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Supplementary Material for:

Undinarchaeota illuminate the evolution of DPANN

Nina Dombrowski1, Tom A. Williams2, Benjamin J. Woodcroft3, Jiarui Sun3, Jun-Hoe Lee4, Bui Quang Minh5, Christian Rinke5, Anja Spang1,5,#

1NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands 2 School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK 3Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Australia 4Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden 5Research School of Computer Science and Research School of Biology, Australian National University, ACT 2601, Australia

#corresponding author. Postal address: Landsdiep 4, 1797 SZ 't Horntje (Texel). Email address: [email protected]. Phone number: +31 (0)222 369 526

Table of Contents

Table of Contents 2 General 3 Evaluating CheckM completeness estimates 3 Screening for contaminants 3 Phylogenetic analyses 4 Informational processing and repair systems 7 Replication and cell division 7 Transcription 7 Translation 8 DNA-repair and modification 9 Stress tolerance 9 Metabolic features 10 Central carbon and energy metabolism 10 Anabolism 13 Purine and pyrimidine biosynthesis 13 degradation and biosynthesis 14 Lipid biosynthesis 15 Vitamin and cofactor biosynthesis 16 Host-symbiont interactions 16 Genes potentially involved in host-symbiont interactions 16 Horizontal gene transfer among Undinarchaeota and other microbial lineages 17 Co-occurrence analyses 18 References 19

Supplementary Figures 1-63 27-89

2 1 General

2 Evaluating CheckM completeness estimates 3 4 Out of 147 archaeal marker genes used by CheckM1 for estimating genome completeness, seven 5 were absent in all twelve Undinarchaeota metagenome-assembled genomes (MAGs) and in some cases 6 were also absent from Cluster 1 and/or Cluster 2 DPANN archaea (see Main Text for definition of the 7 clusters). Here, we briefly want to discuss these marker and the potential consequences for 8 estimating genome completeness. (1) PF01287 encodes translation initiation factor 5A and is absent in all 9 Undinarchaeota. However, when searching for the corresponding arCOG (arCOG04277; Supplementary 10 Table 9) it seems that all archaea, including Undinarchaeota, encode this suggesting that the 11 PFAM is not ideal to search for the presence of this protein in at least some archaea. (2) Rps27e homologs 12 (arCOG04108, PF01667) are almost uniquely lacking in Undinarchaeota (see discussion below) and thus 13 do not seem to be universal for this lineage. (3) Similarly, eif6 homologs (arCOG04176, PF01912) are 14 absent in Undinarchaeota though present in all other archaeal lineages. (4) PF01982/arCOG01904 15 homologs appear to be absent in Undinarchaeota and most Cluster 2 DPANN archaea with the exception 16 of Nanohaloarchaeota. This protein encodes a CTP-dependent riboflavin kinase (RFK) commonly found in 17 archaea. However, as we discuss below vitamin biosynthesis genes are commonly absent in DPANN and 18 thus proteins involved in vitamin biosynthesis are less ideal to determine genome completeness for this 19 clade. (5) PF04127 homologs are absent in almost all DPANN except Altiarchaeota and encode the 20 coenzyme A biosynthesis bifunctional protein (CoaBC), which is involved in vitamin biosynthesis and thus 21 also expected to be absent in most DPANN archaea. (6) TIGR00432/arCOG00989 homologs are absent in 22 all DPANN archaea with the exception of and Altiarchaeota. The gene encodes the tRNA- 23 guanine(15) transglycosylase, which is involved in a unique archaeal pathway for archaeosine-tRNA 24 biosynthesis. (7) TIGR01213/arCOG01015 is absent in most DPANN with the exception of 25 Aenigmarchaeota and Nanoarchaeota. The gene encodes a tRNA-pseudouridine synthase responsible for 26 synthesis of pseudouridine from uracil-54 and uracil-55. Altogether, these findings suggest that the 27 marker gene set used by CheckM includes a subset of genes, which is absent in a large proportion of 28 DPANN archaea and thus may underestimate the completeness of DPANN archaeal genomes. Therefore, 29 we additionally assessed genome-completeness with a set excluding these seven markers and provide the 30 alternative and perhaps more accurate completeness and contamination estimates in parenthesis in Table 31 1 and Supplementary Table S2.

32 Screening for contaminants 33 Contigs were manually investigated for signs of contamination by screening for an abnormal GC- 34 content (~10% difference of average GC-content) and/or taxonomic affiliation based on a BLASTp search 35 against ncbi_nr (Supplementary Table 7; details described in the Methods). We noticed that some 36 Undinarchaeota MAGs (e.g. contig GCA_002494525_5) have a region of ~30 proteins that, based on a 37 BLASTp search, show high similarity to proteins encoded on a fosmid classified as uncultured marine group 38 II/II euryarchaeote_KM3_51_D012. However, phylogenetic analyses of marker proteins encoded in this

3 39 region, revealed that they clustered with homologs of Undinarchaeota rather than with homologs of 40 Marine Group II/III Archaea. Furthermore, we compared the average amino acid (AAI) of the fosmid of 41 KM3_51_D01 with Undinarchaeota, which showed 84% AAI to Undinarchaeales and 59% AAI to 42 Naiadarchaeales, suggesting that this fosmid was incorrectly assigned to and should rather 43 be classified as uncultivated archaeal fosmid.

44 Phylogenetic analyses

45 In published phylogenetic analyses, Undinarchaeota (originally named UAP2) branched sister to 46 all other DPANN archaea3,4. To evaluate this placement and assess DPANN monophyly, we performed in- 47 depth phylogenetic analyses using different sets of representative archaeal taxa (364 and 127 taxa set) 48 and marker proteins as well as using concatenated 16S and 23S rRNA gene sequences (see below). In brief, 49 the initial protein set was based on a selection of 151 markers used in previous studies, such as ribosomal 50 protein marker sets, the Genome Database (GTDB) and the PhyloSift marker set4–7. Notably, 51 initial phylogenetic analyses of single gene trees, including both archaeal, bacterial and eukaryotic 52 homologs of these 151 commonly used markers, revealed that 39 protein did not recover archaeal 53 monophyly suggesting that they are unsuited for concatenated marker protein analyses. In turn, we 54 excluded these 39 markers as well as translation elongation factor aEF-2 (TIGR00490; arCOG01559), which 55 has two paralogs in some archaeal lineages8, from our initial marker set (Supplementary Tables 4-5). 56 To further assess the suitability of marker proteins for concatenated gene trees, we scored the 57 remaining markers based on the recovery of well accepted monophyletic archaeal taxa defined at the 58 order to phylum level (see Methods), i.e. we penalized markers, whenever any of these clades were 59 paraphyletic: Geothermarchaeota, Halobacteria, Methanonatronarchaeales, , 60 , Methanocellales, Methanophagales, Archaeoglobales, , 61 Acidiprofundales, Methanomassiliicoccales, Poseidoniales, (unassigned at order level), 62 Pontarchaea (MG-III), Undinarchaeota, Woesearchaeota, Pacearchaeota, NovelDPANN_1 (UAP1), 63 Parvarchaeota, Nanohaloarchaeota, Aenigmarchaeota, Diapherotrites, Huberarchaeota, Micrarchaeota, 64 Altiarchaeota, , , , , , 65 , Marsarchaeota, , Theionarchaea, Methanofastidiosa, Hadesarchaea, 66 Persephonarchaea, Odinarchaeota, Verstraetearchaeota, , , 67 Heimdallarchaeota, Bathyarchaeota, , , Aigarchaeota, Geoarchaeales, 68 Hydrothermarchaeota and Nanoarchaeota. Violation of monophyly was counted as splits - as described 69 in the methods using a script that we make available in git-bub (count_sister_taxa.py; 70 https://github.com/Tancata/phylo/blob/master/count_sister_taxa.py) - which provided a mean to rank 71 the marker proteins based on congruency and potential events of horizontal gene transfer (HGT). Please 72 note, that we did not make any a priori assumptions regarding the relationship of any of these clades with 73 each other, i.e. our markers did not require that certain clans such as the DPANN are monophyletic. This 74 is important because DPANN monophyly remains debated and we did not want to bias our marker protein 75 assessment. Subsequently, concatenated alignments were created by combining the 25%, 50% and 75% 76 highest (least amount of potential HGTs) - as well as 25% and 50% lowest-scoring (highest amount of 77 potential HGTs) marker proteins (Supplementary Tables 4-5). These datasets were subjected to a variety 78 of Bayesian and Maximum-likelihood-based phylogenetic analyses that differed with respect to model as

4 79 well as data treatment, such as removal of fast-evolving or compositionally heterogeneous sites, and the 80 results are shown in Supplementary Table 6 and Supplementary Figs. 6-56. 81 All our inferences based on the curated marker protein sets recovered a monophyletic DPANN 82 clan and consistently placed Undinarchaeota as an independent lineage branching between two 83 monophyletic DPANN clans, here referred to as Cluster 1 DPANN archaea including Altiarchaeota, 84 Micrarchaeota and Diapherotrites and Cluster 2 DPANN archaea including Nanoarchaeota, 85 Pacearchaeota, Woesearchaeota, Huberarchaeota, Parvarchaeota and Nanohaloarchaeota 86 (Supplementary Figs. 6-41, Supplementary Table 6). In particular, the consistent placement of 87 Altiarchaeota within Cluster 1 is notable, since the evolutionary history of this archaeal lineage remains 88 an ongoing matter of debate9–13. 89 Subsequently and as detailed in the main text, we addressed the effect of using highly incongruent 90 markers with a high degree of splits (i.e. non-monophyletic archaeal taxa, see above) on phylogenetic 91 analyses by inferring phylogenetic trees using 25% and 50% of the lowest ranking markers 92 (Supplementary Tables 4-5). Notably, resulting phylogenetic trees recovered topologies inconsistent with 93 the accepted archaeal taxonomy and confirming the unsuitability of these markers due to conflicting 94 evolutionary signals (Supplementary Figs. 46-49). For instance, in trees inferred using the 25% lowest 95 ranking marker set, known symbionts, such as Nanoarchaeota and Nanohaloarchaeota, clustered with 96 their crenarchaeal or halobacterial hosts, respectively (Supplementary Fig. 46-47). Based on our 97 investigation of horizontal gene transfer events, ~7% and ~12.4% of the proteome of Halobacteria and 98 Nanohaloarchaeota, respectively, have been exchanged horizontally or cluster together due to similar 99 compositional biases (Figure 4a, Supplementary Table S17). Importantly, this suggests that conflicting 100 signals regarding the placement of certain archaeal clades, in particular members of the DPANN archaea, 101 may in part be due to the use of unsuitable markers in phylogenetic reconstructions based on protein 102 concatenations. 103 Considering that previous analyses3,4 suggested that the Undinarchaeota lineage represents an 104 outgroup of all DPANN lineages, we further addressed the reliability of our inferences by accounting for 105 effects imposed by fast-evolving14,15 or compositionally heterogeneous sites16. In particular, and to ensure 106 that the placement of Undinarchaeota is not affected by such artefacts, fast-evolving and compositionally 107 heterogeneous sites were removed using the SlowFaster method14 and chi2 testing17, respectively. In 108 brief, 10%, 20%, 30% and 40% of the most biased sites were removed from alignments generated using 109 the 25% and 50% highest ranked marker proteins both from the 127 and 364 taxa set (Supplementary 110 Table 6, Supplementary Figs. 13-22 and 30-40). All analyses confirmed the placement of Undinarchaeota 111 as an independent lineage emerging between DPANN Cluster 1 and Cluster 2 DPANN archaea. 112 Furthermore, these analyses confirmed the placement of Altiarchaeota within Cluster 1 DPANN. The most 113 notable difference between the treated and untreated alignments was the placement of 114 Methanonatronarchaeia18. In agreement with a recent study addressing the effect of compositional biases 115 and/or fast-evolving sites19, our analyses indicated that Methanonatronarchaeia form a sister lineage of 116 Halobacteria in full alignments, while forming an early branching Methanotecta lineage when biased sites 117 are removed (Supplementary Figs. 13-22, 31-35 and 37-38). In turn, it seems likely that the sisterhood of 118 Halobacteria and Methanonatronarchaeia is due to a phylogenetic artifact perhaps resulting from 119 convergent sequence adaptations to high salinity.

5 120 Next, we investigated tree topologies inferred from several non-curated alignments as well as 121 marker protein sets such as a ribosomal marker set4, the GTDB marker set5 and the PhyloSift markers6 as 122 well as 16S/23S rRNA genes. Unexpectedly, these trees not only showed inconsistent placements for the 123 Undinarchaeota lineage but also for the Altiarchaeota. First of all, an analysis based on an alignment of 34 124 concatenated marker proteins of the PhyloSift marker protein set (alignment length of 5,353 amino acids, 125 Supplementary Fig. 50), placed Altiarchaeota as a separate archaeal lineage emerging in-between DPANN 126 (including Undinarchaeota) as a whole and all other Archaea, respectively (support values of 87.7/89). In 127 this case, the Undinarchaeota lineage represented the first diverging DPANN lineage. Secondly, an 128 alignment consisting of 14 concatenated ribosomal proteins (alignment lengths of 1,974 (trimmed with 129 BMGE) and 2,406 (trimmed with trimAL)) recovered Undinarchaeota as an independent lineage emerging 130 in-between all DPANN (including Altiarchaeota) and all other Archaea (support values of 99.7/100 and 131 99.2/99), respectively (Supplementary Figs. 53-54) as has been assumed previously3,4. Thirdly, in 132 phylogenetic trees recovered from the complete set of 122 archaeal marker proteins used by GTDB 133 (Supplementary Figs. 51-52), Altiarchaeota formed a separate branch forming a sister group to all DPANN 134 Archaea (bootstrap supports of 85.3/98 and; using IQ-tree and bootstrap support 1; using FastTree). Here, 135 Undinarchaeota branched as a sister lineage of Cluster 2 DPANN (Supplementary Table 6). Finally, we 136 performed a concatenated analysis of the 16S and 23S rRNA genes using the 364 taxa set. In contrast to 137 protein phylogenies, these analyses (depending on trimming method and alignment filtering) recovered 138 Undinarchaeota in between Cluster 1 and Cluster 2 DPANN archaea (Supplementary Fig. 4; 93.7/80) or as 139 a sister lineage of the Aenigmarchaeota (Supplementary Fig. 3; 95.7/86), while Altiarchaeota formed a 140 monophyletic cluster with Micrarchaeota and Diapherotrites (88.1/90 bootstrap support) 141 (Supplementary Figs. 3-5). However, these latter analyses recovered several unexpected groupings and 142 trees were characterized by overall low support in deeper branches and were likely affected by long- 143 branch attraction artifacts (LBA)20. In addition, alignments of the concatenated 16S/23S rRNA were 144 relatively short (3,128 nucleotides) and likely harbored insufficient information to resolve deeper 145 branches in the tree as indicated by low support values. Finally, 16S/23S rRNA genes have previously been 146 shown to be good molecular thermometers that reflect the optimal growth temperature of organisms21,22. 147 In turn, the sequence composition of rRNA genes can be biased and impair the accurate assessment of 148 phylogenetic relationships. 149 These analyses highlight the importance of carefully assessing the suitability of marker protein 150 sets as well as of determining the effect of compositional biases on phylogenetic inferences aiming to 151 address archaeal evolution19,23. In particular, many commonly used marker protein sets seem to comprise 152 protein families unsuitable for concatenation: for instance, single-protein tree analyses of the PhyloSift 153 and 122 GTDP markers not only revealed that some markers were exchanged horizontally with bacteria 154 (violation of archaeal monophyly) but also indicated that several of these markers failed to recover 155 monophyly of well-accepted archaeal order- to phylum-level lineages indicating horizontal exchange 156 (Supplementary Tables 4-5). 157 Altogether, our extensive phylogenetic reconstructions provide strong support for a clan 158 consisting of Undinarchaeota as sister lineage of DPANN Cluster 2 archaea, as well as the placement of 159 Altiarchaeota as part of a clan comprising Cluster 1 DPANN archaea. Monophyly of the DPANN clan in turn 160 solely depends on the placement of the root (see Main Text). 161

6 162 Informational processing and repair systems

163 A common feature of symbionts, particularly bacterial endosymbionts, is the loss of genes related 164 to energy production, general biosynthetic pathways, DNA repair mechanisms and to a lesser degree 165 informational processing24. To elucidate whether similar patterns characterize the evolution of 166 Undinarchaeota and DPANN archaea in general, we investigated the presence and absence of core genes 167 involved in replication, transcription, translation and DNA and repair processing.

168 Replication and cell division 169 Undinarchaeota representatives encode most genes related to replication processes 170 (Supplementary Fig. 58, Supplementary Tables 7-10). More specifically, Undinarchaeota MAGs encode 171 two DNA polymerases: DNA polymerase B1 (PolB1, arCOG00328) and the two subunits of the DNA 172 Polymerase D (arCOG04447 and arCOG04455). Additionally, two of the four aquifer representatives 173 encode a DNA polymerase IV (Dpo4, arCOG04582). Furthermore, Undinarchaeota MAGs encode all 174 replication-related proteins commonly found in archaea including ORC1-type DNA replication protein 1 175 (Orc1, arCOG00467) and several helicases including the potential replicative helicase Mcm2 176 (arCOG00439) and a DNA ligase (Lig, arCOG01347). Notably and in agreement with all other analyses and 177 previously published results25, Cluster 2 DPANN archaea and Undinarchaeota encode a fused version of 178 the DNA primase, i.e. PriS and PriL are encoded by one gene (Supplementary Fig. 57, Supplementary 179 Table 11). Finally, they encode DnaG (arCOG04281) and two topoisomerases: type 1 (TopA; arCOG01527) 180 and type 2 topoisomerase 6 (Top6AB; arCOG04143 and arCOG01165), while lacking genes for gyrase or 181 reverse gyrase. However, this is not unexpected since gyrases are more sparsely distributed in archaea 182 (Supplementary Figure 58)26,27. In particular, reverse gyrase seems to be uniquely found in 183 hyperthermophiles (with an optimal growth temperature above 80°C) and thus represents a genetic 184 marker for the adaptation to life at high temperatures13,28–32. In turn, the absence of reverse gyrase 185 homologs in the herein analyzed MAGs suggests that they may not comprise hyperthermophiles. 186 Each Undinarchaeota MAG encodes two paralogs for FtsZ cell division proteins (arCOG02201) as 187 well as a septum site-determining protein MinD (K03609). Additionally, Undinarchaeota representatives 188 encode histones (arCOG02144), chromosome segregation and condensation protein SpcA (K05896)33 as 189 well as the chromosomal protein MC1 (arCOG04743). MC1 is only found in a small number of archaeal 190 lineages and plays a role in DNA bending and compaction in certain Euryarchaeota34–36.

191 Transcription 192 With few exceptions, Undinarchaeota MAGs encode most proteins involved in transcription 193 (Supplementary Fig. 60, Supplementary Tables 7-9), including all core subunits of the RNA polymerase 194 (RpoA1; arCOG04257, RpoA2; arCOG04256, RpoB; arCOG01762, RpoD; arCOG04241, RpoK; arCOG01268, 195 RpoL; arCOG04111, RpoF; arCOG01016, RpoH; arCOG04258, RpoE; arCOG00675, RpoN; arCOG04244 and 196 RpoP; arCOG04341). Similar to many other archaea, Undinarchaeota representatives lack genes for RpoG 197 (arCOG04271) and Rpo13 (arCOG05938)37, which do not seem to be required to form a functional RNA 198 polymerase38. All transcription factors common to archaea, such as the transcription initiation factor IIB 199 (Tfb, arCOG01981), transcription factor S (Tfs; arCOG00579) and transcription factor E (Tfe, arCOG04270),

7 200 are present in Undinarchaeota. Interestingly, Tfs is found in Undinarchaeota and Cluster 2 but not Cluster 201 1 DPANN archaea (Supplementary Fig. 60). Few non-essential genes related to transcription appear to be 202 absent in Undinarchaeota MAGs: these include genes coding for DNA/RNA-binding protein Alba1 203 (arCOG01753) (only present in two aquifer Naiadarchaeales MAGs), as well as the complete absence of 204 Rad3-related DNA helicase (DinG, arCOG00770) in Undinarchaeta, which is involved in nucleotide excision 205 repair39.

206 Translation 207 Undinarchaeota MAGs seem to encode most proteins involved in translation (Supplementary Fig. 208 61, Supplementary Tables 7-10). For example, Undinarchaeota MAGs encode most ribosomal proteins 209 and all archaeal tRNA synthetases. Two notable exceptions are Rpl30e (arCOG01752), which is absent in 210 marine Undinarchaeales, and Rps27e (arCOG04108), which is lacking in all Undinarchaeota 211 representatives. Rpl30e seems also absent in other archaea, such as Halobacteria, Nanohaloarchaeota 212 and most Thermoplasmatales, and may therefore not be essential for building a functional ribosome40,41. 213 On the other hand, Rps27e is found in all analyzed cultivated archaeal taxa and absent in only a subset of 214 so-far uncultivated archaeal lineages such as all Undinarchaeota, Persephonarchaea (MSBL1), 215 Poseidoniales (MG-II) and Pontarchaea (MG-III). Rps27e is likely involved in rRNA processing and is 216 thought to be universally present in archaea and but absent in bacteria40,42. It remains to be 217 determined to what extent the absence of Rps27e in Undinarchaeota impairs the functioning of their 218 ribosomes. 219 Undinarchaeota MAGs also encode most translation-related proteins such as the initiation factors 220 EifA (arCOG01179), Eif2 (arCOG04107), Eif5 (arCOG04277), the elongation factors Tuf (arCOG01561), EF1b 221 (arCOG01988) and FusA (arCOG01559) as well as the potential terminating factor eRF1 (arCOG01742). 222 Other proteins involved in translation that are present in Undinarchaeota MAGs include the ribonuclease 223 P complex (Rnp1-4), ribonuclease Z (Rnz, arCOG00501), ribonuclease J (RnjA, arCOG00546) and 224 endoribonuclease (Nob1, arCOG00721). However, and in contrast to most other archaea, Undinarchaeota 225 seem to lack the translation factor Eif6 (arCOG04176), which has a ribosomal anti-association activity43, 226 and the potential translation initiation ATPase Rli1 (K06174), which plays a role in the dissociation of the 227 two ribosomal subunits44,45. HflX (arCOG00353), which potentially plays a role in ribosome recycling in 228 bacteria and some archaea46, is also absent in Undinarchaeota representatives and it is unclear whether 229 any other proteins can complement the function of these proteins. 230 Undinarchaeota MAGs encode the exosome subunits Rrp4/41/42 (arCOG00678, arCOG01575 and 231 arCOG01574) but lack Csl4 (arCOG00676) as well as any Csl4- containing proteins (i.e. IPR039771, 232 IPR030850). Csl4 plays a role in specificity and regulation of RNA processing47,48 and interacts with DNA 233 primase DnaG (arCOG04281)49. Experimental evidence suggests that a Csl4-Rrp4/41/42 complex (Csl4- 234 exosome) degrades an oligo-A tail more effectively than a Rrp4-Rrp4/41/42 complex (Rrp4-exosome), 235 suggesting that a complex without Csl4 might be still functional but possibly less efficient than the full 236 complex47. Notably, the presence of a putative Rrp4-exosome without Csl4, seems to be a distinctive 237 feature of Undinarchaeota and Cluster 2 DPANN archaea (Supplementary Fig. 61, Supplementary Table 238 9) and indicates a structural difference of their exosomes as compared to Cluster 1 DPANN and other 239 archaea.

8 240 Undinarchaeota MAGs encode the necessary proteins to synthesize translationally modified 241 residues including diphthamide (via Dph2/5/6; arCOG04112, arCOG04161 and arCOG00035)8. However, 242 Undinarchaeota lack most genes related to the pathway for wyosine derivatives. Wyosine is important for 243 post-translational modifications at position 37 of the phenylalanine-specific transfer RNA (tRNAPhe) that 244 is common in archaea and eukaryotes50. Specifically, while Undinarchaeota MAGs encode a potential 245 Trm5 methyltransferase (arCOG00033), they lack the three other biosynthesis genes required for this 246 pathway (Taw1/2/3; arCOG04174, arCOG10124 and arCOG04156). This finding suggests that members of 247 this group can only methylate the N1 position of guanosine-37 and form m1G37 but no other derivatives. 248 Finally, Undinarchaeota MAGs encode several proteins involved in post-translational processes 249 that include the two subunits required to assemble a potential proteasome (PsmAB, arCOG00971 and 250 arCOG00970) as well as a chaperon of the HSP20-family (arCOG01832) and the thermosome chaperonin 251 (ThsA; arCOG01257).

252 DNA-repair and modification 253 A common feature of bacterial organisms with reduced genomes is the absence of key proteins 254 involved in DNA-repair24. However, Undinarchaeota MAGs appear to harbor most proteins related to DNA 255 repair that are typically found in archaea (Supplementary Fig. 58, Supplementary Tables 7-10). Proteins 256 related to recombination and repair that were detected in Undinarchaeota representatives include a 257 holliday junction resolvase (Hjc, arCOG00919), a 5'-3'_exonuclease (Fen1, arCOG04050), type III and V 258 endonucleases (Nth; arCOG00459 and Nfi; arCOG00929), the DNA repair and recombination proteins 259 RadAB (arCOG00415, arCOG00417), the double-strand break repair protein Rad50/Mre11 complex 260 (SbcCD; arCOG00368 and arCOG00397) and the GroEL chaperonin (arCOG01257). However, 261 Undinarchaeota MAGs seem to lack genes for a single-stranded-DNA-specific exonuclease (RecJ; 262 arCOG00427), the Chaperone DnaK (arCOG03060) and the ATP-dependent DNA helicase (DinG, 263 arCOG00770), which are otherwise found in most Archaea including most DPANN archaea. It remains to 264 be assessed, whether other DNA helicases encoded by Undinarchaeota MAGs, such as the DNA double- 265 strand break repair helicase (HerA, arCOG00280) or the uncharacterized ATP-dependent helicase (Lhr, 266 arcog00557), may function in DNA repair and functionally substitute for the lacking enzymes mentioned 267 above. 268 A few proteins related to DNA repair show lineage-specific distributions across the 269 Undinarchaeota representatives. For example, only marine Undinarchaeales but not aquifer 270 Naiadarchaeales MAGs encode the alkylation repair enzyme AlkD (arCOG05122) and the 271 exodeoxyribonuclease III (Xth, arCOG02207) as well as a type 4 uracil-DNA glycosylase (Ugd1m; 272 arCOG00905), which is likely involved in base excision repair51. Naiadarchaeales MAGs on the other hand 273 encode a methylated-DNA--protein-cysteine methyltransferase (Ogt, arCOG02724), involved in the repair 274 of alkylation damage52 and an 8-oxoguanine DNA glycosylase (Ogg, arCOG04357) that is involved in 275 repairing oxidative DNA damage53.

276 Stress tolerance 277 Since it is likely that Undinarchaeota encounter fluctuating environmental conditions in marine 278 and aquifer habitats, we next investigated each MAG for the presence of proteins involved in stress

9 279 tolerance other than repair-related proteins (Supplementary Tables 7-10). Marine Undinarchaeales 280 representatives encode two heat-shock proteins of the HSP20 family54 (arCOG01832 and arCOG01833), 281 two potential glutaredoxins (arCOG02607, arCOG02608) and a Fe/Mn-containing superoxide dismutase 282 (SodA, arCOG04147). Superoxide reductases, which are often found in anaerobic and microaerophilic 283 microorganisms55, appear to be lacking. Two of the aquifer Naiadarchaeales MAGs encode peroxiredoxins 284 (arCOG00310, arCOG00312), which might be involved in oxidative stress tolerance56 and most 285 Undinarchaeota MAGs encode a thioredoxin system (TrxAB; arCOG01972 and arCOG01296) that may play 286 a role in counteracting fluctuations in nutrient availability and oxygen status57. Overall, this suggests that 287 Undinarchaeota utilize several systems to encounter oxidative stress.

288 Metabolic features

289 Central carbon and energy metabolism 290 Carbon metabolism. Next, we investigated key pathways of representatives of Undinarchaeota 291 regarding carbon metabolism and potential modes of energy conservation. All Undinarchaeota MAGs 292 have a low number of genes encoding carbohydrate and peptide transporters as well as carbohydrate 293 degradation enzymes (CAZymes). The only putative transporters were PotE (arCOG00009), involved in 294 amino acid transport, an uncharacterized solute transporter (arCOG00238; IPR001898), which might take 295 up sulfate and/or dicarboxylate with the concomitant uptake of sodium ions58, a phosphate transporter 296 (PitA, arCOG02267) and a potential tripartite tricarboxylate transporter (TTT; arCOG04469, PF01970; 297 Supplementary Tables 7, 9, 13). According to the Transporter Classification DataBase (TCDB), the TTT 298 transporter is homologous to TctA (TCDB ID 2.A.80.2.1), which is predicted to be a putative citrate 299 transporter59. Additionally, all marine Undinarchaeales MAGs encode cation anti-/symporters, such as the 300 Na(+)/H(+) antiporter (KefB; arCOG01953) and the sodium:calcium antiporter (arCOG02881), which may 301 be used to maintain osmic balance in marine environments60,61. Consistently, KefB is only encoded by two 302 aquifer MAGs and arCOG02881 was completely absent in Naiadarchaeales. 303 While Undinarchaeota MAGs encode a small number of peptidases, these may be involved in 304 anabolism rather than catabolism (see below) (Fig. 3, Supplementary Tables 7-9 and 15). In fact, we did 305 not detect any signal peptide in any of the predicted peptidases (as determined by InterProScan including 306 a SignalP search) suggesting that peptidases are located intracellularly. In turn, the most likely substrates 307 used for central metabolism and energy conservation seem to be simple carbohydrates, such as pyruvate 308 or acetate, or nucleic acids. While Undinarchaeota representatives lack specific sugar transporters, simple 309 sugars could perhaps be taken up by passive diffusion62. Nucleic acids might be taken up via pili (encoded 310 by Undinarchaeota MAGs, see below) and degraded into nucleosides via nucleases, such as ribonuclease 311 J (RnjA, arCOG00546), ribonuclease HII (RhnAl; arCOG02942 and RhnB; arCOG04121)63, exonuclease III 312 (XthA, arCOG02207)64, ATP-dependent RNA helicase (DeaD, arCOG00558), or endonuclease YncB 313 (arCOG03192)65. Nucleoside triphosphates might be fed into the nucleoside degradation pathway via the 314 AMP phosphorylase (DeoA, arCOG02013), ribose 1,5-bisphosphate isomerase (arCOG01124) and ribulose 315 1,5-bisphosphate carboxylase (RbcL; RuBisCO, arCOG04443), which would yield 3-phosphoglycerate66–68. 316 This pathway has been discussed to be relevant for a range of DPANN archaea in previous studies68,69. Two 317 Naiadarchaeales MAGs seem to encode a functional group III-b RuBisCO with the same key catalytic

10 318 residues as found in the oxygen-sensitive RuBisCO found in jannaschii70 319 (Supplementary Figure S59a-c). MAGs from marine Undinarchaeales on the other hand encode a group- 320 III-like RuBisCO homolog that, with the exception of the homolog of MAG GCA_002502135, shows 321 substitutions at the catalytic site in position 195 (aspartic acid (D) to glutamic acid (E)) and 196 322 (phenylalanine/leucine/tyrosine (F/L/Y) to glycine (G)) (Supplementary Fig. 59c). The substitution of D by 323 E does not change the property of the side chains, which are both acidic and in turn have a negative 324 charge. The main difference between these two amino acids is the length of the side chain, with E having 325 one methyl-group more than D. On the other hand, even though both F/L/Y and G (Phenylalanine/ 326 Leucine/ Tyrosine and Glycine) are neutral, the side chains of F and Y differ from those of L and G with 327 respect to class (aliphatic versus aromatic). In turn, it remains to be determined, whether the substitution 328 of D by E at position 195 could be compensated by the change of F/L/Y to G at position 196 and whether 329 the RuBisCO-like proteins of marine Undinarchaeales have retained their canonical function. However, 330 the presence of a conserved group-III RuBisCO and other major key genes of the AMP degradation 331 pathway suggests that at least some aquifer Naiadarchaeales might use this pathway to produce 3- 332 phosphoglycerate that can enter the central carbon metabolism. However, it has to be noted that DeoA 333 was only found in one and the RuBisCO only in two out of four Naiadarchaeales genomes. With the 334 exception of MAG SRR2090159.bin1129 all had a relatively low completeness, such that the absence of 335 these genes in several Naiadarchaeales could be either due to genome completeness or be signs of 336 genome streamlining. 337 The gene repertoire of Undinarchaeota suggests that 3-phosphoglycerate produced by the AMP 338 degradation pathway could enter the lower glycolytic pathway via their phosphoglycerate mutase (GpmA; 339 arCOG01993 and ApgM; arCOG01696), enolase (Eno, arCOG01169) and phosphoenolpyruvate synthase 340 (PpsA, arCOG01111), which would yield pyruvate and ATP. Pyruvate kinase (Pk, arCOG04120), which in 341 most archaea converts phosphoenolpyruvate to pyruvate, is absent from Undinarchaeota 342 representatives. The only enzyme that might fulfill this role in Undinarchaeota is PpsA, which is encoded 343 by these MAGs and may be reversible, as reported in certain archaea71–73. Additionally, 9 out of 12 344 Undinarchaeota representatives encode a putative pyruvate dehydrogenase complex (PdhABC; 345 arCOG01054, arCOG01052 and arCOG01706) (found also in some other DPANN archaea (Supplementary 346 Table S9)74), while lacking genes for oxoacid-ferredoxin oxidoreductase complexes (e.g. OorABDG; K00174 347 to K00177, arCOG01599 to arCOG01608), which are common in other archaeal lineages75. Though the 348 functional annotation of pyruvate dehydrogenases is challenging based on sequence information alone, 349 it seems possible that Undinarchaeota members use this complex for the conversion of pyruvate to acetyl- 350 CoA. 351 Acetyl-CoA could be further metabolized to acetate via the ADP-forming acetyl-CoA synthetase 352 (AcdAB; arCOG01340 and arCOG01338), a reaction that would allow the production of ATP. Additionally, 353 three MAGs of the aquifer Naiadarchaeales encode a putative aldehyde as well as alcohol dehydrogenase 354 (PF00171 as well as PF08240 and arCOG01455, respectively). While none of the Undinarchaeota homologs 355 are closely related to experimentally characterized enzymes, it seems possible that these Undinarchaeota 356 representatives are able to ferment 3-phosphoglycerate to pyruvate (generating ATP via the lower 357 glycolytic pathway) and ethanol (to remain redox balance). 358 Key enzymes of the glycolytic pathway, the 6-phosphofructokinase (Pfk, arCOG03370) and 359 pyruvate kinase (Pk, arCOG04120), appear to be absent in Undinarchaeota MAGs (Fig. 3, Supplementary

11 360 Tables 7-9 and 12). Additionally, representatives of the Undinarchaeota lack genes for key proteins of the 361 classical and modified versions of the Entner–Doudoroff (ED) pathway such as the gluconate dehydratase 362 (Gad, arCOG01168) or 2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-phosphogluconate aldolase 363 (K11395). The absence of the upper glycolytic pathway and ED-pathway coincides with the absence of 364 carbohydrate-active enzymes belonging to the glycoside hydrolase (GH) family (Supplementary Table 14), 365 indicating that members of Undinarchaeota are unable to utilize complex carbohydrates as carbon or 366 energy sources. Additionally, Undinarchaeota MAGs lack most genes encoding enzymes linked to the TCA 367 cycle. While representatives of the marine Undinarchaeales might be able to convert oxaloacetate to 368 malate using malate dehydrogenase (Mdh, arCOG00246), MAGs of the aquifer Naiadarchaeales encode a 369 malic enzyme (MaeA, arCOG00853) that might convert malate to pyruvate. 370 Undinarchaeota MAGs encode genes for the initial steps of gluconeogenesis, i.e. the 371 gluconeogenic enzymes that allow the conversion of pyruvate to -6-phosphate, including the 372 phosphoenolpyruvate synthase (PpsA, arCOG01111) and the bifunctional fructose-1,6-bisphosphate 373 aldolase/phosphatase (Fbp, arCOG04180). While Fbp was originally suggested to be present in most 374 archaea76, based on our analyses Fbp is detected in only a few representatives of the DPANN archaea 375 other than Undinarchaeota and ~40% of genomes analyzed from Altiarchaeota (Supplementary Table 9). 376 The presence of Fbp in Undinarchaeota MAGs suggests that members of this group are able to synthesize 377 cellular building blocks via gluconeogenesis using 3-phosphoglycerate. Glyceraldehyde-3-phosphate and 378 fructose-6-phosphate produced during gluconeogenesis might be fed into the non-oxidative pentose- 379 phosphate pathway via a putative transaldolase (TalA, arCOG05061) and transketolase (TktA, 380 arCOG01053) to produce pentoses, such as ribose-5-phosphate. These could subsequently enter into 381 anabolic pathways including the purine biosynthetic pathway. 382 Redox balance. The absence of genes encoding enzymes involved in the oxidative phase of the 383 pentose pathway as well as the lack of isocitrate dehydrogenase (Icd, arCOG01164), NADH 384 dehydrogenases or hydrogenases (Fig. 3, Supplementary Tables 7-9) suggests that Undinarchaeota may 385 use alternative enzymes to reduce NAD(P)+ to NAD(P)H. One possible candidate enzyme for this 386 conversion is the thioredoxin reductase (arCOG01296, TrxB)57, genes for which are present in most 387 Undinarchaeota MAGs. Furthermore, Undinarchaeota MAGs encode glyceraldehyde-3-phosphate 388 dehydrogenase (Gap, arCOG00493), and, in the case of the aquifer Naiadarchaeales representatives, also 389 malic enzyme (MaeA, arCOG00853) and a NAD(P)-dependent glyceraldehyde-3-phosphate 390 dehydrogenase (GapN, arCOG01252). All of these proteins could couple NADPH-generation to central 391 carbon metabolism77. Another enzyme that plays a role in providing organisms with de novo NADP is the 392 NAD kinase (NadK, arCOG01348)76, which is encoded by all aquifer MAGs. The absence of NadK in marine 393 Undinarchaeota is interesting as most bacteria and archaea encode this enzyme78. One of the few 394 characterized organisms that lack NadK is the obligate intracellular bacterium Chlamydia trachomatis that 395 seems to rely on its host for NADP maintenance79. However, based on our analysis homologs of this 396 enzymes seem also to be lacking in certain free-living archaea such as Methanococcales (Supplementary 397 Table S9). 398 Energy metabolism. Undinarchaeota MAGs lack genes encoding membrane-bound complexes 399 belonging to the electron transport chain including NADH dehydrogenases, hydrogenases, cytochromes 400 and terminal oxidases (Supplementary Table 9). Additionally, we could not detect any genes for terminal 401 reductases, such as nitrate/nitrite reductase, sulfite reductase or fumarate reductase in the

12 402 Undinarchaeota MAGs. However, an archaeal-type V-type ATP synthase is encoded by all Undinarchaeota 403 representatives (AtpABCDEFHI; arCOG00868, arCOG00865, arCOG02459, arCOG04101, arCOG00869, 404 arCOG04102, arCOG03363 and arCOG04138). Furthermore, most Undinarchaeota encoded a 405 pyrophosphate-driven (instead of ATP-driven) sodium pump (HppA, arCOG04949), that may use energy 406 conserved by pyrophosphate hydrolysis for proton movement across the membrane80–82. 407 408 Altogether, our analyses of the central carbon and energy metabolism of the herein reconstructed 409 Undinarchaeota representatives indicate that members of this group are restricted to energy 410 conservation using substrate-level phosphorylation. In fact, considering the limited substrate range and 411 absence of various central carbon metabolic pathways as well as membrane-bound complexes, it seems 412 possible that members of the Undinarchaeota rely on other organisms to sustain their living (see below) 413 - a lifestyle common in members of the DPANN4,83. 414

415 Anabolism

416 Purine and pyrimidine biosynthesis 417 Most aquifer Naiadarchaeales MAGs encode enzymes needed to convert ribose-5-phosphate into 418 inosine monophosphate (IMP) (Fig. 3, Supplementary Tables 7-9 and 12), while MAGs from marine 419 Undinarchaeales appear to lack key genes encoding proteins involved in purine biosynthesis. For example, 420 phosphoribosylformylglycinamidine cyclo-ligase (PurM, arCOG00639), phosphoribosylaminoimidazole- 421 succinocarboxamide synthase (PurC, arCOG04421) and phosphoribosylaminoimidazole- 422 succinocarboxamide formyltransferase (PurH, arCOG02824) were only found in either two or three 423 marine Undinarchaeales MAGs while being present in most aquifer representatives. However, it has to be 424 noted that not all steps of the purine biosynthesis pathway have been elucidated in archaea. For instance, 425 it is currently unclear which enzyme catalyzes the conversion of 5-aminoimidazole ribonucleotide to N5- 426 carboxyaminoimidazole ribonucleotide84, which in bacteria is mediated by the N5-CAIR synthase (PurK, 427 arCOG01597). Similarly, genes encoding the guanylate kinase (Gmk, K00942) seem to be absent not only 428 from all Undinarchaeota MAGs but from archaeal genomes in general85 (Supplementary Table 9) and it 429 remains to be determined, which enzyme substitutes this reaction in Archaea. 430 The genes required to convert IMP to purines have a slightly inconsistent occurrence across 431 marine and aquifer Undinarchaeota MAGs. For example, genes for IMP dehydrogenase (GuaB, 432 arCOG00612), which catalyzes the conversion of IMP to xanthosine 5'-phosphate), were only found in 433 three marine Undinarchaeales representatives (GCA_002495465, SRR4028224.bin17 and 434 SRR5007147.bin71) and one aquifer MAG (SRR2090153.bin1042), while genes for GMP synthase (GuaA, 435 K01951), which catalyzes the second step, were present in two additional aquifer MAGs 436 (SRR2090159.bin1129 and SRR2090159.bin1288). Genes encoding the nucleoside diphosphate kinase 437 (Ndk, arCOG04313) and ribonucleoside-triphosphate reductase (NrdD, arCOG04889), required for the 438 formation of dGTP, could be identified in most Undinarchaeota MAGs. Finally, adenylosuccinate 439 synthetase (PurA, arCOG04387), which is required to convert IMP to adenylosuccinate, was only present 440 in three aquifer MAGs, but the genes encoding the proteins involved in the production of dATP (PurB;

13 441 arCOG01747, AdkA; arCOG01039, Ndk; arCOG04313 and NrdD; arCOG04889) were found in most 442 Undinarchaeota MAGs. The lack of GuaB in most aquifer representatives is puzzling, since they harbor 443 genes for most other steps of this pathway. In turn, it remains to be determined whether the absence of 444 this gene is due to genome incompleteness or represent a true biological signal. 445 Next, our analysis of the pyrimidine biosynthesis pathway revealed that Undinarchaeota MAGs 446 encoded most of the proteins necessary to convert carbamoyl phosphate to CTP and UTP85. These proteins 447 include the carbamoyl-phosphate synthase (CarA, arCOG00064) catalyzing the first step in the pathway. 448 Glutamine required by CarA likely cannot be synthesized by Undinarchaeota themselves but must be 449 taken up from the environment (see also discussion on amino acid biosynthesis pathways below). All 450 enzymes required for the conversion of glutamine to uridine monophosphate (UMP), which are encoded 451 by the PyrBCDEF (arCOG00911, arCOG00689, arCOG00603, arCOG00029, arCOG00081) gene cluster, 452 were found in the majority of Undinarchaeota MAGs (Fig. 4, Supplementary Tables 7-9). Furthermore, 453 almost all MAGs encode the enzymes that convert UMP further into dCTP (PyrH; arCOG00858, PyrG; 454 arCOG00063, Ndk; arCOG04313 and NdrD; arCOG04889), dUTP (Dcd, arCOG04048) and dTTP (ThyA; 455 arCOG03214 and Tmk; arCOG01891). Notably, we could not identify genes for thymidylate synthase 456 (ThyA; arCOG03214) or flavin-dependent thymidylate synthase (ThyX; arCOG01883) in most aquifer 457 Naiadarchaeales MAGs while these were present in Undinarchaeales representatives. Considering the 458 presence of all other enzymes of this pathway, it seems possible that the lack of thyA/X genes is due to 459 genome incompleteness.

460 Amino acid degradation and biosynthesis 461 Our analyses of the amino acid metabolism suggested that Undinarchaeota representatives lack 462 most genes encoding enzymes required for amino acid biosynthesis and interconversion (Supplementary 463 Tables 7-9 and 12). The identified genes code for aminopeptidases that might be involved in the turnover 464 of intracellular proteins or general protein processing. For instance, we found genes for leucyl 465 aminopeptidase (PepA; arCOG04322), methionine aminopeptidase (Map; arCOG01001) and a potential 466 membrane-associated serine protease of the S54 family (GlpG, arCOG01768; IPR022764 and 467 IPR035952)86. Aminopeptidases potentially involved in protein hydrolysis include a Xaa-Pro 468 aminopeptidase (PepQ, arCOG01000) and a putative metallopeptidase (arCOG04217). Other enzymes 469 related to amino acid metabolism, which were predicted to be present in Undinarchaeota representatives, 470 could be involved in the interconversion of amino acids and respective organic acids. For example, the 471 putative aspartate aminotransferases encoded by Undinarchaeota MAGs (AspC, arCOG01130) might 472 convert L-aspartate and 2-oxoglutarate to glutamate and oxaloacetate, their serine 473 hydroxymethyltransferase (GlyA, arCOG00070) could be involved in the interconversion of serine and 474 glycine, a glutamate dehydrogenase (GdhA, arCOG01352) might produce glutamate without ammonia 475 assimilation87 and a cysteine desulfurase might interconvert cysteine and alanine (SufS, arCOG00065). The 476 SufS of Undinarchaeota representatives may also function in iron- cluster assembly alongside with 477 SufBCD88 (arCOG01715, arCOG04236, TIGR01981), which are encoded by 10 out of 12 MAGs. Additionally, 478 Undinarchaeota MAGs encode a potential serine-pyruvate aminotransferase (PucG, arCOG00082), which 479 might transaminate L-serine and pyruvate to 3-hydroxypyruvate and alanine. While Undinarchaeota 480 MAGs encode a 3-phosphoglycerate dehydrogenase (SerA, arCOG01754), which catalyzes the first step in

14 481 serine biosynthesis, genes required to mediate the other two steps of this pathway, generally encoded by 482 serB (arCOG00083) and serC (arCOG01158), were absent. However, it seems possible that an 483 uncharacterized aminotransferase might complement the function of SerC. For example, in 484 Methanocaldococcus jannaschii a broad-spectrum class V aminotransferase is sufficient for 485 phosphoserine production89. The gene in the cited study belongs to arCOG00082, a homolog of which is 486 present in Undinarchaeota. Interestingly, this protein has an aminotransferase class V domain 487 (IPR000192) and thus might indeed be involved in serine biosynthesis in Undinarchaeota. Similarly, the 488 function of phosphoserine phosphatase SerB might be mediated by another, so far uncharacterized 489 phosphatase. 490 Altogether, the lack of many genes involved in amino acid metabolism suggests that 491 Undinarchaeota representatives need to acquire amino acids from the environment or a host, for instance 492 using the amino acid transporter PotE (arCOG00009) that is present in all MAGs (Supplementary Table 7). 493 PotE has an amino acid/polyamine transporter domain (IPR002293), but lacks any additional domain that 494 would allow to make more specific predictions regarding the identity of amino acids that could be taken 495 up by this transporter. The lack of other amino acid transport systems could suggest that Undinarchaeota 496 representatives require a host to obtain certain amino acids and other necessary metabolites (see also 497 below) directly.

498 Lipid biosynthesis 499 Previous analyses have revealed that many DPANN archaea lack lipid biosynthesis genes74,90 and 500 it was shown that several cultivated representatives such as N. equitans and potentially 501 Nanohaloarchaeaum antarcticus, acquire their lipids from their respective hosts91–93. Interestingly, 502 especially aquifer Naiadarchaeales MAGs encode for a far more complete gene set for lipid biosynthesis 503 than N. equitans and many other DPANN archaea (Fig. 3, Supplementary Tables 7-9 and 12, 504 Supplementary Figure S62). First of all, all Undinarchaeota MAGs encode the key genes for proteins 505 involved in the mevalonate pathway, which allows the conversion of acetyl-CoA to isopentenyl- 506 diphosphate (IPP). These proteins include HmgB (arCOG01767), HmgA (arCOG04260), Mvk (arCOG01028), 507 MvaD (arCOG02937, IPR029765) and Ipk (arCOG00860). Furthermore, the presence of genes for 508 geranylgeranyl diphosphate synthase (GGPS, arCOG01726), suggests that Undinarchaeota 509 representatives have the ability to convert IPP further to geranylgeranyl diphosphate (GGPP), a precursor 510 of ether-linked lipids94. Undinarchaeota MAGs also encode an undecaprenyl-diphosphate synthase (UppS, 511 arCOG01532) that could convert GGPP to undecaprenyl diphosphate, which is a potential precursor of 512 glycosyl carrier lipids95. Intriguingly, genes for enzymes synthesizing archaeol via the glycerophospholipid 513 pathway seem to be solely encoded by aquifer but absent from marine Undinarchaeota MAGs. For 514 instance, aquifer Naiadarchaeales code for glycerol-1-phosphate dehydrogenase (EgsA, arCOG00982) that 515 transforms glycerone-1-phosphate to glycerol-1-phosphate and is essential to build the backbone of 516 phospholipids96. Furthermore, two aquifer Naiadarchaeales MAGs (SRR2090159.bin1129 and 517 SRR2090159.bin1288) encode phosphoglycerol geranylgeranyltransferase (GGGPS, arCOG01085), which 518 could convert glycerol 1-phosphate and GGPP to geranylgeranyl)glycerol 1-phosphate, catalyzing the first 519 step in archaeal lipid biosynthesis97. While all Undinarchaeota representatives encode a protein assigned 520 to the arCOG00476 family comprising putative digeranylgeranylglyceryl phosphate synthases (DGGGP

15 521 synthase), only the homologs identified in the aquifer MAGs harbor the characteristic DGGGP synthase 522 domain (IPR023547). Finally, all aquifer MAGs encode enzymes for the last steps of the archaeal lipid 523 biosynthesis: these include CDP-archaeol synthase (CarS, arCOG04106)98, as well as archaetidylinositol 524 phosphate synthase (AIP synthase, arCOG00670), archaetidylserine synthase (AS synthase, arCOG00671) 525 and the putative archaetidylserine decarboxylase (Psd, arCOG04470)99. Thus, while aquifer 526 Naiadarchaeales seem to be able to synthesize their own lipids, marine Undinarchaeales representatives 527 instead may rely on lipids or certain intermediates from potential interaction partners.

528 Vitamin and cofactor biosynthesis 529 Undinarchaeota MAGs encode diverse enzymes whose function is dependent on the presence of 530 vitamins and cofactors, such as the thiamine-domain (IPR029061) containing proteins, such as the 531 pyruvate dehydrogenase (PdhA, arCOG01054) and transketolase (Tk, arCOG01051 and arCOG01053). Yet, 532 Undinarchaeota MAGs seem to lack most genes coding for enzymes involved in vitamin biosynthesis 533 pathways (Supplementary Tables 7-9 and 12). The few enzymes present include the nicotinamide- 534 nucleotide adenylyltransferase (NadR, arCOG00972) encoded by all aquifer Naiadarchaeales MAGs and 535 dihydrofolate reductase (FolA, arCOG01490) found in marine Undinarchaeales representatives. 536 Additionally, most Undinarchaeota representatives contain genes coding for a putative dephospho-CoA 537 kinase (CoaE, arCOG01045) and a protein assigned to the arCOG04076 family, which comprises candidate 538 enzymes for GTP-dependent dephospho-CoA kinases100. However, we could not detect genes for other 539 enzymes involved in coenzyme A biosynthesis in any of the Undinarchaeota genomes such as coenzyme 540 A biosynthesis bifunctional protein CoaB (arCOG01704) or phosphopantetheine adenylyltransferase 541 (CoaD, arCOG01223). Additionally, Undinarchaeota MAGs seem to lack genes for transporters specific to 542 coenzymes and vitamins, which would allow the uptake of these compounds (Supplementary Table 13). 543 In turn, this further suggests that the herein analyzed Undinarchaeota representatives may depend on 544 direct contact with a partner organism to acquire vitamins and cofactors.

545 Host-symbiont interactions

546 Comparative genome analyses revealed a limited set of central carbon metabolism related 547 proteins as well as the low number of genes encoding transporters and enzymes involved in vitamin and 548 amino acid biosynthesis, raising the possibility that Undinarchaeota representatives depend on partner 549 organisms for growth. To shed more light onto potential interaction partners, we have analyzed proteins 550 that may be involved in -species interactions and inferred routes of horizontal gene transfer and 551 generated proportionality networks (see Main Text).

552 Genes potentially involved in host-symbiont interactions 553 Cellular appendages, such as pili and the archaellum, and other surface proteins (i.e. LamG- 554 domain containing proteins) represent mechanisms reported to mediate cell-cell interactions4,101. While 555 we did not detect genes encoding subunits of the archaellum102, it has previously been suggested that 556 certain DPANN use pili to interact with their hosts103. Undinarchaeota MAGs have gene clusters encoding 557 several proteins potentially involved in pili formation (VirB11; arCOG01818, TadC; arCOG01808, EppA;

16 558 arCOG02300) as well as an uncharacterized protein with archaeal pilin domains (i.e. 559 arCOG03871/IPR013373) (Supplementary Tables 7-9). The potential VirB11 protein contains a P-loop 560 NTPase domain (IPR027417) and might generate energy from NTP hydrolysis104 and TadC might provide 561 an assembly platform for the assembly of pili105. Prepilins, which are encoded by 10 out of 12 562 Undinarchaeota MAGs, could be transported through the membrane via the sec-transport system 563 (secDEFGY encoded by arCOG03055, arCOG02204, arCOG03054, arCOG02957 and arCOG04169) and 564 modified via potential prepilin peptidases (arCOG02298, arCOG02300 and arCOG02300). Some pili- 565 related proteins seem to be present in aquifer Naiadarchaeales representatives but are not encoded by 566 marine Undinarchaeales MAGs: these include CpaF (an uncharacterized protein with a type II/IV secretion 567 system protein domain: arCOG01819; IPR001482) and uncharacterized proteins in the same genetic 568 region that may functionally be related to pili formation such as a potential surface binding proteins 569 (arCOG05787, arCOG03512). A potential VirB4 ATPase (arCOG04035) on the other hand is only encoded 570 by marine Undinarchaeales MAGs. 571 Surface modification proteins, involved in the modification of S-layers and construction of 572 extracellular matrices, represent additional means that may enable host-symbiont interactions106. While 573 Undinarchaeota MAGs seem to lack S-layer proteins SlaA (arCOG06039) and SlaB (arCOG07272), they 574 encode an uncharacterized S-layer protein (arCOG03418; IPR006454) as well archaeal glycosylation 575 proteins, such as the glycosyltransferase AglA (arCOG01410) and the protein glycotransferase AglB 576 (arCOG02044), that might be involved in S-layer protein N-glycosylation107. AglA and B are encoded in the 577 same genetic region as other archaeal glycosylation proteins (arCOG00899, arCOG03199) and potential 578 membrane-binding proteins (arCOG05092, arCOG00395, arCOG07813 and arCOG02080). Overall, this 579 suggests the presence of an S-layer or the potential of Undinarchaeota to generate an extracellular matrix 580 that might play a role in cell-cell interactions. In support of the latter, we found that some of the longest 581 proteins (~1400 amino acids) present in marine but not aquifer Undinarchaeota representatives encode 582 LamG-like protein domains (arCOG07813; IPR006558), which might be involved in the formation of an 583 extracellular matrix (Supplementary Table S20-23)108. LamG-like proteins in Undinarchaeota are often 584 encoded in the same genetic region as potential S-layer proteins, glycosyltransferases (AglA) or pilus- 585 assembly proteins (TadA). Furthermore, our investigation of a suite of proteins discussed to be involved 586 in cell-interactions74 and present in the Undinarchaeota MAGs shares similarity to proteins involved in cell 587 adhesion( Supplementary Table 22-23). We also identified a hypothetical protein with TSP type-3 repeat 588 domains (IPR028974, arCOG07561) in marine Undinarchaeales MAGs, which may represent another 589 putative extracellular matrix protein. Finally, it is worth mentioning that similar to many other DPANN 590 archaea74,109, Undinarchaeota MAGs do not seem to encode CRISPR-Cas systems, which, among others, 591 are involved in viral defense110.

592 Horizontal gene transfer among Undinarchaeota and other microbial lineages 593 It has previously been shown that intimately interacting organisms can share genes through 594 horizontal gene transfer (HGT). For example, N. equitans, the first cultivated representative of the DPANN, 595 and its host I. hospitalis seem to have exchanged several genes horizontally111,112. To investigate the 596 possibility whether Undinarchaeota representatives have exchanged genes with potential hosts and to 597 pinpoint routes of HGT, we reconstructed protein trees of all proteins present in at least three or more

17 598 Undinarchaeota genomes (520 genes total) and analyzed sisterhood-relationships among taxonomically 599 distinct lineages. In brief, we identified homologs of these 520 Undinarchaeota protein families in a 600 reference set of 364 archaeal, 3020 bacterial and 100 eukaryotic genomes and generated single protein 601 trees. Subsequently, HGT events were identified using a custom script (count_sister_taxa.py; 602 https://github.com/Tancata/phylo/blob/master/count_sister_taxa.py), that allows to determine the next 603 closest sister lineage of any lineage of interest (see Methods for details). Notably, this approach revealed 604 significant fractions of HGT among known DPANN symbiont-host systems (Fig. 4a, b, Supplementary 605 Tables 16-17). Undinarchaeota did not show a dominant fraction of genes shared with a specific lineage, 606 i.e. most genes seemed to be shared with taxonomically closely related DPANN Archaea. The largest 607 number of proteins, that did not cluster with DPANN homologs, seemed to be related to homologs of 608 archaea (16 proteins to Heimdall-, Loki- or Thorarchaeota), Bathyarchaeota (11 proteins), and 609 Thermoplasmata (11 proteins to Thermoplasmatales, Pontarchaea or Poseidoniales) (Supplementary 610 Tables 16-17). Notably, the protein families potentially transferred with these members of these archaeal 611 lineage comprise components of informational processing machineries such as a potential tRNA 612 pseudouridine synthase (arCOG04252; one Bathyarchaeota clustering inside Undinarchaeota), RNA 3'- 613 terminal phosphate cyclase (arCOG04125, transfer to Heimdallarchaeota) and ribosomal protein S19 614 (arCOG04099; transfer to Pontarchaea). Considering that genes for information processing are thought to 615 evolve predominantly vertically but may be exchanged between known symbiont-hosts systems, this 616 opens the possibility that marine Undinarchaeales engage in symbiotic interactions with one of these 617 lineages.

618 Co-occurrence analyses 619 Next, we used a read-based co-occurrence analysis to assess whether MAGs of Undinarchaeota 620 are proportional to other archaeal and bacterial genomes113 (see Methods for details). Unfortunately, we 621 only detected Undinarchaeota in a low number of metagenome datasets, such that this analysis does not 622 have sufficient statistical power to resolve co-proportionality with high support. In turn, we did not detect 623 any significant co-occurrence patterns for members of the Naiadarchaeales and any other taxonomic 624 lineage. In fact, the majority of genomes co-varying with Undinarchaeota MAGs belongs to other DPANN 625 and Patescibacteria/CPR lineages, which are all characterized by small cell sizes and reduced genomes 626 such that these co-occurrence patterns could be due to an artifact resulting from the enrichment of small 627 cells for some of the samples (though interactions among members of these lineages cannot be excluded). 628 The main observation was that marine Undinarchaeales appeared to co-vary with three genomes of the 629 Chloroflexi, all belonging to the order Dehalococcoidales (Supplementary Figure 63). Most members of 630 the Dehalococcoidales have small genomes (i.e. ~1.5 Mb for Dehalococcoides mccartyi 195, which 631 however has a rather large cell size of 0.3-1 µm) and represent free-living heterotrophic bacteria that can 632 use chlorinated compounds as electron acceptors114. While challenging to grow in isolation, 633 Dehalococcoides can be maintained in enrichment cultures, in which they rely on acetate and hydrogen 634 from other community members114. Based on metabolic gene repertoires of members of the 635 Undinarchaeales, which are characterized by the absence of any of the known genes for the various 636 hydrogenase protein families115 (Supplementary Table 7), hydrogen-dependent syntrophy seems unlikely 637 to support interactions with Dehalococcoides. Yet, a symbiotic relationship could be based on exchange

18 638 of acetate or be of parasitic nature as observed in currently known host-symbiont systems93,116–119. It has 639 to be noted, however, that the UAP2-positive metagenomes (see Supplementary Table S1) used for the 640 proportionality analyses differ in respect to sampling method and filtering steps and we cannot exclude 641 that correlation patterns are due to methodological artefacts. Therefore, prospective analyses of a larger 642 number of metagenomes generated with consistent methodology and without filtering steps will be 643 needed to further assess co-proportionality of Undinarchaeota with other organism groups. 644 Yet, since co-occurrence analyses predicted a potential association of marine Undinarchaeales 645 with three Chloroflexi of the order Dehalococcoidales (Supplementary Figure 63) we manually 646 investigated single-gene trees for potential transfers between these groups but could only identify a small 647 fraction of candidate HGTs. For example, a potentially transferred gene encodes a Fe-S cluster assembly 648 ATPase SufC (arCOG04236). In the corresponding phylogeny, two Chloroflexi (Thermogemmatispora 649 carboxidivorans and Ktedonobacter sp.) branch as a sister group of marine Undinarchaeales with low 650 bootstrap support of 41%. Another potential transfer involves a gene for mevalonate kinase 651 (arCOG01028). In particular, the undinarchaeal sequence from GCA_002502135 emerges from within a 652 cluster of Chloroflexi (70% bootstrap support). However, the number of putative HGTs among Chloroflexi 653 and Undinarchaeota are significantly lower than the HGTs detected in other DPANN-host symbiont 654 systems, such as Nanoarchaeota and , and do therefore not provide support for the 655 association Undinarchaeota with members of this bacterial lineage. 656 In turn, further analyses including fluorescence in situ hybridization will be needed to shed further 657 light onto potential interaction partners of Undinarchaeota and test whether certain members of this 658 group indeed interact with members of the Pontarchaea or Chloroflexi. 659

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26 high abundant MAG Environment

● Aquifer

● 750 Marine

MAG SRR2090153.bin1042 500 ● SRR2090159.bin1129 SRR2090153.bin461 SRR2090159.bin1288 GCA_002494525.1 GCA_002501985.1 250 GCA_002687935.1 U_76725 SRR4028224.bin17 SRR5007147.bin71 0 GCA_002502135.1

ERR594345ERR594346ERR599037ERR599062ERR599167 SRR1658343SRR1658344SRR1658462SRR1658465SRR1658466SRR1658468SRR1658472SRR2090152SRR2090153SRR2090155SRR2090157SRR2090158SRR2090159SRR2090160SRR2090161SRR2090162SRR2177951SRR2177956SRR4388699SRR4028193SRR4028224 ERR1662208ERR1662209ERR1662212ERR1662216ERR1662492SRR2981515SRR5007141SRR5007147SRR1509792SRR1509799SRR1169871

low abundant MAG 25

● normalized relative abundance normalized relative

20

●

15 ●

●

10 ● ● ● ● ●

5 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 0 ● ● ● ● ● ● ● ● ●

ERR594345ERR594346ERR599037ERR599062ERR599167 SRR1658343SRR1658344SRR1658462SRR1658465SRR1658466SRR1658468SRR1658472SRR2090152SRR2090153SRR2090155SRR2090157SRR2090158SRR2090159SRR2090160SRR2090161SRR2090162SRR2177951SRR2177956SRR4388699SRR4028193SRR4028224 ERR1662208ERR1662209ERR1662212ERR1662216ERR1662492SRR2981515SRR5007141SRR5007147SRR1509792SRR1509799SRR1169871

Groundwater metagenome Marine metagenome FWM

Supplementary Figure 1 | Abundance of Undinarchaota (UAP2) across 37 metagenomic datasets. Normalized relative abundance of aquifer Naiadarchaeales (light green) and marine Undinarchaeales (dark green) across 37 metagenomes. Relative abundances were normalized by the total read counts. Read mapping was done to metagenomes belonging to different environmental types including groundwater, marine and freshwater metagenomes (FWM). Due to the difference in abundance, MAGs with a relative abundance >50 were plotted separately. Details on the metagenomes can be found in Supplementary Table S1. a

100

75

50

25 Average amino acid identity (%) Average

0 ) 2 1 ( ta o e a h Background rc Sulfolobales (6) a AigarchaeotaKorarchaeota (5) (3) in Altiarchaeota (9) Halobacteria (22) Poseidoniales (9) TheionarchaeaHadesarchaea (2) (4) Marsarchaeota (4) LokiarchaeotaThorarchaeota (2) (7) Parvarchaeota (3) Diapherotrites (8) Methanocellales (2) Methanopyrales (3) Geoarchaeales (3) Pacearchaeota (30)NanoarchaeotaHuberarchaeota (4) (3)d Micrarchaeota (12) ArchaeoglobalesAcidiprofundales (7) (4) ThermoplasmataMethanococcales (6) (7) Thermococcales (11) ThermoprotealesBathyarchaeota (8) (18) Aenigmarchaeotan (7) Methanophagales (3) MethanofastidiosaPersephonarchaea (5) (3) Thaumarchaeota (10) HeimdallarchaeotaWoesearchaeota (5) (39) U MethanomicrobialesMethanosarcinales (6) (12) Methanobacteriales (5) Desulfurococcales (14) VerstraetearchaeotaGeothermarchaeota (6) (3) Nanohaloarchaeota (6) Thermoplasmatales (12)Pontarchaea (MG-III)Hydrothermarchaeota (3) (3) NovelDPANN_1 (UAP1) (2) Methanomassiliicoccales (3) Methanonatronarchaeales (2) b

100

75

50

25 Average amino acid identity (%) Average

0 ) 2 1 ( ta o e a h rc a in d n U _ s v )_ 2 1 ( ta o e a h Undinarchaeota (12)_vs_Sulfolobales (6) rc UndinarchaeotaUndinarchaeota (12)_vs_Aigarchaeota (12)_vs_Korarchaeota (5) (3) a Undinarchaeota (12)_vs_Altiarchaeota (9) Undinarchaeota (12)_vs_Halobacteria (22) Undinarchaeota (12)_vs_Poseidoniales (9) UndinarchaeotaUndinarchaeota (12)_vs_Theionarchaea (12)_vs_HadesarchaeaUndinarchaeota (2) (4) (12)_vs_MarsarchaeotaUndinarchaeota (4) UndinarchaeotaUndinarchaeota (12)_vs_Lokiarchaeota (12)_vs_Thorarchaeota (12)_vs_OdinarchaeotaUndinarchaeota (2) (7) (12)_vs_Parvarchaeota (1) n (3) Undinarchaeota (12)_vs_Diapherotrites (8) Undinarchaeota (12)_vs_Methanocellales (2) Undinarchaeota (12)_vs_MethanopyralesUndinarchaeota (3) (12)_vs_Geoarchaeales (3) UndinarchaeotaUndinarchaeota (12)_vs_PacearchaeotaUndinarchaeotaUndinarchaeota (12)_vs_NovelDPANN_1 (12)_vs_Nanoarchaeota (12)_vs_Huberarchaeotai (30)Undinarchaeota (2) (4) (12)_vs_Micrarchaeota (3) (12) Undinarchaeota (12)_vs_ArchaeoglobalesUndinarchaeota (12)_vs_AcidiprofundalesUndinarchaeota (7)Undinarchaeota (12)_vs_Thermoplasmata (4)(12)_vs_MethanococcalesUndinarchaeota (6)(12)_vs_Thermococcales (7) (11)Undinarchaeota (12)_vs_ThermoprotealesUndinarchaeota (12)_vs_Bathyarchaeota (8) (18) Undinarchaeotad (12)_vs_Aenigmarchaeota (7) Undinarchaeota (12)_vs_Methanophagales (3) UndinarchaeotaUndinarchaeota (12)_vs_Methanofastidiosa (12)_vs_Persephonarchaea (5) Undinarchaeota(3) (12)_vs_ThaumarchaeotaUndinarchaeota (10)Undinarchaeota (12)_vs_Heimdallarchaeota (12)_vs_Woesearchaeota (5) (39)n UndinarchaeotaUndinarchaeota (12)_vs_Methanomicrobiales (12)_vs_Methanosarcinales (6) (12) Undinarchaeota (12)_vs_MethanobacterialesUndinarchaeota (5) (12)_vs_DesulfurococcalesUndinarchaeota Undinarchaeota(12)_vs_Verstraetearchaeota (14) (12)_vs_Geothermarchaeota (6) (3) UndinarchaeotaU (12)_vs_Nanohaloarchaeota (6) Undinarchaeota (12)_vs_ThermoplasmatalesUndinarchaeotaUndinarchaeota (12)_vs_Pontarchaea (12) (12)_vs_Hydrothermarchaeota (MG-III) (3) (3) Undinarchaeota (12)_vs_Methanomassiliicoccales (3) Undinarchaeota (12)_vs_Methanonatronarchaeales (2) Supplementary Figure 2 | Comparing the amino acid identity (AAI) of major archaeal lineages. a, Shared AAI across archaeal lineages. Background: Comparing all archaeal lineages included in the analyses but excluding archaea belonging to the same lineages in order to determine the lowest AAI that defines a cluster. b, AAI of Undinarchaeota compared to all other archaeal lineages to show that the highest identity is when comparing Undinarchaeota to themselves. The lower and upper hinges of the boxplot correspond to the first and third quartiles. The upper/lower whiskers extend from the hinge to the largest/smallest value no further than 1.5* of the inter-quartile range. Data beyond the whiskers are shown as individual data points. Number in brackets: Number of genomes included in each cluster. Raw values are listed in Supplementary Table 3. 100/100 Crenarchaeota--Desulfurococcales---Hyperthermus_butylicus-GCA_000015145.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae--Pyrodictium_delaneyi-GCA_001412615.rrn1 67.3/90 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae--Pyrolobus_fumarii-GCA_000223395.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales--Ignicoccus-Ignicoccus_hospitalis-GCA_000017945.rrn1 364 species 76.4/92 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae--Acidilobus_saccharovorans-GCA_000144915.rrn1 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales---Caldisphaera_lagunensis-GCA_000317795.rrn1 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae--Aeropyrum_pernix-GCA_000011125.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae--Desulfurococcus_amylolyticus-GCA_000020905.rrn1 16S + 23S rRNA genes 89/10099.1/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185.rrn1 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495.rrn1 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae--Staphylothermus_marinus-GCA_000015945.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae--Fervidicoccus_fontis-GCA_000258425.rrn1 100/100 Crenarchaeota-Thermoprotei-Sulfolobales---Sulfurisphaera_tokodaii-GCA_000011205.rrn1 trimmed alignment (TRIMAL) 28.5/80 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285.rrn1 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735.rrn1 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae--Metallosphaera_sedula-GCA_000016605.rrn1 100/99 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae--Acidianus_sulfidivorans-GCA_003201765.rrn1 100/100 Crenarchaeota-Thermoprotei-Thermoproteales---Vulcanisaeta_distributa-GCA_000148385.rrn1 4,462 bp alignment 82.8/94 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385.rrn1 77.5/94 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae--Caldivirga_maquilingensis-GCA_000018305.rrn1 100/100100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae--Pyrobaculum_ferrireducens-GCA_000234805.rrn1 97.1/98 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae--Thermoproteus_tenax-GCA_000253055.rrn1 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae--Thermocladium_modestius-GCA_001315925.rrn1 100/100 Crenarchaeota-Thermoprotei-Thermoproteales---Thermofilum_pendens-GCA_000015225.rrn1 Iqtree,GTR+G Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805.rrn1 100/100 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535.rrn1 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545.rrn1 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595.rrn1 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705.rrn1 36.3/82 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305.rrn1 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005.rrn1 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025.rrn1 99.7/100 Thaumarchaeota-none----Nitrosopumilus_maritimus-GCA_000018465.rrn1 100/100 Thaumarchaeota-none----Cenarchaeum_symbiosum-GCA_000200715.rrn1 89.7/96 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185.rrn1 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185.rrn1 Asgard + TACK 100/100 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055.rrn1 99.6/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925.rrn1 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785.rrn1 5.2/47 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165.rrn1 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115.rrn1 50.7/95 98.6/95 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085.rrn1 92.4/99 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325.rrn1 100/100 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285.rrn1 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965.rrn1 96/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795.rrn1 99.9/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805.rrn1 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625.rrn1 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655.rrn1 99.9/98 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865.rrn1 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665.rrn1 83.9/99 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755.rrn1 99.8/100 90.9/61 94.3/94 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275.rrn1 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465.rrn1 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605.rrn1 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965.rrn1 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015.rrn1 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645.rrn1 Nanoarchaeota Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085.rrn1 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639.rrn1 100/100 Euryarchaeota--Thermococcales--Pyrococcus-Pyrococcus_furiosus-GCA_000007305.rrn1 48.4/74 9 9 / 8 5 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105.rrn1 95.5/100Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105.rrn1 93.9/73 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445.rrn1 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485.rrn1 98.9/100 82.9/67100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585.rrn1 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545.rrn1 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085.rrn1 92.9/71 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545.rrn1 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985.rrn1 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae--Palaeococcus_pacificus-GCA_000725425.rrn1 98.5/8399.8/50 54.8/100 Euryarchaeota--Methanococcales--Methanococcus-Methanococcus_vannielii-GCA_000017165.rrn1 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185.rrn1 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae--Methanothermococcus_okinawensis-GCA_000179575.rrn1 100/100 Euryarchaeota-Methanococci-Methanococcales---Methanotorris_igneus-GCA_000214415.rrn1 95.6/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985.rrn1 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625.rrn1 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305.rrn1 99/100 Euryarchaeota--Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545.rrn1 31.3/63 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525.rrn1 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725.rrn1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295.rrn1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095.rrn1 0 / 4 5 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575.rrn1 94.9/82 9 9 / 8 6 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715.rrn1 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695.rrn1 9 0 / 7 5 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595.rrn1 99.6/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205.rrn1 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215.rrn1 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175.rrn1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125.rrn1 99.4/100 Euryarchaeota-Halobacteria--Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325.rrn1 90.1/69 96.1/66 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735.rrn1 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705.rrn1 31.4/59 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625.rrn1 4 1 / 6 5 99.9/77 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715.rrn1 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685.rrn1 100/10099.6/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975.rrn1 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715.rrn1 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625.rrn1 88.4/100 Euryarchaeota-Halobacteria----Halogeometricum_borinquense-GCA_000172995.rrn1 99.9/100 26.1/65100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae--Haloquadratum_walsbyi-GCA_000237865.rrn1 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765.rrn1 Euryarchaeota-Halobacteria-Haloferacales--Halorubrum-Halorubrum_lacusprofundi-GCA_000022205.rrn1 72.9/90100/100 Euryarchaeota-Halobacteria---Natronomonas-Natronomonas_pharaonis-GCA_000026045.rrn1 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055.rrn1 72.6/88 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae--Halomicrobium_mukohataei-GCA_000023965.rrn1 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae--Halorhabdus_tiamatea-GCA_000470655.rrn1 100/100 Euryarchaeota-Halobacteria-Halobacteriales--Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115.rrn1 81.6/97 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955.rrn1 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805.rrn1 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575.rrn1 100/100 Euryarchaeota--Methanosarcinales--Methanosarcina-Methanosarcina_acetivorans-GCA_000007345.rrn1 43.3/100 98.3/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085.rrn1 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025.rrn1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205.rrn1 100/99 82.6/70 76.2/99 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885.rrn1 99.8/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae--Methanolobus_psychrophilus-GCA_000306725.rrn1 5 1 / 9 9 27.7/70 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae--Methanomethylovorans_hollandica-GCA_000328665.rrn1 97.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae--Methanococcoides_burtonii-GCA_000013725.rrn1 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae--Methanohalophilus_halophilus-GCA_001889405.rrn1 71.6/85 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae--Methanosalsum_zhilinae-GCA_000217995.rrn1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae--Methanohalobium_evestigatum-GCA_000196655.rrn1 60.3/58 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415.rrn1 99.2/98 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445.rrn1 70.1/87 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105.rrn1 94.7/82 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae--Methanospirillum_hungatei-GCA_000013445.rrn1

98.2/84 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae--Methanocorpusculum_labreanum-GCA_000015765.rrn1 Euryarchaeota 51.7/85 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965.rrn1 99.9/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae--Methanoregula_formicica-GCA_000327485.rrn1 82.5/96 Euryarchaeota-Methanomicrobia-Methanomicrobiales---Methanolacinia_petrolearia-GCA_000147875.rrn1 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae--Methanoculleus_bourgensis-GCA_000304355.rrn1 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435.rrn1 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485.rrn1 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405.rrn1 100/87 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915.rrn1 100/87 Euryarchaeota-Archaeoglobi-Archaeoglobales--Archaeoglobus-Archaeoglobus_profundus-GCA_000025285.rrn1 99.7/87 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae--Ferroglobus_placidus-GCA_000025505.rrn1 99.9/87100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae--Geoglobus_acetivorans-GCA_000789255.rrn1 99.9/87 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045.rrn1 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665.rrn1 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625.rrn1 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565.rrn1 55.2/98 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745.rrn1 97.8/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705.rrn1 8.9/78 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225.rrn1 75.5/100Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655.rrn1 100/100 99.1/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055.rrn1 99.9/87 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845.rrn1 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales---Picrophilus_torridus-GCA_000008265.rrn1 Euryarchaeota-Thermoplasmata-Thermoplasmatales---Ferroplasma_acidiphilum-GCA_002078355.rrn1 99.9/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales--Thermoplasma-Thermoplasma_volcanium-GCA_000011185.rrn1 97.8/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915.rrn1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825.rrn1 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135.rrn1 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665.rrn1 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505.rrn1 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395.rrn1 97.5/100Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485.rrn1 99.8/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235.rrn1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205.rrn1 100/100 76.8/99 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435.rrn1 96.9/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545.rrn1 100/100 42.7/98100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555.rrn1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535.rrn1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935.rrn1 98.4/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425.rrn1 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255.rrn1 100/100 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305.rrn1 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805.rrn1 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225.rrn1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985.rrn1 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515.rrn1 84.5/82 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095.rrn1 56.5/80 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815.rrn1 98.1/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315.rrn1 99.4/87 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355.rrn1 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155.rrn1 94.8/99 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995.rrn1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585.rrn1 99.7/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295.rrn1 98.2/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705.rrn1 93.7/9177.3/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475.rrn1 54.8/79 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985.rrn1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115.rrn1 100/10099.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125.rrn1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915.rrn1 8.4/81 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415.rrn1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795.rrn1 88.5/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115.rrn1 79.8/100 100/100 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655.rrn1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415.rrn1 99.2/100 28.3/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085.rrn1 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685.rrn1 99.4/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615.rrn1 98.7/100 96.9/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155.rrn1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075.rrn1 99.8/100 83.4/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015.rrn1 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285.rrn1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115.rrn1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805.rrn1 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065.rrn1 48.8/66 19.5/83 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085.rrn1 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595.rrn1 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265.rrn1 84.2/81 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425.rrn1 69.3/81 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795.rrn1 97.7/84 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035.rrn1 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355.rrn1 96.1/100UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525.rrn1 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935.rrn1 DPANN 100/100 99.8/100UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465.rrn1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17.rrn1 95.7/86 Undinarchaeota UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135.rrn1 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965.rrn1 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641.rrn1 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515.rrn1 98.3/100 100/99 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695.rrn1 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122.rrn1 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165.rrn1 98.2/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475.rrn1 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455.rrn1 93.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495.rrn1 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385.rrn1 99.7/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605.rrn1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915.rrn1 91.6/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355.rrn1 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275.rrn1 88.1/90 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035.rrn1 97.7/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845.rrn1 93.3/99 99.8/99 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785.rrn1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855.rrn1 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565.rrn1 99.9/100Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505.rrn1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795.rrn1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105.rrn1

0.2 Supplementary Figure 3 | Phylogenetic placement of Undinarchaeota based on a concatenated alignment of the 16S and 23S rRNA gene sequences. Sequences were extracted from the 364 species set (of these 238 species encoded 16S and/or 23 rRNA genes). The alignment was trimmed using TRIMAL (alignment length = 4,462 bp) and a maximum-likelihood phylogenetic tree was inferred with the GTR+G model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. Scale bar: Average number of substitutions per site. The tree was artificially rooted using DPANN archaea. 99.9/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615.rrn1 94.8/93 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945.rrn1 364 species 89.2/92 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915.rrn1 100/100 99.6/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325.rrn1 96.8/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795.rrn1 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125.rrn1 98.2/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905.rrn1 16S + 23S rRNA genes 98.4/100 98.9/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185.rrn1 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495.rrn1 99.9/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945.rrn1 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205.rrn1 96.1/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285.rrn1 trimmed alignment (BMGE) 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735.rrn1 45.3/92 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605.rrn1 99.8/91 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765.rrn1 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425.rrn1 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805.rrn1 58.4/76 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055.rrn1 3,128 bp alignment 90.5/78 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305.rrn1 99.8/10099/100 98.4/91 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385.rrn1 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385.rrn1 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925.rrn1 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225.rrn1 Iqtree,GTR+G Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805.rrn1 100/100 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535.rrn1 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545.rrn1 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595.rrn1 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705.rrn1 71.7/89 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305.rrn1 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005.rrn1 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025.rrn1 89.9/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465.rrn1 99.9/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715.rrn1 96.2/100 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185.rrn1 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185.rrn1 100/100 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055.rrn1 5 2 / 9 4 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925.rrn1

100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785.rrn1 Asgard + TACK Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165.rrn1 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115.rrn1 6 4 / 7 9 92/100 91.6/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325.rrn1 100/100 83.3/99 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285.rrn1 99.8/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965.rrn1 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085.rrn1 83/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795.rrn1 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805.rrn1 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625.rrn1 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605.rrn1 100/74 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655.rrn1 0 / 2 4 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865.rrn1 44.2/84 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665.rrn1 73.4/93 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755.rrn1 99.7/96 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275.rrn1 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465.rrn1 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305.rrn1 3 9 / 6 1 81.9/82 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105.rrn1 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105.rrn1 73.6/90Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445.rrn1 92.1/98 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485.rrn1 2.5/52 97.9/91 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585.rrn1 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545.rrn1 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085.rrn1 4 3 / 8 9 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545.rrn1 99.3/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425.rrn1 93.1/91 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985.rrn1 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965.rrn1 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015.rrn1 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645.rrn1 96.4/90 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085.rrn1 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639.rrn1 78.5/99 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165.rrn1 Nanoarchaeota 100/100 99.6/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185.rrn1 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575.rrn1 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415.rrn1 88.3/84 92.1/100Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985.rrn1 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625.rrn1 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305.rrn1 63.6/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545.rrn1 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525.rrn1 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725.rrn1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295.rrn1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095.rrn1 96.3/84 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325.rrn1 94.6/75 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735.rrn1 84.7/69 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625.rrn1 9 9 / 9 4 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705.rrn1 67.4/81 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715.rrn1 100/10046.2/80 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685.rrn1 99.4/99 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975.rrn1 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715.rrn1 99.5/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625.rrn1 20.9/61 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995.rrn1 84.4/94 99.9/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865.rrn1 8 0 / 9 5 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765.rrn1 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205.rrn1 80.5/98 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965.rrn1 46.2/939 7 / 9 6 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655.rrn1 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045.rrn1 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055.rrn1 75.8/70 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805.rrn1 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575.rrn1 97.2/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115.rrn1 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955.rrn1 96.2/100Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345.rrn1 54.1/100 95.8/99 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085.rrn1 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025.rrn1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205.rrn1 81.8/91 87.2/98 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885.rrn1 83.4/99 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725.rrn1 6 7 / 5 4 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665.rrn1 100/1009 1 / 5 5 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725.rrn1 9 0 / 5 5 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995.rrn1 93.1/98 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405.rrn1 79.3/89 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655.rrn1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415.rrn1 98.1/100 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445.rrn1 98.1/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105.rrn1 3 1 / 3 8 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765.rrn1 9 0 / 4 1 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355.rrn1 95.7/76 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965.rrn1 97.5/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485.rrn1 87.9/63 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445.rrn1 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875.rrn1 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435.rrn1 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485.rrn1 100/100 Euryarchaeota 100/94 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405.rrn1 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915.rrn1 98.9/99 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285.rrn1 59.2/89 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505.rrn1 99.1/92 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665.rrn1 99.3/9399.7/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255.rrn1 8 0 / 3 6 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045.rrn1 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625.rrn1 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565.rrn1 44.3/84 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745.rrn1 90.3/84 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705.rrn1 85.8/99 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225.rrn1 78.9/100Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655.rrn1 100/100 95/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055.rrn1 99.9/94 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845.rrn1 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265.rrn1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355.rrn1 98.2/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185.rrn1 98.9/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915.rrn1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825.rrn1 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135.rrn1 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665.rrn1 99.6/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505.rrn1 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395.rrn1 88.3/100Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485.rrn1 99.9/99 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235.rrn1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205.rrn1 100/100 14.5/89 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435.rrn1 97.5/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545.rrn1 100/100 50.9/95100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555.rrn1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535.rrn1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935.rrn1 9 7 / 9 8 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425.rrn1 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255.rrn1 100/100 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305.rrn1 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805.rrn1 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225.rrn1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985.rrn1 99.9/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205.rrn1 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215.rrn1 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175.rrn1 95.5/92Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575.rrn1 90.4/91 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695.rrn1 94.8/41 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595.rrn1 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715.rrn1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125.rrn1 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515.rrn1 81.7/91 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095.rrn1 100/100 9 6 / 9 1 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315.rrn1 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355.rrn1 100/100 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995.rrn1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585.rrn1 91.5/99 58.6/90 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155.rrn1 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815.rrn1 94.2/99 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295.rrn1 78/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705.rrn1 92.6/100 95.7/96 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475.rrn1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985.rrn1 92.2/8294.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125.rrn1 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915.rrn1 97.3/85 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415.rrn1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795.rrn1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115.rrn1 91/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115.rrn1 62.6/100 100/100 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655.rrn1 35.3/95 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415.rrn1 95.2/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085.rrn1 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685.rrn1 98.4/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615.rrn1 39.3/93 98.2/100 98.6/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155.rrn1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075.rrn1 99.9/100 91.1/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015.rrn1 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285.rrn1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115.rrn1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805.rrn1 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065.rrn1 67.8/100 51.7/70 99.8/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085.rrn1 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595.rrn1 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265.rrn1 96.4/96 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425.rrn1 88.9/96 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795.rrn1 94.9/95 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035.rrn1 93.7/80 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355.rrn1 99.7/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965.rrn1

Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641.rrn1 DPANN 80.5/100UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525.rrn1 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935.rrn1 100/100 98.9/100UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465.rrn1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17.rrn1 Undinarchaeota UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135.rrn1 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515.rrn1 96.6/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695.rrn1 99.9/99 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122.rrn1 99.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165.rrn1 95.4/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475.rrn1 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455.rrn1 82.4/99 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495.rrn1 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385.rrn1 99.8/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605.rrn1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915.rrn1 91.9/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355.rrn1 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275.rrn1 95.5/84 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035.rrn1 61.5/99 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845.rrn1 86.3/100 99.6/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785.rrn1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855.rrn1 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565.rrn1 99.7/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505.rrn1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795.rrn1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105.rrn1

0.09 Supplementary Figure 4 | Phylogenetic placement of Undinarchaeota based on a concatenated alignment of the 16S and 23S rRNA gene sequences. Sequences were extracted from the 364 species set (of these 238 species encoded 16S and/or 23 rRNA genes). The alignment was trimmed using BMGE (alignment length = 3,128 bp) and a maximum-likelihood phylogenetic tree was inferred with the GTR+G model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. Scale bar: Average number of substitutions per site. The tree was artificially rooted using DPANN archaea. 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615.rrn1 59.4/59 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945.rrn1 364 species 66.4/59 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325.rrn1 100/100 99.9/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795.rrn1 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125.rrn1 16S + 23S rRNA genes 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905.rrn1 91.6/99 99.1/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495.rrn1 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945.rrn1 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425.rrn1 trimmed alignment (TRIMAL) 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205.rrn1 24.8/72 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285.rrn1 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735.rrn1 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605.rrn1 100/88 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765.rrn1 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385.rrn1 Removal of heterogeneous sites 97.9/99 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385.rrn1 17.2/60 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305.rrn1 Pruner, 10% site removal 100/100100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805.rrn1 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055.rrn1 69.7/80 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925.rrn1 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225.rrn1 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805.rrn1 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535.rrn1 4,016 bp alignment 100/100 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545.rrn1 6.4/71 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595.rrn1 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005.rrn1 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025.rrn1 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705.rrn1 Iqtree,GTR+G Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305.rrn1 99.8/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465.rrn1 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715.rrn1 100/100 96.8/98 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185.rrn1 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185.rrn1 100/100 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055.rrn1 52.7/90 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925.rrn1

100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785.rrn1 Asgard + TACK Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165.rrn1

18.3/62 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115.rrn1 7 4 / 6 9 70.2/99 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325.rrn1 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285.rrn1 28.1/70 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965.rrn1 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085.rrn1 94.2/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795.rrn1 99.7/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805.rrn1 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625.rrn1 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605.rrn1 0 / 6 9 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655.rrn1 0 / 1 8 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865.rrn1 99.4/58 9 5 / 9 8 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755.rrn1 9 9 / 8 4 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275.rrn1 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465.rrn1 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665.rrn1 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305.rrn1 76.5/80 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105.rrn1 92.6/99 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105.rrn1 92.3/85 33.3/76 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445.rrn1 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485.rrn1 97.8/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585.rrn1 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545.rrn1 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085.rrn1 4 9 / 6 7 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545.rrn1 99.8/87 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425.rrn1 47.7/64 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985.rrn1 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965.rrn1 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015.rrn1 100/100 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645.rrn1 98.7/8698.9/71 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085.rrn1 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639.rrn1 Nanoarchaeota 62.4/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165.rrn1 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185.rrn1 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575.rrn1 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415.rrn1 97/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985.rrn1 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625.rrn1 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305.rrn1 36.4/71 98.4/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545.rrn1 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525.rrn1 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725.rrn1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295.rrn1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095.rrn1 0 / 3 6 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575.rrn1 60.6/77 98.9/91 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715.rrn1 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695.rrn1 82.8/84 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595.rrn1 99.8/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205.rrn1 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215.rrn1 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175.rrn1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125.rrn1 97.5/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975.rrn1 19.7/41 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715.rrn1 75.5/52 90.5/47 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715.rrn1 7 9 / 4 5 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685.rrn1 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625.rrn1 100/99 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705.rrn1 100/10095.6/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325.rrn1 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735.rrn1 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625.rrn1 84.9/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995.rrn1 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865.rrn1 36.4/53100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765.rrn1 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205.rrn1 80.6/98100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045.rrn1 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055.rrn1 68.8/59 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965.rrn1 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655.rrn1 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115.rrn1 78.1/98 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955.rrn1 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805.rrn1 63.7/57 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575.rrn1 37.1/66 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445.rrn1 58.3/58 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875.rrn1 99.1/68 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355.rrn1 41.1/51 100/100 68.5/84 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965.rrn1 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485.rrn1 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765.rrn1 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445.rrn1 86.2/94 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105.rrn1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415.rrn1 99.9/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345.rrn1 100/100 26.3/99 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085.rrn1 99/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025.rrn1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205.rrn1 46.9/94 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885.rrn1 Euryarchaeota 99.7/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725.rrn1 95.5/99 100/100 99.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665.rrn1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725.rrn1 100/100 5 0 / 9 0 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995.rrn1 99.3/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405.rrn1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655.rrn1 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435.rrn1 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485.rrn1 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405.rrn1 100/87 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915.rrn1 100/88 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285.rrn1 99.7/87 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505.rrn1 100/87100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255.rrn1 99.9/87 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045.rrn1 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665.rrn1 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625.rrn1 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565.rrn1 76.8/100Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655.rrn1 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055.rrn1 94.8/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845.rrn1 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265.rrn1 98.9/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355.rrn1 99.8/87 5 2 / 9 9 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745.rrn1 100/100 98.3/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705.rrn1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225.rrn1 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185.rrn1 96.4/99 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915.rrn1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825.rrn1 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135.rrn1 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665.rrn1 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505.rrn1 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395.rrn1 93.7/100Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485.rrn1 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235.rrn1 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205.rrn1 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435.rrn1 81.3/100 99.5/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545.rrn1 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555.rrn1 54.7/98 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535.rrn1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935.rrn1 97.9/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425.rrn1 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255.rrn1 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305.rrn1 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805.rrn1 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225.rrn1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985.rrn1 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515.rrn1 45.3/69 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095.rrn1 100/100 86.9/70 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315.rrn1 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355.rrn1 100/100 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995.rrn1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585.rrn1 97.6/100 91.5/70 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155.rrn1 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815.rrn1 99.5/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295.rrn1 98.4/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705.rrn1 98.6/94 80.4/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475.rrn1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985.rrn1 89.8/37 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115.rrn1 99.7/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125.rrn1 100/100 7.7/30 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915.rrn1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415.rrn1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795.rrn1 62.2/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115.rrn1 64.2/100 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655.rrn1 100/100 2 9 / 9 9 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415.rrn1 99.3/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085.rrn1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685.rrn1 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615.rrn1 99/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155.rrn1 95/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075.rrn1 99.9/100 36.8/97 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015.rrn1 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285.rrn1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115.rrn1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805.rrn1 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065.rrn1 76.4/86 83.9/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085.rrn1 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595.rrn1 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265.rrn1 98.8/78 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355.rrn1 38.8/72 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795.rrn1 100/100 97.8/90 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035.rrn1 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425.rrn1 95.5/100UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525.rrn1 100/100

UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935.rrn1 DPANN 100/100 99.5/100UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465.rrn1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17.rrn1 93.1/98 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135.rrn1 Undinarchaeota 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965.rrn1 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641.rrn1 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515.rrn1 98.2/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695.rrn1 100/100 100/100 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122.rrn1 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165.rrn1 99.2/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475.rrn1 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455.rrn1 94/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495.rrn1 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385.rrn1 99.9/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605.rrn1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915.rrn1 92.4/99 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355.rrn1 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275.rrn1 86.4/94 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035.rrn1 98.5/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845.rrn1 95/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785.rrn1 99.9/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855.rrn1 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565.rrn1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505.rrn1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795.rrn1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105.rrn1

0.3 Supplementary Figure 5 | Phylogenetic placement of Undinarchaeota based on a concatenated alignment of the 16S and 23S rRNA gene sequences. Sequences were extracted from the 364 species set (of these 238 species encoded 16S and/or 23 rRNA genes). The alignment was trimmed using TRIMAL and 10% of the most heterogenous sites were removed using an alignment pruner (alignment length = 4,016 bp). A maximum likelihood phylogenetic tree was inferred with the GTR+G model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. Scale bar: Average number of substitutions per site. The tree was artificially rooted using DPANN archaea. 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 95.4/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 364 species 69.9/98 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 35.9/93 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 94.6/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 25% top ranked proteins 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 99.9/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 98.4/97 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 (n=28) Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 100/84 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 trimmed alignment (BMGE) 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/83 94.2/84 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 7,442 amino acids Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 Iqtree, LG+C60+F+R 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 67.3/99 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 32.2/73 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 91.9/99 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 99.1/100 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 90.7/100 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 99.2/100100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185

Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 Asgard + TACK 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 98.2/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 99/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 99.4/100 84.8/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 100/86 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 100/86 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/92100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 92.9/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 93.4/94 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 99.3/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 68.1/81 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 99.7/81 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/98100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 45.2/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 58.4/99 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 99.9/100 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 99.9/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 88.7/88 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 96.5/91 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 98.6/100 83.4/88 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 99/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 89.1/90 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 99.9/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 99.2/91 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/46 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 98.4/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 87.8/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 20.7/82 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/48 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/100 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 99.7/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 8 8 / 4 5 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 99.9/100 93.5/93 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 99.5/93 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 99.2/46 100/100 9 4 / 9 4 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 11.4/48 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 73.5/87 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 87.4/86100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 99.5/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 9 5 / 8 8 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 78.6/100Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 95.8/88 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 99/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 95.2/99 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 98.6/100 92.6/99 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 90.7/93 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 98.2/64 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 99.9/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 99.6/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 49.1/62 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 100/100 Euryarchaeota--Methanopyrales---Methanopyrus_sp_SNP6-GCA_002201895 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 74.3/100 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 90.1/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 99.8/70 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 9 3 / 6 7 100/100 77.3/80 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 72.3/79 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 100/10099.9/83 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 95.3/67 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 99.5/96 99.7/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 58.9/98 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/10018.4/84 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 99.8/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 65.9/100 98/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 94.7/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 82.9/92 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 99.1/93 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 100/100 69.5/85 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 51.4/9499.5/80 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/100 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 93.2/95 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/100 99.7/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 0 / 2 4 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 78.3/68 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 89.1/65 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 100/100 99.9/10098.9/81 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 64.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 68.8/83 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 83.4/99 18.3/93 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 38.7/79 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015

Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 Cluster2 100/100 94.4/94 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 51.4/89 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 91.3/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 100/100 17.5/72 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 99.9/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 87.5/99 100/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 99.8/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 DPANN 97.3/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 99.8/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 78.8/99 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 100/100 99.9/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 96.7/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 7 2 0 / 8 5 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 98/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 Undinarchaeota UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 99.9/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 96.1/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 99.6/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 56.5/99 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 78.9/100 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 45.6/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 69.4/99 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 98.6/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 96.4/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 94.7/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Cluster1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 99.8/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 6 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 25% top ranked proteins (n=28) and the 364 species set. The alignment was trimmed with BMGE (alignment length = 7,422 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 1 can be found in Supplementary Table 6. 127 species 25% top ranked proteins (n=28 trimmed alignment (BMGE) 7,666 amino acids Iqtree, LG+C60+F+R

100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 84.7/49 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 92.1/50 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 99.9/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 74.1/72 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 99.4/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 62.3/70100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/100 99.9/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100 100/77 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/99 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 56.3/85 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota 99.8/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 86.7/95 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 96.1/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 52.6/85 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 99.5/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 41.6/96 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 91.4/76 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 98.2/99 99.9/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 99.6/100 75.1/99 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 9 7 / 9 9 100/10099.4/77 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 16.8/66 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Asgard + TACK 99.9/100 59.6/94 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 13.1/66 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 7 9 / 9 8 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 95.2/87 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 89.5/87 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 54.3/80 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.8/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 99.5/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 Cluster2 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 99.9/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 62.1/98 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 8 8 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 8 9 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 100/100 DPANN 97.1/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 Undinarchaeota 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100

Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 7 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 25% top ranked proteins (n=28) and the 127 species set. The alignment was trimmed with BMGE (alignment length= 7,666 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 2 can be found in Supplementary Table 6. 127 species 25% top ranked proteins (n=28) trimmed alignment (BMGE) 7,666 amino acids Phylobayes, CAT+GTR

0,99 1 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 1 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 1 0,94 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 0,55 1 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 1 1 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 1 1 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 1 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 1 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 0,97 1 1 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 0,99 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 0,98 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 1 1 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 1 1 1 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 1 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 1 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 1 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 Asgard + TACK 1 0,88 1 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 1 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 1 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 1 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 1 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 1 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 1 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 1 1 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 1 0,98 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 1 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 1 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 1 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 1 1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 0,81 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 1 0,87 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 1 1 1 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 1 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 1 0,97 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 1 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 1 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 1 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 1 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 1 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 0,55 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 1 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 1

Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 Euryarchaeota 1 1 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 1 1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 1 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 0,82 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 1 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 1 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 1 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 1 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 0,89 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 1 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 0,99 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 1 1 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 1 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 1 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 1 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 1 0,99 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 1 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 1 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 1 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Cluster2 1 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 1 1 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 1 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 1 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 1 0,99 1 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17

UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 DPANN 1 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 1 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 1 1 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 1 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 1 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 1 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 1 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 1 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 Cluster1 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505

0.5

Supplementary Figure 8 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 25% top ranked proteins (n=28) and the 127 species set. The alignment was trimmed with BMGE (alignment length = 7,666 a). A Bayesian phylogenetic tree was inferred with the CAT+GTR model, run with four chains for a total of 34,260 cycles (25% burn-in). The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 3 can be found in Supplementary Table 6. 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 93.7/75 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 100/99 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 77.1/94 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 96.5/79 364 species 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 99.9/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625

85.3/83 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 100/100 9 9 / 8 3 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 50% top ranked proteins Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 (n=56) Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/51 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 trimmed alignment (BMGE) 99.1/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 92.8/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655

100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 99.9/67 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 99.8/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 12,849 amino acids 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 90.7/50 98.9/99 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 72.4/93 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 100/94 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 Iqtree, LG+C60+F+R 99.5/51 100/100 12.6/38 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 99.1/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 97.9/86 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 82.6/85 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 73.1/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 99.9/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 94.7/85 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 78.7/100Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 99.8/85 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 99.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 89.8/99 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 99.9/100 79.9/99 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635

100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 100/100 97.6/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 99.4/96 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 99.3/96 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/96100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 71.6/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 79.8/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 69.3/99 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 7 6 / 4 2 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 95.6/84 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 99.8/43 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 94.7/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 72.3/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 52.9/95 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 97.4/99 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/81 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/100 8 9 / 8 0 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 54.5/98 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 98.8/100 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 69.8/97 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 97.6/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 91.8/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 92.2/97 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 Asgard + TACK 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 98.5/99 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 88.2/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 97.8/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 71.1/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 88.5/60 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 75.3/61 29.6/44 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 49.5/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 99.6/55 83.3/82 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 92.6/98 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 100/92 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 99.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 89.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 72.9/99 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 100/100 99.7/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 23.8/95 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 98/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 100/100 46.3/97 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 81.5/97 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 33.9/76 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/96 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 34.8/89 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 74.6/92 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 100/84 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 43.1/63 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 29.3/63 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/100 89.7/82 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 100/100 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 99.9/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 51.7/90 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 63.6/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 100/100 1 4 / 776.7/90 3 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015

100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Cluster2 99.9/99 10.9/73 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 17.6/72 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 99.2/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.7/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 99.9/100 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 DPANN Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 26.9/90 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 74.6/72UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 0 / 4 0 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.7/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 100/100 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 99.8/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 53.2/98 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 21.2/99 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/96 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 8 4 / 9 6 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 99.8/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 62.7/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 69.6/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100

Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 Cluster1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.4 Supplementary Figure 9 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. The alignment was trimmed with BMGE (alignment length = 12,849 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 4 can be found in Supplementary Table 6. 100/100 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 70.1/51 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 100/97 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 74.5/81 97.7/71 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 364 species 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 79.6/90 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 99.9/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 94.1/90 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 50% top ranked proteins 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 (n=56) 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/99 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 98.4/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 trimmed alignment (BMGE) 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 89.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 99.9/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 12,849 amino acids 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 74.8/95 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 99.2/100 87.9/97 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 100/98 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 95.1/98 100/100 57.1/98 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Iqtree, Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 99.9/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 LG MFP+MERGE followed by Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 98.8/73 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 8 3 / 7 3 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 NONREV Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 60.4/99 99.9/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 97.7/93 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 89.2/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/93 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 99.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 100/99 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 64.2/97 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 99.9/100 74.6/95 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 96.5/96 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 99.9/84 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 99.9/84 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/84100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 65.6/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 20.6/85 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 73.9/100 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 100/92 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 87.8/50 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 99.2/56 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 99.3/50 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 95.9/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 8 3 / 9 8 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 58.2/96 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 7 7 / 5 8 97.6/99 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 100/89 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 99.9/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/95 100/89 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 48.5/93 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/95 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 95.3/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 98.8/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 56.9/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 Asgard + TACK 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 40.3/79 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 26.9/88 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 99.8/100 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/92 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 99.5/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 70.6/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 57.2/81 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 92.3/83 99.1/93 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 91.3/79 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 6 5 / 9 0 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 100/96 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 99.2/98 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 98.5/96 100/100 76/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 99.8/100 99.3/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 99.1/9099.8/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 7.3/56 8 7 / 9 0 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 82.8/96 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 100/100 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/97 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 26.7/73 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 99.4/96 83.6/76 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 14.1/87 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 15.4/74 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 81.9/81 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 98.6/87 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 100/100 100/100100/89 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 44.9/68 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 99.8/100 99.3/97 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 47.3/100 99.3/99 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 96.1/69 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 99.7/92 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 Cluster2 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 100/100 98/100 35.3/91 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/99 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.7/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 DPANN 39.3/50 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 100/100 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 74.1/99 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/95 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 9 0 0 / 4 6 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.9/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 100/100 83.6/75 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 92.1/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/99 39.1/97 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 84.3/99 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 99.9/85 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 33.9/99 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 77.6/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 0.2 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 Supplementary Figure 10 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked (n=56) and the 364 species set. The alignment was trimmed with BMGE (alignment length = 12,849 aa). An initial ML phylogenetic tree was inferred with the LG model (-m MFP +MERGE) followed by a tree generated with a non-reversible model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was rooted using the non-reversible model. Scale bar: Average number of substitutions per site.Tree statistics for tree number 5 can be found in Supplementary Table 6. 100/100/100/100Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 100/100/100/100 73.4/50/67.6/62 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 99.7/99/99.6/95 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 69.2/67/75/86 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 364 species 100/100/100/10097.9/83/97.3/79 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100/100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 100/100/100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 77.4/86/83.8/93 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 99.9/100/100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100/100/100 100/100/100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 97/86/95.1/94 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 50% top ranked proteins Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100/100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100/100/100 100/100/100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100/100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 (n=56) Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100/100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/93/100/98 100/100/100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100/100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 100/100/100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 99.9/100/98.8/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 trimmed alignment (BMGE) 99.9/100/100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100/100/100 100/100/100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 90.8/100/89.2/99 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100/100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100/100/100 100/100/100/100Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100/100/100 100/100/99.9/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/100/100/100 100/100/100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 12,849 amino acids Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/100/100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100/100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 95.2/91/70/96 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 99.6/100/98.5/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 85/97/85.5/96 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100/100/100 100/98/100/97 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 Iqtree, NONREV model 94.4/91/95.3/96 100/100/100/100 63.4/97/49.9/96 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 99.6/100/99.6/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100/100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 99.4/63/99.4/74 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 73.5/62/84.9/74 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100/100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100/100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100/100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100/100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 64.8/99/65.4/99 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 100/100/100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 98.6/89/97/87 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 86.1/100/86.9/100Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100/100/100 99.9/89/99.9/87 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100/100/100 100/100/100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 100/100/100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100/100/100 100/100/100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100/100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100/100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100/100/100 99.8/100/100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 75.5/92/99.9/99 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100/100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100/100/100 100/100/100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 90.4/97/59.4/92 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100/100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100/99.9/100 31.3/89/69.1/92 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100/100/100 100/100/100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100/100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100/100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100/100/100Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100/100/100 100/100/100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100/100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100/100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100/100/100

Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota 100/100/100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100/100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100/100/100 100/100/100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 85.5/97/97.6/98 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100/100/100Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100/100/100 100/100/100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 99.8/91/99.7/88 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100/100/100 99.8/91/99.8/88 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/91/100/88100/100/100/100Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100/100/100 100/100/100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100/100/100 100/100/100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 50.4/100/64.5/98 100/100/100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100/100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 100/100/100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100/100/100 100/100/100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100/100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 61.4/100/11.6/68 100/100/100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100/100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 71.9/99/65.8/97 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 100/100/100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100/100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 100/100/100/96 100/100/100/100 100/100/100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100/100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100/100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100/100/100 90.3/83/84/64 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100/100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 100/100/100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 97/89/98.8/69 99.9/100/99.8/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 100/100/100/100 100/100/100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100/100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 99.8/86/99.3/65 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100/100/100Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 100/100/100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100/100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100/100/100 100/100/100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 97.8/97/95.5/93 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100/100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 100/100/100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 79.6/97/80.9/91 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100/100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100/100/100 100/100/100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 100/98/100/96 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100/100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 41.1/91/68.2/87 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100/100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100/100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 100/100/100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100/100/100 100/100/100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 100/100/72.9/51 99.5/98/99/95 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765

100/90/100/85 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100/100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100/100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100/100/100 100/100/100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100/100/100 100/100/100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 100/81/100/98 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100/100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100/100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/100/100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100/100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/79/100/98100/86/100/83 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100/100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100/100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100/100/100Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100/100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100/100/100 100/100/100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100/100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 60.8/100/48.6/98 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100/100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100/100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100/100/100 100/100/100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100/100/100 100/100/100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/100/100/98 100/100/100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100/100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100/100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100/100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 100/100/94.2/99 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 99.9/100/99.9/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 98/100/98.7/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 100/100/100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100/100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100/100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100/100/100 100/100/100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100/100/100 99.3/100/100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 55.2/100/56.9/99 100/100/100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 TACK + Asgard + TACK 100/100/100/100100/100/100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 99.1/79/43.7/79 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100/100/100100/100/100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 54/95/27.2/84 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100/100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100/100/100 100/100/100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100/100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 99.2/100/99.5/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100/100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 100/100/100/100Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100/100/100 100/100/100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 27.9/81/100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100/100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100/100/100 100/100/100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 99.6/100/99.6/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100/100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100/100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100/100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100/100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 100/100/100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100/100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100/100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100/100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 100/100/100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 95.4/100/96/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 98.8/100/98.5/100 100/100/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 100/100/100/100 95.9/85/85.2/70 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 93.7/96/97.8/86 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 74.8/85/84.7/85 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 82.1/89/45.2/70 70.9/100/63.3/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 100/100/100/100 100/100/100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 99.6/100/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 100/100/100/10099.5/88/99.5/87 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 100/100/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 41.7/91/27.2/84 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 100/100/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 99.3/98/99.4/97 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 100/100/100/10098.4/99/99.1/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 14.5/90/9.8/79 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 96.9/95/88.5/91 100/100/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 91.3/99/88.3/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 100/100/100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/100/100/100 96.6/96/94.8/88 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 38/53/50.8/57 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/96/100/88 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100/100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 63.4/95/41.5/93 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 100/100/100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 82.5/58/59.5/69100/100/100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 44.8/58/4.2/61 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 15.9/58/15/79100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 98/81/99.1/86 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100/100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 100/100/100/100 100/100/100/100100/92/100/96 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 100/100/100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 99.9/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100/100/100 67.1/72/51.4/84 100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 62/100/42.9/98 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 100/100/100/100 24.7/93/16.2/9483.6/72/86.2/86 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 99.5/95/99.8/99 Cluster2 97.6/90/99/85 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100/100/100 100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 96.8/100/98.1/100 100/100/100/100 30/79/51.9/96 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100/100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100/100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/96/100/98 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.7/100/99.8/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100/100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100/100/100 100/100/100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 79.6/85/22.4/32 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100/100/86 100/100/100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 DPANN 100/100/100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100/100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100/100/100 45.7/95/75.8/99 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100/100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 99.9/100/100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100/100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965

100/100/100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100/100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100/100/100 100/100/100/79 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/100/100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100/100/100 100/100/100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 9 3 / 0 / 9UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 0 / 5 8 / 0 / 5 3 100/100/100/100UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100/100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100/100/100UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.9/100/99.9/100 100/100/100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100/100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100/100/100 Undinarchaeota UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100/100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100/100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 100/100/100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100/87.8/69 100/100/100/100 100/100/100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 100/100/100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100/100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100/100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100/100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100/100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 100/100/100/100 82.4/100/92.8/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100/100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100/100/100 19.3/95/47.2/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100/100/100 100/100/100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/98/100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100/100/100 92.7/98/88.5/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100/100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 99.6/100/99.8/97 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100/100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 6.4/88/44.5/100 59.3/100/75.2/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100/100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845

100/100/100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 Cluster1 100/100/100/100Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 100/100/100/100 100/100/100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.2 Supplementary Figure 11 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. The alignment was trimmed with BMGE (alignment length = 12,849 aa). A ML phylogenetic tree was inferred with the NONREV model. The first two values show the support for the reversible and the second two for the non-reversible model. Values 1 and 3 were generated with an ultrafast bootstrap approximation and 2 and 4 with an SH-like approximate likelihood tests, each run with 1000 replicates. The tree was rooted using the non-reversible model in iqtree v2. Scale bar: Average number of substitutions per site. Tree statistics for tree number 6 can be found in Supplementary Table 6. 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 62.5/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 364 species 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 93.2/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 9.1/45 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 68.3/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 50% top ranked proteins Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 30.4/78 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 (n=56) 75.5/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 97.3/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 trimmed alignment (BMGE) 0 / 4 0 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 95/100 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 87.6/40 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 SR4 recoded 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 99.9/100 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 12,849 amino acids Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 99.9/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 72.6/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Iqtree, C60SR4 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/100 100/100 96.5/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 93/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 99.9/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 79.4/100 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 52.9/100 99.7/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 Asgard + TACK 100/100 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 99.9/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 98.3/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 12.6/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 93.1/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 76.2/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 99.7/100 99.9/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 99.9/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 28.6/81 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 98.7/100 99.6/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 99.8/10099.1/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 99.3/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 51/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 84.9/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 99.4/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 99.5/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 90.2/81 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 84.4/100 99.2/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 76.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 99.4/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 68.1/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 64.1/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 0 / 6 2 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 71.9/70 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 99.9/99 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 79.3/95 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 5.6/67 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 99.7/100 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 82.4/96 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 86.2/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 99.9/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 82.4/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 75/100 99.5/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 0 / 1 0 0 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 100/100 74.2/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 74.7/100 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 99.3/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 15.8/100 98.7/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 99.9/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 96.4/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 98.8/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 99.8/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 Euryarchaeota 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 85.2/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 98.5/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 98.9/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 99.9/100100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 32/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 98/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 99.9/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 25.6/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 97.8/100 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 99.9/100 99.1/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 70.6/81 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 70.5/98 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 89.6/100 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 28.1/78 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 93.3/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 95.5/81 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 98.2/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 97.5/100 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 24.3/10099.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 86.5/66 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 100/100 100/100 54.9/66 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 60.8/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 62.9/98 58.1/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 73.4/80 25/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 100/100 100/100 99.2/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 8 4 / 8 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 54.9/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 100/100 96.3/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 99.9/100 57.6/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 98.8/100 99.5/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 53.7/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 0 / 6 7 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 83.1/87 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 80.3/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 62.7/87 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/100 51.5/97 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 27.5/96 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 99.3/8569.1/98 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 14.8/85 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 85.5/77 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 100/100 99.5/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 49.9/77 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 96.5/84 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 67.7/69 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 0 / 4 3 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 65.8/100 Cluster2 96.4/73 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 96.8/100 93.1/69 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 70.5/100 97.4/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 93.5/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 80.8/69 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 99.8/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 38.7/39 97.7/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 87.8/98 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 DPANN NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 99.3/100 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 99.2/100 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 90.3/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 56/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 64.9/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 99.3/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 96.8/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 7 9 0 / 6 5 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 94.4/92 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 96.1/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 98.7/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 98.2/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 95.7/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 94.9/100 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 96.8/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 99.2/100 23.4/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 93.9/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 87.4/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 49.5/40 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 Cluster1 100/100 42.3/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 23.5/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845

0.4 Supplementary Figure 12 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. The alignment was trimmed with BMGE and recoded into 4 character states (SR4 decoding; alignment length = 12,849 characters). A ML phylogenetic tree was inferred with the C60-SR4 model with an ultrafast bootstrap approximation (left) and SH- like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 7 can be found in Supplementary Table 6. 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 99.9/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 90.7/82 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 99.9/95 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 92.2/98 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 100/1007 6 / 8 2 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 364 species 99.8/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 82.4/90 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 100/100 100/92 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 50% top ranked proteins 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/100 (n=56) Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 100/83 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 95.3/96 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 75.4/89 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/90 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 100/100 7 5 / 8 6 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 removal of fast-evolving sites: Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 99.9/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 95.9/83 96.8/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 100/100 SlowFaster, 10% site removal Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 85.6/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 99.8/100 100/83 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 11,585 amino acids Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 35.5/65 90.1/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 99.7/90 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 10.5/79 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 100/100 Iqtree, LG+C60+F+R Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 65.4/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 99.9/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 98.6/95 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 83.2/99Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 99.5/95 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 99.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 86.2/99 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 83.3/99 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 Euryarchaeota 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 99.8/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 94.8/92 99.6/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 93.1/92 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/97100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 74.7/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 80.6/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 45.5/98 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 100/100 68.3/35 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625

93.6/86 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 100/100 85.2/99 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 80.3/35 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 99.2/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 3 0 / 9 6 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 100/100 100/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 91.1/98 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 99.9/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605

99.4/99 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 36.1/65 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 99.7/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 91.3/75 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 40.4/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 99.5/100 99.8/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 57.2/93 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 92.7/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 96.5/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 59.4/85 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 TACK + Asgard + TACK 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925

100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 99.8/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 97.9/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 96.3/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 93.5/99 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 42.9/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 39.1/94 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 86.2/97 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 39.4/54 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 9 8 / 9 8 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 99.9/81 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 18.3/69 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 33.5/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 99.8/68 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 99.8/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 58.3/96 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 55.9/96 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 100/100 99.3/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 28.9/80 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 89.4/86 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 56.9/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 42.2/99 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 19.7/89 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 24.4/81 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/84 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 99.9/88 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 19.5/59 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 8.3/58100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 9 4 / 8 9 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 100/100100/94 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 66.4/63 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 98.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 9 4 / 7 1 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 13.5/75 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 88.5/9783.9/63 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 Cluster2 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 58.8/92 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 31.1/92 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 100/100 99.9/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 99.4/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265

NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 DPANN 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 34.5/82 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 6 8 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 5 0 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 98.6/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 100/100 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455

100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 46.6/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 0 / 3 6 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/97 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 72.7/96 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035

100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 99.8/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 53.4/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 96.2/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845

Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 Cluster1 100/100 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 99.9/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 13 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. 10% of fast-evolving sites were removed from the alignment with SlowFaster (alignment length = 11,585 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 8 can be found in Supplementary Table 6. 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 99.9/100 93.2/90 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 99.9/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 85.6/95 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 55.2/92 99.7/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 364 species 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 99.6/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 85.5/97 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 99.3/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 99.5/97 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 50% top ranked proteins 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 (n=56) 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 100/95 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 79.9/84 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 100/99 84.3/87 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 99.5/99 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 removal of fast-evolving sites: Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 99.7/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 98.2/95 93.8/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 SlowFaster, 20% site removal 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 66.6/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100 99.8/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 99.1/95 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 10,283 amino acids 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 23.9/61 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 95.1/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Iqtree, LG+C60+F+R Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 2 9 / 9 0 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/93 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 98.8/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 50.7/93 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 99.6/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 91.8/80 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 46.3/96Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 99.8/80 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 99.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 99.5/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 86.3/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 99.8/100 93.7/99 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100

Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 Euryarchaeota 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 96.9/98 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 87.1/92 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 88.8/92 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/93100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 98.7/100 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 7 1 / 9 9 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 93/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 29.2/35 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 100/99 100/94 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 99.9/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 8 0 / 5 6 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 98.1/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 76.2/98 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 97.1/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 7 7 / 9 8 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 99.8/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 98.1/99 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/66 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 100/99 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/99 90.8/64 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 1.1/58 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/98 99.9/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 85.5/99 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 97.7/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 90.9/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 Asgard + TACK 4 0 / 4 7 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 99.4/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 94.8/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 87/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 79.3/99 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 91.7/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 72.5/98 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 95.3/100 9 7 / 3 3 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 6 2 / 9 5 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 46.1/53 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 50.1/31 76.8/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 100/10055.7/44 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 31.9/56 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 82.7/96 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 98.1/92 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 49.6/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 86.8/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 86.7/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 97.7/83 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 81.2/84 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 58.3/85 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 72/100 99.4/99 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 100/100 94.5/96 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 97.4/92 52.7/75 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 93.6/76 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/100 39.6/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 100/100 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 86/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 60.7/81 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 98/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 93.9/99 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 65.3/100

Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 Cluster2 81.2/98 100/100 86.3/81 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 54.6/93 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 100/100 18.4/67 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 100/100 99.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 97.9/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.4/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 DPANN 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 0 / 3 0 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 99.9/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 99.8/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 9 8 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 9 5 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 100/100 99.9/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 99.9/100 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 99.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 100/100 60.5/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 42.9/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/85 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 36.9/74 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 59.9/100 91.4/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Cluster1 100/100 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 14 | Phylogenetic placement Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. 20% of fast-evolving sites were removed from the alignment with SlowFaster (alignment length = 10,283 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root inferred with minimal ancestor deviation (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 9 can be found in Supplementary Table 6. 100/100 99.7/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 33.9/93 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 84.8/9697.8/99 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 94.6/99 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 99.4/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 364 species 99/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 37.3/95 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 98.9/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 98.6/99 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 50% top ranked proteins 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 (n=56) 100/100 99.6/96 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 90.5/88 100/98 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 6 4 / 8 7 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 99.9/98 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 removal of fast-evolving sites: 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 99.4/96 85.6/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 SlowFaster, 30% site removal 99.3/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 99.6/96 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 9,031 amino acids 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 70.5/93 7 9 / 9 9 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 100/100 71.6/98 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 Iqtree, LG+C60+F+R 9 9 / 9 9 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 99.3/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 65.7/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 86.3/99 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 100/100 85.1/98 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 60.5/100 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 99.7/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 38.8/96 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 99.1/100 98.2/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 Euryarchaeota 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 99.9/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 96.3/86 88.1/93 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 90.6/86 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/88100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 98.5/99 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/99 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 87.7/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 99.4/100 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 100/100 89.1/91 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 99.6/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 95.2/96 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 0 / 8 2 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 77.2/90 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 98.6/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 86.3/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 97.9/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 75.8/95 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 99.7/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 98.9/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 100/79 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 100/97 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/97 94.2/77 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 49.9/99 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/94 100/100 99.9/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 96.9/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 91.6/100 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 81.2/100 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 Asgard + TACK 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 49.1/79 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 9 6 / 9 9 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 7 7 / 9 9 97.5/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 100/99 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/99 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 80.4/98 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 59.4/100 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 98/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 96.8/86 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 95.2/65 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 86.4/99 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 76.6/86 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 100/100 98.9/82 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 99.7/100 90.9/86 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 75.7/64 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 99.7/92 9 9 / 9 9 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 91.1/97 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 39.2/96 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 46.8/86 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 99.4/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 73.1/100 100/100 83.7/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 100/100 100/100 86.2/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 99.4/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 74.3/99 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 71.9/63 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 99.9/63 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 96.5/64 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/100 93.9/97 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 1 7 / 5 3 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 80.8/56 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 20.6/49 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 100/10099.7/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 36.7/91 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 94.5/100 80.3/97 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 72.3/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 72.8/9797.3/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 Cluster2 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 72.3/96 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 89.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 100/100 98.2/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 96.4/100 100/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.4/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265

NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 DPANN 100/100 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 23.8/65 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 100/100 99/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 99.9/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 9 9 0 / 9 4 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.8/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 Undinarchaeota UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 99/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 99.7/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 73/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 46.5/100 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 99.7/59 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 57.3/59 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 59.9/99 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 86.7/98 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 99.5/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 15 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. 30% of fast-evolving sites were removed from the alignment with SlowFaster (alignment length = 9,031 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 10 can be found in Supplementary Table 6. 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 100/100 46.8/97 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 64.1/92 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 99.5/9890.8/94 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 9 5 / 9 7 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 364 species 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 87.8/98 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 3 4 / 7 7 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 70.9/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 89.9/84 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 50% top ranked proteins 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 (n=56) 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 63.7/89 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 4 9 / 9 7 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 99.7/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 99.9/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 100/100 11.6/73 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 removal of fast-evolving sites Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 99.6/93 91.4/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 SlowFaster, 40% site removal 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 98.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 99.9/100Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 98.9/94 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 7,651 amino acids 99.7/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 73.1/89 77.8/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 Iqtree, LG+C60+F+R Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 100/100 59.6/96 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 99.7/99 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 99.4/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 56.3/77 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 83.2/99 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 88.9/57 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 83.8/99Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 98.9/58 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 99.9/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 99.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 0 / 1 6 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 98.1/100 98.2/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 98.2/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 92.3/89 7 7 / 9 2 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 97.2/89 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 99.9/94100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 94.2/99 99.8/99 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 23.9/95 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 99.8/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 100/100 82.6/82 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 98.5/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 76.1/81 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 99.5/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 3.8/68 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 5 9 / 7 7 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 99.9/100Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 97.2/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 92.6/96 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 95.2/98 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 79.4/94 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 99/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 98.5/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/90 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 99.2/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/10098.7/90 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 23.1/99 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/98 99.4/100100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 99.2/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 74.6/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 55.4/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 Asgard + TACK 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 80.7/95 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 85.5/99 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 24.4/64 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 93.6/99 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 99.9/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/91 100/91 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 79.4/99 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 54.5/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 97.1/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 89.2/93 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 68.2/40 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 100/97 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 39.1/38 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 90.3/95 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 91.3/54 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 98.4/72 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 99.8/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 99.7/74 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 98.3/99 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 24.2/99 95.3/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 100/100 26.3/72 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 91/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 61.7/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 100/100 90.9/100 99.1/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 78.9/93 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 94.9/81 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 89.1/93 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 97.6/74 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 71.4/96 98.1/81 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 76.2/92 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 99.1/100 73.1/79 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 100/100 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 100/100 91.4/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 53.3/75 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 98.6/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 77.4/98 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 75.5/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015

1 3 / 7 3 100/100 Cluster2 92.6/77 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 60.7/89 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 100/100 68.3/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 100/100 96.7/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 98.3/99 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/99 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 98.3/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 DPANN NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 8.5/55 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 94.4/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 99.5/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 1 0 0 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 9 6 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.8/100 99.8/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 99.4/100 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 99.8/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 100/100 20.5/96 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 19.8/95 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 55.3/88 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 99.7/90 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 99.9/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 34.8/100 97.5/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 99.9/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855

100/100 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 96.3/100 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 16 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. 40% of fast-evolving sites were removed from the alignment with SlowFaster (alignment length = 7,651 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 11 can be found in Supplementary Table 6. 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 100/100 85.8/67 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 99.9/99 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 50.1/62 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 89.4/96 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 364 species 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 76.8/78 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 99.2/79 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 50% top ranked proteins 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 (n=56) 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 100/90 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 96.1/99 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 7 9 / 8 2 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/82 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 100/100 77.2/81 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 removal of heterogeneous sites Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 71.7/86 99.3/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Pruner, 10% site removal Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 75.7/99 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 99.8/90 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 11,565 amino acids Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 65.1/86 8 6 / 9 8 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 99.6/98 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 90.1/97 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 Iqtree, LG+C60+F+R 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 69.1/99 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 97.6/94 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 0 / 1 8 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 100/94 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 75.3/98 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 99.8/100 91.4/99 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 Euryarchaeota 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 99.9/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 99.6/69 99/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 99.8/69 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/69100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 19.8/86 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 81.8/100 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 57.7/99 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 100/100 6 2 / 5 2 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 89.3/78 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 93.8/100 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 72.2/51 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 97.8/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 39.8/86 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 99.9/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 73.4/92 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 96.9/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/69 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 99.8/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/100 89.5/68 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 0.6/56 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 94.9/100 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 44.5/87 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 93.1/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 70.3/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 67.7/90 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 TACK + Asgard + TACK 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 94.6/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 99.8/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 92.4/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 98.3/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 84.7/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 92.3/84 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 82.5/84 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 6 / 9 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 83.8/68 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 99.2/85100/77 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 9 9 / 8 6 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 100/94 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 99.8/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 83.9/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 89.4/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 100/100 99.7/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 47.5/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 96.4/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 68.3/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/100 95.3/96 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 32.1/82 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 99.9/97 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 76.5/100 99.4/97 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 84.3/86 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 99.6/91 43.5/88 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 80.7/88 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/100 75.8/91 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 100/100 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 98.6/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 98.9/87 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 4 6 / 9 8 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 100/100 73.1/87 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 99.8/97 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015

100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Cluster2 54.1/90 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 100/100 1 6 / 8 2 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 57.5/96 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 100/100 99.8/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 97.8/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.9/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 DPANN 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 28.1/80 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 75.8/78UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 0 / 4 0 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.4/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 99.2/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 100/100 65.2/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 58.5/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/96 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 55.1/90 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 72.7/100 33.2/92 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855

100/100 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 99.9/100 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.4 Supplementary Figure 17 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. 10% of heterogeneous sites were removed from the alignment using the chi2 test (alignment length = 11,565 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 12 can be found in Supplementary Table 6. 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 64.1/86 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 99.8/97 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 81.8/92 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 99.9/1004 2 / 9 1 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 364 species 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 3 5 / 8 7 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 100/100 98.6/89 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 50% top ranked proteins 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 (n=56) 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 99.9/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 91.8/97 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 80.4/71 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 99.9/71 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 100/100 74.1/68 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 removal of heterogeneous sites Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 99.9/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 87.6/99 99.6/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 100/100 Pruner, 20% site removal Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 70.3/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655

100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/100 99.9/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 10,280 amino acid Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 81.2/98 58.2/96 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 98.5/97 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 58.3/95 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 100/100 Iqtree, LG+C60+F+R Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 80.2/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 95.9/94 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 3 1 / 9 5 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 99.8/94 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915

100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 99.6/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 36.8/91 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 99.5/100 9 1 / 9 9 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 98.2/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 81.3/78 99/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 97.8/78 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/78100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 5.2/59 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 38.2/96 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 95.6/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 100/100 45.6/74 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 96.4/88 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 99.9/100 98.6/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 6 8 / 7 9 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 98.3/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 64.3/95 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 100/100 99.3/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 69.8/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 99.6/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 81.1/99 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/95 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 93.6/81 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/100 92.8/76 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 20.2/79 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/100 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 85.9/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 85.2/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 80.8/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100

Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 Asgard + TACK 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 63.2/67 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 98.4/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 99.7/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 93.9/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 98.2/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 97.3/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 99.7/100 9 7 / 7 1 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 30.7/73 99.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 83.9/78 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 14.6/59 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 97.7/98 100/97 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 23.3/93 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 9 9 / 7 9 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 98.8/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 67/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 93.3/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 100/100 99.8/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 9.5/81 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 96.3/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 100/100 31.6/81 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 68/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 98.5/92 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 40.1/91 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 15.8/76 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/91 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 90.3/86 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 60.8/81 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 9 9 / 4 8 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 95.1/59 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 20.8/49 100/100 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 82.6/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 76.5/87 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 99.1/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 94.3/92 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 54.7/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 Cluster2 98.7/99 63.4/85 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 27.8/77 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 100/100 85.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 100/100 99.7/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 98.2/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/99 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.9/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265

NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 DPANN 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 23.1/79 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 99.8/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 7 8 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 4 8 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.6/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 Undinarchaeota UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 99.9/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 100/100 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 99.2/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 99.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 84.1/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 61.7/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/96 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 85.2/95 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 73.5/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 73.4/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845

Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 Cluster1 100/100 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 99.9/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.4 Supplementary Figure 18 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. 20% of heterogeneous sites were removed from the alignment using the chi2 test (alignment length = 10,280 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 13 can be found in Supplementary Table 6. 100/100 364 species 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 45.4/93Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 100/100 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 50% top ranked proteins 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 95.2/99 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 (n=56) 99.8/100 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/99 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 removal of heterogeneous sites Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 100/10046.5/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/100100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Pruner, 20% site removal 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 97.4/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 98.2/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 10,280 amino acids 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 100/100 100/100Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 99.2/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 82.4/98100/100 Iqtree, NONREV+R10 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/89 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 99.9/99 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 55.4/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 TACK+A 100/86 97.3/98 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 99.8/88 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 9 9 / 8 8 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/89100/74 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/99 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 96.3/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 100/100Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 87.7/70 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 67.5/76 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 100/100 100/100Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 8 0 / 6 7 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 76.4/68 100/100100/100Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 97.4/6798/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 100/67 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 100/100Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 100/99 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 16.8/95Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 70.9/95 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 9.5/61 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 97.9/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 100/100100/100 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 100/100 74.2/82Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 99.9/95 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 7 7 / 9 7 94.3/82 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 99.7/99100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 100/100Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 100/100 99.7/70 81.3/97 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 83.8/97 100/100Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 99.9/94 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/10098.7/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 99.9/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 46.2/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 85.5/69 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105

92.9/98 Euryarchaeota 97.2/99 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 100/100 100/99 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 79.1/68 100/100 67.5/96 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 93.8/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 82.2/93100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 87.1/93 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 99.9/9499.7/100 62.1/98 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 97.2/94 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 100/100 47.4/100Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 99.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 99.5/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 99.8/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 50.2/92 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 92.7/100 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 100/100Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/10099.3/100Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/98 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 100/100 100/100Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 96.6/95 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/97 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 14.1/8735.3/99 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 99.5/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 22.7/98100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 96.1/88 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 29.1/81 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 98.6/86 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 71.7/87 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 100/100 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 95.9/72 97.7/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 42.9/56 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 99.5/81 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 93.5/73 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 99.8/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 98.7/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 80.2/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 92.7/96100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 99.2/86 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 99.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 91.5/96 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 8 / 7 2 79.5/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 95.2/89 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 51.5/68100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 14.9/61 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 90.6/88100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/58 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 85.9/94 100/100 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 6 6 / 9 4 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Cluster2 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 95.8/99 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 35/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 100/100 99.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 97.3/9998.2/94 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 82.7/99 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 78/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495100/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 DPANN 100/100 100/99 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595100/100 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 100/100 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 100/99 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 82.3/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 0 / 7 7 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 0 / 4 5UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 100/100UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 99.7/100 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 Undinarchaeota UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 80.7/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 76.5/100 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 100/100 100/100Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 89.4/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 100/99 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 9 8 / 9 9 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 29.3/46 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 99.9/100 100/100Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515

100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Cluster1 100/100 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 94.2/99 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 99.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385

0.2 Supplementary Figure 19 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. 20% of heterogeneous sites were removed from the alignment with the chi2 test (alignment length = 10,280 aa). An ML phylogenetic tree was inferred with a non-reversible model (NONREV+R10) with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The root was inferred with the non- reversible model in iqtree. Scale bar: Average number of substitutions per site. Tree statistics for tree number 14 can be found in Supplementary Table 6. 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 99.8/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 53.2/85 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 74.3/8597.3/96 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 7 3 / 9 4 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 99.9/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 364 species 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 99.9/97 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 51.7/88 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 50% top ranked proteins 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 (n=56) 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 99.6/99 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 83.8/84 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 9 0 / 8 2 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 98.4/80 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 100/100 69.2/64 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 removal of heterogeneous sites Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 98.1/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 43.8/85 99.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 Pruner, 30% site removal 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 6 1 / 9 9 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 99.6/99 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 99.9/100 8,995 amino acids Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 81.8/95 50.9/98 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 96.3/84 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 72.7/84 Iqtree, LG+C60+F+R Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 66.7/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 95.3/98 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 58.4/97Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 99.9/98 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 99.8/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 99.7/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 63.3/98 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 98.3/100 80.7/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 100/100 Euryarchaeota Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 45.9/53 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 45.7/53 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 93.5/98 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 100/83 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 98.5/100 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/100 100/100Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 52.2/100 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 77.2/100 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 96.7/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 36.1/57 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 91.6/93 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 99.4/100 99.3/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 82.2/59 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 99.9/100Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 96.4/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 59.6/96 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 98.5/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 66.2/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 99.8/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 2.9/83 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/95 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 97.2/77 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/99 85.1/72 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 12.8/95 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/99 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 63.4/98 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 47.1/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 82.5/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 Asgard + TACK 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 75.2/92 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 99.9/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 99.3/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 99.3/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 95.9/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 96.9/99 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 95.6/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 94.9/64 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 97.6/69 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 93.5/72 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 7 6 / 7 5 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 22.5/54 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 99.5/83 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 36.5/77 97.3/59 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 93.6/82 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 81.4/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 96/100 99.3/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 100/100 48.5/7899.4/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 9.3/91 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 99.6/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 53.6/100 93.3/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 3.7/46 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 6 6 / 8 2 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/90 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/100 89.8/84 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 56.3/86 98.3/73 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 98.7/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/100 43.4/83 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 100/100 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 100/100 57.4/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 86.5/98 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 98.4/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 68.7/89 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 1.3/83 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 Cluster2 86.4/91 100/100 86.1/89 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 88.5/98 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 100/100 89.9/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 100/100 99.4/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 99.9/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 80.2/99 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/99 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.8/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 DPANN 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 46.8/96 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 99.8/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 97.3/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 99.8/100 99.9/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 7 8 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 4 6 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 100/100 99.9/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 99.8/100 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 98.4/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 100/100 67.2/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 17.1/97 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/87 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 69.8/87 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 81.9/100 80.1/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 99.9/100 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 20 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. 30% of heterogeneous sites were removed from the alignment using the chi2 test (alignment length = 8,995 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 15 can be found in Supplementary Table 6. 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 98.6/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 66.7/95 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 64.1/959 2 / 9 8 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325

95.9/99 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 364 species 99.3/99 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 99/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 3 3 / 9 5 99.9/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 100/100 83.1/97 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 50% top ranked proteins 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 (n=56) 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 96.1/87 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 55.3/60 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 91.2/90 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 97.7/91 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 100/100 67.9/54 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 removal of heterogeneous sites Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 97.9/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 62.4/81 99.3/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 Pruner, 40% site removal 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 61.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/100 99.2/90 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 7,710 amino acids 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 91.9/87 54.2/99 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 81.9/72 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Iqtree, LG+C60+F+R 73.3/72 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 29.3/82 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 99.9/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705

58.8/89 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 4.4/19Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 99.7/94 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 99.5/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 99.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 96.4/97 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 8 1 / 9 8 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 96.5/100 98.8/98 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 98.3/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 91.5/98 57.2/42 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 55.1/42 100/66 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/100 100/100Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 0 / 4 0 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 16.6/70 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 98.9/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 29.9/47 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 99.9/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 99.9/10099.9/85 99.7/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 97.3/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1

6 4 / 5 9 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 63.7/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 75.1/81 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 99.3/82 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495

94.8/94 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 99.8/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285

100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 8.7/70 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 99.9/92 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385

100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 94.1/59 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 8 9 / 5 1 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 31.2/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/99 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 87.9/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 79.9/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 57.2/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 100/100 100/100 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 TACK + Asgard + TACK 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925

69.3/96 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 94.9/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 95/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 74.5/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 95.6/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 99.9/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 89/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 93.1/49 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 95.8/52 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 28.3/54 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 81.5/30 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 9 9 / 8 7 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 64.7/78 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 91.1/70 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 94.4/64 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075

89.2/74 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 78.3/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 90.6/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 99.5/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 100/100 5 4 / 7 499.6/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 57.5/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 99.6/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 30.5/89 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 98.2/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185

75.8/99 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 7 0 / 8 8 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 99.7/88 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 87.1/89 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 22.6/74 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 51.7/81 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 26.7/6499.9/97 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395

100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 91.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 90/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 87.7/93 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 99.9/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 1 2 / 7 9 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 100/100 56.9/95 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 98.4/88 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 100/100

Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Cluster2 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 92.4/99 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 43.5/82 69.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 100/100 96.7/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 33.7/87 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085

98.8/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 DPANN NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 37.1/93 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 99.1/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 99/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 99.9/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 99.9/100 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 5 2 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 0 / 4 3 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.2/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 99.4/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 97.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 99.6/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 4.2/22 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 2.5/61 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 99.8/92 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 48.9/90 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035

100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 99.9/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 89.1/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 75/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100

100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 21 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. 40% of heterogeneous sites were removed from the alignment using the chi2 test (alignment length = 7,710 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 16 can be found in Supplementary Table 6. 66.2/54 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 98.8/66 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 81.1/53 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 99.6/9799.9/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 98.5/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 364 species 99.8/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 94.4/98 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 100/100 7.2/44 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 50% top ranked proteins 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 99.9/90 (n=56) 97.6/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 96.6/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 99.6/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 100/100 removal of heterogeneous sites Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 32.9/99 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655

100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 99.8/99 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100 Pruner, 40% site removal Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/100 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 99.4/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 93.9/90 80.5/87 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 100/100 7,710 amino acids Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 80.2/84 100/100 99.6/98 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 77.2/86 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 44.1/97 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 95.8/62 Iqtree, NONREV+R10 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 64.6/61 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 1 6 / 8 7 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 99.9/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 76.6/95 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 27.5/99 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 99.8/96 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 97.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 99.4/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 99.5/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 97.1/99 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 97/100 97.2/99 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 Euryarchaeota 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 77.5/94 99.2/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 91.3/64 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 90.9/64 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 31.1/69100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 35.8/99 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 47.9/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 98.7/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 51.5/44 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 98.4/80 100/71 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 99.8/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 98.9/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 85.4/45 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 97.5/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 23.6/81 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 27.6/85 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 87.5/99 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/100 100/97 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 99.3/82 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 99.4/79 100/94 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 66.2/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/94 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 86.7/99 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 99.8/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 92.9/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 86.7/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 TACK + Asgard + TACK 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 96.6/93 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 97.8/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 89.7/99 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/99 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/99 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 91.1/99 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 90.1/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 100/100 99.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 85.3/91 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 8 3 / 9 4 58.2/75 100/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 100/91 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 100/89 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 87.5/85 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 93.4/79 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 97.5/80 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 90.6/91 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 79.1/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 98.5/100 100/95 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 32.5/79 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 99.9/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 27.3/98 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 100/100 93.3/98 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 80.3/99 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 98.5/99 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 56.6/99 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 33.2/83 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/95 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 94.3/85 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 97.1/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 49.1/88 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 84.6/88 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/100 85.7/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 100/100 97.7/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 97/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 99.2/88 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 6.7/65 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 100/100 71.5/87 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 99.8/87 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 Cluster2 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 77.4/91 91.6/98 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 53.6/72 69.3/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035

100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 97.9/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 100/98 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.8/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265

100/100 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 DPANN 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 62.7/98 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 99.5/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 94.7/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 99.4/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 80.1/95 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 99.8/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 0 / 5 9 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 5 5 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.7/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 74.1/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 93.7/100 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 99.9/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 99.8/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 98/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 99.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 72.8/99 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 79.6/93 35.6/99 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/98 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 Cluster1 100/100 90.8/98 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075

0.2 Supplementary Figure 22 | Phylogenetic placement Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=56) and the 364 species set. 40% of heterogeneous sites were removed from the alignment using the chi2 test (alignment length = 7,710 aa). A ML phylogenetic tree was inferred with a non-reversible model (NONREV+R10) with an ultrafast bootstrap approximation (left) and SH- like approximate likelihood tests (right), each run with 1000 replicates. The tree was rooted using the non- reversible model in iqtree. Scale bar: Average number of substitutions per site. Tree statistics for tree number 17 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57) trimmed alignment (BMGE) 13,496 amino acids Iqtree, LG+C60+F+R

100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 99.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 98.4/83 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100 100/83 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 99.9/99 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/83 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 12.2/50 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 99.7/90 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 91.6/89 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 75.9/83 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 99.6/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 91.6/90 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 55.5/74 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 99.8/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 99.9/81 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 81.8/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 99.9/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 99.7/100 100/100 100/90 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 85.9/89 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 43.8/85 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 97.2/97 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 95.4/94 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Asgard + TACK Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 25.8/82 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 37.5/87 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 99.9/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 80.2/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 33.6/81 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 100/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015

100/100 Cluster2 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 93.7/99 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 8 1 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 5 0 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 DPANN 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 Undinarchaeota 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 99.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 23 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. The alignment was trimmed with BMGE (alignment length = 13,496 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 18 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57) trimmed alignment (BMGE) 13,496 amino acids Iqtree, LG -m MFP+MERGE, followed by NONREV

100 9 7 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 9 9 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100 9 9 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100 100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100 100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100 100 100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 7 3 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 8 3 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100 6 4 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100 9 8 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100 100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815

100 Euryarchaeota 100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 9 1 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 4 3 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 9 3 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 5 7 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 9 8 100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 100 9 8 9 5 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100 100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100 9 5 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100 100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100 9 2 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100 9 7 100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 9 9 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955

Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 Asgard + TACK 100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100 8 3 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100 100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 7 5 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 9 5 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100 100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 9 8 100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 8 8 100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 100 9 5 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100 100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015

100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Cluster2 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100 100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 9 6 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 9 0 6 1 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 100 100 DPANN UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 Undinarchaeota 100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100 100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100 100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100 100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 9 4 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Cluster1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.2 Supplementary Figure 24 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. The aligment was trimmed with BMGE (alignment length= 13,496 aa). An initial ML phylogenetic tree was inferred with the LG model (-m MFP+MERGE) followed by a tree generated with a non-reversible model with an ultrafast bootstrap approximation run with 1000 replicates. The tree was rooted with the non-reversible model in iqtree. Scale bar: Average number of substitutions per site. Tree statistics for tree number 19 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57) trimmed alignment (BMGE) 13,496 amino acids Iqtree, NONREV model 100/100/100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/100/96.1/98 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 99.5/96/97.8/97 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100/100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 87.9/95/99.9/99 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 99.5/96/100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100/100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100/100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 100/96/100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100/100/100 100/100/100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 80.1/79/100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100/100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100/100/100 100/100/100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/90/100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 8.3/41/55.2/69 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100/98.7/88 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100/100/100 100/100/100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 100/100/100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 72.8/82/100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100/43.6/72 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100/100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100/97.9/98 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100/100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795

100/100/100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 Euryarchaeota 100/100/100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100/100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100/100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 78/87/100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100/100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100/100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 99.7/100/99.7/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100/90.5/91 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 100/100/100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100/71.4/55 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100/100/100 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 99.3/100/99.8/90 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100/100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 88.2/62/100/72 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/63/100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 87.8/98/91.2/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 100/100/100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100/100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 98.7/99/98.7/99 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/100/100/97 100/95/100/95 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100/100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 100/100/100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 99.7/95/100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/100/99.9/94 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100/100/100 100/100/100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100/100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100/100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100/100/100 100/100/100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100/100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100/83.5/95 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100/100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 87.8/93/100/100 100/100/100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100/96.4/97 99.1/99/100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 TACK + Asgard + TACK 100/100/99.6/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 100/100/100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100/100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 83.3/87/100/100 100/100/42.8/81 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 8/55/100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100/100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100/100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705

100/100/91.7/72 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100/100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 98.9/100/71.3/94 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 78.1/95/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 100/100/100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 61.3/82/100/100 45.5/99/46.7/97 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100/100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100/100/100 99.8/100/70.3/89 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/98/99.9/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265

100/100/100/98 100/100/100/100 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100/100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100/100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100/100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Cluster2 100/100/100/100 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100/100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100/100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100/100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100/100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100/99.3/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 98.4/99/100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795

100/100/100/98 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 100/100/74.8/91UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0/68/100/100UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 0 / 9 1 / 0 / 4UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 9 100/100/100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100/100/100UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 100/100/100/100 100/100/100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 Undinarchaeota DPANN 100/100/100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100/100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100/100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100/100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 100/100/100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100/100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100/100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100/100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100/100/99 100/100/100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100/100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955

100/100/100/100 100/100/100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100/82.7/91 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385

100/100/100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Cluster1 100/100/100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 100/100/100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.2 Supplementary Figure 25 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. The alignment was trimmed with BMGE (alignment length = 13,496 aa). A ML phylogenetic tree was inferred with the NONREV model. The first two values show the support for the reversible and the second two for the non-reversible mode. Values 1 and 3 were generated with an ultrafast bootstrap approximation and values 2 and 4 with the SH-like approximate likelihood tests, each run with 1000 replicates. The tree was rooted with the non-reversible model in iqtree. Scale bar: Average number of substitutions per site. Tree statistics for tree number 20 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57) trimmed alignment (BMGE) 13,496 amino acids Phylobayes, CAT+GTR

1 1 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 1 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 1 1 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 1 1 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 1 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 1 0,98 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 1 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 1 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 1 1 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 1 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 1 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 1 1 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 1 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 1 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 1 0,51 1 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 0,95 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 1 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 1 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 Asgard + TACK 1 0,96 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 1 1 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 1 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 1 1 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 1 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 1 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 1 1 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 1 1 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 1 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 1 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 1 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 1 1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 0,5 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 1 0,5 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 1 1 1 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 1 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 1 0,5 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 1 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 1 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 1 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 1 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 1 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 0,99 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 1 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 Euryarchaeota 1 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 1 1 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 1 0,91 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 1 1 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 1 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 1 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 0,99 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 1 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 1 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 1 1 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 1 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 1 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 1 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 1 1 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265

NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 Cluster2 1 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 1 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 1 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 1 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 0,74 1 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 1 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 0,6 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 1 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 1 1 1 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 DPANN UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 Undinarchaeota 1 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 1 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 1 1 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 1 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 1 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 1 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 1 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 1 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Cluster1

0.5

Supplementary Figure 26 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. The alignment was trimmed with BMGE (alignment length = 13,496 aa). A Bayesian phylogenetic tree was inferred with the CAT+GTR model with 14,107 cycles (25% burn-in). The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position as inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 21 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57) trimmed alignment (BMGE-FAST) 29,778 amino acids Iqtree, LG+C60+F+R

16.4/62 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 9 9 / 9 9 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 9 7 / 9 9 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 85.9/95 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265

0 / 6 5 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 84.6/79 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 99.3/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 60.5/90 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 92.2/98 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 89.1/97 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325

100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 99.9/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 97.7/98 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785

100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 Asgard + TACK 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 41.5/92 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 99.1/98 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 99.1/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 98.2/99 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 98.1/99 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 92.3/51 96.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 66.9/9599.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 49.8/90 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 94.6/93 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 43.8/47 60.8/94 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 6 6 / 8 7 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 99.8/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 80.8/97 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985

100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota 21.4/72 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095

99.6/93 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 99.9/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 91.6/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 51.6/76 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 5.2/51 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 99.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 6.9/94 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 66.5/92 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.4/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 Cluster2 99.8/100 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 4.4/52 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 99.8/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 8 4 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 8 5 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935

100/100 DPANN UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 100/100 0 / 6 6 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 99.7/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 98.2/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 99.6/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955

100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 99.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.5 Supplementary Figure 27 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. The alignment was trimmed with BMGE-FAST (alignment length= 29,778 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 22 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57) trimmed alignment (BMGE) SR4 recoded 13,496 characters Iqtree, LC60SR4

90.9/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 60.4/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 97.7/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 19.3/99 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 10.3/93 99.3/97 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/97 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 100/97 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 53.4/99 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 91.5/97 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555

72/100 Asgard + TACK 97.2/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 99.9/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 97.5/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 99.3/100 99.2/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 91.5/92 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 98.8/99 88.7/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 98.6/93 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 99.6/93 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 99.9/9397.5/98 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 6.9/99 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 85.2/92 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 98.6/98 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 Euryarchaeota 97.4/98 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 67.3/80 9 9 / 9 9 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 99.8/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 86.9/85 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 80.9/87 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 22.9/99 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 88.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 93.9/94 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 95.7/100 81.3/94 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 98.9/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 71.7/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 100/100 Cluster2 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 99.7/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 9 7 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 9 7 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 97.7/100 94.3/99 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 DPANN UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 Undinarchaeota 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 65.5/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 99.8/100 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 97/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.2 Supplementary Figure 28 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. The alignment was trimmed with BMGE and decoded into 4 character states (SR4 recoding; alignment length = 13,496 characters). A ML phylogenetic tree was inferred with the C60SR4 model with an ultrafast bootstrap approximation (left) and SH- like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 23 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57) trimmed alignment (BMGE) SR4 recoded 13,496 characters Phylobayes, CAT+GTR

0,97 1 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 1 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 1 1 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 1 1 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 1 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 1 0,54 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 1 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 1 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 1 1 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 1 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 1 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 1 1 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 1 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 1 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 1 1 1 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 0,85 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 0,82 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Asgard + TACK 1 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 1 1 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 1 1 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 1 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 1 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 1 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 1 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 1 1 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 1 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 1 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 1 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 1 1 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 1 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 1 1 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 1 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 1 1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 1 1 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 1 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 1 1 1 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 1 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 1 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 1 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 1 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 1 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985

1 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 Euryarchaeota 1 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 1 1 1 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 1 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 0,95 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 1 1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 1 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 0,86 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 1 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 1 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 1 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 1 1 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 1 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 1 0,98 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 1 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 1 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 Cluster2 1 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 1 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 1 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 1 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 1 1 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 1 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0,53 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 1 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 1

UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 DPANN 1 1 1 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 1 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 1 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 1 0,84 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 1 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 0,62 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 1 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 1 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 1 1 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 0,79 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 Cluster1 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505

0.3 Supplementary Figure 29 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. The alignment was trimmed with BMGE and recoded into 4 character states (SR4 decoding; alignment length = 13,496 characters). A Bayesian phylogenetic tree was inferred with the CAT+GTR model. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 24 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57) removal of fast-evolving sites SlowFaster, 10% site removal 12,177 amino acids Iqtree, LG+C60+F+R

100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 98.6/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 88.6/79 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100 99.8/80 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/99 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 99.9/80 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 93.6/84 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 99.2/85 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 60.5/81 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 77.3/85 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 90.9/88 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 84.7/86 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 99.9/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 99.8/92 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 63.5/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 99.9/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 99.6/100 100/100 100/92 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 100/91 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 7 4 / 7 6 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 47.5/86 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 99.2/96 100/100 92.5/94 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805

Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Asgard + TACK Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 30.6/83 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 16.1/90 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 18.2/65 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 91.1/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 46.5/89 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 100/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 Cluster2 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 9 3 / 9 8 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 9 4 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 9 2 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725

100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 DPANN 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 100/100 99.7/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 99.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 30 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. 10% of the fast-evolving sites were removed from the alignment with SlowFaster (alignment length = 12,177 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 25 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57) removal of fast-evolving sites SlowFaster, 20% site removal 10,856 amino acids Iqtree, LG+C60+F+R

100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 93.9/99 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 97.2/57 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100 99.5/58 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 99.9/98 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 99.8/58 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 99.2/98 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 98.7/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 74.2/93 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 57.5/72 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 Euryarchaeota 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 86.2/79 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 84.7/93 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 99.9/99 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 15.8/64 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 99.8/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 99.3/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/100 100/81 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 99.9/98 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 91.6/77 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 61.6/62 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 99.1/99 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 56.9/54 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 100/100

Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Asgard + TACK Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 72.4/94 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 58.7/92 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 85.5/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 46.6/85 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 100/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 99.9/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 100/100 Cluster2 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 91.8/99 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 9 6 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 9 3 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725

100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 DPANN 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 Undinarchaeota 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 31 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. 20% of the fast-evolving sites were removed from the alignment with SlowFaster (alignment length = 10,856 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site.Tree statistics for tree number 26 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57) removal of fast-evolving sites SlowFaster, 30% site removal 9,538 amino acids Iqtree, LG+C60+F+R

100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 95.4/99 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 98.7/65 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100 96.8/64 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 99.6/93 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 98.4/65 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 91.2/98 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 63.6/94 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 69.9/59 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 Euryarchaeota 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 99.7/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 50.6/60 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 7 8 / 8 9 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 99.5/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/99 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 2 8 / 8 1 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 98.6/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 99.5/100 100/100 100/94 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 98.8/93 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 96.3/84 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 67.8/65 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 9 9 / 9 8 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 56.8/59 100/97 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 TACK + Asgard + TACK 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 69.6/92 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 42.2/86 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 99.9/100 99.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315

100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 85.5/99 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 74.8/88 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 100/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 99.7/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 100/100 Cluster2 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 71.7/96 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 9 5 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 9 1 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465

Undinarchaeota DPANN 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785

100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.2 Supplementary Figure 32 | Phylogenetic placement of Undinarchaota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. 30% of the fast-evolving sites were removed from the alignment with SlowFaster (alignment length = 9,538 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 27 can be found in Supplementary Table 6. PN acaa n te ry ro pit t te ot oiin s nerd y iia acso deviation ancestor minimal by inferred SH-like as 28 can be found in Supplementary Table 6. number and position tree for statistics Tree root site. per the (left) substitutions the of number with Averagebar: Scale to 2017). approximation rooted al., et (Tria points artificially rooting bootstrap arrow was tree grey ultrafast The the replicates. and an 1000 archaea alignment with DPANN with run each model an (right), tests LG+C60+F+R likelihood on approximate the based with inferred fast-evolving Undinarchaota the was of 40% of set. species 127 placement aa). the 8,083 A= tree MLlength phylogenetic (alignment SlowFaster with alignment and the from removed were sites (n=57) proteins Phylogenetic ranked top 50% | the with generated 33 Figure Supplementary 100/100 100/100 63.7/81 98.7/92 100/100 100/100 97.2/97 100/100 47.9/90 100/100 100/100 100/99 100/100 100/100 100/100 100/100 98.3/98 100/100 100/100 100/100 100/100 99.7/100 100/100 100/100 100/100 100/100 100/100 32.9/81 100/100 54.4/90 99.4/68 100/100 100/100 100/100 24.5/81 95.9/97 100/100 100/100 98.5/68 1 8 / 6 4 100/100 92.2/99 100/100 100/100 33.3/87 90.6/94 100/100 100/100 86.5/67 100/100 100/100 100/100 100/100 100/100 99.9/97 100/100 5 5 / 9 100/100 100/100 99.9/77 6 7 / 9 8 100/100 100/100 100/100 20.6/65 100/100 100/100 100/100 100/100 100/100 99.9/100 100/100 100/100 99.5/100 100/100 100/100 100/100 98.7/100 100/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 100/100 100/100 100/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 100/100 100/100 100/100 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 98.1/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 100/100 99.6/99 85.2/97 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 8 9 / 5 6 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 100/100 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 99.8/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 9 8 / 0 0 9 / 0 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 0.2 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 37.1/98 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 100/100 6 9 / 3 6 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 Undinarchaeota Iqtree, LG+C60+F+R 8,083 aminoacids SlowFaster, 40%siteremoval removal offast-evolving sites (n=57) ranked proteins 50% top 127 species

Cluster1 Cluster2

DPANN Euryarchaeota TACK + Asgard cl br Aeae ubr f usiuin pr ie Te saitc fr re ubr 9 a b fud in found be can 29 number tree for statistics Tree site. per substitutions Supplementary Table 6. of number Average bar: Scale 2017). al., et (Tria rooting deviation ancestor minimal with inferred position root the shows arrow grey the and DPANNthe with archaea rooted artificially was tree The replicates. 1000 with run each (right), tests likelihood approximate SH-like andwas (left) approximation tree bootstrap ultrafast an with phylogenetic model MLLG+C60+F+R Athe aa).with inferred 12,147 = length (alignment test chi2 the were using sites alignment heterogeneous the the from of removed 10% set. species 127 the and (n=57) proteins ranked top 50% the with generated alignment an on based Undinarchaeota placement Phylogenetic | 34 Figure Supplementary 100/100 100/100 79.6/91 100/100 100/100 100/100 94.9/93 100/100 100/100 100/100 100/100 99.7/100 36.2/86 99.7/98 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 30.9/84 62.8/91 100/100 20.6/69 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/60 100/100 99.9/87 52.1/73 40.8/69 99.9/100 100/100 100/100 100/100 75.8/59 72.6/96 100/100 100/100 100/100 81.9/64 100/77 100/100 100/100 98.7/78 100/100 100/60 100/100 100/100 100/100 100/100 100/100 100/100 99.7/100 100/100 100/100 100/100 100/100 99.7/100 9 9 / 5 9 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 99.8/100 98.7/100 100/100 99.1/82 49.9/80 100/100 100/100 100/100 100/100 100/100 100/100 89.6/99 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 100/100 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 0.3 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 94.8/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 100/100 76.3/83 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 2 4 / 0 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 92.4/99 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 Undinarchaeota

Cluster1 Cluster2 Iqtree, LG+C60+F+R 12,147 aminoacids Pruner, 10%siteremoval removal ofheterogeneoussites (n=57) ranked proteins 50% top 127 species

DPANN TACK + Asgard Euryarchaeota 127 species 50% top ranked proteins (n=57) removal of heterogeneous sites Pruner, 20% site removal 10,797 amino acids Iqtree, LG+C60+F+R 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 99.4/85 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 48.2/74 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/85100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 79.5/92 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 68.5/66 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 96.1/72 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 56.9/66 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 61.7/88 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 Euryarchaeota 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 99.4/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 9 7 / 9 6 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 81.2/93 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 98.2/99 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 99.9/96 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 82.1/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 99.4/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 9 4 / 9 9 100/100 100/88 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 98.9/74 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 81.4/61 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 74.1/92 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 98.7/99 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 93.6/97 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 100/99

Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Asgard + TACK Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 21.7/77 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 59.7/86 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 99.5/86 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 96.4/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 43.3/88 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 Cluster2 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 88.1/98 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 75.5/82UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 0 / 4 3 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 DPANN UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 Undinarchaeota 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 99.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 35 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. 20% of the heterogeneous sites were removed from the alignment with the chi2 test (alignment length = 10,797 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 30 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57 genes) removal of heterogeneous sites Pruner, 20% site removal 9,665 amino acids Iqtree, NONREV+R10

100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 99.4/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 71.9/77 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100 98.2/85 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/99 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/86 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 95.8/63 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 69.9/70 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 44.1/67 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 8 9 / 9 6 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 Euryarchaeota 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 99.8/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 96.7/94 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 82.4/52 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 93.2/64 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/88 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 90.9/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 99.6/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 76.8/98 100/100 100/81 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 99.7/86 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 99.3/68 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 66.2/86 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 97.8/97 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 98.4/97 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Asgard + TACK Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 63.8/90 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 94.8/90 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 80.4/97 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 99.7/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 7 8 / 9 9 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 57.5/90 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 Cluster2 100/100 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 99.1/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/99 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 8 4 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 5 5 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 DPANN 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.8/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 26.6/54 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Cluster1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.2 Supplementary Figure 36 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. 20% of the heterogeneous sites were removed from the alignment with the chi2 test (alignment length = 9,665 aa). A ML phylogenetic tree was inferred with the NONREV model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was rooted using the non- reversible model in iqtree. Scale bar: Average number of substitutions per site. Tree statistics for tree number 31 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57)

100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 removal of heterogeneous sites 99.7/85 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 Pruner, 30% site removal 3.9/52 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/85100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 9,448 amino acids Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 74.6/92 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 Iqtree, LG+C60+F+R 100/100 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 99.2/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 91.9/66 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 84.9/65 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 99.1/67 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 39.5/71 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 99.3/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 99.9/99 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 43.4/69 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 96.4/98 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 99.5/84 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 93.6/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 98.2/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 99.6/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/99 99.4/92 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265

90.7/63 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 91.6/63 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 71.1/92 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 99.2/98 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 74.4/91 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Asgard + TACK 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 44.4/93 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 68.6/89 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 9 9 / 9 0 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 99.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 88.1/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 55.5/89 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.9/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305

100/100 Cluster2 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 90.6/99 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795

100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 3 6 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 0 / 3 0 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525

100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 DPANN 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 Undinarchaeota 99.2/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/99 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 99.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955

100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 37 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. 30% of the heterogeneous sites were removed from the alignment using the chi2 test (alignment length = 9,448 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 32 can be found in Supplementary Table 6. cl br Aeae ubr f usiuin pr ie Te saitc fr re ubr 3 a b fud in found be can 33 number tree for statistics Tree site. per substitutions Supplementary Table of 6. the number with Average rooted bar: artificially rooting. Scale deviation was ancestor minimal tree with inferred Theposition root the replicates. shows SH-like arrow 1000 grey the and with and archaeaDPANN (left) run approximation each bootstrap alignment (right), ultrafast tests an an likelihood with approximate model LG+C60+F+R on the with based phylogenetic inferred MLA aa). was 8,098 = tree length Undinarchaeota (alignment test chi2 the using of alignment the heterogeneous from the removed of placement were 40% sites set. species 127 the Phylogenetic and (n=57) proteins ranked top | 50% the with generated 38 Figure Supplementary 100/97 100/97 6.8/35 100/100 99.8/100 100/100 100/100 100/100 99.9/99 100/100 100/100 16.9/82 100/100 89.4/96 100/100 100/100 98.5/98 100/100 100/100 100/100 100/100 100/100 100/100 50.7/93 100/100 100/100 68.7/90 100/100 99.6/63 19.1/72 100/100 67.8/93 100/100 100/100 100/100 100/100 100/100 100/100 25.3/57 99.8/90 99.8/100 100/100 93.8/69 100/100 100/100 91.4/69 100/100 99.3/63 100/100 100/100 100/100 52.2/85 100/100 81.5/93 100/100 99.8/85 100/100 100/100 98.7/100 100/100 100/100 100/100 100/100 100/100 99.9/100 99.8/100 100/100 100/100 100/100 0 6 / 8 1 100/100 100/100 100/100 98.8/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 100/100 37.1/75 7 7 / 3 9 98.6/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 98.6/100 100/100 100/100 100/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 100/100 100/100 71.3/97 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 0.3 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 99.9/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 99.9/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 8 3 / 0 0 3 / 0 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 87.1/100 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 7 9 / 4 7 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 Undinarchaeota

Cluster1 Cluster2 Iqtree, LG+C60+F+R 8,098 aminoacids Pruner, 40%siteremoval removal ofheterogeneoussites (n=57) ranked proteins 50% top 127 species

DPANN Euryarchaeota TACK + Asgard 127 species 50% top ranked proteins (n=57) removal of heterogeneous sites Pruner, 40% site removal 8,098 amino acids Iqtree, NONREV

100/100 99.7/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 61.6/80 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100 95.4/86 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100 99.8/88 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 98.6/78 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 70.4/77 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 82.1/95 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 63.9/79 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100

100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 99/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 99.6/95 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 55.6/71 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 9 1 / 8 0 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/93 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 91.8/98 99.6/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 98/100 99.6/99 98.6/79 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 98.7/44 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 92.4/44 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 100/100 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 8 2 / 8 8 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 99.6/99 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 63.5/83 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955

Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 Asgard + TACK 100/100 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 86.8/97 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/99 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 58.7/95 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 97.4/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 56.1/96 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 45.1/81 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 100/96 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 99.9/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 Cluster2 41.6/88 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 9 4 / 9 9 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 3 6 0 / 3 4 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725

UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 DPANN 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.8/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 100/100 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 89.4/98 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Cluster1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385

0.2 Supplementary Figure 39 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. 40% of the heterogeneous sites were removed from the alignment using the chi2 test (alignment length = 8,098 aa). A ML phylogenetic tree was inferred with the NONREV model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was rooted with the non-reversible model in iqtree. Scale bar: Average number of substitutions per site. Tree statistics for tree number 34 can be found in Supplementary Table 6. 127 species 50% top ranked proteins (n=57) removal of heterogeneous sites Pruner, 40% site removal 8,098 characters Bayes, CAT + GTR

1 1 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 1 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 1 1 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 0,66 1 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 0,53 1 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 1 1 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 1 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 1 1 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 1 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 1 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 1 0,97 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 1 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 1 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 1 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 1 1 1 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 1 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 Asgard + TACK Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 1 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 1 0,99 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 1 1 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 1 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 1 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 0,96 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 1 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 1 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 1 1 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 1 1 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 1 0,82 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 1 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 1 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 1 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 1 0,76 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 1 1 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 1 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 0,89 1 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 1 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 0,89 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 1 1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 0,89 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 1 1 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 1 1 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915

Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota 1 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 1 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 1 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 0,97 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 0,97 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 1 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 1 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 1 1 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 0,99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 1 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 1 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 0,99 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 1 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 0,97 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 1 1 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 1 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 1 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 1 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 1 1 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 1 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 1 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 1 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 1 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 Cluster2 1 1 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 1 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 1 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 1 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 1 1 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 DPANN UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 Undinarchaeota UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 1 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 1 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 1 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 1 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 1 1 1 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 1 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 1 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 1 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 1 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Cluster1 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785

0.4

Supplementary Figure 40 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% top ranked proteins (n=57) and the 127 species set. 40% of heterogenous sites were removed from the alignment with the chi2 test. A Bayesian phylogenetic tree was inferred with the CAT +GTR model run with two chains for 6,788 cycles (25% burn-in). The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 35 can be found in Supplementary Table 6. 100/100 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 95.2/74 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 68.7/90 9 6 / 7 7 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 364 species 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 44.9/89 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 99.7/91 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 75% top ranked proteins 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 (n=84) 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 100/75 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 97.6/100 100/81 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 10.7/66 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/99 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 trimmed alignment (BMGE) Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 95.3/74 99.9/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 90.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 17,191 amino acids Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/75 100/100 97.1/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 68.2/71 99.9/100 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Iqtree, LG+C60+F+R Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 98.4/95 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 100/96 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 14.1/78 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 84.5/87 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 100/100 81.7/89 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 99.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 53.4/97 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 93.2/99 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 Euryarchaeota 100/100 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 99.1/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 99.8/93 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/93100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/93100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 83.1/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 87.1/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 99.9/100 9 3 / 7 5 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 99.9/76 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 100/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 77.4/73 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 90.6/93 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 48.1/89 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 100/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 29.8/87 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 99.8/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 100/100 95.1/97 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 100/54 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/10093.3/54 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 30.3/95 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 47.5/98 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 97.9/100 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 96.5/100 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 58.6/93100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Asgard + TACK Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 97.1/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 99.9/95 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 78.8/95 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 99.4/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 47.8/100 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 98.4/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 94.1/93 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 96.5/70 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 100/92 45.7/51 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 99.3/56 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 34.5/93 100/100 95.7/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 95/100 100/100100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 99.9/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 95.2/97 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 100/96 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 88.7/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 99.7/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 100/100 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 96.4/98 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 25.1/54 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/97 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 100/100 53.8/97 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 99.8/98 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 75.1/58 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 5 3 / 6 3 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 100/70 97.9/70 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 100/100 100/100 100/100 31.3/61 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 78.8/52 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 100/100 82.3/53 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 Cluster2 75.8/100 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 92.5/52 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 7 7 / 9 6 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 86.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 99.2/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 98.7/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 99.8/100 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 DPANN Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 6.4/40 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 8 2 0 / 7 9 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.5/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 Undinarchaeota UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 32.5/98 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 46/100 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 92/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 94.7/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 47.5/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795

0.4 Supplementary Figure 41 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 75% top ranked proteins (n=84) and the 364 species set. The alignment was trimmed with BMGE (alignment length = 17,191 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 36 can be found in Supplementary Table 6. 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 92/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 364 species 94.9/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 21/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 34.5/100 75% top ranked proteins Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 81.6/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 21.6/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 10.8/100 (n=84) Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 22.2/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 trimmed alignment (BMGE) 100/100Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 93.7/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 SR4 recoded 100/100 100/100Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 17,191 characters 100/100Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 91.2/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/100 78.4/100100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Iqtree, LG+C60+F+R Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 99.4/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 49.9/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_00249548595.8/100 99.8/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 Asgard + TACK 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115100/100 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 99.6/100 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 97.5/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 51/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325100/100 98.5/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 98.7/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 99.6/100 90.2/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 85.2/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 68.5/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 74.5/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 89.5/100100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 73.2/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 88/100 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 97.4/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 85.6/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 99.9/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 99/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 33.8/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 66.2/100 97.3/100Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 50.5/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 99.7/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 62.3/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 52/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 95.7/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 50.5/10099.9/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_00038556547.5/100 99.9/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 71.7/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 45.4/100100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 100/100Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 64/100 23.8/96 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 99.9/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_00040422598.7/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 99.7/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 Euryarchaeota 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 99.8/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 99.1/100100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/100100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425100/100 100/100 69/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 0 / 1 0 0 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 100/100 99.6/100Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 99.9/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 99.7/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 87.4/99 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_00016609595.7/100 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 0 / 1 0 0 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 99.3/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 98.8/100 99.2/100Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125100/100 83.7/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 98.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 0 / 1 0 0 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 99.9/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 99.9/100 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 95.3/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 22.3/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 55.8/100 89.3/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 77.9/100 95.7/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 100/100 99.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 45.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 98.7/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 77.6/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 64.9/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 9 5 / 9 1 99.6/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 0 / 1 0 0 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 17.2/10088.8/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 99.7/100 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 96.3/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 48.3/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 100/1005.3/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 98.4/10017/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 80.2/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 15.7/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 99.8/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 95.9/98100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 52.6/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 9 6 / 9 6 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 99.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 Cluster2 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 98.7/91 91.2/92 0 / 4 4 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 98.4/88 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 37.4/100Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 99.5/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 84/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 78.3/90 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_00000808599/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 57.5/86 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085

NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 DPANN NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_00276326599.6/100 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 95.5/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641100/100 33.6/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 83.8/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 97/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 76.2/83 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 100/100 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 3 6 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 96/100 96.6/98 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288100/100 99/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 100/100 97.8/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 95.4/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 100/100 77.5/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 99.4/100 93.2/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 59.4/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 0 / 1 0 0 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 88.6/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 97.8/100100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100

Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 99.9/100Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795

0.4 Supplementary Figure 42 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 75% top ranked proteins (n=84) and the 364 species set. The alignment was trimmed with BMGE and recoded into 4 character states (SR4 decoding; alignment length = 17,191 characters). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root as inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 37 can be found in Supplementary Table 6. 127 species 75% top ranked proteins (n=85) trimmed alignment (BMGE) 18,824 amino acids Iqtree, LG+C60+F+R

100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 99.9/77 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100 100/78 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/78 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 2 3 / 6 2 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 72.5/68 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/76 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 96.5/97 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 Euryarchaeota 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 85.7/49 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/50 100/99 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 98.7/49 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 71.6/98 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 99.4/100 100/82 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 96.2/81 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 97.3/99 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 98.8/98 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 97.9/99 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 100/100 Asgard + TACK Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 95.1/96 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 16.6/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 99.8/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 91.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 77.5/87 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 Cluster2 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 99.7/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 9 0 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 80.9/98UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 DPANN 99.9/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 99.8/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 43 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 75% top ranked proteins (n=85) and the 127 species set. The alignment was trimmed with BMGE (alignment length = 18,824 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 38 can be found in Supplementary Table 6. 127 species 75% top ranked proteins (n=85) trimmed alignment (BMGE-FAST) 39,615 amino acids Iqtree, LG+C60+F+R

86.3/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 13.4/29 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 37.6/61 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 79.7/62 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 98.4/45 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 64.2/45 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/99 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 9 7 / 9 9 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 99.5/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 96.9/96 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 68.2/96

Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 TACK + Asgard 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 39.4/96 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 98.7/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 99.2/97 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 91.4/95 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 9.4/51 88.9/99 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 91.1/95100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 50.2/88 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 4 5 / 6 6 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 71.5/71 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 99.3/98 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 95.6/72 99.4/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 91.9/72 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 99.9/99 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 67.5/69 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 22.1/63 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 78.4/72 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 91.5/96 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 17.8/85 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 82.1/96 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.3/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305

99.8/100 Cluster2 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 55.3/93 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 8 4 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 8 4 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 DPANN 95.8/99 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 Undinarchaeota 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 99.6/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 99.9/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 99.1/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.5 Supplementary Figure 44 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 75% top ranked proteins (n=85) and the 127 species set. The alignment was trimmed with BMGE-FAST (alignment length = 39,615 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting. Scale bar: Average number of substitutions per site. Tree statistics for tree number 39 can be found in Supplementary Table 6. 127 species 75% top ranked proteins (n=85) trimmed alignment (BMGE) SR4 recoded 18,824 characters Iqtree, LG+C60+F+R

36.9/78 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 95.3/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 96.3/100 76.5/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 100/100 97.4/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 100/96 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 100/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 99.1/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 97.2/66 100/100 39.4/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 Asgard + TACK Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 91.8/94 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 99.5/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 90.9/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 99.2/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100 61.1/69 99.9/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 99.8/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/10095.5/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 99.1/99100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 98.6/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 90.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 97.8/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 7.9/89 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/99 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 99.8/98 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 97.2/99 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 66.2/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 97.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 26.7/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 99.2/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 99.2/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.6/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305

67.7/100 Cluster2 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 99.8/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 79.1/100UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 45.1/100 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.1/100 97.4/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 DPANN UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 78.1/100 99.6/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 98.7/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.2 Supplementary Figure 45 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 75% top ranked proteins (n=85) and the 127 species set. The aligment was trimmed with BMGE and decoded into 4 character states (SR4 recoding; alignment length = 18,824 characters). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 40 can be found in Supplementary Table 6. 99.1/100Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 364 species Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 91.1/100 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 75.5/99 25% lowest ranked proteins Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 85.5/99 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 (n=28) 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 78/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 96.8/99 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 43.2/91 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 100/100 62.6/92 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 trimmed alignment (BMGE) 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 99/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 93.6/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 96.1/100 3,963 amino acids Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 96.7/84 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 98.3/84 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 98.6/84 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 15.6/56 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 Iqtree, LG+C60+F+R 100/100 72.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 99.8/99 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 78.7/99 99.3/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 11.6/70 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 100/100 73.1/99 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 99.9/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 83.5/97 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 56.6/94 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 35.5/89 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 9 8 / 9 9 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 94.6/81 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 99.1/81 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 99.7/92 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 95.9/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 18.6/78 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 99.5/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 89.6/99 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 100/100 99.9/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 94.9/99 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 100/100 99.7/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 9 7 / 9 7 99.8/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 99.9/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 51.3/95 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 94.6/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 99.2/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 99.7/98 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 0.7/39 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 93.9/48 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Altiarchaeota 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 91.5/99 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 99.9/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 99.7/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 95.5/91 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 91.4/90 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 98.7/100 99.8/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 93.6/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 99.9/99 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 97.8/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 99.4/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 80.9/93 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 98.1/99 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 59.5/58 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 100/100 99.4/63 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 99.5/100 Korarchaeota Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 100/99 98.6/61 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 95.4/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 99.5/96 98.1/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 45.5/88 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/97 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 100/98 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 83.6/95 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 47.8/70 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 100/100 97.5/99 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 98.1/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 100/98 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 99.4/98 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 84.1/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 99.8/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 98.3/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 99.6/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 100/98 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 98.8/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 84.4/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 99.6/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 86.5/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 99.8/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 98.6/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 99.9/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 76.9/99 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 99.8/81 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 44.9/81 74.8/77 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 99.7/77 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 100/100 98.5/77 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100 99.7/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 81.7/94 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 98.1/95 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 92.8/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 Halobacteria 80.4/95 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 46.5/58 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 5.4/67 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 99.9/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 98.4/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 99.7/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 50.9/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Nanohaloarchaeota Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 98.9/99 0 / 7 1 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 78.3/95 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 100/100 86.2/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 66.3/79 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 99.5/99 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 84.5/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 97.2/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 82.6/97 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 16.4/93 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 99.4/75 100/100 Methanofastidiosa Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 99.9/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 99.9/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 99.6/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 97/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 62.1/80 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 100/100 100/95 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 99.2/70 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 94.9/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 9.6/21 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 79.5/66 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 48.4/58 90.5/9588.8/46 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 89.8/39 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 9 8 / 9 2 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 93.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 2 3 / 5 8 75.4/96 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 98.7/89 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 100/93 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 99.7/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 64.2/95 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 98.9/90 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 78.8/63 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 74.7/47 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 64.1/43 97.7/96 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 100/93 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 99.6/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 99.8/100 92.9/53 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 99.9/81 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 99.9/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 27.8/97 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 99.6/97 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 100/98 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 99.9/96 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 86.4/86 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 98.7/76 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 100/80 99.9/81 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 9 4 / 8 7 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 9 6 / 8 9 100/87 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/100 34.6/54 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 46.5/74 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 91.8/82 100/89 78.4/78 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 100/87 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 95.8/86 100/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 3 5 / 7 1 99.9/89 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 70.6/83 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 97.3/95 80.7/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 99.7/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 77.8/82 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 99.7/89 100/78 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 91.7/81 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 100/100 66.3/79 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/100 7 6 / 9 7 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 84.5/98 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075

0.4 Supplementary Figure 46 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 25% lowest ranking proteins (n=28) and the 364 species set. The alignment was trimmed with BMGE (alignment length = 3,963 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 41 can be found in Supplementary Table 6. 127 species 25% lowest ranked proteins (n=28) trimmed alignment (BMGE) 3,682 amino acids Iqtree, LG+C60+F+R

3 5 / 4 6 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 45.8/47 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 99.7/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100 95.5/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 99.7/100 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 93.8/99 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 91.9/64 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 76.7/84 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 99.9/100 3 2 / 5 2 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 98.1/65 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 8 7 / 6 8 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 96.8/99 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 7 4 / 8 4 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 91.8/99 76.5/83 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 94.5/93 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 97.6/94 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Altiarchaeota Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 90.3/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 68.4/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 95.1/76 60.8/89 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 98.3/97 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 35.2/40 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 82.2/74 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 Nanoarchaeota 56.3/51 100/94 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 99.4/77 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 99.7/94 100/61 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 64.3/75 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 61.9/98 58.5/88 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 77.9/82 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 97.9/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 82.7/93 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 99.5/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 99.9/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 66.2/89 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 99.9/99 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 0 / 5 2 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 0 / 8 4 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 100/100 96.8/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 Undinarchaeota 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 78.7/67 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 62.7/68 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 91.2/91 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 63.7/90 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 99.8/93 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 95.2/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 95.8/99 27.3/55 99.8/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 5.2/81 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 92.5/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 1 7 / 5 0 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 96.3/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 9 6 / 9 1 99.8/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 86.6/92 72.9/91 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 99.3/91 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 99.9/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 99.9/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 99.7/94 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 78.7/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Nanohaloarchaeota 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 Halobacteria 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 Methanofastidiosa

0.3 Supplementary Figure 47 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 25% lowest ranked proteins (n=28) and the 127 species set. The alignment was trimmed with BMGE (alignment length = 3,682 aa). A ML phylogenetic tree was inferred with the LG+C60+F +R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 42 can be found in Supplementary Table 6. 100/100 91.7/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 89.9/85 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 100/100 98.3/92 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/10099.5/80 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 364 species 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 95.6/97 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 98.6/82 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/100 50% lowest ranked proteins Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 100/100 16.2/77 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 53.5/96 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 (n=56) 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 98.9/97 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 70.6/98 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 99.9/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 100/100 trimmed alignment (BMGE) Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 96.5/97 99.7/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 95.1/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 8,305 amino acids 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/100 94.4/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 9.2/70 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 100/100 Iqtree, LG+C60+F+R 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 94.3/100 99.9/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 86.7/99 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 99.7/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 53.5/62 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 99.4/85 100/100 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 98.9/78 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 78.1/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 97.9/90 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 100/100 82.8/90 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 100/100 Euryarchaeota Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 98.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 9 9 / 8 1 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 100/96 98.9/81 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 100/81 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 99.9/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 99.6/96 100/100 54.3/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 99.4/95 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 99.8/100 81.2/94 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 100/100 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 75.9/84 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 96.8/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 99.5/96 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 93.7/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 90.7/93 99.9/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/96 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 100/93 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 18.4/66 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 100/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 85.7/78 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 95.2/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 98.5/94 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 99.5/99 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 99.7/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 99.9/86 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 2 6 / 5 1 83.4/84 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 9 9 / 7 5 80.9/78 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 91.1/98 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 99.2/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 92.4/100 75.6/99 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 100/91 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 88.9/96 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 69.4/100 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/97 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 26.6/85 Asgard + TACK 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 90.9/82 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/82 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 99.8/81 100/100 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 99.8/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 99.6/99 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 99.8/83 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 58.9/99 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 83.5/98 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 99.4/9998.8/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 92.4/92 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 74.4/94 8 9 / 9 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 97.7/99 9 7 / 9 2 54.7/97 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 100/100 21.5/83 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 97.4/94 98.2/97 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 99.2/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 100/97 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 100/100 58.8/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/97 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 97.8/93 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 98.4/96 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 99.9/100 45.7/74 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 88.2/95 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/95 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 100/100 89.1/99 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 99.9/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/100 43.1/71 99.7/95 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 99.7/100 30.3/86 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 99.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 80.6/94 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 100/100 99.8/100 100/100 99.9/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 99.8/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 46.5/100 8 / 7 0 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 93.1/99 97.3/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285

100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Cluster2 78.3/43 99.3/98 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 100/100 96.6/98 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 95.4/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 99.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 99.5/100 97.5/43 88.8/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 99.6/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 100/100 100/100 100/98 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015

Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 DPANN 92.5/44 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.7/100 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 99.9/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 26.4/83 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 99.4/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 9 3 77.6/95UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 31.2/97 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 99.9/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 99.3/100 98.1/98 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 99.9/100 98.1/95 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 52.2/94 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795

0.3 Supplementary Figure 48 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% lowest ranked proteins (n=56) and the 364 species set. The alignment was trimmed with BMGE (alignment length = 8,305 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 43 can be found in Supplementary Table 6. 127 species 50% lowest ranked proteins (n=57) trimmed alignment (BMGE) 9,133 amino acids Iqtree, LG+C60+F+R

74.6/98 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 93.6/99 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 99.8/99 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100 84.6/95 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/91 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 98.6/91 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/94 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 100/94 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 52.1/90 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 99.6/96 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 99.4/99 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 95.8/90 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 71.8/86 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 99.9/100 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/98 83.9/90 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 98.1/97 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 99.4/95 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 24.1/61 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 94.6/71 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 100/96 100/94 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 88.4/93 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 99.5/99 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 87.4/93 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 99.7/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 99.5/99 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 4 1 / 9 3 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 99.7/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 72.9/95100/99 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 94.1/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 94.4/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Asgard + TACK 81.7/96 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 81.6/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 86.1/94 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 99.6/100 99.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 98.3/61 100/99 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 2 4 / 3 4 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 99.3/55

Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 Cluster2 99.8/93 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 98.5/93 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 99.5/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 99.9/94 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0 / 7 2 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 74.9/80UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 DPANN 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 45.3/90 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 Undinarchaeota 4 9 / 8 5 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 75.2/94 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225

100/94 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 99.9/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 99.7/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.4 Supplementary Figure 49 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 50% lowest ranked proteins (n=57) and the 127 species set. The alignment was trimmed with BMGE (alignment length = 9,133 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 44 can be found in Supplementary Table 6. 100/100 99.4/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 91.3/65 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 99.9/100 98.7/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 356 species 99.7/1007 0 / 6 5 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 42.3/41 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 62.2/41 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 Phylosift marker proteins 44.3/85 99.9/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 62.6/88100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 (n=34) 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 99.6/96 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 99.5/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 trimmed alignment (BMGE) 96.7/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 84.2/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/100 100/100 5,353 amino acids 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 95.4/97 58.1/99 74.5/96 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 99.9/96 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 100/100 66.8/95 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 100/100 Iqtree, LG+C60+F+R 45.3/71 25.8/81 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 19.1/69 100/100 Euryarchaeota-Methanomicrobia-none-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-none-none-none-ANME-1_cluster_archaeon-GCA_003194435 Euryarchaeota-Methanomicrobia-none-none-none-ANME-1_cluster_archaeon-GCA_003336485 87.2/87 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 47.9/86 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 86.2/100 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Marine_Group_II-none-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 100/100 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 Euryarchaeota-Marine_Group_II-none-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 100/100 Euryarchaeota-Marine_Group_III-none-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 3.4/37 Euryarchaeota-Marine_Group_III-none-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Marine_Group_III-none-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 98.7/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 98.5/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 94.1/100Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 Euryarchaeota 100/100 50.3/88 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 99.6/89 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 89.5/89 97.4/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 91.3/98 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 99.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 99.6/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 99.4/98 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 96.8/98 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 100/98 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/100 98.5/100 Euryarchaeota-Methanomicrobia-none-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Methanomicrobia-none-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 37.3/69 100/100 Euryarchaeota-Methanomicrobia-none-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Methanomicrobia-none-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Methanomicrobia-none-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 99.9/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 36.9/91 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 98.7/99 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 99.6/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 47.9/76 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 85.8/73 39.6/84 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 100/99 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 98.8/100 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 100/100 Crenarchaeota-Thermoprotei--Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Acidilobales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Acidilobales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 97.9/97 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 97.1/57 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 99.6/94 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 6 6 / 5 6 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Fervidicoccales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 99.9/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 99.7/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 99.1/95 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 98.2/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 99.9/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 93.1/98 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/99 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 100/100 3 3 / 9 2 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 87.8/98 98.3/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 99.8/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 99.5/100 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 16.6/99 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185

100/100 Asgard + TACK 74.9/95 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 37.5/87 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 94.3/100 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 97.9/100 99.5/100 Thaumarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 Thaumarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Thaumarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 100/100 Thaumarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Thaumarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/100 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 99.9/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 99.5/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 96.7/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 77.1/99 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 93.1/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 99.7/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 95.7/100 85.3/84 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 98/100 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 74.3/81 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 99.8/94 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 83.1/79 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 97.5/95 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 100/94 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 69.4/99 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 52.8/92 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 11.9/72 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 6 4 / 894.7/95 6 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 76.9/64 75.8/64 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 99.5/100 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 98.1/99 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 8 7 / 9 5 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 99.3/97 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/100 100/100 97.2/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 23.3/90 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 3 5 / 8 9 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 98.9/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 97.7/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 12.6/90 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 100/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 89.4/95 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 96.4/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 91.1/96 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100

100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 Cluster2 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 55.1/50 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 100/85 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 64.2/47 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 99.5/100 87.8/99 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 94.3/100 38.1/95 100/10097.8/84 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 100/100 97.5/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 95.7/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 99.7/99 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 76.1/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 9 3 / 8 8 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 DPANN 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 99.8/88 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 99.2/100 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 85.3/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 98.9/100 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 99.7/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 50.7/99 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 87.7/89 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 100/100 99.9/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 99.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 99.9/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 63.1/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/88 74.9/100 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 67.6/88 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 100/99 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 81.9/99 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 0 / 7 8 0 / 5 1 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 99.9/100 98.5/100 99.8/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_bin_140_subBin1-bin_140_subBin1 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 Undinarchaeota 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 99.5/100 89.4/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 50 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the phylosift marker proteins (n=34) and the 356 species set. The alignment was trimmed with BMGE (alignment length = 5,353 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor devation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 45 can be found in Supplementary Table 6. 100/100 98.8/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 99.2/98 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 100/100 99.9/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100100/98 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 100/100 356 species Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 99.2/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 100/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/89100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 GTDB marker proteins Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 100/100 36.7/85 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 (n=122) Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 100/93 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 99.9/95 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 100/100 89.3/95 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 trimmed alignment (BMGE) Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 94.3/98 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 26,843 amino acids 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 69.3/97 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/100 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/93 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 Iqtree, LG+C60+F+R 100/100 100/100 100/100 Euryarchaeota-Methanomicrobia-none-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-none-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-none-none-none-ANME-1_cluster_archaeon-GCA_003194435 98.9/100 100/41 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 69.7/41 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 63.4/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 99.9/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 48.3/29 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 94.2/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 95.9/100 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Marine_Group_II-none-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155

100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 Euryarchaeota 100/100 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 Euryarchaeota-Marine_Group_II-none-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 100/100 Euryarchaeota-Marine_Group_III-none-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Marine_Group_III-none-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 Euryarchaeota-Marine_Group_III-none-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/100 100/100 Euryarchaeota-Methanomicrobia-none-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Methanomicrobia-none-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Methanomicrobia-none-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Methanomicrobia-none-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Methanomicrobia-none-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 95.9/98 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 90.5/96 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 99.7/100 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Crenarchaeota-Thermoprotei-Acidilobales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 100/100 Crenarchaeota-Thermoprotei-Acidilobales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Acidilobales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 82.4/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 100/100 100/83 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 Crenarchaeota-Thermoprotei-Fervidicoccales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 95.1/82 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 98.7/100100/98 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 85.3/98 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 48.2/65 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 35.3/52 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 100/100 100/84 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 95.9/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/100 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 91.1/98 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 99.9/100 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 Asgard + TACK 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 81.9/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 100/100 Thaumarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 Thaumarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Thaumarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Thaumarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Thaumarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 100/95 100/95 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 72.6/73 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 70.7/74 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 100/53 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 35.9/21 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 95.5/56 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 99.9/71 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 100/100 99.9/100 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 99.5/100 99.9/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 100/100 100/100 99.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 44.5/89 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 100/100 100/100 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 68.4/91 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 96.6/64 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 99.4/66 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 99.1/72 100/95 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 100/100 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 100/100 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 54.4/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 100/95 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 100/95 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 100/100 99.2/99 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 99.7/99 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 1 4 / 3 2 99.9/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Cluster2 100/91 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 100/100 10.2/58 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 100/34 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/63 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 70.9/63 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 78.6/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 100/91 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 15.2/77 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 DPANN 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 99.9/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 100/100 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7 bin_34-Ga0181641 100/100 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 9 8 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 81/100 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 99.2/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_bin_140_subBin1-bin_140_subBin1 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 Undinarchaeota UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 85.3/98 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 81.6/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 99.3/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100

Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 99.9/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.2 Supplementary Figure 51 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the GTDB archaeal marker proteins (n=122) and the 356 species set. The alignment was trimmed with BMGE (alignment length = 26,843 aa). A ML phylogenetic tree was inferred with the LG+C60+F +R model using iqtree with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 46 can be found in Supplementary Table 6. 1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 0,998 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 1 1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 356 species 1 1 1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 0,672 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 1 1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 1 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 1 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 GTDB marker proteins 0,8 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 1 1 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 0,998 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 1 1 0,989 (n=122) Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 1 1 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 0,791 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 1 1 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 trimmed alignment (BMGE) 0,772 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 0,996 0,999 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 1 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 1 0,993 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 0,998 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 1 26,843 amino acids 1 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 1 1 1 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 1 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 0,998 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 1 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 0,999 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 1 Fasttree, LG+C60+F+R 1 1 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 1 1 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 1 1 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 1 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 1 1 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 1 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 1 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 0,576 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 1 1 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 1 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 0,519 1 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 1 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 1 1 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 0,998 0,733 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 1 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 1 1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 0,283 1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 1 1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 1 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 Euryarchaeota 1 1 1 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 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Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 0,528 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 1 1 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 0,98 1 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 1 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 1 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 1 1 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 1 1 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 1 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Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 0,996 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 0,999 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 0,423 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 1 0,051 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 0,745 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 1 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 0,969 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 0,874 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 1 0,766 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 0,735 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 1 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 1 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 1 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 1 1 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 0,975 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 0,214 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 0,977 1 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 0,997 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 0,996 1 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 1 1 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 1 1 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 0,598 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 1 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 0,546 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 1 1 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 1 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 1 0,999 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 1 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 0,991 0,999 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 Cluster2 1 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 1 0,789 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 0,961 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 0,999 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 0,478 1 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 1 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 1 1 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 1 1 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 1 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 1 1 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065

Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 DPANN Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 1 1 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 1 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 1 1 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 1 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 1 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 1 1 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 1 1 1 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 1 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 0,999 1 1 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0,786 0,881 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 1 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 1 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 1 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_bin_140_subBin1-bin_140_subBin1 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 1 Undinarchaeota UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 1 1 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 1 0,999 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 1 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 1 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 1 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 0,99 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 1 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 1 0,158 1 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 1 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 1 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 0,986 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 1 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 1 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 1 0,994 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 1 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 Cluster1 1 1 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 1 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.2 Supplementary Figure 52 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the archaeal GTDB marker proteins (n=122) and the 356 species set. The alignment was trimmed using BMGE (alignment length = 26,843 aa). An approximately-ML phylogenetic tree was inferred with the WAG+GAMMA model using fasttree with SH-like approximate likelihood tests run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 47 can be found in Supplementary Table 6. 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 99.7/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 59.6/98 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 100/100 82.2/94 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 356 species Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 49.3/83 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 37.8/42 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 9.8/55 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 Ribosomal proteins 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 99.8/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 77.2/99 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 (n=14) Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 97.8/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 99.6/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 95/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 2 1 / 6 4 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 trimmed alignment (BMGE) 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 96.4/99 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 97.9/98 100/100 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 1,974 amino acids Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 99.7/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 Iqtree, LG+C60+F+R 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 28.7/61 99.3/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 99.9/100 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 22.9/59 72.4/87 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 89.3/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 100/100 99.5/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 86/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/100 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 99.8/100 99.8/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 Asgard + TACK 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 99.4/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 11.7/58 99.7/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 95.4/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 89.1/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 98.9/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 100/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 99.9/100Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 99.8/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 98/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465

97.4/99 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 91.5/99 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 93.3/99 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 99.9/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 96.6/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 67.4/82 99/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 96.2/91 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 61.6/92 99.7/91 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 99.9/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 99.9/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 84.2/98 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/100Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 75.4/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 99.6/100 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 98.1/73 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 99.1/98 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 0 / 5 7 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 70.3/39 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 97.5/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 99.9/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 4 7 / 5 0 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 100/100 98.8/81 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 86.5/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 98.6/74 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 94.4/100Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 99.4/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 46.6/93 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 46.1/95 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 85.1/97 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 95.3/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 100/100 98.1/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 40.1/62 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 98.7/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 56.8/50100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 99.7/99 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 89.2/50 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 67.2/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 99.9/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 92.2/74 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 97.6/47 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 87.4/77 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 57.3/45 91.8/96 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 99.9/100 98/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 76/100 89.5/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 8 2 / 9 9 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 93.8/84 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 26.2/98 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 99.2/99 2 3 / 9 759.6/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 45.7/63 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355

Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 Euryarchaeota Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 53.4/99 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 96.1/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 59.6/99 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 99.9/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 90.4/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 85.8/100Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 99.5/91 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 98.5/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 43.8/95 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 4 8 / 7 3 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 86.3/76 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 96.6/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 100/100 97.5/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 63.5/77 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 100/100 89.2/77 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 93.3/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 98/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 99/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 90.1/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 99.6/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 47.8/93 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 93.2/99 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 19.9/27 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 95.6/97 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 76.7/70 82.1/46 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 99.8/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 97.1/72 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 26.4/30 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 73.1/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 100/100 79.1/82 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 99.5/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 98.5/95 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 93.7/84 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 99.8/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 27.4/86 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 99.2/97 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 79.9/95 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 92.9/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 99.6/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 91.8/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 72.5/89 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 74.8/85 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 74.1/77 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 94.9/99 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 99.9/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 96.7/85 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 77.8/96 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 99.4/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 99.1/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 5 7 / 9 8 92.5/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 97.8/100 79.9/97 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 3.4/42 99.4/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 92.3/99 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 99.5/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 100/100 38.8/79 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 Cluster2 99.9/94 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 89.7/81 6.1/48 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 51.6/85 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 85.6/100 97.4/9398.8/87 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 99.9/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 95.9/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 7 1 / 9 3 98.3/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 99.9/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 80.7/57 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 99.4/94 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 68.3/97 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 100/100 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 DPANN Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 71.1/57 99.9/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 99.8/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 54.4/87 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 92.5/96 100/100 9 9 / 9 2 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 95.2/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 99.9/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 76.9/98 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/98 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 98.8/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 97/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 93.4/99 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 99.8/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 95.6/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 42.2/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 62.4/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 97.8/100 48.9/97 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 94.9/93 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 99.1/83 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 40.5/76 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 80.8/95 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 67.2/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 99.7/99 96.8/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 99.7/100 89.9/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 99.7/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 0 / 8 1 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 99.9/100UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 99.7/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_bin_140_subBin1-bin_140_subBin1 33.2/77 98.8/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 Undinarchaeota UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 78.6/98 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 4.4/44 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288

0.4 Supplementary Figure 53 | Phylogenetic placement of Undinarchaeota based on an alignment generated with the 14 ribosomal proteins and the 356 species set. The alignment was trimmed with BMGE (alignment length = 1,974 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 48 can be found in Supplementary Table 6. 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 12.1/84 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 9 0 / 9 1 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 99.8/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 356 species 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 96.2/71 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 22.3/64 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 99.9/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 ribosomal proteins 92.7/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 48.9/92 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 (n=14) 95.8/99 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 99.9/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 45.8/94 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 10.1/87 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 trimmed alignment (TRIMAL) Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 0.6/57 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 36.6/87 100/100 2,406 amino acid 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Iqtree, LG+C60+F+R 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 38.1/82 96.2/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 100/100 99.7/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 4 5 / 7 1 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 28.7/37 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 89.7/99 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 99.7/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 76.9/100 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100

99.9/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 Asgard + TACK 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 99.9/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 75.7/100 100/100 91.5/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 50.5/99 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 99.8/100 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 99.9/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 99.9/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 99.7/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 98.3/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 62.9/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 97.7/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 99.8/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 84.6/95 17.5/88 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 72.8/94 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 99.8/100 99.3/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 99.8/94100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 68.5/97 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 74.5/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 98/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 97.3/83 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 95.2/99 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 64.8/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 34.8/40 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 98.9/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 64.5/49 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 99.7/98 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 99/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 99.7/90 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 96.6/100 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 99.3/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 43.6/88 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 35.7/94 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 82.8/95 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 99.5/100 100/10096.3/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 71.7/68 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 88.7/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 99.2/99 39.3/67 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 81.7/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 0 / 5 1100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 100/100 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 98.2/93 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 49.6/95 24.6/84 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 49.3/92 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 93.9/92 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 100/100 99.8/100 99.9/99 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 98.9/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 97.7/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 97/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 83.7/96 99.7/100 57.8/90 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 99.2/98 99.8/99 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 59.7/86 100/100 64.3/94

Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 66.6/98 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 81.5/98 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 48.6/97 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 97.6/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 45.7/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 99.2/97 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 99.4/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 12.7/73 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 74.4/89 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 98.8/91 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 100/100 19.3/90 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 94.6/91 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 96.8/100 99.1/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 79.3/99 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 98.7/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 94.4/100 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 92.6/73 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 99.2/98 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 65.3/72 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 68.6/60 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 97.4/95 87.3/66 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 97.6/63 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 99.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 42.9/52 98.7/100 79.4/98 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 15.5/90 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 98.8/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 59.9/98 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 98.2/98 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 85.1/7291.4/99 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 100/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 54.7/96 2 5 / 8 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 99.6/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 93.1/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 99.9/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 94.8/100 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 92.2/96 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 51.9/94 63.3/91 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 96.3/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 100/100 99.8/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 95.7/96 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 77.7/96 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 97.6/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 97.9/100 99.3/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015 45.3/96 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 99.8/100 100/100 99.6/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 6.8/1758.6/96 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 38.5/98 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 100/100 99.7/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 100/100 76.1/99 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 99.9/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 9 8 / 9 9 35.9/86 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 Cluster2 62.7/98 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 40.4/98 9 5 / 9 993.3/98 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 99.9/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 95.8/100 95.9/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 9 8 / 9 0 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 99.4/97 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 96.8/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 DPANN 100/100 99.7/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 70.5/96 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 99.3/100 97.9/88 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 96.5/100 99.6/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 97.9/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 70.9/99 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 97.5/100 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 53.2/81 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 99.6/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 97.3/99 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 99.9/100 99.8/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 77.6/100 80.8/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 70.2/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 96.9/92 31.6/97 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 9 8 / 9 8 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 99.8/97 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 9.8/81 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 82.1/88 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 99.2/99 83.9/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 96.1/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 99.8/100 92.5/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 Cluster1 100/100 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 0 / 8 0 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 100/100 99.9/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 72.6/97 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_bin_140_subBin1-bin_140_subBin1 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 99.9/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 Undinarchaeota 12.3/71 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461

0.4 Supplementary Figure 54 | Phylogenetic placement Undinarchaeota lineage based on an alignment generated with 14 ribosomal proteins and the 356 species set. The alignment was trimmed with TRIMAL (alignment length = 2,406 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor deviation rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 49 can be found in Supplementary Table 6. 100/100 98.7/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halobiforma-Halobiforma_lacisalsi-GCA_000226975 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronobacterium-Natronobacterium_gregoryi-GCA_000230715 99.4/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halopiger-Halopiger_xanaduensis-GCA_000217715 100/100 99.9/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_turkmenica-GCA_000025325 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/10070.2/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrialba-Natrialba_magadii-GCA_000025625 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Haloterrigena-Haloterrigena_daqingensis-GCA_001971705 364 species Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natronococcus-Natronococcus_occultus-GCA_000328685 99.8/89 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Halostagnicola-Halostagnicola_larsenii-GCA_000517625 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halomicrobium-Halomicrobium_mukohataei-GCA_000023965 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Halorhabdus-Halorhabdus_tiamatea-GCA_000470655 87.1/86 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_pharaonis-GCA_000026045 Euryarchaeota-Halobacteria-Halobacteriales-Haloarculaceae-Natronomonas-Natronomonas_moolapensis-GCA_000591055 99.6/100 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Halogeometricum-Halogeometricum_borinquense-GCA_000172995 82.6/91 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloquadratum-Haloquadratum_walsbyi-GCA_000237865 48 marker proteins 100/100 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Halobacteria-Haloferacales-Halorubraceae-Halorubrum-Halorubrum_lacusprofundi-GCA_000022205 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halalkalicoccus-Halalkalicoccus_jeotgali-GCA_000196895 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_salinarum-GCA_000006805 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halobacterium-Halobacterium_hubeiense-GCA_001488575 100/100 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halanaeroarchaeum-Halanaeroarchaeum_sulfurireducens-GCA_001011115 100/96 Euryarchaeota-Halobacteria-Halobacteriales-Halobacteriaceae-Halodesulfurarchaeum-Halodesulfurarchaeum_formicicum-GCA_001886955 40.1/93 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanospirillaceae-Methanospirillum-Methanospirillum_hungatei-GCA_000013445 trimmed alignment (BMGE) 100/100 99.1/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanosphaerula-Methanosphaerula_palustris-GCA_000021965 100/100 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanoculleus-Methanoculleus_bourgensis-GCA_000304355 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanomicrobiaceae-Methanolacinia-Methanolacinia_petrolearia-GCA_000147875 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 99.7/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanococcoides-Methanococcoides_burtonii-GCA_000013725 99.9/100 95.9/96 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalophilus-Methanohalophilus_halophilus-GCA_001889405 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanolobus-Methanolobus_psychrophilus-GCA_000306725 9,534 amino acids Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanomethylovorans-Methanomethylovorans_hollandica-GCA_000328665 82.2/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanohalobium-Methanohalobium_evestigatum-GCA_000196655 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosalsum-Methanosalsum_zhilinae-GCA_000217995 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_acetivorans-GCA_000007345 99.6/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_siciliae-GCA_000970085 100/96 100/100 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_mazei-GCA_000970205 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 100/100 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_thermophila-GCA_000969885 Iqtree, LG+C60+F+R Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 100/100 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_conradii-GCA_000251105 96.3/95 97.8/100 100/100 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003336485 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 97.3/98 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 97.3/99 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_profundus-GCA_000025285 100/100 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_veneficus-GCA_000194625 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_sulfaticallidus-GCA_000385565 100/100 99.9/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_acetivorans-GCA_000789255 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Geoglobus-Geoglobus_ahangari-GCA_001006045 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 99.6/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S43_B8-GCA_001629235 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S41_B6-GCA_001629245 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G35-GCA_002457155 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S30_B12-GCA_001629205 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S03_B6-GCA_001628435 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G37-GCA_002457555 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote_MED-G36-GCA_002457595 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 100/100 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi3-GCA_001875355 53.2/70 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 100/100 100/100 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_BRNA1-GCA_000350305 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanoplasma-Methanoplasma_termitum-GCA_000800805 94.9/78 92.2/73 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomassiliicoccus-Methanomassiliicoccus_intestinalis-GCA_000404225 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA184-GCA_002495185 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M11B2D-GCA_002900545 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B2D-GCA_002900555 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 80.2/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-uncultured_archaeon-GCA_000965745 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_B_DKE-GCA_002204705 23.3/70 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_A-plasma-GCA_000447225 100/100 93.5/79 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Picrophilaceae-Picrophilus-Picrophilus_torridus-GCA_000008265 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Ferroplasmaceae-Ferroplasma-Ferroplasma_acidiphilum-GCA_002078355 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_volcanium-GCA_000011185 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 Euryarchaeota 45.7/94 100/100 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_divulgatum-GCA_900090055 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_Gpl-GCA_001856845 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 100/100 100/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 99.9/100 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_MAR08-339-GCA_000327505 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_JdFR-45-GCA_002011395 98.8/87 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_sp_-GCA_002878135 99.9/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_pacificus-GCA_002214485 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_profundus-GCA_002214585 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_thioreducens-GCA_002214545 87.8/43 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_piezophilus-GCA_001647085 100/100 99.8/43 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_horikoshii-GCA_000011105 100/43100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_barophilus-GCA_000151105 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_paralvinellae-GCA_000517445 100/100 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_sibiricus-GCA_000022545 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Thermococcus-Thermococcus_litoralis-GCA_000246985 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 100/100 94.4/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_B15fssc0709_Meth_Bin003-GCA_001587695 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin055-GCA_001587715 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_U1lsi0528_Bin089-GCA_001587675 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-GCA_001515185 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 96.2/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_N21-GCA_001515215 99.7/100 100/100 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259I09-GCA_001548995 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_aeolicus-GCA_000017185 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanothermococcus-Methanothermococcus_okinawensis-GCA_000179575 54.9/76 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanotorris-Methanotorris_igneus-GCA_000214415 100/100 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_vulcanius-GCA_000024625 98.6/86 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_infernus-GCA_000092305 100/100 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanosphaera-Methanosphaera_stadtmanae-GCA_000012545 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobacterium-Methanobacterium_paludis-GCA_000214725 11.8/48 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanobrevibacter-Methanobrevibacter_smithii-GCA_000016525 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 100/100 96.8/99 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B60_G1-B60_G1 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_SNP6-GCA_002201895 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_saccharovorans-GCA_000144915 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 Crenarchaeota-Thermoprotei-Desulfurococcales-Caldisphaeraceae-Caldisphaera-Caldisphaera_lagunensis-GCA_000317795 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Aeropyrum-Aeropyrum_pernix-GCA_000011125 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Hyperthermus-Hyperthermus_butylicus-GCA_000015145 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrodictium-Pyrodictium_delaneyi-GCA_001412615 70.1/89 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Desulfurococcus-Desulfurococcus_amylolyticus-GCA_000020905 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermosphaera-Thermosphaera_aggregans-GCA_000092185 97/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Thermogladius-Thermogladius_calderae-GCA_000264495 83.7/90 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Staphylothermus-Staphylothermus_marinus-GCA_000015945 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_islandicus-GCA_001481685 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Fervidicoccaceae-Fervidicoccus-Fervidicoccus_fontis-GCA_000258425 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfurisphaera-Sulfurisphaera_tokodaii-GCA_000011205 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Sulfolobus-Sulfolobus_acidocaldarius-GCA_000012285 100/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Metallosphaera-Metallosphaera_sedula-GCA_000016605 97.6/100 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Acidianus-Acidianus_sulfidivorans-GCA_003201765 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 9 8 / 9 1 Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermocladium-Thermocladium_modestius-GCA_001315925 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_distributa-GCA_000148385 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Vulcanisaeta-Vulcanisaeta_thermophila-GCA_001748385 32.9/81 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Pyrobaculum-Pyrobaculum_ferrireducens-GCA_000234805 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Thermoproteus-Thermoproteus_tenax-GCA_000253055 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_uzonense-GCA_000993805 99.2/100 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_OSP_B-GCA_003019445 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_OSP_D-GCA_003019545 100/100 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Crenarchaeota_archaeon_SCGC_AAA471-B05-GCA_000380705 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_mesodigestum-GCA_001717005 100/100 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA76-GCA_002507395 100/100 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 Verstraetearchaeota-none-none-none-none-Verstraetearchaeota_archaeon_UBA156-GCA_002504985 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717085 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003141855 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003165195 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon-GCA_003133625 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group-6_archaeon_AD8-1-GCA_001273385 89/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG_4_8_14_3_um_filter_42_8-GCA_002782745 99.8/100 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_JdFR-04-GCA_002010925 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA2-GCA_001399795 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_ex4484_40-GCA_002254475 100/100 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_16_57_9-GCA_001776015 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_52_12-GCA_001774245 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_B23-GCA_001593875 92.6/100 100/100 Bathyarchaeota-none-none-none-none-miscellaneous_Crenarchaeota_group_archaeon_SMTZ-80-GCA_001273495 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA185-GCA_002495485 66.5/100 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 Thaumarchaeota-none-none-none-Nitrosopelagicus-Nitrosopelagicus_brevis-GCA_000812185 100/100 Thaumarchaeota-none-Cenarchaeales-Cenarchaeaceae-Cenarchaeum-Cenarchaeum_symbiosum-GCA_000200715 100/100 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_N4-GCA_000723185 Thaumarchaeota-none-none-none-Nitrosotenuis-Nitrosotenuis_aquarius-GCA_002787055 Asgard + TACK 100/100 100/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_13_1_20CM_2_39_20-GCA_001920395 100/100 Thaumarchaeota-none-none-none-Nitrosotalea-Nitrosotalea_devanaterra-GCA_900065925 100/100 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 97.8/98 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 98.6/100 Thaumarchaeota-none-none-none-none-Thaumarchaeota_archaeon_RBG_16_49_8-GCA_001830115 100/100 100/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-14-GCA_002011085 99.9/100 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 99.7/100 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_JGI_0000106-J15-GCA_000405685 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-E14-GCA_000402965 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_SCGC_AAA471-F17-GCA_000405905 98.9/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-45-GCA_001563335 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ-45-GCA_001563465 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP11T_1-GCA_002825515 100/100 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP8T_1-GCA_002825465 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_MP9T_1-GCA_002825535 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 58.5/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon-GCA_003662865 100/100 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_2-GCA_001940725 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon-GCA_002728275 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_LC_3-GCA_001940645 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 Korarchaeota-none-none-none-none-Korarchaeota_archaeon_NZ13-K-GCA_003344655 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 94.5/100 100/100 Woesearchaeota-none-none-none-none-archaeon-GCA_002688925 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002730625 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686855 65.3/75 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR11-GCA_000806135 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687795 96.3/76 41.8/83 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_33_12-GCA_002762865 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_47_18-GCA_001872825 9 7 / 9 7 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 100/100 94.1/85 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002687275 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_37_12-GCA_002762795 99.5/85 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR3-GCA_000806075 100/99 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR4-GCA_000806095 99.1/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG1_02_57_44-GCA_001871415 100/100 97.2/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA525-GCA_002498125 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA153-GCA_002503705 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_9-GCA_002762915 99.3/100 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002685855 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002686295 99.8/98100/100 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002867475 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG11_big_fil_rev_8_21_14_0_20_43_8-GCA_002762705 4.7/30 6 8 / 4 1 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_36_11-GCA_002762845 100/79 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_24-GCA_002763025 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 96.5/99 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG_4_10_14_0_2_um_filter_33_13-GCA_002792115 Woesearchaeota-none-none-none-none-archaeon-GCA_002688265 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA119-GCA_002505945 100/100 99.8/84 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 Woesearchaeota-none-none-none-none-archaeon-GCA_002688355 15.1/56 Woesearchaeota-none-none-none-none-archaeon-GCA_002687185 99.2/93 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 76.6/82 Woesearchaeota-none-none-none-none-archaeon-GCA_002687815 100/100 100/100 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002687825 100/10099.3/81 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon-GCA_002688095 Woesearchaeota-none-none-none-none-Nanoarchaeota_archaeon_SCGC_AAA011-G17-GCA_000402515 Woesearchaeota-none-none-none-none-archaeon-GCA_002688325 99.9/94 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR17-GCA_000805995 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR18-GCA_000806155 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002689985 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002731115 79.8/87 Pacearchaeota-none-none-none-none-archaeon_BMS3Abin17-GCA_002897655 100/100 65.6/82 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_19FT_COMBO_34_9-GCA_001786415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_16_35_8-GCA_001786425 99.9/91 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR13-GCA_000805965 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002686355 100/100 100/100 100/100 92.1/83 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR1-GCA_000806055 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_71-GCA_002254395 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_32_14-GCA_002763085 91.9/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA92-GCA_002497285 53.6/73 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_9_14_0_2_um_filter_39_13-GCA_002788615 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_219-GCA_002794155 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_34_76-GCA_002763075 97.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002687255 84.5/97 100/100 9 9 / 7 6 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688015

Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA73-GCA_002496015 Cluster2 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_30_48-GCA_002763155 74.8/98 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG_4_10_14_0_2_um_filter_05_32_18-GCA_002792685 100/100 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688335 99/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688875 58.8/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_RBG_13_36_9-GCA_001786395 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 100/100 100/100 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_31-GCA_002254805 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_UBA284-GCA_002499185 96.4/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_59-GCA_002763115 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 100/100 Parvarchaeota-none-none-none-none-Parvarchaeum_acidiphilum_Arman4-GCA_002412065 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 99.9/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 86.1/100 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 98.3/100 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanobsidianus-Nanobsidianus_stetteri-GCA_000387965 100/100 DPANN 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100 100/100 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_10_14_0_8_um_filter_31_133-GCA_002785105 Huberarchaeota-none-none-none-none-HuberarchaeaCG_4_9_14_3_um_filter_31_125-GCA_002790315 100/100 Huberarchaeota-none-none-none-none-Euryarchaeota_archaeon_HGW-Euryarchaeota-1-GCA_002841675 100/100 100/100 Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 34.5/86 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_14-GCA_002255055 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_56-GCA_002254685 99.9/100 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_GMQ_bin_18-1-Ga0181639 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 100/100 100/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g19-GCA_001563905 100/93 99.9/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 100/100 98.9/93 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_PL-Br10_U2g27-GCA_001564035 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 Euryarchaeota-Nanohaloarchaeota-none-none-Nanosalinarum-Nanosalinarum_sp_J07AB56-GCA_000220355 0 / 7 8 0 / 5 1 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.9/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 100/100 Undinarchaeota UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 100/100 Micrarchaeota-none-none-none-Micrarchaeum-Micrarchaeum_sp_AZ1-GCA_001896515 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 Micrarchaeota-none-none-none-none-Candidatus_Micrarchaeota_archaeon_ARMAN-2-Ga0052122 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_29-GCA_002778455 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_55_41-GCA_001871605 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_60_11-GCA_002792915 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_59_7-GCA_002778425 65.7/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_51_15-GCA_001871495 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 94.3/100 100/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG11_big_fil_rev_8_21_14_0_20_37_9-GCA_002762975 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002687735 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 85.2/99 Diapherotrites-none-none-none-none-Diapherotrites_archaeon-GCA_002688035 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 83.3/92 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 99.1/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_43-GCA_002254945 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 27.8/72 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_SCG-GCA_001723845 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_WOR_SM1_86-2-GCA_001723855 100/100 Cluster1 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG_4_10_14_0_8_um_filter_32_851-GCA_002791795 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_A3-GCA_002083985 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105

0.3 Supplementary Figure 55 | Phylogenetic placement of Undinarchaeota based on an alignment generated with 48 universal marker proteins and the 364 species set. The alignment was trimmed with BMGE (alignment length = 9,534 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was artificially rooted with the DPANN archaea and the grey arrow shows the root position inferred with minimal ancestor rooting (Tria et al., 2017). Scale bar: Average number of substitutions per site. Tree statistics for tree number 50 can be found in Supplementary Table 6. 215 species 48 marker proteins trimmed alignment (BMGE)

70.1/100 99.6/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Desulfurococcaceae-Ignicoccus-Ignicoccus_hospitalis-GCA_000017945 Crenarchaeota-Thermoprotei-Desulfurococcales-Pyrodictiaceae-Pyrolobus-Pyrolobus_fumarii-GCA_000223395 100/100 Crenarchaeota-Thermoprotei-Desulfurococcales-Acidilobaceae-Acidilobus-Acidilobus_sp_7A-GCA_003431325 96.1/100 100/100 Crenarchaeota-Thermoprotei-Sulfolobales-none-none-Sulfolobales_archaeon_Acd1-GCA_000389735 8677 amino acids Crenarchaeota-Thermoprotei-Sulfolobales-Sulfolobaceae-Zestosphaera-Zestosphaera_tikiterensis-GCA_003056265 100/100 100/100 Crenarchaeota-Thermoprotei-Thermoproteales-Thermofilaceae-Thermofilum-Thermofilum_pendens-GCA_000015225 Crenarchaeota-Thermoprotei-Thermoproteales-Thermoproteaceae-Caldivirga-Caldivirga_maquilingensis-GCA_000018305 100/100 Marsarchaeota-none-none-none-none-Marsarchaeota_G2_archaeon_ECH_B_1-GCA_003019535 100/10085/99 Marsarchaeota-none-none-none-none-Marsarchaeota_G1_archaeon_BE_D-GCA_003019595 Iqtree, LG+C60+F+R 100/100 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_archaeon_OSPB-1-Ga0009305 Crenarchaeota-Thermoprotei-Geoarchaeales-Geoarchaeaceae-none-Geoarchaeota_GBS-NAG1-Ga0213453 100/100 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanosuratus-Methanosuratus_petracarbonis-GCA_001717015 Verstraetearchaeota-Methanomethylia-Methanomethyliales-Methanomethyliaceae-Methanomethylicus-Methanomethylicus_oleusabulum-GCA_001717025 100/100 100/100 Thaumarchaeota-none-Nitrosopumilales-Nitrosopumilaceae-Nitrosopumilus-Nitrosopumilus_maritimus-GCA_000018465 100/96 Thaumarchaeota-Nitrososphaeria-Nitrososphaerales-Nitrososphaeraceae-Nitrososphaera-Nitrososphaera_viennensis-GCA_000698785 98.8/100 Thaumarchaeota-Nitrososphaeria-Nitrosocaldales-Nitrosocaldaceae-Nitrosocaldus-Nitrosocaldus_cavascurensis-GCA_900248165 100/100 94.4/100 Geothermarchaeota-none-none-none-Candidatus_Geothermarchaeota-Candidatus_Geothermarchaeota_archaeon_B21_G17-B21_G17 Geothermarchaeota-none-none-none-none-Geothermarchaeota_archaeon_JdFR-13-GCA_002011075 100/100 Aigarchaeota-none-none-none-Caldiarchaeum-Caldiarchaeum_subterraneum-GCA_000270325 100/100 Aigarchaeota-none-none-none-none-Aigarchaeota_archaeon_NZ13_MG1-GCA_003056285 99.9/100 65.2/88 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_UBA233-GCA_002507245 99.8/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_CG07_land_8_20_14_0_80_47_9-GCA_002779555 100/100 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_BA1-GCA_001399805 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_60_20-GCA_001775965 Bathyarchaeota-none-none-none-none-Bathyarchaeota_archaeon_RBG_13_38_9-GCA_001775955 100/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_SMTZ1-83-GCA_001563325 100/100 99.9/100 Thorarchaeota-none-none-none-none-Thorarchaeota_archaeon_AB_25-GCA_001940705 TACK+Asgard 69.5/100 100/100 Lokiarchaeota-none-none-none-none-Lokiarchaeota_archaeon_CR_4-GCA_001940655 Odinarchaeota-none-none-none-none-Odinarchaeota_archaeon_LCB_4-GCA_001940665 100/100 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_AB_125-GCA_001940755 Heimdallarchaeota-none-none-none-none-Heimdallarchaeota_archaeon_B3-JM-08-GCA_003144275 100/100 Korarchaeota-none-none-none-Korarchaeum-Korarchaeum_cryptofilum-GCA_000019605 83.3/90 Korarchaeota-none-none-none-none-Korarchaeota_archaeon-GCA_002899815 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_BMIXfssc0709_Meth_Bin006-GCA_001587575 100/100 Euryarchaeota-Thermococci-Methanofastidiosa-none-none-Arc_I_group_archaeon_ADurb1013_Bin02101-GCA_001587595 100/100 100/100 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-GCA_001595795 Euryarchaeota-Theionarchaea-none-none-none-Theionarchaea_archaeon_DG-70-1-GCA_001595815 100/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Pyrococcus-Pyrococcus_furiosus-GCA_000007305 99.3/100 Euryarchaeota-Thermococci-Thermococcales-Thermococcaceae-Palaeococcus-Palaeococcus_pacificus-GCA_000725425 100/100 0/88 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_DG-33-1-GCA_001515195 100/100 Euryarchaeota-Hadesarchaea-none-none-none-Hadesarchaea_archaeon_YNP_45-GCA_001515205 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA259E19-GCA_001549095 Euryarchaeota-Persephonarchaea-none-none-none-candidate_divison_MSBL1_archaeon_SCGC-AAA261D19-GCA_001549175 100/100 68.8/99 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosaetaceae-Methanothrix-Methanothrix_soehngenii-GCA_000204415 Euryarchaeota-Methanomicrobia-Methanosarcinales-Methanosarcinaceae-Methanosarcina-Methanosarcina_barkeri-GCA_000970025 99.9/81 Euryarchaeota-Methanomicrobia-Methanocellales-Methanocellaceae-Methanocella-Methanocella_arvoryzae-GCA_000063445 100/100 51.6/72 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanocorpusculaceae-Methanocorpusculum-Methanocorpusculum_labreanum-GCA_000015765 Euryarchaeota-Methanomicrobia-Methanomicrobiales-Methanoregulaceae-Methanoregula-Methanoregula_formicica-GCA_000327485 99.1/99 100/100 94.3/90 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194425 Euryarchaeota-Methanomicrobia-Methanophagales-none-none-ANME-1_cluster_archaeon-GCA_003194435 100/100 Euryarchaeota-Halobacteria-Natrialbales-Natrialbaceae-Natrinema-Natrinema_pellirubrum-GCA_000230735 100/100 100/81 Euryarchaeota-Halobacteria-Haloferacales-Haloferacaceae-Haloferax-Haloferax_mediterranei-GCA_000306765 100/100 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanohalarchaeum-Methanohalarchaeum_thermophilum-GCA_001914405 Euryarchaeota-Methanonatronarchaeia-Methanonatronarchaeales-Methanonatronarchaeaceae-Methanonatronarchaeum-Methanonatronarchaeum_thermophilum-GCA_002153915 100/100 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Archaeoglobus-Archaeoglobus_fulgidus-GCA_000008665 Euryarchaeota-Archaeoglobi-Archaeoglobales-Archaeoglobaceae-Ferroglobus-Ferroglobus_placidus-GCA_000025505 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_group_II_euryarchaeote_REDSEA-S11_B3N4-GCA_001628485 100/100 100/100 Euryarchaeota-Thalassoarchaea-Thalassoarchaea-none-none-Marine_Group_II_euryarchaeote-GCA_003324635 100/100 22/92 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Epi1-GCA_001875345 Euryarchaeota-Pontarchaea-Pontarchaea-none-none-Marine_Group_III_euryarchaeote_CG-Bathy1-GCA_001875425 98.5/9955.3/97 Euryarchaeota-Thermoplasmata-Methanomassiliicoccales-Methanomassiliicoccaceae-Methanomethylophilus-Methanomethylophilus_alvus-GCA_000300255 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_UBA61-GCA_002503985 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_HGW-Thermoplasmata-1-GCA_002838935 100/100 Euryarchaeota-Thermoplasmata-none-none-none-Thermoplasmata_archaeon_M9B1D-GCA_002900535 88.5/92 100/100 Euryarchaeota 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Thermoplasmataceae-Thermoplasma-Thermoplasma_acidophilum-GCA_000195915 100/100 Euryarchaeota-Thermoplasmata-Thermoplasmatales-Cuniculiplasmataceae-Cuniculiplasma-Cuniculiplasma_sp_C_DKE-GCA_002204655 Euryarchaeota-Thermoplasmata-Thermoplasmatales-none-none-Thermoplasmatales_archaeon_I-plasma-GCA_001856825 Euryarchaeota-none-none-none-Aciduliprofundum-Aciduliprofundum_boonei-GCA_000025665 100/100 Euryarchaeota-Hydrothermarchaeota-none-none-Candidatus_Hydrothermarchaeota-Candidatus_Hydrothermarchaeota_archaeon_B51_G15-B51_G15 38.8/80 Euryarchaeota-Hydrothermarchaeota-none-none-none-Hydrothermarchaeota_archaeon_JdFR-18-GCA_002011125 100/100 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_kandleri-GCA_000007185 100/99 Euryarchaeota-Methanopyri-Methanopyrales-Methanopyraceae-Methanopyrus-Methanopyrus_sp_KOL6-GCA_002201915 100/100 Euryarchaeota-Methanococci-Methanococcales-Methanococcaceae-Methanococcus-Methanococcus_vannielii-GCA_000017165 99.5/81 Euryarchaeota-Methanococci-Methanococcales-Methanocaldococcaceae-Methanocaldococcus-Methanocaldococcus_fervens-GCA_000023985 100/100 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanobacteriaceae-Methanothermobacter-Methanothermobacter_marburgensis-GCA_000145295 Euryarchaeota-Methanobacteria-Methanobacteriales-Methanothermaceae-Methanothermus-Methanothermus_fervidus-GCA_000166095 97.4/95 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR15-GCA_000830295 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_45_16-GCA_002762785 19.3/70 33.6/88 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon-GCA_002688315 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_44_13-GCA_002762985 100/100 Woesearchaeota-none-none-none-none-archaeon_GW2011_AR20-GCA_000830315 100/100 Woesearchaeota-none-none-none-none-Woesearchaeota_archaeon_UBA489-GCA_002505585 70.4/99 100/100 Pacearchaeota-none-none-none-none-archaeon_GW2011_AR19-GCA_000806015 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon-GCA_002688415 35.6/90 100/100 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG10_big_fil_rev_8_21_14_0_10_35_13-GCA_002763035 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_CG06_land_8_20_14_3_00_35_12-GCA_002780285 Pacearchaeota-none-none-none-none-Pacearchaeota_archaeon_ex4484_26-GCA_002254495 100/100 Parvarchaeota-none-none-none--Parvarchaeum_acidophilus-GCA_002412085 100/100 99.9/99 Parvarchaeota-none-none-none-none-Parvarchaeota_archaeon_UBA449-GCA_002503305 58.7/99 NovelDPANN_1-none-none-none-none-archaeon_CG10_big_fil_rev_8_21_14_0_10_43_11-GCA_002763265 NovelDPANN_1-none-none-none-none-archaeon_CG07_land_8_20_14_0_80_38_8-GCA_002779595 100/100 100/100 Nanoarchaeota-none-Nanoarchaeales-Nanopusillaceae-Nanopusillus-Nanopusillus_acidilobi-GCA_001552015 100/100 Nanoarchaeota-none-none-none-none-Nanoarchaeota_archaeon_NZ13-N-GCA_003344645 Nanoarchaeota-none-Nanoarchaeales-Nanoarchaeaceae-Nanoarchaeum-Nanoarchaeum_equitans-GCA_000008085 100/100

Aenigmarchaeota-none-none-none-none-archaeon_GW2011_AR5-GCA_000806115 Cluster2 100/100 Aenigmarchaeota-none-none-none-none-archaeon-GCA_002688965 100/100 Aenigmarchaeota-none-none-none-none-Aenigmarchaeota_archaeon_ex4484_224-GCA_002254545 100/100 Aenigmarchaeota-none-none-none-none-Candidatus_Aenigmarchaeota_archaeon_DRTY-7_bin_34-Ga0181641 80.4/100 100/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_B1-Br10_U2g1-GCA_001563875 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SW_7_43_1-GCA_003009795 99.4/100 Euryarchaeota-Nanohaloarchaeota-none-none-none-Nanohaloarchaea_archaeon_SG9-GCA_001761425 0/82 0/52 UAP2-none-none-none-none-archaeon_UBA490-GCA_002494525 100/100 UAP2-none-none-none-none-archaeon_UBA140-GCA_002501985 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-U_76725 100/100 UAP2-none-none-none-none-Euryarchaeota_archaeon-GCA_002687935 100/100 100/100 UAP2-none-none-none-none-archaeon_UBA55-GCA_002495465 99.8/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_U_76725-SRR4028224.bin17

UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR5007147.bin71-SRR5007147.bin71 DPANN 100/100 UAP2-none-none-none-none-archaeon_UBA543-GCA_002502135 100/100 Undinarchaeota UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin1042-SRR2090153.bin1042 100/100 94.3/98 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1129-SRR2090159.bin1129 100/100 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090153.bin461-SRR2090153.bin461 UAP2-none-none-none-none-Candidatus_UAP2_archaeon_SRR2090159.bin1288-SRR2090159.bin1288 100/100 99.9/100 Diapherotrites-none-none-none-Iainarchaeum-Iainarchaeum_andersonii-GCA_000402355 100/100 Diapherotrites-none-none-none-none-archaeon_GW2011_AR10-GCA_000830275 100/100 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG10_big_fil_rev_8_21_14_0_10_31_34-GCA_002763225 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_34_12-GCA_002779065 Diapherotrites-none-none-none-none-Diapherotrites_archaeon_CG08_land_8_20_14_0_20_30_16-GCA_002779075 100/100 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG1_02_47_40-GCA_001871475 99.9/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_CG_4_10_14_0_2_um_filter_49_7-GCA_002792955 100/100 100/100 Micrarchaeota-none-none-none-none-Thermoplasmatales_archaeon_ARMAN-GCA_002204695 100/100 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_Mia14-GCA_002214165 Micrarchaeota-none-none-none-none-Micrarchaeota_archaeon_UBA97-GCA_002507385 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_IMC4-GCA_001742785 100/100 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_ex4484_2-GCA_002254565 100/100 Euryarchaeota-none-Altiarchaeales-none-Altiarchaeum-Altiarchaeum_sp_CG03_land_8_20_14_0_80_32_618-GCA_002785505 Euryarchaeota-none-Altiarchaeales-none-none-Altiarchaeales_archaeon_HGW-Altiarchaeales-1-GCA_002841105 100/100 Cluster1 100/100 Bacteria_Proteobacteria-Gammaproteobacteria-Enterobacterales-Enterobacteriaceae-Escherichia-Escherichia_coli-GCA_000005845 65.5/100 Bacteria_Proteobacteria-Gammaproteobacteria-Alteromonadales-Alteromonadaceae-Alteromonas-Alteromonas_macleodii-GCA_000172635 100/100 Bacteria_Proteobacteria-Gammaproteobacteria-Oceanospirillales-Alcanivoracaceae-Alcanivorax-Alcanivorax_borkumensis-GCA_000009365 Bacteria_Proteobacteria-Gammaproteobacteria-Chromatiales-Chromatiaceae-Allochromatium-Allochromatium_vinosum-GCA_000025485 100/100 Bacteria_Proteobacteria-Gammaproteobacteria-Nevskiales-Sinobacteraceae-Steroidobacter-Steroidobacter_denitrificans-GCA_001579945 97.5/100 100/100 Bacteria_Proteobacteria-Betaproteobacteria-Rhodocyclales-Rhodocyclaceae-Azospira-Azospira_oryzae-GCA_000236665 95.8/100 Bacteria_Proteobacteria-Betaproteobacteria-Burkholderiales-Comamonadaceae-Comamonas-Comamonas_thiooxydans-GCA_001418295 Bacteria_Proteobacteria-Betaproteobacteria-Neisseriales-Neisseriaceae-Simonsiella-Simonsiella_muelleri-GCA_002951835 Bacteria_Proteobacteria-Zetaproteobacteria-Mariprofundales-Mariprofundaceae-Mariprofundus-Mariprofundus_ferrooxydans-GCA_000153765 21.7/82 100/100 Bacteria_Proteobacteria-Alphaproteobacteria-Rhodobacterales-Rhodobacteraceae-Roseobacter-Roseobacter_denitrificans-GCA_000014045 99.7/100 Bacteria_Proteobacteria-Alphaproteobacteria-Sphingomonadales-Sphingomonadaceae-Zymomonas-Zymomonas_mobilis-GCA_000175255 99.3/93 Bacteria_Proteobacteria-Alphaproteobacteria-Rhizobiales-Xanthobacteraceae-Xanthobacter-Xanthobacter_autotrophicus-GCA_000017645 100/100 Bacteria_Proteobacteria-Alphaproteobacteria-Caulobacterales-Caulobacteraceae-Brevundimonas-Brevundimonas_denitrificans-GCA_002770575 61.7/89 100/100 58.1/88 Bacteria_Proteobacteria-Alphaproteobacteria-Rhodospirillales-Acetobacteraceae-Acidiphilium-Acidiphilium_multivorum-GCA_000202835 Bacteria_Proteobacteria-Alphaproteobacteria-Rhodospirillales-Rhodospirillaceae-Thalassospira-Thalassospira_marina-GCA_002844375 Bacteria_Proteobacteria-Alphaproteobacteria-none-none-Candidatus_Puniceispirillum-Candidatus_Puniceispirillum_marinum-GCA_000024465 99.4/94 Bacteria_Proteobacteria-Alphaproteobacteria-Magnetococcales-Magnetococcaceae-Magnetococcus-Magnetococcus_marinus-GCA_000014865 100/100 93.2/100 Bacteria_Proteobacteria-Deltaproteobacteria-Desulfobacterales-Desulfobacteraceae-Desulfobacterium-Desulfobacterium_autotrophicum-GCA_000020365 Bacteria_Proteobacteria-Deltaproteobacteria-Desulfobacterales-Desulfobacteraceae-Desulfotignum-Desulfotignum_balticum-GCA_000421285 99.9/94 Bacteria_Proteobacteria-Deltaproteobacteria-Desulfobacterales-Desulfobulbaceae-Desulfurivibrio-Desulfurivibrio_alkaliphilus-GCA_000092205 59/94 99.6/99 Bacteria_Proteobacteria-Deltaproteobacteria-Syntrophobacterales-Syntrophaceae-Desulfobacca-Desulfobacca_acetoxidans-GCA_000195295 68.1/58 Bacteria_Proteobacteria-Deltaproteobacteria-Desulfovibrionales-Desulfohalobiaceae-Desulfonatronovibrio-Desulfonatronovibrio_hydrogenovorans-GCA_000686525 94.1/9866.5/92 Bacteria_Proteobacteria-Deltaproteobacteria-Syntrophobacterales-Syntrophaceae-Syntrophus-Syntrophus_aciditrophicus-GCA_000013405 Bacteria_Proteobacteria-Deltaproteobacteria-Desulfuromonadales-Geobacteraceae-Geoalkalibacter-Geoalkalibacter_subterraneus-GCA_000827125 99.9/99 Bacteria_Proteobacteria-Deltaproteobacteria-Myxococcales-Myxococcaceae-Myxococcus-Myxococcus_xanthus-GCA_000012685 83.4/59 Bacteria_Proteobacteria-Oligoflexia-Bacteriovoracales-Halobacteriovoraceae-Halobacteriovorax-Halobacteriovorax_marinus-GCA_000210915 96.8/100 99.6/58 Bacteria_Deferribacteres-Deferribacteres-Deferribacterales-Deferribacteraceae-Deferribacter-Deferribacter_desulfuricans-GCA_000010985 Bacteria_Chrysiogenetes-Chrysiogenetes-Chrysiogenales-Chrysiogenaceae-Chrysiogenes-Chrysiogenes_arsenatis-GCA_000469585 99.8/83 Bacteria_Proteobacteria-Epsilonproteobacteria-Campylobacterales-Helicobacteraceae-Sulfurimonas-Sulfurimonas_denitrificans-GCA_000012965 100/86 Bacteria_Nitrospinae-Nitrospinia-Nitrospinales-Nitrospinaceae-Nitrospina-Nitrospina_gracilis-GCA_000341545 Bacteria_Nitrospirae-Nitrospira-Nitrospirales-Nitrospiraceae-Nitrospira-Nitrospira_moscoviensis-GCA_001273775 100/98 Bacteria_Acidobacteria-Holophagae-Holophagales-Holophagaceae-Geothrix-Geothrix_fermentans-GCA_000428885 Bacteria_Candidatus_Aminicenantes-none-none-none-Candidatus_Aminicenans-Candidatus_Aminicenans_sakinawicola-GCA_000493965 83.8/100 54/58 100/100 Bacteria_Verrucomicrobia-Opitutae-Opitutales-Opitutaceae-Opitutus-Opitutus_terrae-GCA_000019965 Bacteria_Lentisphaerae-Lentisphaeria-Victivallales-none-none-Victivallales_bacterium_CCUG_44730-GCA_002998355 84.1/100 Bacteria_Kiritimatiellaeota-Kiritimatiellae-Kiritimatiellales-Kiritimatiellaceae-Kiritimatiella-Kiritimatiella_glycovorans-GCA_001017655 100/100 Bacteria_Candidatus_Omnitrophica-none-none-none-none-Omnitrophica_bacterium_RIFCSPHIGHO2_02_FULL_45_28-GCA_001805325 99.3/99 Bacteria_Candidatus_Omnitrophica-none-none-none-none-Candidatus_Omnitrophica_bacterium_CG_4_10_14_0_2_um_filter_44_9-GCA_002792715 99.8/100 99.5/94 100/100 Bacteria_Planctomycetes-Planctomycetia-Planctomycetales-Planctomycetaceae-Blastopirellula-Blastopirellula_marina-GCA_000153105 Bacteria_Planctomycetes-Phycisphaerae-Phycisphaerales-Phycisphaeraceae-Phycisphaera-Phycisphaera_mikurensis-GCA_000284115 Bacteria_Planctomycetes-Planctomycetia-Candidatus_Brocadiales-Candidatus_Brocadiaceae-Candidatus_Kuenenia-Candidatus_Kuenenia_stuttgartiensis-GCA_900232105 Bacteria_Candidatus_Hydrogenedentes-none-none-none-none-Candidatus_Hydrogenedentes_bacterium_UBA6118-GCA_002422525 100/100 Bacteria_Bacteroidetes-Bacteroidia-Bacteroidales-Porphyromonadaceae-Porphyromonas-Porphyromonas_asaccharolytica-GCA_000212375 100/100 Bacteria_Bacteroidetes-Bacteroidia-Bacteroidales-Rikenellaceae-Millionella-Millionella_massiliensis-GCA_900104655 95.7/64 100/100 100/100 Bacteria_Bacteroidetes-Flavobacteriia-Flavobacteriales-Crocinitomicaceae-Crocinitomix-Crocinitomix_algicola-GCA_001661595 100/100 Bacteria_Bacteroidetes-Flavobacteriia-Flavobacteriales-Flavobacteriaceae-Algibacter-Algibacter_aquaticus-GCA_001747085 Bacteria_Bacteroidetes-Cytophagia-Cytophagales-Cytophagaceae-Cytophaga-Cytophaga_aurantiaca-GCA_000379725 100/100 35.1/78 Bacteria_Chlorobi-Chlorobia-Chlorobiales-Chlorobiaceae-Chlorobium-Chlorobium_limicola-GCA_000020465 Bacteria_Ignavibacteriae-Ignavibacteria-Ignavibacteriales-Ignavibacteriaceae-Ignavibacterium-Ignavibacterium_album-GCA_000258405 89.7/100 43.8/84 Bacteria_none-none-none-none-none-candidate_division_KSB1_bacterium_RBG_16_48_16-GCA_001771235 Bacteria_Candidatus_Marinimicrobia-none-none-none-none-Candidatus_Marinimicrobia_bacterium_408169-GCA_002256485 96.3/91 Bacteria_Fibrobacteres-Chitinivibrionia-Chitinivibrionales-Chitinivibrionaceae-Chitinivibrio-Chitinivibrio_alkaliphilus-GCA_000474745 100/9597.9/85 Bacteria__Fermentibacteria-_Fermentibacteria-_Fermentibacterales-_Fermentibacteraceae-_Fermentibacter-_Fermentibacter_daniensis-GCA_001618605 Bacteria 98.5/100 Bacteria_Gemmatimonadetes-Gemmatimonadetes-Gemmatimonadales-Gemmatimonadaceae-Gemmatimonas-Gemmatimonas_phototrophica-GCA_000695095 94.8/65 Bacteria_Candidatus_Latescibacteria-none-none-none-none-Latescibacteria_bacterium_UBA6620-GCA_002433075 100/91 Bacteria_Candidatus_Cloacimonetes-none-none-none-Candidatus_Cloacimonas-Candidatus_Cloacimonas_acidaminovorans-GCA_000146065 Bacteria_candidate_division_Zixibacteria-none-none-none-none-candidate_division_Zixibacteria_bacterium_RBG-1-GCA_000447245 99.8/70 Bacteria_Spirochaetes-Spirochaetia-Spirochaetales-Spirochaetaceae-Salinispira-Salinispira_pacifica-GCA_000507245 Bacteria_candidate_division_WOR-3-none-none-none-none-candidate_division_WOR-3_bacterium_UBA1063-GCA_002316275 100/100 27.9/99 Bacteria_Chloroflexi-Anaerolineae-Anaerolineales-Anaerolineaceae-Ornatilinea-Ornatilinea_apprima-GCA_001306115 Bacteria_Chloroflexi-Ardenticatenia-Ardenticatenales-Ardenticatenaceae-Candidatus_Promineofilum-Candidatus_Promineofilum_breve-GCA_900066015 100/100 Bacteria_Chloroflexi-Dehalococcoidia-Dehalococcoidales-Dehalococcoidaceae-Dehalococcoides-Dehalococcoides_mccartyi-GCA_000011905 99.8/77 99/100 Bacteria_Chloroflexi-Chloroflexia-Herpetosiphonales-Herpetosiphonaceae-Herpetosiphon-Herpetosiphon_aurantiacus-GCA_000018565 100/100 Bacteria_Chloroflexi-Ktedonobacteria-Thermogemmatisporales-Thermogemmatisporaceae-Thermogemmatispora-Thermogemmatispora_carboxidivorans-GCA_000702505 92.7/75 Bacteria_candidate_division_AD3-none-none-none-none-candidate_division_AD3_bacterium-GCA_003162415 82.1/100 100/100 Bacteria_Cyanobacteria-none-Pleurocapsales-Dermocarpellaceae-Stanieria-Stanieria_cyanosphaera-GCA_000317575 70.8/92 100/100 Bacteria_Cyanobacteria-none-Nostocales-Scytonemataceae-Scytonema-Scytonema_hofmannii-GCA_000346485 Bacteria_Cyanobacteria-none-Synechococcales-Prochlorotrichaceae-Prochlorothrix-Prochlorothrix_hollandica-GCA_000332315 Bacteria_Cyanobacteria-none-Synechococcales-Prochloraceae-Prochlorococcus-Prochlorococcus_marinus-GCA_000015645 99.5/74 Bacteria_Armatimonadetes-Chthonomonadetes-Chthonomonadales-Chthonomonadaceae-Chthonomonas-Chthonomonas_calidirosea-GCA_000427095 Bacteria_candidate_division_WPS-2-none-none-none-none-candidate_division_WPS-2_bacterium-GCA_003243975 100/100 5.8/63 100/100 Bacteria_Actinobacteria-Actinobacteria-Micrococcales-Micrococcaceae-Micrococcus-Micrococcus_luteus-GCA_000023205 64.1/99 Bacteria_Actinobacteria-Actinobacteria-Micrococcales-Microbacteriaceae-Leucobacter-Leucobacter_salsicius-GCA_000350525 Bacteria_Actinobacteria-Actinobacteria-Micrococcales-Dermatophilaceae-Mobilicoccus-Mobilicoccus_pelagius-GCA_000247995 100/100 Bacteria_Actinobacteria-Actinobacteria-Propionibacteriales-Propionibacteriaceae-Cutibacterium-[Propionibacterium]_namnetense-GCA_001642025 100/100 100/100 Bacteria_Actinobacteria-Actinobacteria-Frankiales-Frankiaceae-Frankia-Frankia_alni-GCA_000058485 100/100 Bacteria_Actinobacteria-Actinobacteria-Corynebacteriales-Mycobacteriaceae-Mycobacterium-Mycobacterium_aquaticum-GCA_002086485 99.9/99 Bacteria_Actinobacteria-Acidimicrobiia-Acidimicrobiales-Acidimicrobiaceae-Acidithrix-Acidithrix_ferrooxidans-GCA_000949295 Bacteria_Actinobacteria-Thermoleophilia-Solirubrobacterales-Conexibacteraceae-Conexibacter-Conexibacter_woesei-GCA_000025265 100/100 100/100 Bacteria_Firmicutes-Bacilli-Bacillales-Bacillaceae-Oceanobacillus-Oceanobacillus_iheyensis-GCA_000011245 Bacteria_Firmicutes-Bacilli-Bacillales-Staphylococcaceae-Staphylococcus-Staphylococcus_xylosus-GCA_000706685 86.7/80 99.5/90 Bacteria_Firmicutes-Bacilli-Lactobacillales-Leuconostocaceae-Weissella-Weissella_halotolerans-GCA_000420365 57.5/78100/100 Bacteria_Firmicutes-Clostridia-Clostridiales-Clostridiaceae-Clostridium-Clostridium_cellulovorans-GCA_000145275 100/100 Bacteria_Firmicutes-Clostridia-Clostridiales-Ruminococcaceae-Ruminococcus-Ruminococcus_albus-GCA_000179635 Bacteria_Firmicutes-Clostridia-Clostridiales-Peptococcaceae-Peptococcus-Peptococcus_niger-GCA_900101835 Bacteria_Firmicutes-Negativicutes-Veillonellales-Veillonellaceae-Negativicoccus-Negativicoccus_massiliensis-GCA_900155405 34/55 Bacteria_Synergistetes-Synergistia-Synergistales-Synergistaceae-Acetomicrobium-Acetomicrobium_mobile-GCA_000266925 Bacteria_Fusobacteria-Fusobacteriia-Fusobacteriales-Fusobacteriaceae-Psychrilyobacter-Psychrilyobacter_atlanticus-GCA_000426625

0.5 Supplementary Figure 56 | Phylogenetic placement of Undinarchaeota based on an alignment generated with 48 universal marker proteins and the 127 archaeal + 88 bacterial species set. The alignment was trimmed with BMGE (alignment length = 8,677 aa). A ML phylogenetic tree was inferred with the LG+C60+F+R model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. The tree was rooted using bacteria (black labels) as outgroup. Scale bar: Average number of substitutions per site. Tree statistics for tree number 51 can be found in Supplementary Table 6. PriL (canonical)

PriL (fused)

Euryarchaeota TACK Asgard 0.8 DPANN Cluster 1 DPANN Cluster 2 Undinarchaeota

PriS (fused)

90-99.9/90-100 80-89.9/80-100 100/100 PriS (canonical) 90-100/90-99.9 80-100/80-89.9

Supplementary Figure 57 | Phylogenetic history of the primase subunits PriS and PriL in archaea. An alignment was generated for all PriS and PriL sequences found in 364 archaea that was trimmed using TRIMAL (alignment length = 512 amino acids). The canonical PriS and PriL genes are encoded by two genes with the exception for most DPANN archaea that encode a fused version of the primase (Supplementary Table 10). These fused versions were split before aligning all sequences (n=585 sequences; see Methods for details). A maximum-likelihood phylogenetic tree was inferred with the LG+F+C10 model with an ultrafast bootstrap approximation (left) and SH-like approximate likelihood tests (right), each run with 1000 replicates. Bootstrap values above certain thresholds are indicated with colored circles. Scale bar: Average number of substitutions per site. DNA Polymerase Replication factors Helicase Topoisomerase Repair and Recombination Methylase Chromatin Cell_cycle Halobacteria (22) Occurence (%) Methanomicrobiales (6) 100 Methanosarcinales (12) Methanocellales (2) Methanophagales (3) 75 Archaeoglobiales(7) Methanonatronarchaeia (2) 50 Thermoplasmatales (11) Aciduliprofundales (4) Methanomassiliicoccales (4) 25 o_UBA184 (2) Poseidoniales (9) 0 Pontarchaea (MG-III) (3) o_DHVEG−1 (4) Thermococcales (11) Methanofastidiosa (5) Theionarchaea (2)

Hadesarchaea (4) Euryarchaeota Persephonarchae (3) Methanococcales (7) Methanobacteriales (5) Hydrothermarchaeota (3) Methanopyrales (3) Crenarchaeota (28) Marsarchaeota (4) Geoarchaeota (3) Verstraetearchaeota (6) Bathyarchaeota (18) Thaumarchaeota (10) Geothermarchaeota (3) Aigarchaeota (5) Korarchaeota (3) TACK+A Asgard (15) Woesearchaeota (39) Pacearchaeota (30) Nanoarchaeota (4) Parvarchaeota (3) NovelDPANN_1 (2) Huberarchaeota (3) Aenigmarchaeota (7) Nanohaloarchaeota (6) marine Undinarchaeales (8)

aquifer Naiadarchaeales (4) DPANN Micrarchaeota (12) Diapherotrites (8) Altiarchaeales (9)

Lig hjc Rgy Nth Nfo Nfi OgtOgg Pol4PolXOrc1 GinSPriSPriL LigNPcn1RfcSRfcL XthA Udg1 AlkD UvrB MjaII Dcm MC1Smc FtsZ Rkd1 RPA2RPA3 DnaG FEN1RnhARnhB MPH1BRR2 SrmBDna2 TopAGyrAGyrB TopB SbcCSbcDNurA NucS DinG HerARadARadB UvrA UvrC MthTIMthZI MjaIIIMjaV HmvAScpAScpB Alba1ELP3 MinD Rkd2CetZ1CdvACdvBVps4 Pol−PolB1−PolB2−B3 MCM2 MUS81 Top6ATop6B HmfAB Cren−1 SSO0112 DNA_met actin_like PolD_large SSB/RPA1 PolD_small RecJ/Cdc45

PolB−casposon−associated Supplementary Figure 58 | Presence of key replication proteins across major archaeal lineages. Heatmap of presence/absence patterns of key proteins are summarized across the total number of genomes included in each phylogenetic cluster (shown in percent). TACK + A = TACK + Asgard. Number in brackets = number of genomes analyzed for each phylogenetic cluster. Supplementary Table 19 lists the proteins used to generate the plot and Supplementary Table 9 lists the raw values. a

Group IV-phage-like

Group IV/RLP

(L)

Group II/III Group II (E) (F) Group III-a (B)

Group III-c 100 9 9

100

100

100

9 1 b 9 5 RubisCO Motif 100

(J) Marine 100

5 2

100 Group I

9 5 100

100 (A)

100 Probability (C) 100 9 3

9 7

7 8 5762 120 172 174 176 195196 198 200 201 291 292 324 331 376 377 400 401

8 8

8 1

0.4 9 9

1 7

100 8 7 c RubisCO Motif

100 9 2 5762 120 172 174 176 195196 198 200 201 291 292 324 331 376 377 400 401 9 9

100 100 Synechococcus elongatus PCC_6301: YP_170840 ET N K K G D F KDEHRHKS GGG (A) 100

100 Rhodobacter capsulatus ATCC11166: P50922 ET N K K G D F KDEHRHKS GGG (B) Methanocaldococcus jannaschii DSM_2661: AAB99239 ET N K K G D L KDEHRHKS GGG (C) (G) Thermococcus kodakaraensis KOD1: BAD86479 ET N K K G D Y KDEHRHKS GGG (D) (K) Marine 5 0 Methanococcoides burtonii DSM_6242: YP_566926 ET N K K G D F KDEHRHKS GGS (E) 87 9 4 86 5 2 9 3 897 67 48 7 01 1009 3 Perigrinibacteria PER_GWF2_38_29: KKQ68902 ES N K K G D F KDEHRHKS GGG (F) WS6 GWF2_39_15: KKR05836 ES N K K G H F KDEHRHKS GGG (G)

68 84 0 WS6 GWC1_33_20: KKP44747 ET N K K G Q G KDEHRHKS GGG (H) Group III-like 100 Aquifer: SRR2090153.bin461_00930 ------HR- HKSGGG (I) Aquifer: SRR2090159.bin1288_00760 ENKKGDT L KDEHRHKS GGG (I) Marine: GCA_002502135_04940 ENKKGDT F KDEHRHKS GGG (J) 100 Marine: GCA_002494525_04240 ENKKGET G KDEHRHKS GGG (K) Marine: GCA_002501985_03190 ENKKGET G KDEHRHKS GGG (K) Marine: GCA_002687935_06810 ENKKGET G KDEHRHKS GGG (K) Marine: U_76725_01980 ENKKGET G KDEHRHKS GGG (K) (I)Aquifer Marine: GCA_002495465_03690 ENKKGDT G KDEHRHKS GGG (K) Marine: SRR4028224.bin17_03970 ENKKGDT G KDEHRHKS GGG (K) Marine: SRR5007147.bin71_02210 ENKKGDT G KDEHRHKS GGG (K)

Bacillus subtilis str. 168: CAB13232 GS K KV G DKDEHPL LSSAGG (L) Group III-b (D) CCCRRR C R CCCCRRCR RRR Supplementary Figure 59 | Diversity of RubisCO proteins in archaea. a, ML phylogenetic analysis of the RubisCO protein extracted from marine Undinarchaeales (dark green) and aquifer Naiadarchaeales MAGs (light green) that were added to an alignment from Jaffe et al., 2019 (n=786 sequences). The alignment was trimmed using BMGE (alignment length = 397 aa). A ML phylogenetic tree was inferred with the LG+G model with an ultrafast bootstrap approximation with 1000 replicates. Scale bar: Average number of substitutions per site. b, Probability plot of the occurence of each amino acid of the catalytic site of the RubisCO protein across 786 sequences. Color-coding is based on the hydrophobicity score. c, Conservation of the catalytic site of selected amino acid sequences of the catalytic site compared to the reference sequence of Synechococcus elongatus PCC_6301 as described by Jaffe et al., 2019. Differences in amino acid sequence compared to the reference are colored based on their hydrophobicity score and conserved sites are colored in grey. The position of each amino acid in the alignment is indicated at the top of the scheme and information on whether an amino acid represents a catalytic site (C) or RubisCO binding site (R) is indicated at the bottom. (A)-(L) = Reference sequences for different RubisCO groups. RNA Polymerases Transcription factors Transcription Halobacteria (22) Occurence (%) Methanomicrobiales (6) 100 Methanosarcinales (12) Methanocellalles (2) Methanophagales (3) 75 Archaeoglobales (7) Methanonatronarchaeales (2) Thermoplasmatales (11) 50 Aciduliprofundales (4) Methanomassiliicoccales (4) o_UBA184 (2) 25 Poseidoniales (9) Pontarchaea (MG-III) (3) 0 o_DHVEG−1 (4)

Thermococcales (11) Euryarchaeota Methanofastidiosa (5) Theionarchaea (2) Hadesarchaea (4) Persephonarchaea (3) Methanococcales (7) Methanobacteriales (5) Hydrothermarchaeota (3) Methanopyrales (3) Crenarchaeota (28) Marsarchaeota (4) Geoarchaeota (3) Verstraetearchaeota (6) Bathyarchaeota (18) Thaumarchaeota (10) Geothermarchaeota (3) Aigarchaeota (5) Korarchaeota (3) TACK+A Asgard (15) Woesearchaeota (39) Pacearchaeota (30) Nanoarchaeota (4) Parvarchaeota (3) NovelDPANN_1 (2) Huberarchaeota (3) Aenigmarchaeota (7) Nanohaloarchaeota (6) marine Undinarchaeales (8) aquifer Naiadarchaeales (4) DPANN Micrarchaeota (12) Diapherotrites (8) Altiarchaeales (9)

TBP TFB TFE TFS Spt4 Rpo4 RPB5 RPB7 RPB8 LysM NusG NusA Alba1 RPB11 RPB10 RPC12 Rpo13 EGD2

RpoC/Rpo3 RpoB/Rpo2RpoA/Rpo1Rpo6/RpoZ RpoC/Rpo11

Supplementary Figure 60 | Presence of key transcription-related proteins across major archaeal lineages. Heatmap of presence/absence patterns of key proteins are summarized across the total number of genomes included in each phylogenetic cluster (shown in percent). TACK + A = TACK + Asgard. Number in brackets = number of genomes analyzed for each phylogenetic cluster. Supplementary Table 19 lists the proteins used to generate the plot and Supplementary Table 9 lists the raw values. Ribosome Halobacteria (22) Occurence (%) Methanomicrobiales (6) Methanosarcinales (12) 100 Methanocellales (2) Methanophagales (3) Archaeoglobales (7) 75 Methanonatronarchaeales (2) Thermoplasmatales (11) Aciduliprofundales (4) 50 Methanomassiliicoccales (4) o_UBA184 (2) Poseidoniales (9) 25 Pontarchaea (MG-III) (3) o_DHVEG−1 (4) Thermococcales (11) 0 Methanofastidiosa (5) Theionarchaea (2) Hadesarchaea (4) Euryarchaeota Persephonarchaea (3) Methanococcales (7) Methanobacteriales (5) Hydrothermarchaeota (3) Methanopyrales (3) Crenarchaeota (28) Marsarchaeota (4) Geoarchaeota (3) Verstraetearchaeota (6) Bathyarchaeota (18) Thaumarchaeota (10) Geothermarchaeota (3) Aigarchaeota (5) Korarchaeota (3) TACK+A Asgard (15) Woesearchaeota (39) Pacearchaeota (30) Nanoarchaeota (4) Parvarchaeota (3) NovelDPANN_1 (2) Huberarchaeota (3) Aenigmarchaeota (7) Nanohaloarchaeota (6) marine Undinarchaeales (8) aquifer Naiadarchaeales (4) DPANN Micrarchaeota (12) Diapherotrites (8) Altiarchaeales (9)

L1 L2 L3 L4 L5 S2 S3 S4 S5 S7 S8 S9 L6P L10 L11 L13 L14 L15 L18 L22 L23 L24 L29 L30 S4E S8E S10S11 S12S13S14 S17 S19 S25S26 S30 HflX L7AE L13E L15E L18EL19EL20AL21E L24E L30EL31EL32EL34E L37EL38EL39EL40EL41EL44E S3AE S15P S17E S19ES24E S27E PelARsgA S27AE S6E/S10 L10AE/L16 S28E/S33 L35AE/L33AL37AE/L43A L14E/L6E/L27E

L12E/L44/L45/RPP1/RPP2

tRNA_synthetases TFs Exosome DBS WBS Translation Posttranslation Halobacteria (22) Methanomicrobiales (6) Methanosarcinales (12) Methanocellales (2) Methanophagales (3) Archaeoglobales (7) Methanonatronarchaeales (2) Thermoplasmatales (11) Aciduliprofundales (4) Methanomassiliicoccales (4) o_UBA184 (2) Poseidoniales (9) Pontarchaea (MG-III) (3) o_DHVEG−1 (4) Thermococcales (11) Methanofastidiosa (5) Theionarchaea (2) Hadesarchaea (4) Euryarchaeota Persephonarchaea (3) Methanococcales (7) Methanobacteriales (5) Hydrothermarchaeota (3) Methanopyrales (3) Crenarchaeota (28) Marsarchaeota (4) Geoarchaeota (3) Verstraetearchaeota (6) Bathyarchaeota (18) Thaumarchaeota (10) Geothermarchaeota (3) Aigarchaeota (5) Korarchaeota (3) TACK+A Asgard (15) Woesearchaeota (39) Pacearchaeota (30) Nanoarchaeota (4) Parvarchaeota (3) NovelDPANN_1 (2) Huberarchaeota (3) Aenigmarchaeota (7) Nanohaloarchaeota (6) marine Undinarchaeales (8) aquifer Naiadarchaeales (4) DPANN Micrarchaeota (12) Diapherotrites (8) Altiarchaeales (9)

Tuf IleS TyrS InfB Rli1 Csl4 LigT Rnz AlaSArgSAsnSCysSGlnS HisS LeuSLysSLysUMetGPheSSerSProSThrSTrpS ValS SUI1 EIF6 FusA Rrp4 Dph2Dph5Dph6 Trm5 EndAFau1 RtcB RnjA Rnp2Rnp3Rnp4TgtA DnaJDnaKGrpEGroLHtpX Pan1PcmThsA GRS1 EIF1A EIF2AEIF2B EIF2GEIF4AEIF5a EFB1 eRF1 Rrp41Rrp42DnaG TYW1TYW2TYW3 Nob1 RCL1 Rnp1 Hsp16Hsp19PsmAPRE1 EIF2B−like Archaease

Supplementary Figure 61 | Presence of key translation-related proteins across major archaeal lineages. Heatmap of presence/absence patterns of key proteins are summarized across the total number of genomes included in each phylogenetic cluster (shown in percent). TACK + A = TACK + Asgard. DBS = Diphthamide biosynthesis. WBS = Wybutosine biosynthesis. Number in brackets = number of genomes analyzed for each phylogenetic cluster. Supplementary Table 19 lists the proteins used to generate the plot and Supplementary Table 9 lists the raw values. Mevalonate Archaeol biosynthesis Halobacteria (22) Occurence (%) Methanomicrobiales (6) 100 Methanosarcinales (12) Methanocellaceae (2) Methanophagales (3) 75 Archaeoglobi (7) Methanonatronarchaeia (2) 50 Thermoplasmatales (11) Aciduliprofundum (4) 25 Methanomassiliicoccales (4) o_UBA184 (2) Poseidoniales (9) 0 Pontarchaea (MG-III) (3) o_DHVEG−1 (4) Thermococcales (11)

Methanofastidiosa (5) Euryarchaeota Theionarchaea (2) Hadesarchaea (4) Persephonarchaeota (3) Methanococcales (7) Methanobacteria (5) Hydrothermarchaeota (3) Methanopyri (3) Crenarchaeota (28) Marsarchaeota (4) Geoarchaeota (3) Verstraetearchaeota (6) Bathyarchaeota (18) Thaumarchaeota (10) Geothermarchaeota (3) Aigarchaeota (5) Korarchaeota (3) Asgard (15) Asgard + TACK Woesearchaeota (39) Pacearchaeota (30) Nanoarchaeota (4) Parvarchaeota (3) NovelDPANN_1 (2) Huberarchaeota (3) Aenigmarchaeota (7) Nanohaloarchaeota (6)

marine Undinarchaeales (8) DPANN aquifer Naiadarchaeales (4) Micrarchaeota (12) Diapherotrites (8) Altiarchaeales (9)

Ipk Asd MvK M3k UbiA* GGR CarS ASS HmgB HmgA mvaD GFPS EgsA PgsA M3P5K

GGGP_synthase

Supplementary Figure 62 | Presence of key lipid-related proteins across major archaeal lineages. Heatmap of presence/absence patterns of key proteins are summarized across the total number of genomes included in each phylogenetic cluster (shown in percent). TACK + A = TACK + Asgard. Number in brackets = number of genomes analyzed for each phylogenetic cluster. Supplementary Table 19 lists the proteins used to generate the plot and Supplementary Table 9 lists the raw values. *In Undinarchaeota only the Naidarchaeales UbiA contains a DGGGP synthase domain required for this enzyme to function in lipid biosynthesis. Category

● Undinarcheales ● ● Correlating organism ● ● 4 ● Genome

● GCA_002494525.1

GCA_002501985.1

GCA_002687935.1

U_76725 2 GCA_002502135.1

● o__Dehalococcoidales_1 (GCA_002685815.1) ● o__Dehalococcoidales_2 Logratio (GCA_002688105.1)

● o__Dehalococcoidales_3 (GCA_0026884351.1) 0 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

−2

ERR594345ERR594346ERR599037ERR599062ERR599167 SRR1658343SRR1658344SRR1658462SRR2090152SRR2090153SRR2090155SRR2090157SRR2090158SRR2090159SRR2090160SRR2090161SRR2090162SRR2177951SRR2177956SRR4388699SRR4028193SRR4028224 SRR2981515SRR5007141SRR5007147SRR1509792SRR1509799

groundwater metagenomes marine metagenomes

Supplementary Figure 63 | Determining co-correlations signals of Undinarchaeota with a potential host. 37 metagenomes containing reads assigned to Undinarchaeota (Supplementary Table 1) were aligned to a reference database of 6,890 archaeal and bacterial genomes. Proportionality was calculated based on normalized relative abundances and centered log-ratio transformation. Genomes shown in this graph were proportional (ρ ≥ 0.9) to more than one Undinarchaeota MAG and thus were inferred as Undinarchaeota co- correlated.