The two-domain tree of life is linked to a new root for the Archaea Kasie Raymanna, Céline Brochier-Armanetb, and Simonetta Gribaldoa,1 aInstitut Pasteur, Department of Microbiology, Unit Biologie Moléculaire du Gène chez les Extrêmophiles, 75015 Paris, France; and bUniversité de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved April 17, 2015 (received for review November 02, 2014) One of the most fundamental questions in evolutionary biology is restricted taxonomic sampling, notably for the outgroup, may also the origin of the lineage leading to eukaryotes. Recent phyloge- generate or mask potential tree reconstruction artifacts (16). All nomic analyses have indicated an emergence of eukaryotes from these considerations emphasize that we have not yet found a way within the radiation of modern Archaea and specifically from a group out of the phylogenomic impasse caused by the use of universal comprising Thaumarchaeota/“Aigarchaeota” (candidate phylum)/ trees to investigate the relationships among Archaea and eu- Crenarchaeota/Korarchaeota (TACK). Despite their major im- karyotes (12). plications, these studies were all based on the reconstruction of Here, we have applied an original two-step strategy that we universal trees and left the exact placement of eukaryotes with re- proposed a few years ago which involves separately analyzing the spect to the TACK lineage unclear. Here we have applied an original markers shared between Archaea and eukaryotes and between two-step approach that involves the separate analysis of markers Archaea and Bacteria (12). This strategy allowed us to use a larger shared between Archaea and eukaryotes and between Archaea and taxonomic sampling, more markers and thus more positions, have Bacteria. This strategy allowed us to use a larger number of markers higher-quality alignments, and detect potential tree reconstruction and greater taxonomic coverage, obtain high-quality alignments, and artifacts more easily. With respect to previous analyses, we obtained alleviate tree reconstruction artifacts potentially introduced when phylogenies that are fully resolved and consistent between datasets analyzing the three domains simultaneously. Our results robustly in- and with the systematics of each domain, demonstrating the rele- dicate a sister relationship of eukaryotes with the TACK superphylum vance of our approach. Comparison of the results obtained from EVOLUTION that is strongly associated with a distinct root of the Archaea that lies the Archaea/eukaryote (A/E) and the Archaea/Bacteria (A/B) within the Euryarchaeota, challenging the traditional topology of the datasets robustly indicates that eukaryotes are sister to the TACK archaeal tree. Therefore, if we are to embrace an archaeal origin for superphylum but also that this topology is strongly linked to a root eukaryotes, our view of the evolution of the third domain of life will for the tree of the Archaea lying within the Euryarchaeota. have to be profoundly reconsidered, as will many areas of investiga- This topology is in contrast to the traditional root between tion aimed at inferring ancestral characteristics of early life and Earth. Euryarchaeota and the TACK superphylum (17, 18), which we demonstrate as likely being the product of an artifact resulting methanogenesis | Tree of Life | ancient evolution | site-heterogeneous from the combination of noise introduced by fast-evolving posi- model | archaeal phylogeny tions and the use of an overly simplistic evolutionary model. s was suggested by a few early phylogenetic analyses (1–3), Results Aover the past five years a number of universal trees of life A/E Dataset. Universal trees obtained in previous analyses have rooted on the branch leading to Bacteria have supported an left the precise relationship of eukaryotes to the TACK superphylum emergence of eukaryotes from within the radiation of modern unclear (10). We sought to clarify this placement by assembling Archaea (4–11), with a specific link to a group comprising a large supermatrix of 72 markers shared between Archaea and Thaumarchaeota/“Aigarchaeota” (candidate phylum)/Cren- eukaryotes—the A/E dataset—totaling 17,892 amino acid positions archaeota/Korarchaeota (the TACK superphylum) (5). This finding has very important consequences, because it clearly defines Significance that an organism endowed with characteristics of a modern archaeon was the starting point for the process of eukaryogenesis An archaeal origin for eukaryotes is an exciting recent finding. (12, 13). Although these analyses used sophisticated approaches, Nevertheless, it has been based largely on the reconstruction of they were all based on the reconstruction of universal trees of universal trees. The use of an alternative strategy based on life and a restricted taxonomic sampling, in particular for the markers shared between Archaea and eukaryotes and Archaea bacterial outgroup. Moreover, these studies have left the and Bacteria bypasses potential problems linked to the analysis precise relationship of eukaryotes with the TACK lineages of the three domains simultaneously. Comparison of the unclear (10) and showed intradomain phylogenies that were phylogenies obtained by these two complementary sets of only partially resolved and often inconsistent between differ- markers supports a sister relationship between eukaryotes and ent analyses and with well-established relationships. In fact, the Thaumarchaeota/“Aigarchaeota” (candidate phylum)/Cren- analyzing the three domains at once reduces the number of archaeota/Korarchaeota lineage but also robustly indicates a markers and unambiguously aligned positions that can be used root of the tree of Archaea that challenges the traditional to- for phylogenetic reconstruction and may produce artifacts pology of this domain. This sensibly changes our perspective of because of the very large interdomain distances (14). Fur- the ancient evolution of the Archaea, early life, and Earth. thermore, the inclusion of very fast-evolving lineages may distort the phylogeny within each domain and bias the in- Author contributions: C.B.-A. and S.G. designed research; K.R. performed research; K.R., ference of interdomain relationships. Such is the case, for C.B.-A., and S.G. analyzed data; and K.R., C.B.-A., and S.G. wrote the paper. example, of the recently proposed archaeal superphylum The authors declare no conflict of interest. DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, This article is a PNAS Direct Submission. Nanohaloarchaeota, and Nanoarchaeota) (15), which has 1To whom correspondence should be addressed. Email: [email protected]. shown conflicting placements in recent universal trees (9, 11), This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. and may not even be monophyletic. Finally, the use of very 1073/pnas.1420858112/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1420858112 PNAS Early Edition | 1of6 Downloaded by guest on September 26, 2021 Candidatus Korarchaeum cryptofilum OPF8 KOR Physcomitrella patens Desulfurococcus kamchatkensis 1221n 1 1 Pyrolobus fumarii 1A Selaginella moellendorffii 1 Desulfurococcales VIRIDIPLANTAE Arabidopsis thaliana 1 1 Ignicoccus hospitalis KIN4_I 1 Metallosphaera sedula DSM 5348 Chlamydomonas reinhardtii 1 1 Sulfolobales Micromonas pusilla 1 1 Sulfolobus tokodaii str. 7 Dictyostelium discoideum 1 Thermofilum pendens Hrk 5 CREN Vulcanisaeta moutnovskia 768-28 AMOEBOZOA Monosiga brevicollis 1 1 1 Homo sapiens 1 Caldivirga maquilingensis IC-167 Thermoproteales 1 1 1 Thermoproteus tenax Kra 1 OPISTHOKONTA Saccharomyces cerevisiae 1 1 Pyrobaculum aerophilum str. IM2 Batrachochytrium dendrobatidis 0.98 Thalassiosira pseudonana Candidatus Caldiarchaeum subterraneum ‘AIG’ Phaeodactylum tricornutum 1 Candidatus Nitrosoarchaeum limnia SFB1 ALVEOLATA 1 1 1 Aureococcus anophagefferens 1 Nitrosopumilus maritimus SCM1 Nitrosopumilales STRAMENOPILES Paramecium tetraurelia 1 1 1 Cenarchaeum symbiosum A Cenarchaeales THAUM Tetrahymena thermophila 1 Candidatus Nitrososphaera gargensis Ga9.2 Thermococcus litoralis DSM 5473 Leishmania major 2.09 1 EUGLENOZOA 1 Thermococcus barophilus MP Trypanosoma brucei 1 1 Thermococcales Naegleria gruberi Pyrococcus yayanosil CH1 HETEROLOBOSEA 1 Pyrococcus abyssi GE5 Methanotorris igneus Kol 5 1 Methanococcus vannielii SB Methanococcales 1 Methanocaldococcus infernus ME 1 1 1 Methanocaldococcus jannaschii DSM 2661 Methanothermus fervidus DSM 2088 1 Methanobacterium sp. SWAN-1 1 Methanobrevibacter smithii ATCC 35061 Methanobacteriales 1 Methanothermobacter thermautotrophicus str. Delta H 1 Aciduliprofundum boonei T469 DHEV2 1 Ferroplasma acidarmanus fer1 1 Thermoplasmatales uncultured marine group II euryarchaeote Marine Group II 0.93 Candidatus Methanomethylophilus alvus Mx1201 EURY 1 Methanomassiliicoccus luminyensis Methanomassiliicoccales Ferroglobus placidus DSM 10642 1 1 Archaeoglobus veneficus SNP6 Archaeoglobales 1 Archaeoglobus profundus DSM 5631 1 Archaeoglobus fulgidus DSM 4304 Methanocorpusculum labreanum Z 1 Methanoregula boonei 6A8 Methanomicrobiales 1 1 1 Methanoculleus marisnigri JR1 Haloferax volcanii DS2 1 Natrialba magadii ATCC 43099 Halobacteriales 1 1 Haloarcula marismortui ATCC 43049 Methanococcoides burtonii DSM 6242 1 1 Methanosarcina mazei Go1 Methanosarcinales Methanosaeta harundinacea 6Ac 1 Methanocella arvoryzae MRE50 1 Methanocella