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Home , Andalucia incarcerata, Botryobasidium, Collodictyon, Collodictyonidae, Euglenozoa, Eumetazoa

ABCK01000081.1 Lentisphaera araneosa Lentisphaerae−bacterium−GWF2−50−93 CP001998CoraliomargaritaakajimensisDSM45221 CP000975MethylacidiphiluminfernorumV4 −bacterium−GWF2−62−7 Supplementary Figure 1. Chronogram of 308 archaeal, bacterial, and eukaryotic generated using PhyloBayes with a CIR AE001273.1 Chlamydia trachomatis clock model and conservative calibration points. Chronogram was built based on an alignment of concatenated universal, ASLA01000001.1 Omnitrophica bacterium SCGC AAA252−B19 A252B19DRAFT contig 0 0.1 C single-copy . Branch lengths indicate time in thousands of years. Error bars represent the 95% confdence intervals for each CP001848.1 Pirellula staleyi DSM 6068 node. TARA−PSW−MAG−00018 AQYQ01000001.1 Hydrogenedentes bacterium Elusimicrobia−bacterium−GWA2−66−18 Elusimicrobia−bacterium−RBG−16−66−12 Elusimicrobia−bacterium−RIFOXYA2−FULL−69−6 Supplementary Figure 1. Chronogram of 308 archaeal, bacterial, and eukaryotic genomes generated using PhyloBayes with a CIR clock model and conservative fossil calibration points. Chronogram was built based on an alignment of concatenated universal, single-copy genes. Branch lengths indicate time in thousands of years. Error bars representElusimicrobia−bacte the 95% confdencerium−GWD2−63−28 intervals for each node. CP001698SpirochaetathermophilaDSM6192 CP001841TreponemaazotonutriciumZAS9 CP001843TreponemaprimitiaZAS2 Treponema−sp−GWA1−62−8 Treponema−sp−RIFOXYC1−FULL−61−9 CP002116SpirochaetasmaragdinaeDSM11293 −bacterium−GWC2−52−13 Spirochaetes−bacterium−GWB1−36−13 AE006470ChlorobiumtepidumTLS CP001099ChlorobaculumparvumNCIB8327 CP000096ChlorobiumluteolumDSM273 CP000607ChlorobiumphaeovibrioidesDSM265 CP000108ChlorobiumchlorochromatiiCaD3 CP001110PelodictyonphaeoclathratiformeBU1 CP000492ChlorobiumphaeobacteroidesDSM266 CP001097ChlorobiumlimicolaDSM245 CP001108ProsthecochlorisaestuariiDSM271 CP001100ChloroherpetonthalassiumATCC35110 AP006841.1 Bacteroides fragilis AP010656CandidatusAzobacteroidespseudotrichonymphaegenomovarCFP2 CP003418.1 Ignavibacterium album CP003418.1 Ignavibacterium album JCM 16511 ASZK01000001.1 Marinimicrobia bacterium CP018099.1 Caldithrix abyssi LJNC01000001.1 Latescibacteria bacterium candidate−division−Zixibacteria−bacterium−RBG−16−53−22 AQYP01000001.1 Cloacimonetes bacterium JGI 0000039−G13 WWE1 1DRAFT contig 131.132 C CP002158.1 Fibrobacter succinogenes CP007127.1 Gemmatirosa kalamazoonesis strain KBS708 phage−like extrachromosal element AE017180GeobactersulfurreducensPCA CP000698GeobacteruraniireducensRf4 CP001390GeobacterdaltoniiFRC32 CP001124GeobacterbemidjiensisBem CP000482PelobacterpropionicusDSM2379 Geobacteraceae−bacterium−GWC2−48−7 Desulfuromonadales−bacterium−GWD2−54−10 Pelobacteraceae−bacterium−GWB2−53−15 Geobacteraceae−bacterium−GWB2−52−12 Geobacteraceae−bacterium−GWC2−53−11 Geobacteraceae−bacterium−GWC2−55−20 Geobacteraceae−bacterium−GWF2−54−21 CP001089GeobacterlovleyiSZ CP000142PelobactercarbinolicusDSM2380 AP010904DesulfovibriomagneticusRS1 CP001649DesulfovibriosalexigensDSM2638 CP003220DesulfovibriodesulfuricansND132 TARA−PSW−MAG−00013 Desulfovibrionales−bacterium−GWA2−65−9 CP003221DesulfovibrioafricanusstrWalvisBay CP001629DesulfomicrobiumbaculatumDSM4028 CP002683ThermodesulfatatorindicusDSM15286 CP001087DesulfobacteriumautotrophicumHRM2 Desulfobacula−sp−GWF2−41−7 TARA−PSW−MAG−00026 CP001322DesulfatibacillumalkenivoransAK01 CP001940DesulfurivibrioalkaliphilusAHT2 Deltaproteobacteria−bacterium−RIFOXYD12−FULL−53−23 Deltaproteobacteria−bacterium−RIFOXYD12−FULL−55−16 Deltaproteobacteria−bacterium−RIFOXYD12−FULL−56−24 Deltaproteobacteria−bacterium−RIFOXYD12−FULL−50−9 CP002364DesulfobulbuspropionicusDSM2032 CP002085DesulfarculusbaarsiiDSM2075 CP000478SyntrophobacterfumaroxidansMPOB CP002629DesulfobaccaacetoxidansDSM11109 CP000769AnaeromyxobacterspFw1095 HG422173.1 Nitrospina gracilis MGDO01000001.1 Candidatus Tectomicrobia bacterium AM406670AzoarcusspBH72 Rhodocyclales−bacterium−GWA2−65−19 CP000089DechloromonasaromaticaRCB CP001715CandidatusAccumulibacterphosphatiscladeIIAstrUW1 CP003153DechlorosomasuillumPS CP000529PolaromonasnaphthalenivoransCJ2 CP001013LeptothrixcholodniiSP6 CP002039HerbaspirillumseropedicaeSmR1 CP001965SideroxydanslithotrophicusES1 Gallionellales−bacterium−GWA2−59−43 Hydrogenophilales−bacterium−RIFOXYD1−FULL−62−11 BX950851PectobacteriumatrosepticumSCRI1043 CP001654DickeyadadantiiEch703 CP001616TolumonasauensisDSM9187 CP001157AzotobactervinelandiiDJ Pseudomonadales−bacterium−GWC1−66−9 TARA−ION−MAG−00014 TARA−ANW−MAG−00006 TARA−ANW−MAG−00019 CP000544HalorhodospirahalophilaSL1 CP001896AllochromatiumvinosumDSM180 CP002738MethylomonasmethanicaMC09 CP002985AcidithiobacillusferrivoransSS3 AP007255MagnetospirillummagneticumAMB1 CP003046RhodospirillumrubrumF11 AP010946AzospirillumspB510 FQ311868Azospirillumlipoferum4B HE577327AzospirillumbrasilenseSp245 CP000613RhodospirillumcentenumSW CP001189GluconacetobacterdiazotrophicusPA15 AP009384AzorhizobiumcaulinodansORS571 CP000781XanthobacterautotrophicusPy2 CP001016BeijerinckiaindicasubspindicaATCC9039 CP001280MethylocellasilvestrisBL2 CP001349MethylobacteriumnodulansORS2060 AP012206BradyrhizobiumjaponicumUSDA6 CP000494BradyrhizobiumspBTAi1 CU234118BradyrhizobiumspORS278 BA000012MesorhizobiumlotiMAFF303099 CP002279MesorhizobiumopportunistumWSM2075 CP002447MesorhizobiumciceribiovarbiserrulaeWSM1271 CP002292RhodomicrobiumvannieliiATCC17100 CP001312RhodobactercapsulatusSB1003 CP000471MagnetococcusmarinusMC1 DS022297.1 Mariprofundus ferrooxydans AP012048ArcobacterspL CP001999ArcobacternitrofigilisDSM7299 CP002355SulfuricurvumkujienseDSM16994 Sulfuricurvum−sp−GWF2−44−89 Sulfuricurvum−sp−RIFOXYD12−FULL−44−77 Sulfuricurvum−sp−RIFCSPHIGHO2−12−FULL−44−8 Sulfurimonas−sp−GWF2−37−8 Sulfurimonas−sp−RIFOXYD12−FULL−33−39 Candidatus−Lambdaproteobacteria−bacterium−RIFOXYD12−FULL−49−8 Candidatus−Lambdaproteobacteria−bacterium−RIFOXYD2−FULL−50−16 CP001968DenitrovibrioacetiphilusDSM12809 CP002347CalditerrivibrionitroreducensDSM19672 CP002432.1 Desulfurispirillum indicum CP001147ThermodesulfovibrioyellowstoniiDSM11347 LDXN01000001.1 Candidatus Dadabacteria bacterium CP001472.1 Acidobacterium capsulatum LDXP01000001.1 Candidatus Rokubacteria bacterium AE017263.1 Mesoplasma florum L1 complete −bacterium−GWE2−51−13 Firmicutes−bacterium−GWF2−51−9 CP003107PaenibacillusterraeHPL003 CP000673ClostridiumkluyveriDSM555 CP001666ClostridiumljungdahliiDSM13528 CP000721ClostridiumbeijerinckiiNCIMB8052 CP002160Clostridiumcellulovorans743B CP002582ClostridiumlentocellumDSM5427 FP929038CoprococcuscatusGD7 CP000724AlkaliphilusmetalliredigensQYMF CP002987AcetobacteriumwoodiiDSM1030 CP000679CaldicellulosiruptorsaccharolyticusDSM8903 CP002219Caldicellulosiruptorhydrothermalis108 CP003001Caldicellulosiruptorlactoaceticus6A CP002171ThermoanaerobacteriumthermosaccharolyticumDSM571 CP000612DesulfotomaculumreducensMI1 CP002780DesulfotomaculumruminisDSM2154 CP002736DesulfotomaculumcarboxydivoransCO1SRB CP002770DesulfotomaculumkuznetsoviiDSM6115 CP000860CandidatusDesulforudisaudaxviatorMP104C CP001720DesulfotomaculumacetoxidansDSM771 CP002028ThermincolapotensJR CP000930HeliobacteriummodesticaldumIce1 CP002547SyntrophobotulusglycolicusDSM8271 CP003108DesulfosporosinusorientisDSM765 CP002048SyntrophothermuslipocalidusDSM12680 −bacterium−GWC2−53−9 AQYX01000001.1 Atribacteria bacterium Actinobacteria−bacterium−RBG−13−35−12 Candidatus−Margulisbacteria−bacterium−GWD2−39−127 Candidatus−Margulisbacteria−bacterium−GWE2−39−32 BA000019NostocspPCC7120 CP002059Nostocazollae0708 CP001344CyanothecespPCC7425 CP000393TrichodesmiumerythraeumIMS101 CP001291CyanothecespPCC7424 CP002198CyanothecespPCC7822 CP001701CyanothecespPCC8802 CP001842CandidatusAtelocyanobacteriumthalassa TARA−ASW−MAG−00003 CP000239SynechococcusspJA33Ab Candidatus−Melainabacteria−bacterium−GWA2−34−9 CP002801FrankiasymbiontofDatiscaglomerata CP007139.1 Fimbriimonas ginsengisoli CP000804RoseiflexuscastenholziiDSM13941 −bacterium−RBG−13−52−12 CP011210.1 Microgenomates Beckwithbacteria bacterium GW2011 GWC1 49 16 Candidatus−Gottesmanbacteria−bacterium−RBG−16−52−11 LBRO01000001.1 Candidatus Levybacteria bacterium GW2011 GWB1 36 18 US07 C0001 LBSV01000001.1 Candidatus Roizmanbacteria bacterium GW2011 GWC2 37 13 US40 C0001 LBSJ01000001.1 Candidatus Daviesbacteria bacterium GW2011 GWA1 36 8 US28 C0001 LCAG01000001.1 Candidatus Curtissbacteria bacterium GW2011 GWA1 41 11 UU34 C0001 LBWK01000001.1 Candidate division WS6 bacterium GW2011 GWF2 39 15 UT34 C0001 MEWK01000001.1 Candidate division WWE3 bacterium LBUC01000001.1 Candidatus Falkowbacteria bacterium GW2011 GWF2 38 1205 US73 C0001 LCPI01000001.1 Candidatus Jorgensenbacteria bacterium GW2011 GWA1 48 13 UY26 C0001 LCQM01000001.1 Candidatus Kaiserbacteria bacterium MNZT01000079.1 Candidatus Wirthbacteria bacterium AE000513.1 Deinococcus radiodurans AE009951.2 Fusobacterium nucleatum CP001818.1 Thermanaerovibrio acidaminovorans CP001251.1 Dictyoglomus turgidum MNXV01000056.1 Caldisericum sp. CG2 30 36 11 cg2 3.0 scaffold 1022 c AE000512.1 Thermotoga maritima AP011112HydrogenobacterthermophilusTK6 CP001931ThermocrinisalbusDSM14484 AquifexaeolicusVF5 AQTE01000001.1 Calescamantes bacterium AE000666MethanothermobacterthermautotrophicusstrDeltaH CP001710MethanothermobactermarburgensisstrMarburg CP000742MethanococcusvannieliiSB CP000743MethanococcusaeolicusNankai3 CP002792MethanothermococcusokinawensisIH1 CP002737MethanotorrisigneusKol5 CP001787MethanocaldococcusvulcaniusM7 CP001901MethanocaldococcusspFS40622 L77117MethanocaldococcusjannaschiiDSM2661 CP002009MethanocaldococcusinfernusME AE008384MethanosarcinamazeiGo1 AE010299MethanosarcinaacetivoransC2A CP000099MethanosarcinabarkeristrFusaro CP001994MethanohalophilusmahiiDSM5219 CP002565MethanosaetaconciliiGP6 AM114193MethanocellaarvoryzaeMRE50 CP003243MethanocellaconradiiHZ254 CP000254MethanospirillumhungateiJF1 CP000780Methanoregulaboonei6A8 CP001338MethanosphaerulapalustrisE19c CP000559MethanocorpusculumlabreanumZ CP001365.1 Halorubrum lacusprofundi ATCC 49239 1 CP011267.1 Geoglobus ahangari strain 234 AQRS01000001.1 Candidatus Iainarchaeum andersonii SCGC AAA011−E11 A11E11DRAFT contig 42 0.43 C CP010514.1 Candidatus Nanopusillus acidilobi strain 7A MFWN01000001.1 Candidatus Pacearchaeota archaeon RBG 13 36 9 RBG 13 scaffold 10120 MGFI01000001.1 Candidatus Woesearchaeota archaeon CP012986.1 Nanohaloarchaea archaeon MFRS01000001.1 Candidatus Micrarchaeota archaeon MNUF01000070.1 Candidatus Aenigmarchaeota archaeon CG1 02 38 14 cg1 0.2 scaffold 1045 c AE006641.1 Sulfolobus solfataricus CP000968.1 Candidatus Korarchaeum cryptofilum OPF8 CP007536.1 Nitrososphaera viennensis CP007536.1 Nitrososphaera viennensis EN76 Candidatus−Bathyarchaeota−archaeon−RBG−16−57−9 CP Thorarchaeota WOR bin SMTZ1 83 LRSK01000001.1 Candidatus Thorarchaeota archaeon SMTZ1−83 WOR1 30 36 10184 Archaea Lokiarchaeota RBG 13 Lokiarchaeota 45 8 MBAA01000194.1 Candidatus Lokiarchaeota archaeon MDVT01000001.1 Candidatus Odinarchaeota archaeon LCB 4 OdinLCB4 contig000001 MEHH01000001.1 Candidatus Heimdallarchaeota archaeon AB 125 HeimAB125 contig000001 AE017261.1 Picrophilus torridus Streptophytina Embryophyta Tracheophyta Euphyllophyta Spermatophyta Magnoliophyta Liliopsida commelinids Poales Poaceae BEP Ehrhartoideae Oryzeae Oryza sativa Archaeplastida Viridiplantae Streptophyta Streptophytina Embryophyta Tracheophyta Euphyllophyta Spermatophyta Magnoliophyta Liliopsida commelinids Poales Poaceae PACMAD clade Panicoideae Andropogoneae Sorghum bicolor Archaeplastida Viridiplantae Streptophyta Streptophytina Embryophyta Tracheophyta Euphyllophyta Spermatophyta Magnoliophyta Liliopsida commelinids Poales Poaceae PACMAD clade Panicoideae Andropogoneae Zea mays mays cv. B73 Archaeplastida Viridiplantae Streptophyta Streptophytina Embryophyta Tracheophyta Euphyllophyta Spermatophyta Magnoliophyta eudicotyledons core eudicotyledons rosids fabids Fabales Fabaceae Papilionoideae Phaseoleae Glycine max cultivar Williams 82 Archaeplastida Viridiplantae Streptophyta Streptophytina Embryophyta Tracheophyta Euphyllophyta Spermatophyta Magnoliophyta eudicotyledons core eudicotyledons rosids fabids Malpighiales Salicaceae Saliceae Populus trichocarpa Opisthokonta Metazoa Coelomata Protostomia Arthropoda Insecta Dicondylia Ricinus communis Archaeplastida Viridiplantae Streptophyta Streptophytina Embryophyta Tracheophyta Euphyllophyta Spermatophyta Magnoliophyta eudicotyledons core eudicotyledons rosids malvids Brassicales Brassicaceae Camelineae Arabidopsis thaliana Eukaryota Archaeplastida Viridiplantae Chlamydomonadales Volvocaceae Volvox carteri f. nagariensis 69 1b Eukaryota Archaeplastida Viridiplantae Chlorophyta Prasiolales Prasiolales Chlorella sp. NC64A Eukaryota Archaeplastida Viridiplantae Chlorophyta Mamiellales Micromonas pusilla NOUM17 RCC 299 Eukaryota Alveolata annulata Ankara clone C9 Eukaryota stramenopiles Bacillariophyta Bacillariophyceae Bacillariophycidae Naviculales Phaeodactylaceae Phaeodactylum tricornutum CCAP 10551 Eukaryota stramenopiles Bacillariophyta Coscinodiscophyceae Thalassiosirophycidae Thalassiosirales Thalassiosiraceae Thalassiosira pseudonana CCMP1335 Eukaryota Haptophyceae Pavlovales Pavlovaceae Pavlova lutheri Eukaryota Opisthokonta Fungi Blastocladiomycetes Blastocladiales Blastocladiaceae Allomyces macrogynus ATCC 38327 Eukaryota stramenopiles Blastocystis hominis Eukaryota Opisthokonta Fungi Fungi incertae sedis Early diverging fungal lineages Kickxellales Kickxellaceae Coemansia reversa NRRL 1564 Eukaryota Opisthokonta Fungi saccharomyceta dothideomyceta Dothideomycetidae Capnodiales Mycosphaerellaceae mitosporic Mycosphaerellaceae Cryptococcus neoformans var. neoformans B 3501A Eukaryota Opisthokonta Fungi Dikarya Agaricomycetes incertae sedis Botryobasidium botryosum Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetes incertae sedis Corticiales Corticiaceae Phanerochaete chrysosporium RP 78 Eukaryota Opisthokonta Metazoa Eumetazoa Bilateria Coelomata Protostomia Annelida Polychaeta Palpata Canalipalpata Sabellida Serpulidae lacrymans lacrymans S7.9 Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetidae Agaricales Strophariaceae Hypholoma sublateritium Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetidae Agaricales Tricholomataceae Gymnopus luxurians Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetidae Agaricales Tricholomataceae Laccaria bicolor S238N H82 LACBI Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetidae Agaricales Schizophyllaceae Schizophyllum commune H4 8 Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetes incertae sedis Polyporales Coriolaceae Postia placenta Mad 698 R POSPL Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetidae Agaricales Psathyrellaceae Coprinopsis cinerea strain okayama7130 Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Malasseziales Malasseziaceae Malassezia globosa CBS Eukaryota Opisthokonta Fungi Dikarya Ascomycota saccharomyceta Pezizomycotina leotiomyceta sordariomyceta Hypocreomycetidae Cordycipitaceae mitosporic Cordycipitaceae Beauveria bassiana CH draft genome Eukaryota Opisthokonta Opisthokonta incertae sedis vibrans Eukaryota Jakobida incarcerata Eukaryota Katablepharidophyta Eukaryota Mycetozoa Dictyosteliida Dictyostelium discoideum AX4 Eukaryota Opisthokonta Metazoa Eumetazoa Bilateria Coelomata Deuterostomia Chordata Tunicata Appendicularia Oikopleuridae Oikopleura dioica Eukaryota unclassified triciliatum Eukaryota Euglenida Euglenales Euglenaceae gracilis Eukaryota Euglenozoa Trypanosomatidae Leishmania JPCM5 MCANES98LLM 877 Eukaryota Euglenozoa Kinetoplastida Trypanosomatidae brucei TREU927 Eukaryota Jakobida Histionidae americana Eukaryota Jakobida Jakobidae libera Eukaryota Alveolata Apicomplexa Aconoidasida Piroplasmida bovis T2Bo Eukaryota Heterolobosea Acrasida Guttulinaceae Guttulinopsis vulgaris Eukaryota Chlorarachniophyceae Bigelowiella natans CT868681.1 tetraurelia chromosome undetermined scaffold 99 Eukaryota Alveolata Ciliophora Intramacronucleata Peniculida Parameciidae Paramecium tetraurelia d4 2 Eukaryota Alveolata Ciliophora Intramacronucleata Oligohymenophorea Hymenostomatida Tetrahymenina Tetrahymenidae pyriformis Eukaryota Alveolata Ciliophora Intramacronucleata Oligohymenophorea Hymenostomatida Tetrahymenina Tetrahymenidae Tetrahymena thermophila SB210 Macronucleus DS572673.1 Entamoeba histolytica HM−1IMSS scf 1104750517515 genomic scaffold Eukaryota Amoebozoa Entamoebidae Entamoeba histolytica HM 1IMSS Eukaryota Heterolobosea Psalteriomonadidae marylandensis Eukaryota Heterolobosea gruberi strain NEG M genomic NAEGR Eukaryota Fornicata Diplomonadida Hexamitidae Giardiinae lamblia ATCC 50803 strain WB C6 Eukaryota Parabasalia vaginalis G3 Eukaryota Cryptophyta theta nucleomorph

4270 3420 2560 1710 854 0 Supplementary Figure 2. Chronogram of 308 archaeal, bacterial, and eukaryotic genomes generated using PhyloBayes with a ABCK01000081.1 Lentisphaera araneosa UGAM clock model and conservative fossil calibration points. Chronogram was built based on an alignment of concatenated univer- Lentisphaerae−bacterium−GWF2−50−93 sal, single-copy genes. Branch lengths indicate time in thousands of years. Error bars represent the 95% confdence intervals for CP001998CoraliomargaritaakajimensisDSM45221 each node. CP000975MethylacidiphiluminfernorumV4 Verrucomicrobia−bacterium−GWF2−62−7 AE001273.1 Chlamydia trachomatis ASLA01000001.1 Omnitrophica bacterium SCGC AAA252−B19 A252B19DRAFT contig 0 0.1 C CP001848.1 Pirellula staleyi DSM 6068 TARA−PSW−MAG−00018 AQYQ01000001.1 Hydrogenedentes bacterium Elusimicrobia−bacterium−GWA2−66−18 Elusimicrobia−bacterium−RBG−16−66−12 Elusimicrobia−bacterium−RIFOXYA2−FULL−69−6 Elusimicrobia−bacterium−GWD2−63−28 CP001698SpirochaetathermophilaDSM6192 CP001841TreponemaazotonutriciumZAS9 CP001843TreponemaprimitiaZAS2 Treponema−sp−GWA1−62−8 Treponema−sp−RIFOXYC1−FULL−61−9 CP002116SpirochaetasmaragdinaeDSM11293 Spirochaetes−bacterium−GWC2−52−13 Spirochaetes−bacterium−GWB1−36−13 AE006470ChlorobiumtepidumTLS CP001099ChlorobaculumparvumNCIB8327 CP000096ChlorobiumluteolumDSM273 CP000607ChlorobiumphaeovibrioidesDSM265 CP000108ChlorobiumchlorochromatiiCaD3 CP001110PelodictyonphaeoclathratiformeBU1 CP000492ChlorobiumphaeobacteroidesDSM266 CP001097ChlorobiumlimicolaDSM245 CP001108ProsthecochlorisaestuariiDSM271 CP001100ChloroherpetonthalassiumATCC35110 AP006841.1 Bacteroides fragilis AP010656CandidatusAzobacteroidespseudotrichonymphaegenomovarCFP2 CP003418.1 Ignavibacterium album CP003418.1 Ignavibacterium album JCM 16511 ASZK01000001.1 Marinimicrobia bacterium CP018099.1 Caldithrix abyssi LJNC01000001.1 Latescibacteria bacterium candidate−division−Zixibacteria−bacterium−RBG−16−53−22 AQYP01000001.1 Cloacimonetes bacterium JGI 0000039−G13 WWE1 1DRAFT contig 131.132 C CP002158.1 Fibrobacter succinogenes CP007127.1 Gemmatirosa kalamazoonesis strain KBS708 phage−like extrachromosal element AE017180GeobactersulfurreducensPCA CP000698GeobacteruraniireducensRf4 CP001390GeobacterdaltoniiFRC32 CP001124GeobacterbemidjiensisBem CP000482PelobacterpropionicusDSM2379 Geobacteraceae−bacterium−GWC2−48−7 Desulfuromonadales−bacterium−GWD2−54−10 Pelobacteraceae−bacterium−GWB2−53−15 Geobacteraceae−bacterium−GWB2−52−12 Geobacteraceae−bacterium−GWC2−53−11 Geobacteraceae−bacterium−GWC2−55−20 Geobacteraceae−bacterium−GWF2−54−21 CP001089GeobacterlovleyiSZ CP000142PelobactercarbinolicusDSM2380 AP010904DesulfovibriomagneticusRS1 CP001649DesulfovibriosalexigensDSM2638 CP003220DesulfovibriodesulfuricansND132 TARA−PSW−MAG−00013 Desulfovibrionales−bacterium−GWA2−65−9 CP003221DesulfovibrioafricanusstrWalvisBay CP001629DesulfomicrobiumbaculatumDSM4028 CP002683ThermodesulfatatorindicusDSM15286 CP001087DesulfobacteriumautotrophicumHRM2 Desulfobacula−sp−GWF2−41−7 TARA−PSW−MAG−00026 CP001322DesulfatibacillumalkenivoransAK01 CP001940DesulfurivibrioalkaliphilusAHT2 Deltaproteobacteria−bacterium−RIFOXYD12−FULL−53−23 Deltaproteobacteria−bacterium−RIFOXYD12−FULL−55−16 Deltaproteobacteria−bacterium−RIFOXYD12−FULL−56−24 Deltaproteobacteria−bacterium−RIFOXYD12−FULL−50−9 CP002364DesulfobulbuspropionicusDSM2032 CP002085DesulfarculusbaarsiiDSM2075 CP000478SyntrophobacterfumaroxidansMPOB CP002629DesulfobaccaacetoxidansDSM11109 CP000769AnaeromyxobacterspFw1095 HG422173.1 Nitrospina gracilis MGDO01000001.1 Candidatus Tectomicrobia bacterium AM406670AzoarcusspBH72 Rhodocyclales−bacterium−GWA2−65−19 CP000089DechloromonasaromaticaRCB CP001715CandidatusAccumulibacterphosphatiscladeIIAstrUW1 CP003153DechlorosomasuillumPS CP000529PolaromonasnaphthalenivoransCJ2 CP001013LeptothrixcholodniiSP6 CP002039HerbaspirillumseropedicaeSmR1 CP001965SideroxydanslithotrophicusES1 Gallionellales−bacterium−GWA2−59−43 Hydrogenophilales−bacterium−RIFOXYD1−FULL−62−11 BX950851PectobacteriumatrosepticumSCRI1043 CP001654DickeyadadantiiEch703 CP001616TolumonasauensisDSM9187 CP001157AzotobactervinelandiiDJ Pseudomonadales−bacterium−GWC1−66−9 TARA−ION−MAG−00014 TARA−ANW−MAG−00006 TARA−ANW−MAG−00019 CP000544HalorhodospirahalophilaSL1 CP001896AllochromatiumvinosumDSM180 CP002738MethylomonasmethanicaMC09 CP002985AcidithiobacillusferrivoransSS3 AP007255MagnetospirillummagneticumAMB1 CP003046RhodospirillumrubrumF11 AP010946AzospirillumspB510 FQ311868Azospirillumlipoferum4B HE577327AzospirillumbrasilenseSp245 CP000613RhodospirillumcentenumSW CP001189GluconacetobacterdiazotrophicusPA15 AP009384AzorhizobiumcaulinodansORS571 CP000781XanthobacterautotrophicusPy2 CP001016BeijerinckiaindicasubspindicaATCC9039 CP001280MethylocellasilvestrisBL2 CP001349MethylobacteriumnodulansORS2060 AP012206BradyrhizobiumjaponicumUSDA6 CP000494BradyrhizobiumspBTAi1 CU234118BradyrhizobiumspORS278 BA000012MesorhizobiumlotiMAFF303099 CP002279MesorhizobiumopportunistumWSM2075 CP002447MesorhizobiumciceribiovarbiserrulaeWSM1271 CP002292RhodomicrobiumvannieliiATCC17100 CP001312RhodobactercapsulatusSB1003 CP000471MagnetococcusmarinusMC1 DS022297.1 Mariprofundus ferrooxydans AP012048ArcobacterspL CP001999ArcobacternitrofigilisDSM7299 CP002355SulfuricurvumkujienseDSM16994 Sulfuricurvum−sp−GWF2−44−89 Sulfuricurvum−sp−RIFOXYD12−FULL−44−77 Sulfuricurvum−sp−RIFCSPHIGHO2−12−FULL−44−8 Sulfurimonas−sp−GWF2−37−8 Sulfurimonas−sp−RIFOXYD12−FULL−33−39 Candidatus−Lambdaproteobacteria−bacterium−RIFOXYD12−FULL−49−8 Candidatus−Lambdaproteobacteria−bacterium−RIFOXYD2−FULL−50−16 CP001968DenitrovibrioacetiphilusDSM12809 CP002347CalditerrivibrionitroreducensDSM19672 CP002432.1 Desulfurispirillum indicum CP001147ThermodesulfovibrioyellowstoniiDSM11347 LDXN01000001.1 Candidatus Dadabacteria bacterium CP001472.1 Acidobacterium capsulatum LDXP01000001.1 Candidatus Rokubacteria bacterium AE017263.1 Mesoplasma florum L1 complete genome Firmicutes−bacterium−GWE2−51−13 Firmicutes−bacterium−GWF2−51−9 CP003107PaenibacillusterraeHPL003 CP000673ClostridiumkluyveriDSM555 CP001666ClostridiumljungdahliiDSM13528 CP000721ClostridiumbeijerinckiiNCIMB8052 CP002160Clostridiumcellulovorans743B CP002582ClostridiumlentocellumDSM5427 FP929038CoprococcuscatusGD7 CP000724AlkaliphilusmetalliredigensQYMF CP002987AcetobacteriumwoodiiDSM1030 CP000679CaldicellulosiruptorsaccharolyticusDSM8903 CP002219Caldicellulosiruptorhydrothermalis108 CP003001Caldicellulosiruptorlactoaceticus6A CP002171ThermoanaerobacteriumthermosaccharolyticumDSM571 CP000612DesulfotomaculumreducensMI1 CP002780DesulfotomaculumruminisDSM2154 CP002736DesulfotomaculumcarboxydivoransCO1SRB CP002770DesulfotomaculumkuznetsoviiDSM6115 CP000860CandidatusDesulforudisaudaxviatorMP104C CP001720DesulfotomaculumacetoxidansDSM771 CP002028ThermincolapotensJR CP000930HeliobacteriummodesticaldumIce1 CP002547SyntrophobotulusglycolicusDSM8271 CP003108DesulfosporosinusorientisDSM765 CP002048SyntrophothermuslipocalidusDSM12680 Actinobacteria−bacterium−GWC2−53−9 AQYX01000001.1 Atribacteria bacterium Actinobacteria−bacterium−RBG−13−35−12 Candidatus−Margulisbacteria−bacterium−GWD2−39−127 Candidatus−Margulisbacteria−bacterium−GWE2−39−32 BA000019NostocspPCC7120 CP002059Nostocazollae0708 CP001344CyanothecespPCC7425 CP000393TrichodesmiumerythraeumIMS101 CP001291CyanothecespPCC7424 CP002198CyanothecespPCC7822 CP001701CyanothecespPCC8802 CP001842CandidatusAtelocyanobacteriumthalassa TARA−ASW−MAG−00003 CP000239SynechococcusspJA33Ab Candidatus−Melainabacteria−bacterium−GWA2−34−9 CP002801FrankiasymbiontofDatiscaglomerata CP007139.1 Fimbriimonas ginsengisoli CP000804RoseiflexuscastenholziiDSM13941 Chloroflexi−bacterium−RBG−13−52−12 CP011210.1 Microgenomates Beckwithbacteria bacterium GW2011 GWC1 49 16 Candidatus−Gottesmanbacteria−bacterium−RBG−16−52−11 LBRO01000001.1 Candidatus Levybacteria bacterium GW2011 GWB1 36 18 US07 C0001 LBSV01000001.1 Candidatus Roizmanbacteria bacterium GW2011 GWC2 37 13 US40 C0001 LBSJ01000001.1 Candidatus Daviesbacteria bacterium GW2011 GWA1 36 8 US28 C0001 LCAG01000001.1 Candidatus Curtissbacteria bacterium GW2011 GWA1 41 11 UU34 C0001 LBWK01000001.1 Candidate division WS6 bacterium GW2011 GWF2 39 15 UT34 C0001 MEWK01000001.1 Candidate division WWE3 bacterium LBUC01000001.1 Candidatus Falkowbacteria bacterium GW2011 GWF2 38 1205 US73 C0001 LCPI01000001.1 Candidatus Jorgensenbacteria bacterium GW2011 GWA1 48 13 UY26 C0001 LCQM01000001.1 Candidatus Kaiserbacteria bacterium MNZT01000079.1 Candidatus Wirthbacteria bacterium AE000513.1 Deinococcus radiodurans AE009951.2 Fusobacterium nucleatum CP001818.1 Thermanaerovibrio acidaminovorans CP001251.1 Dictyoglomus turgidum MNXV01000056.1 Caldisericum sp. CG2 30 36 11 cg2 3.0 scaffold 1022 c AE000512.1 Thermotoga maritima AP011112HydrogenobacterthermophilusTK6 CP001931ThermocrinisalbusDSM14484 AquifexaeolicusVF5 AQTE01000001.1 Calescamantes bacterium AE000666MethanothermobacterthermautotrophicusstrDeltaH CP001710MethanothermobactermarburgensisstrMarburg CP000742MethanococcusvannieliiSB CP000743MethanococcusaeolicusNankai3 CP002792MethanothermococcusokinawensisIH1 CP002737MethanotorrisigneusKol5 CP001787MethanocaldococcusvulcaniusM7 CP001901MethanocaldococcusspFS40622 L77117MethanocaldococcusjannaschiiDSM2661 CP002009MethanocaldococcusinfernusME AE008384MethanosarcinamazeiGo1 AE010299MethanosarcinaacetivoransC2A CP000099MethanosarcinabarkeristrFusaro CP001994MethanohalophilusmahiiDSM5219 CP002565MethanosaetaconciliiGP6 AM114193MethanocellaarvoryzaeMRE50 CP003243MethanocellaconradiiHZ254 CP000254MethanospirillumhungateiJF1 CP000780Methanoregulaboonei6A8 CP001338MethanosphaerulapalustrisE19c CP000559MethanocorpusculumlabreanumZ CP001365.1 Halorubrum lacusprofundi ATCC 49239 chromosome 1 CP011267.1 Geoglobus ahangari strain 234 AQRS01000001.1 Candidatus Iainarchaeum andersonii SCGC AAA011−E11 A11E11DRAFT contig 42 0.43 C CP010514.1 Candidatus Nanopusillus acidilobi strain 7A MFWN01000001.1 Candidatus Pacearchaeota archaeon RBG 13 36 9 RBG 13 scaffold 10120 MGFI01000001.1 Candidatus Woesearchaeota archaeon CP012986.1 Nanohaloarchaea archaeon MFRS01000001.1 Candidatus Micrarchaeota archaeon MNUF01000070.1 Candidatus Aenigmarchaeota archaeon CG1 02 38 14 cg1 0.2 scaffold 1045 c AE006641.1 Sulfolobus solfataricus CP000968.1 Candidatus Korarchaeum cryptofilum OPF8 CP007536.1 Nitrososphaera viennensis CP007536.1 Nitrososphaera viennensis EN76 Candidatus−Bathyarchaeota−archaeon−RBG−16−57−9 Archaea CP Thorarchaeota WOR bin SMTZ1 83 LRSK01000001.1 Candidatus Thorarchaeota archaeon SMTZ1−83 WOR1 30 36 10184 Archaea Lokiarchaeota RBG 13 Lokiarchaeota 45 8 MBAA01000194.1 Candidatus Lokiarchaeota archaeon MDVT01000001.1 Candidatus Odinarchaeota archaeon LCB 4 OdinLCB4 contig000001 MEHH01000001.1 Candidatus Heimdallarchaeota archaeon AB 125 HeimAB125 contig000001 AE017261.1 Picrophilus torridus Archaeplastida Viridiplantae Streptophyta Streptophytina Embryophyta Tracheophyta Euphyllophyta Spermatophyta Magnoliophyta Liliopsida commelinids Poales Poaceae BEP clade Ehrhartoideae Oryzeae Oryza sativa Archaeplastida Viridiplantae Streptophyta Streptophytina Embryophyta Tracheophyta Euphyllophyta Spermatophyta Magnoliophyta Liliopsida commelinids Poales Poaceae PACMAD clade Panicoideae Andropogoneae Sorghum bicolor Archaeplastida Viridiplantae Streptophyta Streptophytina Embryophyta Tracheophyta Euphyllophyta Spermatophyta Magnoliophyta Liliopsida commelinids Poales Poaceae PACMAD clade Panicoideae Andropogoneae Zea mays mays cv. B73 Archaeplastida Viridiplantae Streptophyta Streptophytina Embryophyta Tracheophyta Euphyllophyta Spermatophyta Magnoliophyta eudicotyledons core eudicotyledons rosids fabids Fabales Fabaceae Papilionoideae Phaseoleae Glycine max cultivar Williams 82 Archaeplastida Viridiplantae Streptophyta Streptophytina Embryophyta Tracheophyta Euphyllophyta Spermatophyta Magnoliophyta eudicotyledons core eudicotyledons rosids fabids Malpighiales Salicaceae Saliceae Populus trichocarpa Opisthokonta Metazoa Eumetazoa Bilateria Coelomata Protostomia Ecdysozoa Panarthropoda Arthropoda Mandibulata Pancrustacea Hexapoda Insecta Dicondylia Ricinus communis Archaeplastida Viridiplantae Streptophyta Streptophytina Embryophyta Tracheophyta Euphyllophyta Spermatophyta Magnoliophyta eudicotyledons core eudicotyledons rosids malvids Brassicales Brassicaceae Camelineae Arabidopsis thaliana Eukaryota Archaeplastida Viridiplantae Chlorophyta Chlorophyceae Chlamydomonadales Volvocaceae Volvox carteri f. nagariensis 69 1b Eukaryota Archaeplastida Viridiplantae Chlorophyta Trebouxiophyceae Prasiolales Prasiolales incertae sedis Chlorella sp. NC64A Eukaryota Archaeplastida Viridiplantae Chlorophyta Mamiellophyceae Mamiellales Micromonas pusilla NOUM17 RCC 299 Eukaryota Alveolata Apicomplexa Aconoidasida Piroplasmida Theileriidae Theileria annulata Ankara clone C9 Eukaryota stramenopiles Bacillariophyta Bacillariophyceae Bacillariophycidae Naviculales Phaeodactylaceae Phaeodactylum tricornutum CCAP 10551 Eukaryota stramenopiles Bacillariophyta Coscinodiscophyceae Thalassiosirophycidae Thalassiosirales Thalassiosiraceae Thalassiosira pseudonana CCMP1335 Eukaryota Haptophyceae Pavlovales Pavlovaceae Pavlova lutheri Eukaryota Opisthokonta Fungi Blastocladiomycota Blastocladiomycetes Blastocladiales Blastocladiaceae Allomyces macrogynus ATCC 38327 Eukaryota stramenopiles Blastocystis hominis Eukaryota Opisthokonta Fungi Fungi incertae sedis Early diverging fungal lineages Kickxellomycotina Kickxellales Kickxellaceae Coemansia reversa NRRL 1564 Eukaryota Opisthokonta Fungi Dikarya Ascomycota saccharomyceta Pezizomycotina leotiomyceta dothideomyceta Dothideomycetes Dothideomycetidae Capnodiales Mycosphaerellaceae mitosporic Mycosphaerellaceae Cryptococcus neoformans var. neoformans B 3501A Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetes incertae sedis Cantharellales Botryobasidiaceae Botryobasidium botryosum Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetes incertae sedis Corticiales Corticiaceae Phanerochaete chrysosporium RP 78 Eukaryota Opisthokonta Metazoa Eumetazoa Bilateria Coelomata Protostomia Lophotrochozoa Annelida Polychaeta Palpata Canalipalpata Sabellida Serpulidae Serpula lacrymans lacrymans S7.9 Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetidae Agaricales Strophariaceae Hypholoma sublateritium Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetidae Agaricales Tricholomataceae Gymnopus luxurians Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetidae Agaricales Tricholomataceae Laccaria bicolor S238N H82 LACBI Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetidae Agaricales Schizophyllaceae Schizophyllum commune H4 8 Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetes incertae sedis Polyporales Coriolaceae Postia placenta Mad 698 R POSPL Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricomycetidae Agaricales Psathyrellaceae Coprinopsis cinerea strain okayama7130 Eukaryota Opisthokonta Fungi Dikarya Basidiomycota Ustilaginomycotina Exobasidiomycetes Malasseziales Malasseziaceae Malassezia globosa CBS Eukaryota Opisthokonta Fungi Dikarya Ascomycota saccharomyceta Pezizomycotina leotiomyceta sordariomyceta Sordariomycetes Hypocreomycetidae Hypocreales Cordycipitaceae mitosporic Cordycipitaceae Beauveria bassiana CH draft genome Eukaryota Opisthokonta Opisthokonta incertae sedis Eukaryota Jakobida Eukaryota Katablepharidophyta Roombia truncata Eukaryota Amoebozoa Mycetozoa Dictyosteliida Dictyostelium discoideum AX4 Eukaryota Opisthokonta Metazoa Eumetazoa Bilateria Coelomata Deuterostomia Chordata Tunicata Appendicularia Oikopleuridae Oikopleura dioica Eukaryota unclassified eukaryotes Collodictyonidae Collodictyon triciliatum Eukaryota Euglenozoa Euglenida Euglenales Euglenaceae Eukaryota Euglenozoa Kinetoplastida Trypanosomatidae Leishmania Leishmania Leishmania infantum JPCM5 MCANES98LLM 877 Eukaryota Euglenozoa Kinetoplastida Trypanosomatidae TREU927 Eukaryota Jakobida Histionidae Reclinomonas americana Eukaryota Jakobida Jakobidae Jakoba libera Eukaryota Alveolata Apicomplexa Aconoidasida Piroplasmida Babesiidae Babesia bovis T2Bo Eukaryota Heterolobosea Acrasida Guttulinaceae Guttulinopsis vulgaris Eukaryota Rhizaria Cercozoa Chlorarachniophyceae Bigelowiella natans CT868681.1 Paramecium tetraurelia chromosome undetermined scaffold 99 Eukaryota Alveolata Ciliophora Intramacronucleata Oligohymenophorea Peniculida Parameciidae Paramecium tetraurelia d4 2 Eukaryota Alveolata Ciliophora Intramacronucleata Oligohymenophorea Hymenostomatida Tetrahymenina Tetrahymenidae Tetrahymena pyriformis Eukaryota Alveolata Ciliophora Intramacronucleata Oligohymenophorea Hymenostomatida Tetrahymenina Tetrahymenidae Tetrahymena thermophila SB210 Macronucleus DS572673.1 Entamoeba histolytica HM−1IMSS scf 1104750517515 genomic scaffold Eukaryota Amoebozoa Archamoebae Entamoebidae Entamoeba histolytica HM 1IMSS Eukaryota Heterolobosea Psalteriomonadidae Sawyeria marylandensis Eukaryota Heterolobosea Schizopyrenida Vahlkampfiidae strain NEG M genomic NAEGR Eukaryota Fornicata Diplomonadida Hexamitidae Giardiinae Giardia lamblia ATCC 50803 strain WB C6 Eukaryota Parabasalia Trichomonadida Trichomonadidae G3 Eukaryota Cryptophyta Pyrenomonadales Geminigeraceae Guillardia theta nucleomorph

4350 3480 2610 1740 870 0 nifH nifD nifK

nxrA nirB nrfA

napA narG nasA

nitrogen fixation nirS nirK denitrification from nitrate denitrification from nitrite nitrification DNRA

Supplementary Figure 3. Histograms and density plots of all speciation, loss, duplication and horizontal transfer (HGT) events. All events are shown in blue, HGT events alone are shown in norB nosZ green. Events were inferred by reconcil- ing phylogenetic trees of nitrogen-cy- cling genes with a chronogram generat- ed using a UGAM clock model and conservative calibration points. Y-axis represents proportion of all events (blue) or HGT events only (green). Borders around graphs indicate the metabolic process that the gene is involved in. Histograms are ordered according to the earliest time point at which a speciation, loss, duplication, or HGT event occurred. anfD anfK

vnfD vnfK

Supplementary Figure 4. Histograms and density plots of all speciation, loss, duplication, and HGT events (blue) and just horizontal gene transfer events (green) for anf and vnf genes inferred from the species chronogram generated using the CIR clock model with conservative calibration points. anfD anfK

vnfD vnfK

Supplementary Figure 5. Histograms and density plots of all speciation, loss, duplication, and HGT events (blue) and just horizontal gene transfer events (green) for anf and vnf genes inferred from the species chronogram generated using the UGAM clock model with conservative calibration points.