a. Institut Pasteur, Departement de Microbiologie, … · Institut Pasteur, Departement de Microbiologie, Unite Biologie Moleculaire du Gene chez les Extremophiles, 28 rue du Docteur

The 2 Domains Tree of Life is linked to a new root for the Archaea

Kasie Raymanna, Céline Brochier-Armanetb, and Simonetta Gribaldoa1

a. Institut Pasteur, Departement de Microbiologie, Unite Biologie Moleculaire du Gene chez les

Extremophiles, 28 rue du Docteur Roux Paris, France 75015

b. Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie

Evolutive, 43 bd du 11 novembre 1918 Villeurbanne, France 69622

Supporting Information (SI Appendix)

Supplementary Methods

Data. In order to gather a set of widely distributed and sure orthologous markers,

we followed a very conservative and strict semi-automatic protocol.

Local databases were constructed using 132, 211, and 31 complete archaeal,

bacterial, and eukaryotic genomes, respectively, which were downloaded from the

National Center for Biotechnology Information (NCBI http://www.ncbi.nlm.nih.gov/).

An all-against-all BLASTP (1) search was performed on the local archaeal

database. Homologous sequences were clustered into protein families using SiLiX

(2) with a minimum threshold of 70% length overlap and 30% identity. Large

paralogous protein families were split using the MCL clustering algorithm as

implemented in BioLayout (3). The taxonomic distribution of each protein family

was determined and absences were verified by additional BLASTP and TBLASTN

searches. We extracted 230 protein families present in more than 95% of the 132

archaeal genomes. These were used to build HHM profiles and perform HMMER

searches (4) on the local database of 31 eukaryotes and 211 bacteria. Protein

families present in more than 90% of the eukaryotic and/or bacterial genomes were

retained. Each protein family was aligned with MUSCLE v3.8.31 (5), and trimmed

Raymann et al. 2015

using the software BMGE (6) with a BLOSUM30 matrix. Phylogenies of individual

proteins were inferred using PhyML v3.1 (7) and RAxML v7.2.8 (8) with substitution

models chosen using the ProteinModelSelection script available from the RAxML

website (http://sco.h-its.org/exelixis/software.html), with a gamma distribution with

four discrete classes of sites (Γ4) and an estimated alpha parameter. The branch

robustness of the ML trees was estimated with the non-parametric bootstrap

procedure implemented in PhyML (100 replicates of the original dataset), and the

rapid bootstrap method implemented in RAxML (500 replicates of the original

dataset). All individual trees were visually inspected, and protein families where

Archaea and Bacteria were not monophyletic, or showed intermixing of well

defined orders or phyla (hinting at a large number of horizontal gene transfers or

insufficiently clear phylogenetic signal) were discarded. This step also allowed us

to identify and remove eukaryotic proteins of bacterial/mitochondrial origin.

In order to decrease the computational time of the analysis, the taxonomic

sampling was then reduced to 49 archaea, 67 bacteria, and 18 eukaryotes,

keeping at least three representatives for each archaeal order, bacterial phylum,

and eukaryote super group when possible. To further identify potential intra-

domain gene transfers, we separately realigned and trimmed the bacterial and

archaeal sequences and used Prunier (9) to identify and remove specific

sequences detected as a source of inconsistency with their respective reference

trees (bootstrap threshold 70%, depth 2: i.e. inducing an inconsistency involving at

least two nodes supported by bootstrap value >70%). The reference trees were

calculated based on a concatenation of 29 universal markers used by Williams et

Raymann et al. 2015

al. (10).

Following this step, the datasets maintaining at least 90% taxonomic coverage

were kept, leading to a final list of 81 widely distributed, well-conserved and

verified orthologous protein markers, 9 of which are uniquely shared between

Archaea and Bacteria and 35 uniquely shared between Archaea and eukaryotes

(Fig. S1). The markers were concatenated into three large supermatrices (A/B

supermatrix, 46 proteins and 10,986 positions), Archaea/eukaryotes (A/E

supermatrix, 72 proteins and 17,892 positions), and universal (A/B/E supermatrix,

37 proteins and 9,090 positions). Of these, 9 are uniquely shared between

Archaea and Bacteria and 35 are uniquely shared between Archaea and

eukaryotes (Fig. S1). Missing characters are not biased across taxa and datasets

(Fig. S1).

Supermatrix phylogenetic analysis. Phylogenetic trees of the supermatrices

were obtained by Maximum Likelihood and Bayesian analysis. PhyloBayes 3.3b

(11) was used to perform Bayesian analysis using the CAT+GTR model and a

gamma distribution with four categories of evolutionary rates was used to model

the heterogeneity of site evolutionary rates. The supermatrices were also recoded

using the Dayhoff6 recoding scheme as implemented in PhyloBayes 3.3b and

analyzed with the same model parameters. For each data set, two independent

chains were run until convergence. Convergence was assessed by evaluating the

discrepancy of bipartition frequencies and between independent runs, with a bpdiff

cutoff <0.3. The first 500 trees were discarded as burn in and the posterior

consensus was computed by selecting one tree out of every 5. Maximum likelihood

Raymann et al. 2015

analyses were performed using PhyML v 3.1 (7), with the LG+Γ4 model, chosen

using the ProteinModelSelection script available from the RAxML website

(http://sco.h-its.org/exelixis/software.html). The branch robustness of the ML trees

was estimated with the non-parametric bootstrap procedure implemented in

PhyML (100 replicates of the original dataset).

Hypothesis testing. Alternative candidate topologies were created using

TreeGraph2 (12). The per-site log likelihood values were calculated for each

topology under the LG+Γ4 model using RAxML (8). The alternative topologies

were then statistically evaluated using the approximately unbiased (AU) test (13)

as implemented in CONSEL (14).

Removal of noise from the data. A site-by-site removal of noisy positions was

carried out on the A/E and A/B datasets using the Slow-Fast method (15). To do

so, the sequences from each dataset were subdivided into established

monophyletic groups as follows: 16 bacterial phyla (Actinobacteria,

Bacteroidetes/Chlorobi, Chloroflexi, Cyanobacteria, Deinococcus-Thermus,

Firmicutes, PVC_Chlamydiae, PVC_Planctomycetes, PVC_Verrucomicrobia,

Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria,

Epsilonproteobacteria, Gammaproteobacteria, Spirochaetes, Thermotogae), 12

archaeal orders/phyla (Desulfurococcales/Sulfolobales, Thermoproteales,

Archaeoglobales, Halobacteriales, Methanobacteriales, Methanococcales,

Methanocellales, Methanomicrobiales, Methanosarcinales,

Thermoplasmatales/Marine Group II/DHVE2/Methanomassiliicoccales,

Thermococcales, Korarchaeota, Thaumarchaeota/Aigarchaeota), and 4 eukaryotic

Raymann et al. 2015

groups (Alveolata/Stramenopiles, Viridiplantae, Euglenozoa/Heterolobosea,

Opisthokonta/Amoebozoa). All of the considered groups contained 3 or more taxa

except Korarchaeota, which was therefore considered alone.

The evolutionary rate at sites within each group was estimated with the program

SlowFaster (16) and this led to the construction of different supermatrices each

corresponding to progressive removal of fast-evolving sites. These supermatrices

were then subjected to Maximum Likelihood (LG+Γ4) and Bayesian analysis

(CAT+GTR+Γ4). For each supermatrix, the support values (bootstrap value or

posterior probability) at defined nodes of interest were recovered from the ML and

BI trees and their corresponding bipartitions, and plotted using R (R Development

Core Team 2014).

Supplementary references

1. Altschul SF et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of

protein database search programs. Nucleic Acids Res 25:3389–3402.

2. Miele V, Penel S, Duret L (2011) Ultra-fast sequence clustering from similarity

networks with SiLiX. BMC Bioinformatics 12:116.

3. Theocharidis A, van Dongen S, Enright AJ, Freeman CT (2009) Network

visualization and analysis of gene expression data using BioLayout Express(3D).

Nat Protoc 4:1535–1550.

4. Johnson LS et al. (2010) Hidden Markov model speed heuristic and iterative

HMM search procedure. BMC bioinformatics 11:431.

5. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced

time and space complexity. BMC bioinformatics 5:113.

6. Criscuolo A, Gribaldo S, (2010) BMGE (Block Mapping and Gathering with

Entropy): a new software for selection of phylogenetic informative regions from

multiple sequence alignments. BMC Evol Biol 10:210.

7. Guindon S et al. (2010) New algorithms and methods to estimate maximum-

Raymann et al. 2015

likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol

59:307–321.

8. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic

analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690.

9. Abby SS, Tannier E, Gouy MM, Daubin V (2009) Detecting lateral gene

transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics

11:324–324.

10. Williams TA, Foster PG, Nye TM, Cox CJ, Embley TM (2012) A congruent

phylogenomic signal places eukaryotes within the Archaea. Philos Trans R Soc

Lond B Biol Sci 279:4870–4879

11. Lartillot N et al. (2009) PhyloBayes 3: a Bayesian software package for

phylogenetic reconstruction and molecular dating. Bioinformatics 25:2286–2288.

12. Stöver BC, Müller KF (2010) TreeGraph 2: combining and visualizing evidence

from different phylogenetic analyses. BMC Bioinformatics 11:7.

13. Shimodaira H, Shimodaira H (2002) An approximately unbiased test of

phylogenetic tree selection. Syst Biol 51:492–508.

14. Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of

phylogenetic tree selection. Bioinformatics 17:1246–1247.

15. Brinkmann HH, Philippe HH, (1999) Archaea sister group of Bacteria?

Indications from tree reconstruction artifacts in ancient phylogenies. Mol Biol Evol

16:817–825.

16. Kostka M, Uzlikova M, Cepicka I, Flegr J (2008) SlowFaster, a user-friendly

program for slow-fast analysis and its application on phylogeny of Blastocystis.

BMC Bioinformatics 9:341

Raymann et al. 2015

Fig. S1. List of markers used in this study and details on character distribution for each of the three supermatrices. Highlighted in gray are the orthologous markers uniquely shared between Archaea and Bacteria or Archaea and eukaryotes, and in white are the orthologous universal markers. Overlap with the 29 universal markers dataset from Williams et al. (7) are shown in blue font. The few differences with our dataset are likely due to the use of a larger and different taxonomic sampling and the exclusion of highly reduced genomes. For each marker, the corresponding COG name and general description are also indicated.

COG0528 Uridylate kinase Nucleotide transport and metabolismCOG0358/3 DNA primase (bacterial type) General function prediction only eplication; recombination and repair COG0343/1 Queuine/archaeosine tRNA-ribosyltransferase Translation; ribosomal structure and biogenesisCOG0462 Phosphoribosylpyrophosphate synthetase Nucleotide transport and metabolism Amino acid transport and metabolism COG0195 Transcription elongation factor TranscriptionCOG0012 Predicted GTPase, probable translation factor Translation; ribosomal structure and biogenesisCOG0250 Transcription antiterminator TranscriptionCOG0126 3-phosphoglycerate kinase Energy production and conversionarbohydrate transport and metabolism COG0149 Triosephosphate isomerase Energy production and conversionarbohydrate transport and metabolism COG0017 Aspartyl/asparaginyl-tRNA synthetases Translation; ribosomal structure and biogenesisCOG5256 Translation elongation factor EF-1alpha (GTPase) Translation; ribosomal structure and biogenesisCOG0541 Signal recognition particle GTPase Intracellular trafficking; secretion; and vesicular transportCOG0459 Chaperonin GroEL (HSP60 family) Posttranslational modification; protein turnover; chaperonesCOG0052 Ribosomal protein S2 Translation; ribosomal structure and biogenesisCOG0103 Ribosomal protein S9 Translation; ribosomal structure and biogenesisCOG0102 Ribosomal protein L13 Translation; ribosomal structure and biogenesisCOG0049 Ribosomal protein S7 Translation; ribosomal structure and biogenesisCOG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit TranscriptionCOG0085 DNA-directed RNA polymerase, beta subunit/140 kD subunit TranscriptionCOG0090 Ribosomal protein L2 Translation; ribosomal structure and biogenesisCOG0092 Ribosomal protein S3 Translation; ribosomal structure and biogenesisCOG0093 Ribosomal protein L14 Translation; ribosomal structure and biogenesisCOG0094 Ribosomal protein L5 Translation; ribosomal structure and biogenesisCOG0098 Ribosomal protein S5 Translation; ribosomal structure and biogenesisCOG0201 Preprotein translocase subunit SecY Intracellular trafficking; secretion; and vesicular transportCOG0080 Ribosomal protein L11 Translation; ribosomal structure and biogenesisCOG0081 Ribosomal protein L1 Translation; ribosomal structure and biogenesisCOG0480 Translation elongation factors (GTPases) Translation; ribosomal structure and biogenesisCOG0533 Metal-dependent proteases with possible chaperone activity Posttranslational modification; protein turnover; chaperonesCOG0532 Translation initiation factor 2 (IF-2; GTPase) Translation; ribosomal structure and biogenesisCOG1156 Archaeal/vacuolar-type H+-ATPase subunit B Energy production and conversionCOG0470 ATPase involved in DNA replication General function prediction only eplication; recombination and repair COG0048 Ribosomal protein S12 Translation; ribosomal structure and biogenesisCOG0100 Ribosomal protein S11 Translation; ribosomal structure and biogenesisCOG0552 Signal recognition particle GTPase Intracellular trafficking; secretion; and vesicular transport COG0099 Ribosomal protein S13 Translation; ribosomal structure and biogenesisCOG0087 Ribosomal protein L3 Translation; ribosomal structure and biogenesisCOG0088 Ribosomal protein L4 Translation; ribosomal structure and biogenesisCOG0096 Ribosomal protein S8 Translation; ribosomal structure and biogenesisCOG5257 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) Translation; ribosomal structure and biogenesisCOG0030 Dimethyladenosine transferase (rRNA methylation) Translation; ribosomal structure and biogenesisCOG0200 Ribosomal protein L15 Translation; ribosomal structure and biogenesisCOG0130/1 Pseudouridine synthase Translation; ribosomal structure and biogenesisCOG1222 ATP-dependent 26S proteasome regulatory subunit Posttranslational modification; protein turnover; chaperonesCOG0020 Undecaprenyl pyrophosphate synthase General function prediction only eplication; recombination and repair ipid transport and metabolismCOG0062/1 Uncharacterized conserved protein Nucleotide transport and metabolismunction unknown

Archaea/Bacteria

Raymann et al. 2015

COG1718 Serine/threonine protein kinase involved in cell cycle control Signal transduction mechanisms, Cell cycle control; cell division; chromosome partitioning COG1632 Ribosomal protein L15E Translation; ribosomal structure and biogenesisCOG1889 Fibrillarin-like rRNA methylase Translation; ribosomal structure and biogenesisCOG1269 Archaeal/vacuolar-type H+-ATPase subunit I Energy production and conversionCOG0051 Ribosomal protein S10 Translation; ribosomal structure and biogenesisCOG1890 Ribosomal protein S3AE Translation; ribosomal structure and biogenesisCOG1500 Predicted exosome subunit Translation; ribosomal structure and biogenesisCOG1471 Ribosomal protein S4E Translation; ribosomal structure and biogenesisCOG2147 Ribosomal protein L19E Translation; ribosomal structure and biogenesisCOG0197 Ribosomal protein L16/L10E Translation; ribosomal structure and biogenesisCOG1093 Translation initiation factor 2, alpha subunit (eIF-2alpha) Translation; ribosomal structure and biogenesisCOG1976 Translation initiation factor 6 (eIF-6) Translation; ribosomal structure and biogenesisCOG1867 N2,N2-dimethylguanosine tRNA methyltransferase Translation; ribosomal structure and biogenesisCOG2101 TATA-box binding protein (TBP), component of TFIID and TFIIIB TranscriptionCOG0638 20S proteasome, beta subunit Posttranslational modification; protein turnover; chaperonesCOG1155 Archaeal/vacuolar-type H+-ATPase subunit A Energy production and conversionCOG0470/1 ATPase involved in DNA replication Replication; recombination and repairCOG0423 Glycyl-tRNA synthetase (class II) Translation; ribosomal structure and biogenesisCOG0186 Ribosomal protein S17 Translation; ribosomal structure and biogenesisCOG0097 Ribosomal protein L6P/L9E Translation; ribosomal structure and biogenesisCOG0091 Ribosomal protein L22 Translation; ribosomal structure and biogenesisCOG1358 Ribosomal protein HS6-type (S12/L30/L7a) Translation; ribosomal structure and biogenesisCOG0456 Acetyltransferases General function prediction only COG0522/3 Ribosomal protein S4 and related proteins Translation; ribosomal structure and biogenesisCOG1095 DNA-directed RNA polymerase, subunit E' TranscriptionCOG1717 Ribosomal protein L32E Translation; ribosomal structure and biogenesisCOG1394 Archaeal/vacuolar-type H+-ATPase subunit D Energy production and conversionCOG1631 Ribosomal protein L44E Translation; ribosomal structure and biogenesisCOG1498 Protein implicated in ribosomal biogenesis, Nop56p homolog Translation; ribosomal structure and biogenesisCOG0585 Uncharacterized conserved protein Nucleotide transport and metabolismunction unknown COG0592 DNA polymerase sliding clamp subunit (PCNA homolog) Replication; recombination and repairCOG2139 Ribosomal protein L21E Translation; ribosomal structure and biogenesisCOG1537 Predicted RNA-binding proteins General function prediction only COG1241 Predicted ATPase involved in replication control, Cdc46/Mcm family Replication; recombination and repairCOG0258 5'-3' exonuclease (including N-terminal domain of PolI) General function prediction only eplication; recombination and repair COG0017 Aspartyl/asparaginyl-tRNA synthetases Translation; ribosomal structure and biogenesisCOG5256 Translation elongation factor EF-1alpha (GTPase) Translation; ribosomal structure and biogenesisCOG0541 Signal recognition particle GTPase Intracellular trafficking; secretion; and vesicular transportCOG0459 Chaperonin GroEL (HSP60 family) Posttranslational modification; protein turnover; chaperonesCOG0052 Ribosomal protein S2 Translation; ribosomal structure and biogenesisCOG0103 Ribosomal protein S9 Translation; ribosomal structure and biogenesisCOG0102 Ribosomal protein L13 Translation; ribosomal structure and biogenesisCOG0049 Ribosomal protein S7 Translation; ribosomal structure and biogenesisCOG0086 DNA-directed RNA polymerase, beta' subunit/160 kD subunit TranscriptionCOG0085 DNA-directed RNA polymerase, beta subunit/140 kD subunit TranscriptionCOG0090 Ribosomal protein L2 Translation; ribosomal structure and biogenesisCOG0092 Ribosomal protein S3 Translation; ribosomal structure and biogenesisCOG0093 Ribosomal protein L14 Translation; ribosomal structure and biogenesisCOG0094 Ribosomal protein L5 Translation; ribosomal structure and biogenesisCOG0098 Ribosomal protein S5 Translation; ribosomal structure and biogenesisCOG0201 Preprotein translocase subunit SecY Intracellular trafficking; secretion; and vesicular transportCOG0080 Ribosomal protein L11 Translation; ribosomal structure and biogenesisCOG0081 Ribosomal protein L1 Translation; ribosomal structure and biogenesisCOG0480 Translation elongation factors (GTPases) Translation; ribosomal structure and biogenesisCOG0533 Metal-dependent proteases with possible chaperone activity Posttranslational modification; protein turnover; chaperonesCOG0532 Translation initiation factor 2 (IF-2; GTPase) Translation; ribosomal structure and biogenesisCOG1156 Archaeal/vacuolar-type H+-ATPase subunit B Energy production and conversionCOG0470 ATPase involved in DNA replication General function prediction only eplication; recombination and repair COG0048 Ribosomal protein S12 Translation; ribosomal structure and biogenesisCOG0100 Ribosomal protein S11 Translation; ribosomal structure and biogenesisCOG0552 Signal recognition particle GTPase Intracellular trafficking; secretion; and vesicular transport COG0099 Ribosomal protein S13 Translation; ribosomal structure and biogenesisCOG0087 Ribosomal protein L3 Translation; ribosomal structure and biogenesisCOG0088 Ribosomal protein L4 Translation; ribosomal structure and biogenesisCOG0096 Ribosomal protein S8 Translation; ribosomal structure and biogenesisCOG5257 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) Translation; ribosomal structure and biogenesisCOG0030 Dimethyladenosine transferase (rRNA methylation) Translation; ribosomal structure and biogenesisCOG0200 Ribosomal protein L15 Translation; ribosomal structure and biogenesisCOG0130/1 Pseudouridine synthase Translation; ribosomal structure and biogenesisCOG1222 ATP-dependent 26S proteasome regulatory subunit Posttranslational modification; protein turnover; chaperonesCOG0020 Undecaprenyl pyrophosphate synthase General function prediction only eplication; recombination and repair ipid transport and metabolismCOG0062/1 Uncharacterized conserved protein Nucleotide transport and metabolismunction unknown

Archaea/Eukarya

Fig. S1

Raymann et al. 2015

AE Dataset % positions present in each taxa!!

!" #!" $!" %!" &!" '!" (!" )!" *!" +!" #!!"

&%+&*#,-.//012"

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%%%#&(,O5?2F5645038"

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%'##(!,:56@/6AJ51"

'$%*&(,:H16@2F38"

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&%#*+',:.61@2?/;;28"

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$+('&%,I9813F/0505"

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%+)+&*,M45S32;20L10828"

#!&#+%!,:?/065F22"

**!)$&,:2L0138"

%&)'#',T45P/6"

&+!*++,ED54?B5=D10828"

(+&&$+,<H345622"

(+%((#,-@101U?38"

#*)&$!,:=B16453=/=6/9B"

%##&'*,MM5;F256?B5134"

'+##,I=B164/9B2;5"

&'%'+#,VB/892=5;28"

%++'&+,:81F3;5"

%!+*!!,7@/;?5022"

$)$*&&,<5.A882"

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#&'&*#,<95=108"

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&#!%'*,:;5.615034"

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$$&%$',-H3;L2F38"

')$'&(,-96/H30F38"

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Fig. S1

Raymann et al. 2015

AB Dataset % positions present in each taxa!!

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&%+&*#,-.//012"##&$%+&,34256710828"

$)&*'&,6497201"%(!!+',:.9;2<<2=/7428"

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'&'(+',A9B/C/06C72;264")'($)$,3.7982<210828"

'#)&#),DE97F64"#!*!)#$,@<6420G10828"

&'(&&$,@.//012"$'#$$#,HF2/<9;168"

$+$&#',AI102C72J;908"&$!$&),@842CK22"

&*'+#),3K1E972068"+*'!'%,L4/6C0/F8529"

%!+*!#,A7/8164"$&%#(&,M1CK10/N1018"

('%+%,D8E"(+()&+,-.96490022"$(+!*&,O1</0N9C68"

'$#!&',P/<19729"$)$'(+,Q497284/7C62"

&$!**+,RN97F2191"$$*&#!,S167/E919"%%+()!,:94.2=9729"

+$('(+,-CK174/EK2<9"%+!$%(,:9=B1<22"

&)+&%%,D9;2I2EK2<9"%*$(%*,Q9;20/0G;K28"

'&(&#&,MI1817?"')%!(%,@20=17068"$&%$)&,A4972?49"

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$((+&!,P79I2/C/<17908"$!%#$&,A17GCK79164"%&+)&#,-46;202EK2<9"(&+(%*,A79I2/F2;C72T"%!&%)#,@E9<6I2;/<9"

*(+$#!,@KGI7/CK1749<28"#)*%!(,3917/EK2<64"%#($)&,Q96790?9;68"

%%''&%,O=6497/T2I908"**()%*,DS2C7/8/97;K916"

$(+)+*,DK6C;K208/022"')''&!,UE9<<2I9"&&(&($,-42764"'$%*&+,A<2C/79<28"

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%*#)(&,V0/I/864"'&)''+,S49N9I22"

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Fig. S1

Raymann et al. 2015

ABE Dataset % positions present in each taxa!

!" #!" $!" %!" &!" '!" (!" )!" *!" +!" #!!"

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Fig. S1

Raymann et al. 2015

0.3

Dictyostelium discoideum AX4

Batrachochytrium dendrobatidis JAM81

Methanococcoides burtonii DSM 6242

Thermococcus barophilus MP

Metallosphaera sedula DSM 5348

Methanocella paludicola SANAE

Methanomassiliicoccus luminyensis

Archaeoglobus fulgidus DSM 4304

Methanoregula boonei 6A8

Natrialba magadii ATCC 43099

Pyrolobus fumarii 1A

Nitrosopumilus maritimus SCM1

Homo sapiens

Aureococcus anophagefferens

Methanosarcina mazei Go1

Trypanosoma brucei brucei strain 927_4 GUTat10.1

Candidatus Methanomethylophilus alvus Mx1201

Pyrococcus yayanosii CH1Pyrococcus abyssi GE5

Candidatus Korarchaeum cryptofilum OPF8

Methanocaldococcus infernus ME

Vulcanisaeta moutnovskia 768-28

Chlamydomonas reinhardtii

Methanosaeta harundinacea 6Ac

Methanocella arvoryzae MRE50

Haloarcula marismortui ATCC 43049

Sulfolobus tokodaii str. 7

Methanocella conradii HZ254

Phaeodactylum tricornutum CCAP 1055_1

Tetrahymena thermophila

Candidatus Nitrosoarchaeum limnia SFB1

Naegleria gruberi strain NEG-M

Pyrobaculum aerophilum str. IM2Thermofilum pendens Hrk 5

Micromonas pusilla CCMP1545

Ignicoccus hospitalis KIN4_I

Methanobacterium paludis

Saccharomyces cerevisiae S288c

Caldivirga maquilingensis IC-167

Thermoproteus tenax Kra 1

Thermococcus litoralis DSM 5473

Selaginella moellendorffii

Candidatus Caldiarchaeum subterraneum

uncultured marine group II euryarchaeote

Arabidopsis thaliana

Methanothermus fervidus DSM 2088

Aciduliprofundum boonei T469

Ferroglobus placidus DSM 10642Archaeoglobus veneficus SNP6

Methanobrevibacter smithii ATCC 35061

Methanotorris igneus Kol 5

Physcomitrella patens subsp. patens

Archaeoglobus profundus DSM 5631

Methanocaldococcus jannaschii DSM 2661

Haloferax volcanii DS2

Desulfurococcus kamchatkensis 1221n

Methanococcus vannielii SB

Methanoculleus marisnigri JR1

Paramecium tetraurelia strain d4-2

Methanocorpusculum labreanum Z

Candidatus Nitrososphaera gargensis Ga9.2Cenarchaeum symbiosum A

Monosiga brevicollis MX1

Leishmania major strain Friedlin

Thalassiosira pseudonana CCMP1335

Methanothermobacter thermautotrophicus str. Delta H

Ferroplasma acidarmanus fer1

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Cenarchaeum symbiosum AParamecium tetraurelia strain d4-2




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Pyrococcus yayanosii CH1








Homo sapiens











Pyrococcus abyssi GE5










Methanomassiliicoccus luminyensisFerroglobus placidus DSM 10642




Archaeoglobus veneficus SNP6




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Fig. S2. A) Unrooted Maximum likelihood phylogeny of the A/E supermatrix with the LG+Γ4 model. The tree was calculated by PhyML. The scale bar represents the average number of substitutions per site. Values at nodes represent support calculated by nonparametric bootstrap from 100 resamples of the original dataset. B) Unrooted Bayesian phylogeny of the A/E supermatrix with the LG+Γ4 model. The tree was calculated by Phylobayes. The scale bar represents the average number of substitutions per site. Values at nodes represent posterior probabilities.

Raymann et al. 2015

0.3












Thermococcus barophilus MPThermococcus litoralis DSM 5473


Methanobacterium sp. SWAN-1


Cenarchaeum symbiosum A





















Homo sapiens














Sulfolobus tokodaii str. 7Metallosphaera sedula DSM 5348









Ferroglobus placidus DSM 10642






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Fig. S3. Unrooted Bayesian phylogeny of the A/E supermatrix with a Dayhoff6 recoding scheme. The tree was calculated by Phylobayes (CAT+GTR+Γ4). The scale bar represents the average number of substitutions per site. Values at nodes represent posterior probabilities. For clarity, the branch leading to eukaryotes has been shortened, and the real length is indicated.

Raymann et al. 2015

Fig.%S4.%Removal(of(noisy(data(from(the(A/E(supermatrix.%The(X(axis(indicates(the(name(of(the(supermatrix(and(its(number(of(posi=ons,(where(removal(of(fastest@evolving(sites(proceeds(from(leB(to(right((from(the(original(supermatrix(to(progressively(less(noisy(and(smaller(supermatrices).(Trees(corresponding(to(each(supermatrix(were(inferred(by(Phylobayes(with(the(CAT+GTR+Γ4(model.(The(Y(axis(represents(support(of(each(matrix(for(an(external(placement(of(eukaryotes(with(respect(to(the(TACK(or(Euryarchaeota(as(indicated(by(the(support(at(the(nodes(corresponding(to(the(monophylies(of(these(two(archaeal(groups.(Note(that(the(drop(in(support(for(the(monophyly(of(the(TACK(observed(in(supermatrices(S5(to(S0(is(due(to(a(general(lack(of(phylogene=c(signal(that(leaves(the(rela=onships(among(TACK(and(eukaryotes(unresolved(because(of(very(poor(support(at(nodes((trees(corresponding(to(all(the(supermatrices(of(the(graph(are(provided(as(Dataset(SI).(((

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Raymann et al. 2015

0.4


























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Haloferax volcanii DS2Natrialba magadii ATCC 43099




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A B

Fig. S5. A) Unrooted Bayesian phylogeny of a supermatrix of 35 markers uniquely shared between Archaea and eukaryotes (6629 amino acid positions, highlighted in gray in Fig. S1). B) Unrooted Bayesian phylogeny of Archaea and eukaryotes with a supermatrix of 37 universal markers (10319 amino acid positions, highlighted in white in Fig. S1). The trees were calculated by Phylobayes (CAT+GTR+Γ4). The scale bar represents the average number of substitutions per site. Values at nodes represent posterior probabilities.

Raymann et al. 2015

Fig. S6. A) Unrooted Bayesian phylogeny of the A/B supermatrix with the LG+Γ4 model. The tree was calculated by Phylobayes. The scale bar represents the average number of substitutions per site. Values at nodes represent posterior probabilities.

0.2

Allochromatium vinosum DSM 180


Anaerolinea thermophila UNI-1

Actinosynnema mirum DSM 43827



Opitutus terrae PB90-1

Treponema azotonutricium ZAS-9

Isosphaera pallida ATCC 43644

Petrotoga mobilis SJ95

Bacteroides fragilis 638R


Legionella longbeachae NSW150





Rhodopirellula baltica SH 1

Syntrophobacter fumaroxidans MPOB



Natranaerobius thermophilus JW_NM-WN-LFLactococcus garvieae ATCC 49156

Thermomicrobium roseum DSM 5159




Kineococcus radiotolerans SRS30216



Nitrosomonas europaea ATCC 19718Chromobacterium violaceum ATCC 12472



Thiobacillus denitrificans ATCC 25259

Kosmotoga olearia TBF 19.5.1


Dehalococcoides ethenogenes 195

Pedobacter heparinus DSM 2366

Listeria innocua Clip11262

Bartonella bacilliformis KC583

Novosphingobium aromaticivorans DSM 12444

Gloeobacter violaceus PCC 7421

Cytophaga hutchinsonii ATCC 33406

Caldilinea aerophila DSM 14535 = NBRC 104270






Truepera radiovictrix DSM 17093

Anabaena variabilis ATCC 29413

Akkermansia muciniphila ATCC BAA-835

Borrelia afzelii PKo



Coraliomargarita akajimensis DSM 45221

Simkania negevensis Z

Phycisphaera mikurensis NBRC 102666

Chlamydia muridarum Nigg




Helicobacter acinonychis str. Sheeba

Thermotoga maritima MSB8

Leptospira biflexa serovar Patoc strain Patoc 1 Ames


Methylacidiphilum infernorum V4


Burkholderia ambifaria AMMD

Brachyspira hyodysenteriae WA1

Desulfobulbus propionicus DSM 2032

Methanothermus fervidus DSM 2088Methanococcus vannielii SB


Streptosporangium roseum DSM 43021




Herpetosiphon aurantiacus DSM 785

Candidatus Protochlamydia amoebophila UWE25

Alteromonas macleodii str. Black Sea 11


Stigmatella aurantiaca DW4_3-1

Acetobacter pasteurianus IFO 3283-01-42C

Synechococcus elongatus PCC 6301

Nocardia cyriacigeorgica GUH-2


Marinithermus hydrothermalis DSM 14884

Acinetobacter baumannii 1656-2

Catenulispora acidiphila DSM 44928





Nautilia profundicola AmH

Pelobacter carbinolicus DSM 2380


Acidaminococcus fermentans DSM 20731


Trichodesmium erythraeum IMS101


Deinococcus deserti VCD115

Dinoroseobacter shibae DFL 12

Planctomyces brasiliensis DSM 5305

Rhodothermus marinus DSM 4252Chlorobaculum parvum NCIB 8327

Fervidobacterium nodosum Rt17-B1

Waddlia chondrophila WSU 86-1044



Arcobacter butzleri ED-1

Cyanothece sp. PCC 7424



Heliobacterium modesticaldum Ice1

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Dehalococcoides mccartyi 195

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Kineococcus radiotolerans SRS30216 = ATCC BAA-149












Nitrosomonas europaea ATCC 19718
















Lactococcus garvieae ATCC 49156







Chromobacterium violaceum ATCC 12472




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Raymann et al. 2015

Fig. S6 B) Unrooted Maximum likelihood phylogeny of the A/B supermatrix with the LG+Γ4 model. The tree was calculated by PhyML. The scale bar represents the average number of substitutions per site. Values at nodes represent support calculated by nonparametric bootstrap from 100 resamples of the original dataset. Both trees support the traditional root of the Archaea (root 2 in Fig. 3). !

0.2






























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Methanothermus fervidus DSM 2088Methanococcus vannielii SB
































Rhodothermus marinus DSM 4252Chlorobaculum parvum NCIB 8327










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Raymann et al. 2015

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S14

S12

S11

S10 S9 S7 S6 S5 S4 S3 S2 S0

SF Supermatrix (# of positions)

(287

)

(885

)

(151

8)

(186

2)

(217

5)

(245

6)

(300

4)

(325

2)

(349

7)

(377

6)

(430

7)

(458

6)

(486

8)

(539

8)

(571

3)

(621

6)

(696

5)

(742

0)

(765

9)

(847

0)

(102

06)

(116

1)

(109

86)

Orig

Phylobayes CAT+GTR+Γ4 PhyML LG+Γ4

AB b

ranc

h le

ngth

S43 S3

1

S27

S26

S24

S20

S19

S18

S16

S15

S14

S12

S11

S10 S9 S7 S6 S5 S4 S3 S2 S0

SF Supermatrix (# of positions)

(287

)

(885

)

(151

8)

(186

2)

(217

5)

(245

6)

(300

4)

(325

2)

(349

7)

(377

6)

(430

7)

(458

6)

(486

8)

(539

8)

(571

3)

(621

6)

(696

5)

(742

0)

(765

9)

(847

0)

(102

06)

(116

1)

(109

86)

Orig

●

●

●

●● ●

●

●●

●●

●

●

●●

●

●

●

●

●

●

●

●

01

23

45●

●

●

●●

●

●

●

●

●●

●

●●

●●

●●

●● ●

●

●

0.0

0.5

1.0

1.5

Fig. S7. Evolution of the length of the branch leading to the bacterial outgroup upon progressive removal of fastest evolving sites during the Slow-Fast analysis described in Figure 4 with the site-homogeneous LG+Γ4 model (left) and with the site-heterogenous CAT+GTR+Γ4 model (right).

Raymann et al. 2015

0.8

































Simkania negevensis ZMethylacidiphilum infernorum V4






























Acidaminococcus fermentans DSM 20731Natranaerobius thermophilus JW_NM-WN-LF






























Homo sapiens












Actinosynnema mirum DSM 43827Nocardia cyriacigeorgica GUH-2


Stigmatella aurantiaca DW4_3-1Syntrophobacter fumaroxidans MPOB






















0.97

1

1

0.99

1

0.99

0.99

11

0.51

0.99

1

0.99

1

0.99

1

1

0.99

1

1

1

1

0.99

0.98

1

1

0.99

1

0.99

1

1

0.99

1

1

0.93

0.99

1

0.98

0.97

1

1

1

1

1

1

1

1

1

1

1

1

0.96

0.98

1

1

1

1

0.99

0.99

1

0.76

0.99

0.98

1

1

1

1

1

0.99

0.99

1

0.95

0.99

1

1

1

1

1

1

0.95

1

1

1

1

1

0.98

1

1

0.98

1

1

1

1

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1

1

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1

1

1

0.99

0.51

0.99

1

1

1

1

0.990.99

1

0.99

1

1

1

0.99

0.98

1

1

10.99

1

1

1

1

1

0.990.99

0.99

1


Fig. S8. Unrooted Bayesian phylogeny of the A/B/E supermatrix after removal of Korarchaeota with the CAT+GTR+Γ4 model. The tree was calculated by Phylobayes. The scale bar represents the average number of substitutions per site. Values at nodes represent posterior probabilities.

Raymann et al. 2015

0.5


Homo sapiens

































































11

1

1

1

1

1

1

1

1

1

1

1

1

0.93

1

1

1

1

1

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1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

11

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

11

1

10.98.


1

AE CAT+GTR original matrix 17892 positions

Supplementary Datasets

Individual trees corresponding to removal of noisy data from the A/E, A/B, and A/B/E supermatrices.

AE CAT+GTR original matrix 17892 positions

Raymann et al. 2015

!"#

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AE CAT+GTR S30 17506 positions


Raymann et al. 2015

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Raymann et al. 2015

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Raymann et al. 2015

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Raymann et al. 2015

0.4


















Pyrobaculum aerophilum str. IM2Thermoproteus tenax Kra 1

































Methanocella conradii HZ254Methanosaeta harundinacea 6Ac
































































100

9 5

100

100

100

100

8 6

100

7 2

100

100

100

6 1

7 8

9 7

4 4

9 7

9 9

100

100

100

100

100

9 3

9 8

100

9 1

100

5 6

8 2

100

2 5

1 4

100

8 6

100

100

100

8 7

1 2

100

100

100

100

100

100

100

100

100

100

6

9 6

100

5 9100

8 1

100

100

100100

100

100

9 8

9 8

100

8 5

8 6

100

9 7

100

100

100

9 7

100

100

100

9 9

100

100

100

100

100

100

100

100

100

100

100

1007 5

100

100

9 3

100

100

9 3

7 8

9 9

100

3 9

5 6

100

100

100

100

100

100

8 5

100

100

100

100

100

100

AB ML LG original matrix 10986 positions

Raymann et al. 2015

0.3

Thermomicrobium roseum DSM 5159@

Caldilinea aerophila DSM 14535 = NBRC 104270@

Methanocella conradii HZ254@

Nitrosomonas europaea ATCC 19718@

Pyrococcus abyssi GE5@

Methanocaldococcus infernus ME@

Chlorobaculum parvum NCIB 8327@

Archaeoglobus profundus DSM 5631@

Pelobacter carbinolicus DSM 2380@

Natrialba magadii ATCC 43099@

Candidatus Methanomethylophilus alvus Mx1201@

Desulfurococcus kamchatkensis 1221n@

Thermotoga maritima MSB8@

Methanocella arvoryzae MRE50@

Phycisphaera mikurensis NBRC 102666@

Methanococcus vannielii SB@

uncultured marine group II euryarchaeote@

Sulfolobus tokodaii str. 7@

Borrelia afzelii PKo@

Chlamydia muridarum str. Nigg@

Streptosporangium roseum DSM 43021@

Lactococcus garvieae ATCC 49156@

Haloarcula marismortui ATCC 43049@

Synechococcus elongatus PCC 6301@

Metallosphaera sedula DSM 5348@

Brachyspira hyodysenteriae WA1@

Akkermansia muciniphila ATCC BAA-835@

Candidatus Caldiarchaeum subterraneum@

Opitutus terrae PB90-1@

Cenarchaeum symbiosum A@

Desulfobulbus propionicus DSM 2032@

Cyanothece sp. PCC 7424@

Leptospira biflexa serovar Patoc strain Patoc 1 Ames@

Methanobacterium sp. SWAN-1@

Caldivirga maquilingensis IC-167@

Herpetosiphon aurantiacus DSM 785@

Candidatus Nitrososphaera gargensis Ga9.2@

Allochromatium vinosum DSM 180@

Kosmotoga olearia TBF 19.5.1@Fervidobacterium nodosum Rt17-B1@

Nitrosopumilus maritimus SCM1@

Petrotoga mobilis SJ95@

Methanoculleus marisnigri JR1@

Cytophaga hutchinsonii ATCC 33406@

Thermoproteus tenax Kra 1@

Pyrolobus fumarii 1A@

Methanobrevibacter smithii ATCC 35061@

Truepera radiovictrix DSM 17093@Marinithermus hydrothermalis DSM 14884@

Kineococcus radiotolerans SRS30216 = ATCC BAA-149@

Candidatus Nitrosoarchaeum limnia SFB1@

Candidatus Protochlamydia amoebophila UWE25@

Helicobacter acinonychis str. Sheeba@

Burkholderia ambifaria AMMD@Chromobacterium violaceum ATCC 12472@

Acinetobacter baumannii 1656-2@

Methanomassiliicoccus luminyensis@

Thermofilum pendens Hrk 5@

Acidaminococcus fermentans DSM 20731@

Methanococcoides burtonii DSM 6242@

Trichodesmium erythraeum IMS101@

Pedobacter heparinus DSM 2366@

Thiobacillus denitrificans ATCC 25259@

Natranaerobius thermophilus JW_NM-WN-LF@

Candidatus Korarchaeum cryptofilum OPF8@

Planctomyces brasiliensis DSM 5305@

Waddlia chondrophila WSU 86-1044@

Gloeobacter violaceus PCC 7421@

Syntrophobacter fumaroxidans MPOB@

Vulcanisaeta moutnovskia 768-28@

Methanoregula boonei 6A8@

Pyrococcus yayanosii CH1@

Actinosynnema mirum DSM 43827@

Isosphaera pallida ATCC 43644@

Methanocella paludicola SANAE@

Archaeoglobus veneficus SNP6@

Anabaena variabilis ATCC 29413@

Alteromonas macleodii str. Black Sea 11@

Nocardia cyriacigeorgica GUH-2@

Ignicoccus hospitalis KIN4_I@

Catenulispora acidiphila DSM 44928@

Methanosaeta harundinacea 6Ac@

Coraliomargarita akajimensis DSM 45221@

Thermococcus barophilus MP@

Methanotorris igneus Kol 5@

Rhodothermus marinus DSM 4252@

Arcobacter butzleri ED-1@

Bacteroides fragilis 638R@

Ferroglobus placidus DSM 10642@

Stigmatella aurantiaca DW4_3-1@

Pyrobaculum aerophilum str. IM2@

Methanothermobacter thermautotrophicus str. Delta H@

Methanosarcina mazei Go1@

Methanothermus fervidus DSM 2088@

Anaerolinea thermophila UNI-1@Heliobacterium modesticaldum Ice1@

Dinoroseobacter shibae DFL 12 = DSM 16493@

Treponema azotonutricium ZAS-9@

Legionella longbeachae NSW150@

Haloferax volcanii DS2@

Deinococcus deserti VCD115@

Methylacidiphilum infernorum V4@

Novosphingobium aromaticivorans DSM 12444@Bartonella bacilliformis KC583@

Simkania negevensis Z@

Methanocorpusculum labreanum Z@

Listeria innocua Clip11262@

Thermococcus litoralis DSM 5473@

Archaeoglobus fulgidus DSM 4304@

Rhodopirellula baltica SH 1@

Nautilia profundicola AmH@

Dehalococcoides mccartyi 195@

Aciduliprofundum boonei T469@

Methanocaldococcus jannaschii DSM 2661@

Ferroplasma acidarmanus fer1@

Acetobacter pasteurianus IFO 3283-01-42C@

9 9

9 9

100

100

100

100

9 9

9 8

100

100100

100

100

6 5

100

100

8 2

6 9

100

100

100

5 4

9 7

100

100

100

2 8

100

100

9 4

2 7

100

5 7

100

100

100

100

100

100

100

9 1

1 8

100

100

100

100

7 59 6

9 9

7 7

6 4

100

7 0

6 7

100

3 7

100

100

8 1

100

100

100

100

9 6

100

2 5

6 5

100

9 3

100

100

1008 5

100

100

100

8 9

100

100

100

100

100

100

100

9 7

100

100

100

100

100

100

8 9

100

100

100

100

9 7

9 3

100

100

100100

100

9 3

9 6

100

100

9 7

9 8

9 1

100

9 0

7 2

100

AB ML LG S43 10206 positions

Raymann et al. 2015

0.3










Chlamydia muridarum str. Nigg@Planctomyces brasiliensis DSM 5305@























Chromobacterium violaceum ATCC 12472@







Natranaerobius thermophilus JW_NM-WN-LF@Nocardia cyriacigeorgica GUH-2@

Fervidobacterium nodosum Rt17-B1@


















Methanosaeta harundinacea 6Ac@Methanocella conradii HZ254@


Novosphingobium aromaticivorans DSM 12444@




Heliobacterium modesticaldum Ice1@



Marinithermus hydrothermalis DSM 14884@










Bartonella bacilliformis KC583@



Burkholderia ambifaria AMMD@



Kosmotoga olearia TBF 19.5.1@








Ferroglobus placidus DSM 10642@Archaeoglobus profundus DSM 5631@











Anaerolinea thermophila UNI-1@








Truepera radiovictrix DSM 17093@


100

8 7

100

2 6

100

6 0

100

100

100

8 0

100

100

100

100

1009 4

100

100

9 7

7 3

100 100

8 5

100

100

100

100

100

100

4 6

100

100

100

6 3

100

9 69 6

7 0

9 8

100

7 8

100

100

100

100

5 8

8 2

100

100

100

8 2

100

9 3

100

8 8

5 6

100

100

100

9 7

9 9

100

100

100

100

100

9 8

9 5

100

7 4

100

9 9

100

5 9

100

100

100 100

100

6 3

100

100

100

100

9 5

7 7

9 2

100

100

100

100

9 9

4 8100

7 1

1 1

100

5 5

100

9 6

100

5 7

100

2 4

1009 7

100

8 6

9 5

100

5 2

100

9 99 8


Raymann et al. 2015

0.3















Methanosarcina mazei Go1@Methanococcoides burtonii DSM 6242@









Cytophaga hutchinsonii ATCC 33406@Stigmatella aurantiaca DW4_3-1@











































































Thermoproteus tenax Kra 1@Vulcanisaeta moutnovskia 768-28@















100

100

5 5

9 4

100

100

100

4 7

1005 0

100

9 9

100

100

6 7

100

100

9 1

9 9

100

100

100

100

8 3

100

100

9 5

100

100

100

100

100

100

100

5 2

100

100

100

4 0

9 0

100

100

4 9

9 4

100

5

9 7

9 1

9 9

9 4

100

100

100

100

6 9

5 9

100

9 8

5 7

100

100

5 1

100

100

7 5

100

6 9

9 8

100

100

100

100

7 5

9 4

100

9 2

100

100

100

100

100

7 7

9 9

100

100

100

8 5

100

100

100

5 3

100

100

100

100

100

9 7

4 3

100

7 6

100

9 2

9 8

5 0

8 5

7 6

5 2

100

8 1

100

100

9 7

100

9 6


Raymann et al. 2015

0.3










Novosphingobium aromaticivorans DSM 12444@Acetobacter pasteurianus IFO 3283-01-42C@










































Allochromatium vinosum DSM 180@Legionella longbeachae NSW150@































































100

5 0

100

100

100

100

100

9 6

100

100

5 4

9 7

7 9

100

100

8 3

100

100

100

9 8

100

7 7

6 3

100

100

100

100

100

9 9

100

100

100

100

9 78 8

100

7 9

9 5

100

9 0

100

100

5 7

100

7 8

4 1

100

9 6

100

9 5

6 2

9 1

100

4 9

7 4

100

9 9

100

8 5

9 6

100

100

5 7

7 4

100

100

100

100

100

4 6

6 8

9 8

5 1

100

100

100

2 7

100

100

8 7

4 4

9 4

100

100

9 9

100

100

100

6 4

100

100

100

100

9 9

8 9

100

7 0

9 7

100

100

100

100

100

9 4

100

100

6 6

6 2

100

8 2

100

100

100

100


Raymann et al. 2015

0.2





























Candidatus Nitrososphaera gargensis Ga9.2@Candidatus Caldiarchaeum subterraneum@

























Planctomyces brasiliensis DSM 5305@Rhodopirellula baltica SH 1@


Haloferax volcanii DS2@Haloarcula marismortui ATCC 43049@



























Candidatus Protochlamydia amoebophila UWE25@Simkania negevensis Z@






























100

9 4

100

100

4 8

9 5

100

100

100

100

7 4

100

100

100

8 3

100

100

100

7 9

6 1

100

6 2

100

100

100

7 0

9 6

100

100

6 7

7 3

100

100

100

100

100

100

100

100

100

100

7 7

9 3

100

100

7 2

9 8

9 9

100

100

5 0

100

9 9

100

7 7

100

100

8 0

100

100

100

9 4

9 5

9 0

100

100

100

100

6 5

100

100

1009 8

100

3 5

6 5

100

9 6

100

9 3

100

7 2

100

5 2

100

100

2 6

100

5 9

100

100

8 0

100

8 7

5 4

8 0

6 88 6

5 1

100

100100

100

100

100

9 7

9 4

8 0

2 4

100

100

9 8

100

100


Raymann et al. 2015

0.2




























Acidaminococcus fermentans DSM 20731@Heliobacterium modesticaldum Ice1@
























































































100

5 7

7 4

100

100

8 9

100

7 3

100

1 6

8 9

100

100

4 5

100

100

9 4

100

100

8 5

9 25 8

100

100

9 7

100

8 7

100

7 2

8 8

100

100

100

100

7 7

5 5

100

100

9 8

100

9 5100

100

100

100

5 3

100

100

100

9 9

100

9 8

100

9 9

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2 0

100

5 2

100

8 3

100

100

100

8 2

7 0

100

6 5

5 7

5 1

6 4

4 7

100

100

9 9

100

100

100

100

6 7

100

7 8

100

1 4

100

100

100

100

100

1009 5

100

100

100

9 0 100

8 3

100

8 0

6 5

100

9 1

100

4 1

100

9 1

9 3

100

100

100

4 7

100

100

100

100


Raymann et al. 2015

0.2




















































































































9 3

100

100

100

100

100

9 0

9 9

100

7 3

7 2

100

8 6

100

8 5

9 9100

9 06 7

100

100

8 0

8 8

8 3

100

100

100

6 7

100

100

100

100

100

6 5

7 3

100

100

100

8 9

8 4

100

100

100

100

100

100

100

100

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8 8

7 4

9 4

3 1

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5 9

100

100

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3 6

100

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9 7

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7 1

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9 0

2 9

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100

100

100

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5 8

5 6

100

100

100

9 7

100

100

100

6 9

100

100

100

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7 9

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9 9

5 8

100

100

5 3

100

6 3

100

100

9 2

100

9 7100

9 9

100

100

100

4 2

100

7 1100


Raymann et al. 2015

0.2



























Methanoculleus marisnigri JR1@Methanoregula boonei 6A8@



Opitutus terrae PB90-1@Coraliomargarita akajimensis DSM 45221@































Burkholderia ambifaria AMMD@Chromobacterium violaceum ATCC 12472@











































Dehalococcoides mccartyi 195@Thermomicrobium roseum DSM 5159@









100

8 5

100

100

8 6

4 5

100

100

9 9

9 7

100

100

8 3

100

100

100

8 0

100

9 3

8 9

100

7 3

100

100

9 6

100

100

100

100

9 0

100

6 1

8 8

6 8

100

100

100

100

100

100

6 6

100

8 1

8 3

100

3 8

100

6 9

9 9

100

9 6

8 0

100

2 9

2 7

8 8

8 2

8 5

100

100

8 1

100

100

100

100

5 4

5 4

100

6 5

6 6

100

100

100

7 5

100

9 9

100

5 3

7 5

100

100

5 6

9 9

6 3

100

100

9 9

7 5

100

100

9 9

9 0

100

100

100

9 5

5 4

7 4

100

100

100

100

100

100

100

100

9 7

1 6

100

9 5

100

9 9

9 4

100


Raymann et al. 2015

0.2








Caldivirga maquilingensis IC-167@Candidatus Caldiarchaeum subterraneum@




























































Natrialba magadii ATCC 43099@Archaeoglobus fulgidus DSM 4304@



Deinococcus deserti VCD115@Truepera radiovictrix DSM 17093@











































9 0

100

100

100

9 9

9 2

100

100

9 1

100

100

100

100

9 8

5 0

5 6

8 9

100

100

8 9

9 9

100

4 5

8 5

100

100

3 5

100

4 2

100

100

7 4

100

100

100

8 9

5 2

3 1

100

100

100100

7 3

6 3

100

100

7 5

9 8

100

100

7 8

100

7 3

100

5 5

6 5

100

100

100

100

100

100

6 3

100

100

100

9 4

100

100

6 9

9 8

100

100

2 5

8 1

100

5 6

100100

6 0

9 7

100

7 7

100

6 1

100

100

100

100

100

9 5

9 9

4 4

100

9 2

9 0

100

100

100

8 7

100

100

100

9 4

9 9

100

9 2

7 7

100

7 0

7 5

100

100

100


Raymann et al. 2015

0.2














































uncultured marine group II euryarchaeote@Methanomassiliicoccus luminyensis@











Dinoroseobacter shibae DFL 12 = DSM 16493@Nitrosomonas europaea ATCC 19718@


Methanocella arvoryzae MRE50@Methanoculleus marisnigri JR1@























































100

100

8 3

100

9 2

100

100

8 1

100

4 7

7 6

100

100

7 8

100

7 9

6 2

100

5 0

100

9 9

8 6

100

100

100

7 0

100

9 9

100

100

100

100

100

8 8

100

100

100

100

5 7

100

9 3

5 9

6 0

100

4 0

100

100

6 1

8 8

7 5

100

100

100

100

100

100

9 7

5 1

100

4 4

100

100

100

7 9

100

100

100

100

100

100

100

9 5

7 5

100

5 9

100

100

6 8

100

7 2

8 9

100

2 7

6 0

100

100

9 1

6 9

9 8

100

100

100

100

6 5

100

9 7

100

7 0

100

100

8 7

7 1

2 5

8 9

7 6

100

8 3

100

9 7

4 6

100

100

100

100


Raymann et al. 2015

0.2




























Nocardia cyriacigeorgica GUH-2@Actinosynnema mirum DSM 43827@























































































9 7

100

7 4

100

100

5 9

2 1

7 7

100

100

100

100

9 6

100

100

100

8 7

8 2

7 2

100

100

9 3

100

5 9

100

6 3

7 0

100

100

1007 1

100

2 7

7 49 8

100

100

7 2

100

4 4

100

100

100100

100

7 9

100

100

3 3

9 7

6 0

100100

100

6 5

6 8

8 3

8 5

9 2

5 9

100

9 9

8 4

100

100

100

100

9 9

100

100

100

100

100

7 1

8 1

100

100

100

100

9 9

9 4

100

100

100

6 1

9 0

100

8 1

6 5

5 6

5 3

4 6

100

100

100

100

9 9

100

100

100

7 2

100

100

6 6

100

9 8

7 6

100

7 8

6 0

100

100

100

100


Raymann et al. 2015

0.2
























































Thermococcus litoralis DSM 5473@Thermococcus barophilus MP@




























































100

7 1

100

100

6 6

4 2

100

6 0

6 9

100

3 0

4 1

100

9 7

100

100

100

5 9

6 9

100

100

9 9

6 6

9 9

100

8 1

100

100

9 9

100

9 9

100

100

9 0

9 8

5 3

100

2 1

100

100

100

100

100

3 7

100

1009 8

100

100

100

100

100

9 3

100

8 2

9 6

9 8

100

9 2

8 2

6 4

100

9 5

8 3

4 6

100

8 4

100

100

6 3

8 2

100

100

7 5

5 6

100

100

100

7 4

6 7

9 4

5 8

100

100

100

100

9 9

7 8

100

100

100

100

9 5

6 6

3 3

100

6 4

7 5

100

100

6 0

100

8 1

9 2

6 8

100

100

100

100

9 4

6 0

100

100

4 7


Raymann et al. 2015

0.2







Cytophaga hutchinsonii ATCC 33406@Phycisphaera mikurensis NBRC 102666@












































Desulfurococcus kamchatkensis 1221n@Metallosphaera sedula DSM 5348@









Bartonella bacilliformis KC583@Desulfobulbus propionicus DSM 2032@






















































4 5

100

3 2

3 9

8 3

100

9 8

100

100

9 1

9 3

9 9

100

100

100

100

6 3

5 6

8 6

100100

100

100

100

100

7 7

100

100

8 4

100

100

5 5

6 6

100

9 5

8 1

100

2 8

100

100

5 7

100

100

9 8

6 7

100

4 8

9 5

100

9 4

3 9

5 8

9 3

100

100

9 4

9 6

100

5 7

100

100

100

9 8

5 1

6 8

100

6 5

100

9 1

100

100

100

100

5 2

100

9 7

8 7100

100

100

100

8 6

6 5

100

100

100

100

6 7

7 4

100

100

100

4 4

8 7

2 5

100

100

100

100

5 3

100

8 4

100

100

100

3 8

100

9 7

9 8

100

6 4

5 3 6 0

6 5


Raymann et al. 2015

0.2



























































































Methanoregula boonei 6A8@Methanoculleus marisnigri JR1@

























9 4

100

100

100

8 8

5 09 4

9 0

100

100

3 9

100

6 0

7 4

100

100

100

100

100

100

100

100

100

5 8

9 7

9 7

5 8

4 6

5 8

100

8 6

100

6 5

100

4 6

100

100

100

5 1

5 0

100

100

5 7

100

100

100

100

3 0

100

100

6 2

100

100

2 8

9 1

3 5

100

8 9

100

6 4

100

6 7

100

100

9 5

100

100

4 8

100

100

3 7

100

9 9

100

5 7

100

100

100

7 1

6 9

3 1

9 8

9 7

8 2

100

100

3 7

6 7

100

100

6 1

100

9 6

100

7 0

100

100

6 2

100

9 9

9 5

7 3

7 3

1 6

9 4

8 1

9 9

100

9 3

3 7

8 7

7 7

100

100


Raymann et al. 2015

0.1





















































































































100

100

100

100

100

7 1

100

9 4

6 4

2 46 7

6 6

100

100

9 9

4 6

100

100

100

8 4

100

9 1

6 8

100

100

9 3

6 5 4 3

100

9 7

5 2

7 2

6 1

8 0

100

100

100

100

7 3

9 9

100

5 3

3 8

8 5

100

9 7

2 4

100

100

100

6 7

5 9

100

100

100100

9 8

7 0

5 8

5 9

9 7

100

2 9

100

3 0

9 9

9 0

100

100

100

100

4 1

100

100

100

100

9 1

9 8

100

6 4

9 24 1

9 3

100

100

5 5

9 7

8 3

9 8

4 1

7 1

5 6

100

100

2 4

5 1

100

100

9 5

9 0

100

100

100

100

100

100

100

8 1

100

8 4

9 2

5 5

100

4 8


Raymann et al. 2015

0.1









































Herpetosiphon aurantiacus DSM 785@Streptosporangium roseum DSM 43021@





















Borrelia afzelii PKo@Brachyspira hyodysenteriae WA1@









































Pelobacter carbinolicus DSM 2380@Stigmatella aurantiaca DW4_3-1@











9 8

100

6 0

1008 7

5 7

4 3

100

7 4

4 8

100

100

7 8

100

9 2

5 9

9 8

100

8 3

8 8

100

8 1

9 5

5 2

9 9

2 1

9 9

9 9

100

7 8

3 5

100

5 8

100

6 0

6 5

100

9 8

9 9

9 6

9 8

100

100

100

100

100

100

100

100

9 8

100

9 3

6 3

100

9 6

4 3

7 2

100

8 0

4 8

7 4

6 1

100

100

5 7

4 8

100

5 2

9 1

5 3

100

100

100

100

6 9

8 5

100

7 9

4 9

100

100

100

100

100

5 4

9 5

100

100

9 6

100

5 0

100

6 2

7 6

100

8 7

100

100

5 7

9 6

5 5

9 6

100

9 8

100

100

9 7

100

100

4 8

100

100

8 6

4 3


Raymann et al. 2015

0.09


































































Methanobrevibacter smithii ATCC 35061@Methanothermobacter thermautotrophicus str. Delta H@













































Candidatus Korarchaeum cryptofilum OPF8@Pyrococcus yayanosii CH1@




1 73

100

9 1

100

100

9 1

6 4

6 5

9 7

3 9

7 5

8 4

100

4 0

100

7 2

100

8 5

3

6 6

100

9 8

9 7

8 5

100

2 8

100

2 4

9 6

100

9 8

6 7

100

5 9

100

100

100

100

100

100

100

4 5

4 0

7 2

5 4

9 6

100

100

9 8

9 1

100

6 0

1 2

7 7

100100

8 5

7 7

9 9

9 1

6 1

9 9

2 0

6 3

9 9

100

100

8 7

4 5

100

100

100

100

100

8 5

100

2 8

3 4

9 5

7 9

6 4

100

100

100

100

100

9 1

100

100

6 9

9 2

100

7 0

100

6 1

8 0

2 9

3 3

7 8

100

9 6

3 0

7 3

3 2

9 6

100

6 6

6 2

100

5 2

5 1

100

8 6


Raymann et al. 2015

0.08





































Methanothermus fervidus DSM 2088@Methanotorris igneus Kol 5@












































































Metallosphaera sedula DSM 5348@Pyrolobus fumarii 1A@


7 89 7

4 6

4 7

100

9 8

8 5

9 1

9 9

2 1

100

8

100

8 0

5 9

2 3

4 33 5

1 4

100

9 7

100

100

100100

100

4 6

100

5 5

100

3 2

6 9

100

100

5 1

8 4

100

3 9

100

100

8 8

8 0

7 2

100

9 9

8 7

100

9 7

100

5 5

100

8 2

100

5 0

8 8

100

100

100

7 6

100

100

100

4

8 8

100

8 5

9 6

100

7 7

8 6

7 5

4 9

5 3

6 5

8 9

8 5

5 7

8 1

100100

9 9

9 2

7 8

100

100

100

9 9

100

4 8

6 2

4 8

100

100

9 8

5 8

4 7

2 7

100

7 7

9 9

9 9

6 2

100

7 31 6

9 8

9 9

100

9 0

8 87 3

6 5

5 9

2


Raymann et al. 2015

0.07




















































































Marinithermus hydrothermalis DSM 14884@Deinococcus deserti VCD115@































7 6

100

2 2

5

100

100

9 8100

100

9 1

100

4 5

9 3

100

4 1

100

4 3

8 4

100

8 3

100

5 9

7 6

100

1 3

4 1

6 8

6 4

7 8

7

6 9

8 9

1

7 4

9 8100

7 3

1009 8

100

1 1

3 3

9 9

3 8

7 2

5 6

100

4 4

3 5

9 2

2 2

5 6

100

5 6

8 5

8 0

100

3 2

7 6

100

100

3 8

5 5

9 7

100

6 7

100

100

6 4

7 4

7 3

100

8 1

100

6 5

100

3 6

100

9 5

8 1

7 5

8 4

100

7 2

6 5

6 9100

9 9

9 5

5 0

7 9100

4 3

2 7

100

100

7 6

9 4

3 2

5 2

8 7

9 9

7 0

6 8

7 8

6 3

9 7

9 6

3 5

100

9 1

100

100

5 8


Raymann et al. 2015

0.06


































Streptosporangium roseum DSM 43021@Kosmotoga olearia TBF 19.5.1@


















































































4 4

9 2

5 5

100

3 3

2 5

100

8 3

100

100

8 4

4 1

9 5

100

4 7

9 8

6 0

4 8

100

100

1 49 5

5 8

9 9

2 3

2 2

2 5

9 5

9 6

4 1

100

100

6 6

9 2

6 2

100

5 9

8 4

100

7 0

9 9

6 0

8 4

9 6

8 4

8 1

100

3 6

100

3 4

9 9

100

100

100

1009 2

8 2

9 7

100

100

9 9

5 9

5 7

7 4

100

7 9

100

7 4

3 8

7 8

9 9

2 0

9 6

5 8

9 2

5 7

100

5 72 4

3 7

8 2

6 3

5 8

5 5

100

4 6

100

9 5

100

6 4

9 8

1 6

3 1

100

8 9

6 6

3 5

7

9 4

3 7

5 4

7 0

8 7

8 9

5 1

100

9 5

7 1

9 5

4 7

7 1

8 1

7 4

8 0


Raymann et al. 2015

0.05

























Planctomyces brasiliensis DSM 5305@Isosphaera pallida ATCC 43644@




























Methanococcus vannielii SB@Methanotorris igneus Kol 5@







Nitrosomonas europaea ATCC 19718@Thiobacillus denitrificans ATCC 25259@






















































100

2 0

6 8

100

3 9

100

4 6

9 0

4 6

4 6

8 5

8 0

8 1

9 6

1 1

7 2

3 8

8 3

2 1

9 4

2 1

100

4 3

2 6

100

100

3 0

6 6

5 3

100

100

9 6

3 2

8 2

2

3 5

100

3 2

3 9

9 8

8 8

2 2

6 2

0

1 6

9 9

100

7 8

6 3

9 9

100

3 4

100

3

5 0

5 7

8

1 4

1 1

4 1

2 8

1 0

5 3

1

8 4

2 4

23 1

100

3 3

5

2 5

3 1

8 1

5 6

7 1

4 0

4 6

4 7

4 0

9 3

2 5

6 6

9 8

6 5

8 0

9

9 3

3

5 3

7 6

7 1

100

5 9

3 8

2 5

7 7

5 5

8 9

100

8 3

7 3

100

7 8

4

5 5

9 2

9 9

2

5 6

6 1

4 36 7

4 8


Raymann et al. 2015

0.03

















Planctomyces brasiliensis DSM 5305@Phycisphaera mikurensis NBRC 102666@


































Nitrosopumilus maritimus SCM1@Cenarchaeum symbiosum A@































































2

8 6

1 0

2

2

6 3

2

2

2

0

2

5 9

2

3 8

1 5

3 4

100

2

8 6

0

4 5

6

1 3

5 7

5 2

2

6 2

2

4 7

2

8

6 6

7 5

7 7

4 5

2

1 7

100

7 7

1 3

7 1

2

2

1 3

7

1 2

8

2

8 9

6 8 2

8 4

2

2

1 7

7 9

2

1 3

5 5

0

2

9

8 6

2

7 5

5

2

8 6

1 3

4

2

1 2

6 1

0

0

0

2

2

8

5 6

5

4 5

1 2

1 3

0

6 7

2

5 7

2

0

0

3

0

1 3

5 2

1 2

6 0

2

2 9

6 3

4 8

6

2

2

2

9 1

1 1

0

5 8

6 4

3

2

4 9

8


Raymann et al. 2015

0.6


























Rhodopirellula baltica SH 1Planctomyces brasiliensis DSM 5305


























uncultured marine group II euryarchaeoteAciduliprofundum boonei T469































































0.99

0.99

0.94

0.98

0.99

0.98

1

0.99

1

1

1

1

1

1

0.99

1

1

1

1

0.99

0.91

1

1

0.98

1

1

1

0.99

1

1

1

0.99

1

0.99

1

1

0.99

1

0.99

0.94

1

11

1

1

0.99

1

1

0.99

1

1

1

0.99

0.99

1

0.98

0.99

1

0.6

0.99

0.99

1

1

0.99

0.99

0.98

0.99

0.99

0.99

1

1

0.99

0.99

1

1

0.99

1

0.79

0.99

1

1

0.98

0.92

1

1

0.99

0.99

1

1

0.78

0.99

0.99

1

0.99

0.99

1

1

1

0.98

1

0.98

1

0.99

0.99

1

1

0.99

0.99

1

1

0.99

1

1

0.99

AB CAT+GTR S43 10206 positions

Raymann et al. 2015

0.6





































































Methylacidiphilum infernorum V4Opitutus terrae PB90-1














































1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0.94

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

11

11

1

1

1

1

1

1

0.97

1

1

1

1

1

1

0.99

1

1

1

1

1

1

1

1

1

1

1

1

1

0.99

1

1

1

0.97

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0.87

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1


Raymann et al. 2015

0.5
















































































































Thermoproteus tenax Kra 1Pyrobaculum aerophilum str. IM2




1

1

1

1

1

1

0.96

1

0.99

0.99

1

1

1

0.99

1

1

1

0.77

1

0.99

1

1

1

0.99

0.99

0.88

0.86

1

1

1

0.59

0.99

1

0.99

1

1

0.95

1

0.99

11

0.99

1

1

0.99

0.99

0.99

0.88

1

1

1

1

1

1

0.97

0.99

0.99

0.99

1

0.99

1

1

1

0.98

1

1

1

0.99

0.99

1

1

0.86

0.99

1

1

1

0.99

1

0.99

1

0.99

0.99

1

1

1

0.99

0.99

1

1

0.99

1

0.99

1

0.990.99

0.99

0.99

0.97

0.97

1

0.99

1

0.99

0.98

1

1

1

0.99

0.99

0.7

0.99

1

0.99

0.99


Raymann et al. 2015

0.5









































Heliobacterium modesticaldum Ice1Natranaerobius thermophilus JW_NM-WN-LF

Acinetobacter baumannii 1656-2Methanotorris igneus Kol 5




























Novosphingobium aromaticivorans DSM 12444Bartonella bacilliformis KC583

















Dinoroseobacter shibae DFL 12Acetobacter pasteurianus IFO 3283-01-42C


























1

1

0.99

0.99

1

1

0.99

0.99

0.99

0.99

0.99

1

1

1

0.72

0.92

0.99

1

1

1

0.99

0.99

0.98

1

1

0.71

0.99

1

1

0.99

1

1

0.99

1

1

10.85

0.98

1

0.99

1

0.99

0.71

0.95

0.94

1

1

0.99

0.71

1

0.99

1

1

0.99

1

1

1

1

0.99

1

1

1

1

0.5

0.99

0.99

0.99

0.99

0.99

1

1

0.99

0.99

0.99

1

0.99

1

1

0.79

1

1

1

1

0.99

1

1

0.99

1

1

0.99

0.99

1

1

0.99

0.99

0.99

1

0.99 1

1

1

0.99

1

0.99

0.99

0.99

0.99

0.98

1

1

1

1


Raymann et al. 2015

0.5




















































Herpetosiphon aurantiacus DSM 785Thermomicrobium roseum DSM 5159














































Streptosporangium roseum DSM 43021Trichodesmium erythraeum IMS101

















1

0.96

1

1

0.99

0.99

1

1

0.99

0.99

0.99

1

0.58

0.99

1

0.99

0.96

0.99

0.99

0.98

1

0.88

1

0.99

0.99

1

1

1

1

0.99

1

0.99

1

1

0.94

1

1

0.98

1

1

1

1

1

1

1

0.99

0.92

1

1

1

1

1

0.99

1

1

1

1

0.97

0.99

1

0.99

1

0.99

0.99

1

1

1

0.99

1

1

0.7

1

1

0.99

1

1

0.98

1

0.96

1

0.99

1

1

1

0.99

1

1

0.99

0.98

0.99

1

1

1

1

0.99

0.99

1

1

0.99

1

1

1

0.99

1

1

1

1

0.99

0.99

1

1

1

1

0.99


Raymann et al. 2015

0.5





























































































Thermomicrobium roseum DSM 5159Dehalococcoides ethenogenes 195























0.99

1

1

0.99

1

1

0.99

1

1

0.8

1

0.99

0.99

1

0.99

0.99

1

0.99

1

1

0.99

1

0.99

1

1

0.980.99

1

0.99

0.99

0.99

1

1

0.99

1

1

1

0.99

0.56

1

1

1

0.99

1

1

1

1

0.99

0.99

1

0.99

1

1

0.99

1

0.99

1

0.99

0.99

1

1

1

1

1

1

0.56

1

1

0.86

1

1

1

1

1

1

0.94

0.99

0.99

1

1

0.98

1

0.99

0.99

1

1

1

1

1

1

0.9

1

0.99

0.99

0.98

1

1

1

1

11

0.99

0.99

0.99

0.991

0.54

0.99

0.57

0.98

1

0.99

1


Raymann et al. 2015

0.5


















































































Haloarcula marismortui ATCC 43049Natrialba magadii ATCC 43099


































0.99

1

0.62

0.99

0.99

1

1

1

1

0.99

0.99

1

1

1

0.99

1

1

1

1

1

1

0.99

0.97

1

1

1

0.99

1

1

0.89

0.91

1

1

1

1

1

0.99

1

0.99

1

1

0.99

1

0.99

1

1

0.96

0.57

1

0.99

1

1

0.99

0.99

0.98

0.99

0.99

1

1

1

1

0.99

0.99

0.99

0.99

0.9

1

0.98

0.99

0.99

0.99

0.99

0.99

0.97

1

1

1

0.99

0.77

1

1

1

0.99

0.99

0.99

0.99

1

1

0.79

1

1

1

1 1

1

1

0.99

1

0.97

1

0.66

0.99

0.99

1

1

1

1

0.69

0.61

1

1

1

0.99

1


Raymann et al. 2015

0.5















































Thermococcus litoralis DSM 5473Thermococcus barophilus MP

































































Methanocella conradii HZ254Methanocella paludicola SANAE



1

1

1

0.96

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0.97

0.98

1

1

1

1

0.92

0.95

1

1

1

1

1

1

1

1

1

1

1

0.97

0.99

1

1

1

1

1

1

1

1

0.79

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0.82

1

1

1

1

1

1

10.99

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0.74

0.98

1

1

0.99

1

0.95

1

1

1

1

1

1

1

1

1

1

0.941

1

1


Raymann et al. 2015

0.4





















































































































0.99

0.97

1

1

1

1

1

1

1

1

1

1

1

11

1

0.93

1

1

1

1

1

1

1

0.97

0.99

1

1

1

1

0.98

1

1

1

1

1

1

1

1

1

0.96

1

1

1

1

1

1

0.99

1

1

1

1

1

1

1

1

0.85

1

1

1

0.85

0.941

0.81

1

1

1

1

0.88

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0.97

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1


Raymann et al. 2015

0.4

































Trichodesmium erythraeum IMS101Acidaminococcus fermentans DSM 20731



















































































1

1

1

1

0.83

1

1

1

1

1

1

1

1

1

0.54

1

0.97

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

0.98

1

0.91

1

1

1

1

11

1

1

1

0.99

1

1

1

1

1

1

1

1

1

1

1

1

0.79

1

1

1

0.99

1

1

1

1

1

1

10.9

1

0.99

1

1

1

1

1

0.98

0.52

1

1

1

0.91

1

1

0.76

1

1

1

1

1

1

1

1

0.99

0.99

1

1

0.99

1

1

0.78

0.94

1

1

1

0.75

0.95

1

1

1

1

1

1


Raymann et al. 2015

0.4












Methanobacterium sp. SWAN-1Methanobrevibacter smithii ATCC 35061


























































Candidatus Protochlamydia amoebophila UWE25Chlamydia muridarum str. Nigg


































Candidatus Caldiarchaeum subterraneumPyrobaculum aerophilum str. IM2










1

1

1

1

1

1

1

0.7

1

1

1

0.97

1

0.97

1

1

1

1

0.99

1

0.7

11

1

1

1

1

0.98

1

1

1

1

1

1

0.88

1

1

1

1

1

1

0.83

1

1

1

0.99

1

1

1

1

1

0.64

0.99

1

1

1

1

1

1

0.96

1

1

1

10.9

1

1

0.74

0.66

1

1

1

1

1

1

0.65

1

1

0.81

1

0.87

1

1

1

1

0.7

0.99

1

1

1

1

1

0.99

1

1

1

1

10.96

1

1

0.99

1

1

1

11

1

1

1

1

1

1


Raymann et al. 2015

0.4






























Deinococcus deserti VCD115Kosmotoga olearia TBF 19.5.1






















































































1

0.97

1

1

1

1

1

0.66

0.99

1

0.99

0.99

1

1

1

1

0.890.64

0.59

0.941

0.71

1

1

0.78

1

1

1

0.651

0.99

1

0.99

1

1

1

1

1

1

1

1

0.96

0.7

0.99

1

1

1

1

1

1

10.97

1

1

1

1

1

1

0.97

1

1

1

1

11

1

0.89

1

1

0.99

1

1

1

1

1

1

11

1

1

0.99

1

1

1

0.98

1

1

0.73

1

1

0.71

1

1

1

1

1

1

1

1

1

1

0.99

1

1

0.56

1

1

1

1

1

1

1

1

0.99


Raymann et al. 2015

0.3





























































































Catenulispora acidiphila DSM 44928Kineococcus radiotolerans SRS30216























1

1

1

0.95

1

1

1

1

1

1

1

1

0.72

1

1

1

1

1

1

0.78

0.59

0.86

1

1

1

1

1

1

0.7

1

1

1

1

1

1

1

1

1

0.95

1

0.97

1

0.98

1

0.65

1

1

1

1

1

1

0.62

1

1

0.59

0.99

0.98

0.72

0.61

1

1

1

1

0.94

1

1

1

1

1

0.99

0.83

0.7

1

1

1

1

0.77

1

1

1

1

1

0.99

0.99

1

1

0.89

1

1

1

1

1

1

1

1

1

1

1

1

0.8

1

1

1

1

1

1

1

1

0.67

1

1

1

1


Raymann et al. 2015

0.3
















Trichodesmium erythraeum IMS101Streptosporangium roseum DSM 43021

























































Methylacidiphilum infernorum V4Akkermansia muciniphila ATCC BAA-835










































1

0.88

1

1

0.88

0.52

1

0.98

0.99

1

1

1

0.54

1

0.8

1

1

1

1

1

1

1

1

1

1

0.99

1

0.79

0.98

0.68

0.5

1

1

0.93

1

1

1

1

1

0.89

1

1

1

0.5

1

1

1

1

1

1

1

0.94

1

11

1

1

11

1

0.97

1

1

0.99

1

0.75

0.93

1

1

1

0.51

1

1

0.89

1

1

0.89

1

1

0.99

0.94

1

1

1

0.71

1

1

1

11

1

0.59

1

1

1

1

1

1

1

0.94

1

1

1

1

1

1

1

11

1

1


Raymann et al. 2015

0.3







































Opitutus terrae PB90-1Methylacidiphilum infernorum V4

Thermotoga maritima MSB8Fervidobacterium nodosum Rt17-B1













































Methanobacterium sp. SWAN-1Methanobrevibacter smithii ATCC 35061





























0.71

1

0.99

1

0.98

1

0.59

1

1

1

1

0.99

0.98

1

1

0.96

0.95

1

1

1

1

1

1

0.91

1

0.65

1

1

0.92

1

1

1

0.91

1

1

1

1

1

1

1

1

0.95

0.57

1

1

1

0.75

1

1

1

1

0.96

0.99

0.95

0.97

0.92

1

1

1

1

0.63

1

1

1

0.75

1

1

1

1

1

1

11

1

1

1

0.89

0.92

0.62

0.64

1

1

1

1

0.92

0.99

1

1

1

1

0.99

1

1

1

1

1

1

0.68

1

1

1

1

1

1

0.99

1

0.86

1

1

1


Raymann et al. 2015

0.3













































Methanothermus fervidus DSM 2088Methanobacterium sp. SWAN-1















Actinosynnema mirum DSM 43827Kineococcus radiotolerans SRS30216























































1

1

0.97

1

1

1

0.91

1

1

1

11

0.62

1

0.96

0.54

0.54

1

1

0.99

1

1

1

1

0.55

1

0.68

0.57

1

0.99

0.52

1

1

0.99

1

1

1

1

0.81

0.98

1

1

0.6

1

0.65

1

1

1

1

1

1

0.76

0.99

1

1

0.86

0.62

0.92

1

0.64

1

1

0.99

1

1

1

1

0.83

1

1

1

1

1

1

0.98

1

1

1

1

1

1

0.99

1

1

1

1

1

1

0.53

1

1

1

1

0.97

1

0.85

1

0.69

1

1

0.67

1

1

1

1

1

1

1


Raymann et al. 2015

0.2





















































































































1

1

1

1

0.78

1

1

1

1

0.87

0.93

0.96

0.87

1

1

0.8

1

0.87

1

0.8

0.98

1

0.74

0.54

1

0.95

1

0.71

0.99

1

1

1

0.63

0.5

1

1

1

1

1

1

1

0.71

0.5

1

1

0.99

1

1

1

0.97

1

0.85

1

1

1

1

0.56

1

1

1

1

0.99

1

1

1

0.99

1

1

10.61

1

0.68

1

1

1

1

1

1

0.98

1

1

1

1

1

1

0.95

0.93

1

0.99

1

1

0.92

1

1

0.81

0.91

0.96

1

0.98

1

0.97

1

0.96

0.63

1

1

0.97

1

0.93

1


Raymann et al. 2015

0.2





















































































































1

1

0.73

1

1

1

1

1

1

1

0.99

0.99

0.85

1

1

1

1

1

0.65

1

0.99

0.56

1

1

0.97

1

1

0.99

0.98

1

1

0.83

0.85

1

1

1

1

1

0.78

1

1

0.74

0.97

0.99

1

0.95

0.99

1

1

0.99

1

0.58

1

10.99

1

1

0.51

0.99

1

1

10.92

1

0.99

1

1

1

1

0.55

0.85

1

0.681

1

1

1

1

1

1

0.64

1

0.94

1

1

1

1

1

0.99

1

1

1

1

0.98

1

0.72

1

0.77

0.97

0.96

0.73

1

0.67

1

0.93

0.78

0.67

1

1

1


Raymann et al. 2015

0.2






















Chlamydia muridarum str. NiggCandidatus Protochlamydia amoebophila UWE25






























































































10.99

0.99

1

0.93

0.67

0.52

1

1

0.87

1

1

1

1

0.89

0.83

0.96

0.66

0.99

1

1

0.99

0.89

1

1

1

0.67

1

1

0.76

0.98

0.74

0.59

0.78

1

0.511

0.78

0.6

1

0.57

1

1

0.97

1

0.98

1

0.99

0.91

0.99

1

1

1

0.93

1

1

0.77

1

1

0.62

1

0.68

1

1

0.99

1

0.99

0.77

0.95

0.94

0.99

1

1

1

0.99

1

0.51

0.7

0.82

1

0.99

1

0.99

0.96

0.93

0.99

1

1

1

0.99

0.74

0.58

0.78

1

0.79

1

0.62

1

1

0.99

1

0.6

1

1

0.99

0.83

1

1

1

1

1

0.64

0.91


Raymann et al. 2015

0.09





















































































































1

1

0.52

1

0.79

1

1

0.680.84

1

1

0.99

0.51

1

1

11

1

1

1

0.51

1

1

0.99

0.99

0.9

0.99

1

1

0.7

0.95

0.92

1

0.51

0.56

1

0.88

1

1

1

0.95

1

0.95

0.8

1

0.99

1

1

1

1

0.98

0.99

1

1

1

1

1

0.95

0.9

0.82

0.95

1

1

0.99

0.95

0.95

1

1

0.98

0.93

0.9

1

0.75

0.92

1

0.95

0.98

1

0.97

0.6

0.99

1

0.92

0.78

1

0.82

0.73

1

0.93

1

0.99

0.99

1

1

0.68

1

0.96

0.99

1

0.69

1

0.96

1

1

0.890.58

0.65


Raymann et al. 2015

0.07





































Nitrosopumilus maritimus SCM1Cenarchaeum symbiosum A















































































1

1

1

0.93

0.95

0.96

1

0.8

1

0.85

11

0.99

0.5

0.97

1

1

0.99

0.99

1

0.65

0.84

0.83

0.69

0.99

0.92

0.99

0.51

0.6

0.96

0.65

1

0.52

0.99

0.8

1

0.97

1

0.99

0.96

0.89

0.611

1

1

1

1

1

1

0.66

0.97

1

1

1

0.89

1

0.99

0.9

0.98

0.82

0.79

0.94

0.98

0.99

1

0.83

0.580.93

1

0.98

0.95

0.99

1

0.98

1

1

1

0.96

0.81

0.88

1

0.96

1

0.92

1

0.78

1

0.54

1

1

1

1

0.59


Raymann et al. 2015

0.02













Allochromatium vinosum DSM 180Desulfobulbus propionicus DSM 2032










Kosmotoga olearia TBF 19.5.1Rhodothermus marinus DSM 4252




























































































0.99

0.99

0.99

0.83

1

0.99

0.93

0.99

1

0.65

0.78

0.99

0.99

0.97

0.87

0.99

0.69

1


Raymann et al. 2015

Documents

a. Institut Pasteur, Departement de Microbiologie, … · Institut Pasteur, Departement de Microbiologie, Unite Biologie Moleculaire du Gene chez les Extremophiles, 28 rue du Docteur