SUPPLEMENTARY INFORMATIONharvardphylogenetics.weebly.com/uploads/2/1/1/0/... · SUPPLEMENTARY INFORMATION 6 | RESEARCH 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0 10 20 30 40 50 60 70 80

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SUPPLEMENTARY INFORMATIONdoi:10.1038/nature12130

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Supplementary Table 1. The Taxonomy of the Organisms Used in this Study Organism (acronym) Taxonomy

Yeasts Kluyveromyces waltii (Kwal) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae

Kluyveromyces thermotolerans (Kthe) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae Saccharomyces kluyveri (Sklu) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae

Kluyveromyces lactis (Klac) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae Eremothecium gossypii (Egos) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae

Zygosacharomyces rouxii (Zrou) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae Kluyveromyces polysporus (Kpol) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae

Candida glabrata (Cgla) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae Saccharomyces castellii (Scas) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae Saccharomyces bayanus (Sbay) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae

Saccharomyces kudriavzevii (Skud) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae Saccharomyces mikatae (Smik) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae

Saccharomyces paradoxus (Spar) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae Saccharomyces cerevisiae (Scer) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae

Candida lusitaniae (Clus) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae Candida dubliniensis (Cdub) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae

Candida albicans (Calb) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae Candida tropicalis (Ctro) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae

Candida parapsilosis (Cpar) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae Lodderomyces elongisporus (Lelo) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae;

Pichia stipitis (Psti) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae Candida guilliermondii (Cgui) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae Debaryomyces hansenii (Dhan) Fungi;Ascomycota;Saccharomycetes;Saccharomycetaceae

Verterbrates Xenopus tropicalis (Xtro) Animalia;Chordata;Aphibia;Anura;Pipidae

Gallus gallus (Ggal) Animalia;Chordata;Aves;Galliformes;Phasianidae Monodelphis domestica (Mdom) Animalia;Chordata;Monodelphis;Mammalia;Didelphimorphia

Bos taurus (Btau) Animalia;Chordata;Mammalia;Artiodactyla;Bovidae Equus caballus (Ecab) Animalia;Chordata;Mammalia;Perissodactyla;Equidae

Canis familiaris (Cfam) Animalia;Chordata;Mammalia;Carnivora;Canidae Macaca mulatta (Mmul) Animalia;Chordata;Mammalia;Primates;Cercopithecidae Pongo pygmaeus (Ppyg) Animalia;Chordata;Mammalia;Primates;Hominidae

Homo sapiens (Hsap) Animalia;Chordata;Mammalia;Primates;Hominidae Pan troglodytes (Ptro) Animalia;Chordata;Mammalia;Primates;Hominidae

Rattus norvegicus (Rnor) Animalia;Chordata;Mammalia;Rodentia;Muridae Mus musculus (Mmus) Animalia;Chordata;Mammalia;Rodentia;Muridae Cavia porcellus (Cpor) Animalia;Chordata;Mammalia;Rodentia;Caviidae

Danio rerio (Drer) Animalia;Chordata;Actinopterygii;Cypriniformes;Cyprinidae

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Oryzias latipes (Olat) Animalia;Chordata;Actinopterygii;Beloniformes;Adrianichthyidae Tetraodon nigroviridis (Tnig) Animalia;Chordata;Actinopterygii;Tetraodontiformes;Tetraodontidae

Takifugu rubripes (Trub) Animalia;Chordata;Actinopterygii;Tetraodontiformes;Tetraodontidae Gasterosteus aculeatus (Gacu) Animalia;Chordata;Actinopterygii;Gasterosteiformes;Gasterosteidae

Metazoa Strongylocentrotus purpuratus (Spur) Animalia;Echinodermata;Echinoidea;Echinoida;Strongylocentrotidae

Branchiostoma floridae (Bflo) Animalia;Chordata;Leptocardii;Amphioxiformes;Branchiostomidae Ciona intestinalis (Cint) Animalia;Chordata;Ascidiaceae;Enterogona;Cionidae Mus musculus (Mmus) Animalia;Chordata;Mammalia;Rodentia;Muridae Gallus gallus (Ggal) Animalia;Chordata;Aves;Galliformes;Phasianidae Homo sapiens (Hsap) Animalia;Chordata;Mammalia;Primates;Hominidae

Xenopus tropicalis (Xtro) Animalia;Chordata;Aphibia;Anura;Pipidae Danio rerio (Drer) Animalia;Chordata;Actinopterygii;Cypriniformes;Cyprinidae

Helobdella robusta (Hrob) Animalia;Annelida;Clitellata;Rhynchobdellida;Glossiphoniidae Lottia gigantea (Lgig) Animalia;Mollusca;Gastropoda;Patellogastropoda;Lottiidae

Caenorhabditis elegans (Cele) Animalia;Nematoda;Secernentea;Rhabditida;Rhabditidae Schistosoma mansoni (Sman) Animalia;Platyhelminthes;Digenea;Strigeidida

Ixodes scapularis (Isca) Animalia;Arthropoda;Arachnida;Ixodida;Ixodidae Daphnia pulex (Dpul) Animalia;Arthropoda;Branchiopoda;Cladocera;Daphniidae Apis mellifera (Amel) Animalia;Arthropoda;Insecta;Hymenoptera;Apidae

Tribolium castaneum (Tcas) Animalia;Arthropoda;Insecta;Coleoptera;Tenebrionidae Drosophila melanogaster (Dmel) Animalia;Arthropoda;Insecta;Diptera;Drosophilidae

Bombyx mori (Bmor) Animalia;Arthropoda;Insecta;Lepidopteroa;Bombycidae Monosiga brevicollis (Mbre) hoanoflagellida;Codonosigidae

Nematostella vectensis (Nvec) Animalia;Cnidaria;Anthozoa;Actiniaria;Edwardsiidae Trichoplax adhaerens (Tadh) Animalia;Placozoa;Tricoplacia;Tricoplaciformes;Trichoplacidae


SUPPLEMENTARY INFORMATION RESEARCH

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Supplementary Table 2.Bipartitions that Significantly Conflict with the Bipartitions Recovered in the Concatenation Phylogeny of 23 Yeast Genomes

Primary Tree Bipartition GSF IC [Conflicting Bipartition]:GSF value Kthe, Kwal 99 0.96 None

Calb, Cdub 98 0.95 None

Sbay, Scer, Skud, Smik, Spar 99 0.97 None

Calb, Cdub, Cgui, Clus, Cpar, Ctro, Dhan, Lelo, Psti 95 0.90 None

Calb, Cdub, Ctro 90 0.78 None

Cpar, Lelo 89 0.77 None

Calb, Cdub, Cpar, Ctro, Lelo 86 0.76 None

Scer, Spar 77 0.54 [Sbay,Skud,Smik,Spar]:8; [Smik,Spar]:5

Cgla, Kpol, Sbay, Scas, Scer, Skud, Smik, Spar, Zrou 62 0.59 [Calb,Cdub,Cgla,Cgui,Clus,Cpar,Ctro,Dhan,Lelo,Psti]:6;

[Calb,Cdub,Cgui,Clus,Cpar,Ctro,Dhan,Lelo,Psti,Zrou]:5

Scer, Smik, Spar 60 0.30 [Sbay,Skud,Smik]:14; [Sbay,Scer,Skud,Spar]:11; [Sbay,Skud,Smik,Spar]:8; [Skud,Smik]:7 ; [Scer,Skud,Spar]:6

Scer, Skud, Smik ,Spar 52 0.06 [Sbay,Skud]:29; [Sbay,Skud,Smik]:14; [Sbay,Scer,Smik,Spar]:11; [Sbay,Scer,Skud,Spar]:11; [Sbay,Skud,Smik,Spar]:8

Calb, Cdub, Cpar, Ctro, Lelo, Psti 45 0.11 [Cgui,Clus,Dhan,Psti]:20; [Dhan,Psti]:11; [Cgui,Dhan,Psti]:10;

[Calb,Cdub,Cgui,Clus,Cpar,Ctro,Dhan,Lelo]:8; [Calb,Cdub,Clus,Cpar,Ctro,Lelo]:5; [Clus,Dhan,Psti]:5

Kthe, Kwal, Sklu 41 0.32

[Agos,Kthe,Kwal]:9; [Calb,Cdub,Cgui,Clus,Cpar,Ctro,Dhan,Kthe, Kwal,Lelo,Psti]:9; [Klac,Sklu]:8; [Agos,Klac,Kthe,Kwal]:7; [Agos,

Klac,Sklu]:7; [Agos,Sklu]:7; [Cgla,Kpol,Kthe,Kwal,Sbay,Scas, Scer,Skud,Smik,Spar,Zrou]:6; [Klac,Kthe,Kwal]:5; [Cgla,Kpol,

Sbay,Scas,Scer,Sklu,Skud,Smik,Spar,Zrou]:5

Agos, Klac 36 0.09

[Agos,Cgla,Kpol,Kthe,Kwal,Sbay,Scas,Scer,Sklu,Skud,Smik,Spar,Zrou]:17; [Cgla,Klac,Kpol,Kthe,Kwal,Sbay,Scas,Scer,Sklu,Skud,

Smik,Spar,Zrou]:13; [Agos,Kthe,Kwal,Sklu]:13; [Klac,Kthe,Kwal, Sklu]:10; [Agos,Kthe,Kwal]:9; [Klac,Sklu]:8; [Agos,Sklu]:7; [Cgla,

Klac,Kpol,Sbay,Scas,Scer,Skud,Smik,Spar,Zrou]:7; [Klac,Kthe, Kwal]:5

Agos, Klac, Kthe, Kwal, Sklu 31 0.04

[Agos,Calb,Cdub,Cgui,Clus,Cpar,Ctro,Dhan,Klac,Lelo,Psti]:19; [Calb,Cdub,Cgui,Clus,Cpar,Ctro,Dhan,Klac,Lelo,Psti]:17; [Agos, Calb,Cdub,Cgui,Clus,Cpar,Ctro,Dhan,Lelo,Psti]:13; [Calb,Cdub, Cgui,Clus,Cpar,Ctro,Dhan,Kthe,Kwal,Lelo,Psti]:9; [Agos,Cgla, Klac,Kpol,Sbay,Scas,Scer,Skud,Smik,Spar,Zrou]:7; [Cgla,Klac, Kpol,Sbay,Scas,Scer,Skud,Smik,Spar,Zrou]:7; [Cgla,Kpol,Kthe, Kwal,Sbay,Scas,Scer,Skud,Smik,Spar,Zrou]:6; [Cgla,Kpol,Sbay,

Scas,Scer,Sklu,Skud,Smik,Spar,Zrou]:5

Cgla, Sbay, Scas, Scer, Skud, Smik, Spar 29 0.12 [Cgla,Kpol]:12; [Kpol,Scas]:10; [Kpol,Sbay,Scas,Scer,Skud,Smik,

Spar,Zrou]:9; [Kpol,Sbay,Scas,Scer,Skud,Smik,Spar]:8; [Cgla,



RESEARCH

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Zrou]:8; [Kpol,Sbay,Scer,Skud,Smik,Spar]:8; [Sbay,Scer,Skud, Smik,Spar,Zrou]:7; [Sbay,Scas,Scer,Skud,Smik,Spar,Zrou]:7;

[Cgla,Kpol,Scas]:6; [Agos,Klac,Kpol,Kthe,Kwal,Sbay,Scas,Scer, Sklu,Skud,Smik,Spar,Zrou]:6; [Scas,Zrou]:5

Sbay, Scas, Scer, Skud, Smik, Spar 29 0.02 [Cgla,Sbay,Scer,Skud,Smik,Spar]:20; [Cgla,Scas]:17; [Kpol,

Scas]:10; [Kpol,Sbay,Scer,Skud,Smik,Spar]:8; [Sbay,Scer,Skud, Smik,Spar,Zrou]:7; [Cgla,Kpol,Scas]:6; [Scas,Zrou]:5

Calb, Cdub, Cgui, Cpar, Ctro, Dhan, Lelo, Psti 29 0.01

[Cgui,Clus,Dhan]:24; [Cgui,Clus,Dhan,Psti]:20; [Cgui,Clus]:20; [Calb,Cdub,Clus,Cpar,Ctro,Dhan,Lelo,Psti]:16; [Clus,Dhan]:12; [Calb,Cdub,Clus,Cpar,Ctro,Lelo,Psti]:9; [Calb,Cdub,Cgui,Clus, Cpar,Ctro,Dhan,Lelo]:8; [Calb,Cdub,Cgui,Clus,Cpar,Ctro,Lelo, Psti]:6; [Clus,Dhan,Psti]:5; [Calb,Cdub,Clus,Cpar,Ctro,Lelo]:5

Cgui, Dhan 29 0.02

[Cgui,Clus]:20; [Calb,Cdub,Cpar,Ctro,Dhan,Lelo,Psti]:18; [Calb,Cdub,Clus,Cpar,Ctro,Dhan,Lelo,Psti]:16; [Clus,Dhan]:12; [Dhan,Psti]:11; [Calb,Cdub,Cgui,Cpar,Ctro,Lelo,Psti]:6; [Calb,

Cdub,Cgui,Clus,Cpar,Ctro,Lelo,Psti]:6; [Clus,Dhan,Psti]:5

Cgla, Kpol, Sbay, Scas, Scer, Skud, Smik, Spar 24 0.02

[Kpol,Zrou]:17; [Cgla,Sbay,Scas,Scer,Skud,Smik,Spar,Zrou]:15; [Kpol,Sbay,Scas,Scer,Skud,Smik,Spar,Zrou]:9; [Cgla,Zrou]:8;

[Sbay,Scer,Skud,Smik,Spar,Zrou]:7; [Sbay,Scas,Scer,Skud,Smik, Spar,Zrou]:7; [Calb,Cdub,Cgla,Cgui,Clus,Cpar,Ctro,Dhan,Lelo,

Psti]:6; [Scas,Zrou]:5



a Maximum likelihood species phylogeny inferred using the GARLI software

b Bayesian inference species phylogeny inferred using the MrBayes software

0.2

Kluyveromyces lactis (Klac)

Candida parapsilosis (Cpar)

Pichia stipitis (Psti)

Saccharomyces bayanus (Sbay)

Candida lusitaniae (Clus)

Saccharomyces mikatae (Smik)

Debaryomyces hansenii (Dhan)

Candida dubliniensis (Cdub)Candida albicans (Calb)Candida tropicalis (Ctro)

Lodderomyces elongisporus (Lelo)

Kluyveromyces waltii (Kwal)

Eremothecium gossypii (Egos)Zygosaccharomyces rouxii (Zrou)

Kluyveromyces polysporus (Kpol)

Saccharomyces kudriavzevii (Skud)

Saccharomyces castellii (Scas)

Candida guilliermondii (Cgui)

Candida glabrata (Cgla)

Saccharomyces cerevisiae (Scer)

Saccharomyces kluyveri (Sklu)Kluyveromyces thermotolerans (Kthe)

Saccharomyces paradoxus (Spar)

0.1


Candida lusitaniae (Clus)Candida dubliniensis (Cdub)Candida albicans (Calb)Candida tropicalis (Ctro)

Pichia stipitis (Psti)Lodderomyces elongisporus (Lelo)

Kluyveromyces thermotolerans (Kthe)

Eremothecium gossypii (Egos)


Kluyveromyces lactis (Klac)Saccharomyces kluyveri (Sklu)





Saccharomyces bayanus (Sbay)Saccharomyces kudriavzevii (Skud)





Zygosaccharomyces rouxii (Zrou)

Supplementary Figure 1 | The topology of the yeast phylogeny recovered from concatenation analyses using one other maximum likelihood software (GARLI) and one other Bayesian inference (MrBayes) software was identical to the topology recovered by maxi-mum likelihood analysis using the RAxML software. a, The yeast species phylogeny recovered from concatenation analysis of 1,070 genes using maximum likelihood as implemented in the GARLI software. All internodes received 100% bootstrap support. b, The yeast species phylogeny recovered from concatenation analysis of 1,070 genes using Bayesian inference as implemented in the MrBayes software. All internodes had 100% posterior probability.



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0 10 20 30 40 50 60 70 80 90 100

2 conflicting bipartitions with support values X and 100-X3 conflicting bipartitions with values X, 95-X, and 5 of which only the two highest are used to calculate IC3 conflicting bipartitions with values X, 85-X, and 15 of which only the two highest are used to calculate IC3 conflicting bipartitions with values X, 75-X, and 25 of which only the two highest are used to calculate IC

Inte

rnod

e C

erta

inty

Support Value X

Supplementary Figure 2 | Representative values of the new measure Internode Certainty (IC) for a range of representative support values of two most prevalent and conflicting bipartitions for a given internode. Each plot on the graph depicts how IC (Y-axis) varies in response to the relative support of conflicting bipartitions on a given internode. IC can be measured on any given set of trees. For example, if the entire set of gene trees (GTs) is used, the IC value of a given internode will reflect the amount of information available for that internode in the set GTs by considering the internode’s gene support frequency jointly with the frequency of the most prevalent bipartition that conflicts with the internode. If the set of bootstrap replicate trees for a given gene is used, then IC will be calculated based on bootstrap support values. From the right to the left of the graph, the first of the four plots shown with triangle symbols corresponds to the case of only two conflicting biparti-tions for one internode with support values X and 100–X. For example, given 100 total GTs, if 60 of them support bipartition 1, the remaining 40 will support the conflicting bipartition. The second, third and fourth of the four plots (shown with diamond, circle, and square symbols, respectively) correspond to case where there are three conflicting bipartitions for one internode, but only the two most prevalent ones are considered. For example, in the plot with the diamond symbols, given 100 total GTs, if 60 of them support bipartition 1, 35 will support the conflicting bipartition 2, because conflicting bipartition 3 has been set to be supported by 5 GTs. Thus, when the two most prevalent ones are considered, the percentage of GTs supporting the first bipartition will be equal to 60/(60+35), whereas the percentage of GTs supporting the second bipartition will be 35/(60+35). The reason that the number of GTs that support the third conflicting bipartition is not included is because we want IC to measure the magnitude of certainty conveyed by the two most prevalent bipartitions. This way, IC will equal zero when the two most prevalent bipartitions are equally prevalent (in this example that would be the case if bipartitions 1 and 2 were each supported by 42.5 GTs each).



a Removing all sites containing gaps

b Removing all sites with ≥50% gaps

Concatenationphylogeny

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Candida albicans (Calb)

Debaryomyces hansenii (Dhan)Candida guilliermondii (Cgui)







Kluyveromyces polysporus (Kpol)Zygosaccharomyces rouxii (Zrou)




Candida tropicalis (Ctro)


Candida dubliniensis (Cdub)

Saccharomyces kluyveri (Sklu)




0.2








Candida dubliniensis (Cdub)Candida albicans (Calb)


Kluyveromyces thermotolerans (Kthe)Kluyveromyces waltii (Kwal)

Kluyveromyces lactis (Klac)Saccharomyces kluyveri (Sklu)



Kluyveromyces polysporus (Kpol)Candida glabrata (Cgla)





Saccharomyces bayanus (Sbay)Concatenation

phylogeny

eMRC phylogeny






















eMRC phylogeny






















33/0.0930/0.04

98/0.9537/0.26

95/0.90

28/0.00

59/0.5322/0.01

28/0.1029/0.02

98/0.9748/0.05

54/0.2470/0.48

30/0.04

44/0.07 87/0.7385/0.73

89/0.7698/0.95

95/0.88

99/0.9642/0.33

36/0.1032/0.05

29/0.01 30/0.03

45/0.0987/0.77

90/0.7898/0.94

90/0.75

61/0.5823/0.02

30/0.1629/0.02

99/0.9752/0.06

59/0.2775/0.46

c Removing genes whose alignment length following gap removal is ≤70% of the length of the original alignment (374 genes retained)

eMRC phylogeny






















100/1.00

98/0.9537/0.26

34/0.0831/0.05

29/0.01 30/0.02

43/0.1086/0.82

88/0.7499/0.97

89/0.77

63/0.5225/0.04

33/0.1629/0.03

99/0.9755/0.10

59/0.3076/0.55

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Candida lusitaniae (Clus)Candida dubliniensis (Cdub)


Pichia stipitis (Psti)Lodderomyces elongisporus (Lelo)

Candida tropicalis (Ctro)Candida parapsilosis (Cpar)


Candida glabrata (Cgla)Saccharomyces castellii (Scas)





Zygosaccharomyces rouxii (Zrou)Kluyveromyces polysporus (Kpol)







Supplementary Figure 3 | Removal of sites containing gaps or of poorly aligned genes does not significantly improve the yeast phylog-eny inferred by concatenation and eMRC approaches. Each panel shows the yeast species phylogeny inferred from concatenation analysis (left panel) and from extended majority rule consensus (eMRC) analysis (right panel). All internodes of phylogenies inferred by concatenation received 100% bootstrap support unless otherwise indicated. Values near internodes of phylogenies inferred by eMRC analysis correspond to gene support frequency and internode certainty, respectively. a, Concatenation (left) and eMRC (right) phylogenies of all 1,070 genes follow-ing removal of all sites containing gaps. b, Concatenation (left) and eMRC (right) phylogenies of all 1,070 genes following removal of all sites where ≥50% of the character states are gaps. c, Concatenation (left) and eMRC (right) phylogenies of the 374 genes whose alignment length following removal of all gaps is ≥70% of the length of the original alignment.



RESEARCH

Excluding Candida lusitaniae (Clus)

b Excluding Kluyveromyces polysporus (Kpol)













Candida parapsilosis (Cpar)Candida tropicalis (Ctro)







37/0.13

98/0.9442/0.31

31/0.05

95/0.88

eMRC phylogeny

61/0.5723/0.01

29/0.1230/0.03

99/0.9752/0.05

58/0.2875/0.5499/0.96

90/0.8084/0.68

89/0.7643/0.02

48/0.06










Saccharomyces cerevisiae (Scer)Candida lusitaniae (Clus)










95/0.89

eMRC phylogeny

99/0.9539/0.31

36/0.1031/0.04

66/0.5542/0.20

35/0.0499/0.96

53/0.0661/0.30

77/0.54

28/0.00 29/0.02

98/0.9591/0.79

91/0.7787/0.78

46/0.10

a

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Saccharomyces castellii (Scas)Candida glabrata (Cgla)














c Excluding Candida glabrata (Cgla)

0.2Candida albicans (Calb)
















Candida guilliermondii (Cgui)Debaryomyces hansenii (Dhan)






eMRCphylogeny




















98/0.9640/0.26

36/0.1030/0.03

96/0.88

66/0.6030/0.02

52/0.2699/0.98

51/0.0560/0.28

76/0.51

27/0.00

29/0.02

46/0.09

86/0.74

98/0.9590/0.79

89/0.77

Supplementary Figure 4 | Removal of one or more unstable or fast-evolving species has, if any, a minor and local effect on the yeast phylogeny inferred by concatenation and eMRC approaches. Each panel shows the yeast species phylogeny inferred from concatenation analysis (left panel) and from extended majority rule consensus (eMRC) analysis (right panel) following removal of one or more unstable or fast-evolving species from the analysis. All internodes of phylogenies inferred by concatenation received 100% bootstrap support unless other-wise indicated. Values near internodes of phylogenies inferred by eMRC analysis correspond to gene support frequency and internode certainty, respectively. a, Concatenation (left) and eMRC (right) phylogenies of all 1,070 genes following the removal of the unstable taxon Candida lusitaniae. b, Concatenation (left) and eMRC (right) phylogenies of all 1,070 genes following the removal of the fast-evolving and unstable taxon Kluyveromyces polysporus. c, Concatenation (left) and eMRC (right) phylogenies of all 1,070 genes following the removal of the fast-evolving and unstable taxon Candida glabrata.



d Excluding Saccharomyces castellii (Scas)

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eMRCphylogeny




















99/0.9641/0.31

34/0.0830/0.04

95/0.90

62/0.5425/0.01

40/0.1699/0.97

52/0.0660/0.28

77/0.54

28/0.00

29/0.02

46/0.10

86/0.7690/0.77

90/0.7898/0.94

Excluding Eremothecium gossypii (Egos)

Excluding Kluyveromyces lactis (Klac) f

e


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Candida parapsilosis (Cpar)Lodderomyces elongisporus (Lelo)


Saccharomyces cerevisiae (Scer)Saccharomyces paradoxus (Spar)

















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Lodderomyces elongisporus (Lelo)Candida parapsilosis (Cpar)














Saccharomyces castellii (Scas)Saccharomyces bayanus (Sbay)

Saccharomyces mikatae (Smik)Concatenationphylogeny




















95/0.90

eMRC phylogeny

99/0.9550/0.23

37/0.01

61/0.5323/0.01

29/0.1229/0.02

99/0.9752/0.06

60/0.3178/0.55

29/0.0029/0.02

45/0.09

85/0.7489/0.74

90/0.7898/0.96




















95/0.86

eMRC phylogeny

98/0.9644/0.16

40/0.04

59/0.5123/0.01

29/0.1229/0.02

99/0.9753/0.06

60/0.3078/0.57

29/0.0229/0.00

45/0.11

85/0.7590/0.79

90/0.78

98/0.96

Supplementary Figure 4 | ...continued. d, Concatenation (left) and eMRC (right) phylogenies of all 1,070 genes following the removal of the unstable taxon Saccharomyces castellii. e, Concatenation (left) and eMRC (right) phylogenies of all 1,070 genes following the removal of the fast-evolving and unstable taxon Eremothecium gossypii. f, Concatenation (left) and eMRC (right) phylogenies of all 1,070 genes following the removal of the fast-evolving and unstable taxon Kluyveromyces lactis.


1 0 | W W W. N A T U R E . C O M / N A T U R E

RESEARCH

Excluding Eremothecium gossypii (Egos) and Kluyveromyces lactis (Klac)

Excluding Eremothecium gossypii (Egos), Kluyveromyces lactis (Klac) and Candida glabrata (Cgla)

g

h

0.2Candida dubliniensis (Cdub)







Lodderomyces elongisporus (Lelo)Pichia stipitis (Psti)





Zygosaccharomyces rouxii (Zrou)Saccharomyces kluyveri (Sklu)




Saccharomyces kudriavzevii (Skud)Saccharomyces mikatae (Smik)



0.2










Pichia stipitis (Psti)Candida guilliermondii (Cgui)



Candida tropicalis (Ctro)Candida parapsilosis (Cpar)

Saccharomyces kluyveri (Sklu)Kluyveromyces thermotolerans (Kthe)





96/0.87

eMRCphylogeny



















99/0.9666/0.29

57/0.4221/0.01

29/0.1228/0.02

98/0.9752/0.06

60/0.3076/0.53

29/0.00 29/0.02

46/0.10

86/0.7489/0.74

90/0.7898/0.96

96/0.85

eMRC phylogeny


















99/0.9565/0.25

60/0.4327/0.02

49/0.2198/0.98

50/0.0460/0.28

75/0.52

28/0.0028/0.01

46/0.10

86/0.75

89/0.77

89/0.7798/0.94

Supplementary Figure 4 | ...continued. g, Concatenation (left) and eMRC (right) phylogenies of all 1,070 genes following the removal of both Eremothecium gossypii and Kluyveromyces lactis. h, Concatenation (left) and eMRC (right) phylogenies of all 1,070 genes following the removal of Eremothecium gossypii, Kluyveromyces lactis and Candida glabrata.

W W W. N A T U R E . C O M / N A T U R E | 1 1


b

a

0

10

30

40

excluding Egosexcluding Cglaexcluding Klacexcluding Egos, Klacexcluding Cgla, Klacexcluding Egos, Cglaexcluding Egos, Cgla, Klac

50

20

Calb,C

dub

Calb,C

dub,C

tro

Cpar,L

elo

Calb,C

dub,C

par,C

tro,Le

lo

Calb,C

dub,C

par,C

tro,Le

lo,Psti

Cgui,D

han

Calb,C

dub,C

gui,C

par,C

tro,D

han,L

elo,Psti

Calb,C

dub,C

gui,C

lus,C

par,C

tro,D

han,L

elo,Psti

Egos,K

lac

Kthe,K

wal

Kthe,K

wal,Sklu

Egos,K

lac,K

the,K

wal,Sklu

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r,Zrou

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Cgla,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Sbay,S

cas,S

cer,S

kud,S

mik,Spa

r

Scer,S

kud,S

mik,Spa

r

Sbay,S

cer,S

kud,S

mik,Spa

r

Scer,S

mik,Spa

r

Scer,S

par

Cha

nge

in G

SF c

ompa

red

to d

efau

lt an

alys

is

Candid

a

bipartit

ions

Sacch

aromyce

s

bipartit

ions

-10

selecting [Cgla,Sbay,Scer,Skud,Smik,Spar]selecting [Cgla,Kpol,Sbay,Scas,Scer,Skud,Smik,Spar, Zrou]selecting [Calb,Cdub,Ctro]

0

10

30

40

50

20

Cha

nge

in G

SF c

ompa

red

to d

efau

lt an

alys

is

-10

Calb,C

dub

Calb,C

dub,C

tro

Cpar,L

elo

Calb,C

dub,C

par,C

tro,Le

lo

Calb,C

dub,C

par,C

tro,Le

lo,Psti

Cgui,D

han

Calb,C

dub,C

gui,C

par,C

tro,D

han,L

elo,Psti

Calb,C

dub,C

gui,C

lus,C

par,C

tro,D

han,L

elo,Psti

Egos,K

lac

Kthe,K

wal

Kthe,K

wal,Sklu

Egos,K

lac,K

the,K

wal,Sklu

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r,Zrou

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Cgla,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Sbay,S

cas,S

cer,S

kud,S

mik,Spa

r

Sbay,S

cer,S

kud,S

mik,Spa

r

Scer,S

kud,S

mik,Spa

r

Scer,S

mik,Spa

r

Scer,S

par

Candid

a

bipartit

ions

Sacch

aromyce

s

bipartit

ions

Supplementary Figure 5 | Removal of fast-evolving and unstable species or the exclusive use of genes that recover specific bipartitions has a minor and typically local effect on GSF values of internodes of the yeast phylogeny. The X-axis shows the 20 bipartitions present in the yeast phylog-eny suggested by concatenation analysis and the Y-axis the percent change in gene support frequency (GSF) observed for each bipartition between the treatment and the default analysis. Only GSF changes ≥3% are shown. a, The individual or combined removal of E. gossypii (Egos), K. lactis (Klac), and C. glabrata (Cgla), three of the fastest evolving species as well as of those whose phylogenetic position is most unstable from the dataset has a minor and local effect on the GSF of neighboring internodes. Note that removal of species in the Saccharomyces lineage does not change the GSF of bipartitions in the Candida lineage. b, The selection of genes whose individual topologies recover well-established bipartitions of the yeast phylogeny has a minor effect on the GSF of internodes of the yeast phylogeny. Note that the [C. albicans, C. dubliniensis, C. tropicalis] (abbreviated [Calb, Cdub, Ctro]) bipartition has 90% GSF in the eMRC phylogeny reconstructed from the 1,070 individual gene trees, the [C. glabrata, K. polysporus, S. bayanus, S. castellii, S. cerevisiae, S. kudriavzevii, S. mikatae, S. paradoxus, Z. rouxii] (abbreviated [Zrou, Kpol, Cgla, Sbay, Skud, Smik, Scer, Spar]) biparti-tion has 62% GSF, and the [C. glabrata, S. bayanus, S. cerevisiae, S. kudriavzevii, S. mikatae, S. paradoxus] (abbreviated [Cgla, Sbay, Skud, Smik, Scer, Spar]) bipartition has 20% GSF. This last bipartition does not appear in the eMRC phylogeny but several independent rare genomic changes strongly suggest that it is the correct one.

Change in GSF when removing fast-evolving and unstable species

Change in GSF when using only genes that supportspecific, likely correct, bipartitions



RESEARCH

0.2

0.3

0.4

0.5

0.1

0

-0.1

-0.2Cha

nge

in IC

com

pare

d to

def

ault

anal

ysis

excluding Egosexcluding Cglaexcluding Klacexcluding Egos, Klacexcluding Cgla, Klacexcluding Egos, Cglaexcluding Egos, Cgla, Klac

Calb,C

dub

Calb,C

dub,C

tro

Cpar,L

elo

Calb,C

dub,C

par,C

tro,Le

lo

Calb,C

dub,C

par,C

tro,Le

lo,Psti

Cgui,D

han

Calb,C

dub,C

gui,C

par,C

tro,D

han,L

elo,Psti

Calb,C

dub,C

gui,C

lus,C

par,C

tro,D

han,L

elo,Psti

Egos,K

lac

Kthe,K

wal

Kthe,K

wal,Sklu

Egos,K

lac,K

the,K

wal,Sklu

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r,Zrou

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Cgla,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Sbay,S

cas,S

cer,S

kud,S

mik,Spa

r

Scer,S

kud,S

mik,Spa

r

Sbay,S

cer,S

kud,S

mik,Spa

r

Scer,S

mik,Spa

r

Scer,S

par

Candid

a

bipartit

ions

Sacch

aromyce

s

bipartit

ions

- 0.1

0

0.1

0.2

0.3

0.4

0.5

Cha

nge

in IC

com

pare

d to

def

ault

anal

ysis

selecting {Cgla,Sbay,Scer,Skud,Smik,Spar}selecting {Cgla,Kpol,Sbay,Scas,Scer,Skud,Smik,Spar, Zrou}selecting {Calb,Cdub,Ctro}

Calb,C

dub

Calb,C

dub,C

tro

Cpar,L

elo

Calb,C

dub,C

par,C

tro,Le

lo

Calb,C

dub,C

par,C

tro,Le

lo,Psti

Cgui,D

han

Calb,C

dub,C

gui,C

par,C

tro,D

han,L

elo,Psti

Calb,C

dub,C

gui,C

lus,C

par,C

tro,D

han,L

elo,Psti

Egos,K

lac

Kthe,K

wal

Kthe,K

wal,Sklu

Egos,K

lac,K

the,K

wal,Sklu

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r,Zrou

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Cgla,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Sbay,S

cas,S

cer,S

kud,S

mik,Spa

r

Scer,S

kud,S

mik,Spa

r

Sbay,S

cer,S

kud,S

mik,Spa

r

Scer,S

mik,Spa

r

Scer,S

par

Candid

a

bipartit

ions

Sacch

aromyce

s

bipartit

ions

a

b

Change in IC when removing fast-evolving and unstable species

Change in IC when using only genes that supportspecific, likely correct, bipartitions

Supplementary Figure 6 | Removal of fast-evolving and unstable species or the exclusive use of genes that recover specific bipartitions has a minor and typically local effect on IC values of internodes of the yeast phylogeny. The X-axis shows the 20 bipartitions present in the yeast phylog-eny suggested by concatenation analysis and the Y-axis the percent change in Internode Certainty (IC) observed for each bipartition between the treatment (removal of fast-evolving and unstable species or of genes that fail to recover specific clades) and the default analysis (all species and genes included). Only GSF changes ≥3% are shown. a, The individual or combined removal of E. gossypii (Egos), K. lactis (Klac), and C. glabrata (Cgla), three of the fastest evolving species as well as of those whose phyloge-netic position is most unstable from the dataset has a minor and local effect on the IC of neighboring internodes. b, The selection of genes whose individual topologies recover well-established bipartitions of the yeast phylogeny has a minor effect on the IC of internodes of the yeast phylogeny. Note that the [C. albicans, C. dubliniensis, C. tropicalis] (abbreviated [Calb, Cdub, Ctro]) bipartition has 90% GSF in the extended majority rule consensus (eMRC) phylogeny reconstructed from the 1,070 individual gene trees, the [C. glabrata, K. polysporus, S. bayanus, S. castellii, S. cerevisiae, S. kudriavzevii, S. mikatae, S. paradoxus, Z. rouxii] (abbreviated [Zrou, Kpol, Cgla, Sbay, Skud, Smik, Scer, Spar]) biparti-tion has 62% GSF, and the [C. glabrata, S. bayanus, S. cerevisiae, S. kudriavzevii, S. mikatae, S. paradoxus] (abbreviated [Cgla, Sbay, Skud, Smik, Scer, Spar]) bipartition has 20% GSF. This last bipartition does not appear in the eMRC phylogeny but, as discussed in the main text, several indepen-dent rare genomic changes strongly suggest that it is the correct one.



a

b

Using only genes that recover the [Calb,Cdub,Ctro] bipartition

Using only genes that recover the [Cgla,Kpol,Sbay,Scas,Scer,Skud,Smik,Spar,Zrou] bipartition

Concatenationphylogeny0.3
























0.2












































96/0.90

eMRC phylogeny

99/0.9642/0.33

36/0.0931/0.04

63/0.5924/0.02

29/0.1129/0.02

99/0.9953/0.06

61/0.3078/0.57

30/0.01

47/0.13

30/0.03

89/0.77100/1.00

90/0.76

99/0.95




















Candida lusitaniae (Clus)98/0.92

eMRC phylogeny

99/0.9641/0.24

37/0.03

100/1.00

28/0.01

31/0.0336/0.15

29/0.0199/0.98

54/0.0762/0.31

79/0.57

32/0.01 28/0.01

47/0.10

86/0.6990/0.76

91/0.8099/0.96

Using only genes that recover the [Cgla,Sbay,Scas,Scer,Skud,Smik,Spar] bipartition


0.3







Candida guilliermondii (Cgui)Pichia stipitis (Psti)














c





















97/0.92

eMRC phylogeny

99/0.9641/0.31

35/0.0630/0.01

71/0.6228/0.00

51/0.21100/1.00

100/0.9655/0.09

60/0.3679/0.63

32/0.02

44/0.08

31/0.03

83/0.6689/0.75

93/0.81100/1.00

Supplementary Figure 7 | Selection of genes that support specific bipartitions has, if any, a minor and local effect on the yeast phylog-eny inferred by concatenation and eMRC approaches. Each panel shows the yeast species phylogeny inferred from concatenation analysis (left panel) and from extended majority rule consensus (eMRC) analysis (right panel) following the selection and use of genes that recover specific bipartitions. All internodes of phylogenies inferred by concatenation received 100% bootstrap support unless otherwise indicated. Values near internodes of phylogenies inferred by eMRC analysis correspond to gene support frequency and internode certainty, respectively. a, Concatenation (left) and eMRC (right) phylogenies using only the genes that recover the [C. albicans, C. dubliniensis, C. tropicalis] (abbreviated [Calb, Cdub, Ctro]) bipartition. b, Concatenation (left) and eMRC (right) phylogenies using only the genes that recover the [C. glabrata, K. polysporus, S. bayanus, S. castellii, S. cerevisiae, S. kudriavzevii, S. mikatae, S. paradoxus, Z. rouxii] (abbreviated [Zrou, Kpol, Cgla, Sbay, Skud, Smik, Scer, Spar]) bipartition. c, Concatenation (left) and eMRC (right) phylogenies using only the genes that recover the [C. glabrata, S. bayanus, S. cerevisiae, S. kudriavzevii, S. mikatae, S. paradoxus] (abbreviated [Cgla, Sbay, Skud, Smik, Scer, Spar]) bipartition. This last bipartition does not appear in the eMRC phylogeny but, as discussed in the main text, several independent rare genomic changes strongly suggest that it is the correct one.



RESEARCH

Selecting the 100 most slowly-evolving genes

100/1.00

eMRC phylogeny





















97/0.92

29/0.07

18/0.0411/0.00

60/0.4122/0.01

26/0.1027/0.03

97/0.9245/0.05

40/0.0847/0.16

29/0.01 23/0.00

86/0.6943/0.2274/0.66

95/0.8675/0.54


0.06












Saccharomyces kudriavzevii (Skud)Saccharomyces bayanus (Sbay)











9882

99

95

79

63

Supplementary Figure 8 | Selection of the 100 slowest-evolving genes has a large, negative effect on GSF and IC values of internodes of the yeast phylogeny inferred by concatenation and eMRC approaches. Each panel shows the yeast species phylogeny inferred from concatenation analysis (left panel) and from extended majority rule consensus (eMRC) analysis (right panel) following the selection and use of the 100 slowest-evolving genes. All internodes of phylogenies inferred by concatenation received 100% bootstrap support unless otherwise indicated. Values near internodes of phylogenies inferred by eMRC analysis correspond to gene support frequency and internode certainty, respectively.



00.10.20.30.40.50.60.70.80.9

1

Using only sites that contain single radical substitutions

Using only indels

Using only sites that contain a single substitution betweenphysicochemically different amino acids

Using only sites that contain a single rare but conserved amino acid substitution or indels

Inte

rnod

e C

erta

inty

Calb,C

dub

Calb,C

dub,C

tro

Cpar,L

elo

Calb,C

dub,C

par,C

tro,Le

lo

Calb,C

dub,C

par,C

tro,Le

lo,Psti

Cgui,D

han

Calb,C

dub,C

gui,C

par,C

tro,D

han,L

elo,Psti

Calb,C

dub,C

gui,C

lus,C

par,C

tro,D

han,L

elo,Psti

Egos,K

lac

Kthe,K

wal

Kthe,K

wal,Sklu

Egos,K

lac,K

the,K

wal,Sklu

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r,Zrou

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Cgla,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Sbay,S

cas,S

cer,S

kud,S

mik,Spa

r

Scer,S

kud,S

mik,Spa

r

Sbay,S

cer,S

kud,S

mik,Spa

r

Scer,S

mik,Spa

r

Scer,S

par

Candid

a

bipartit

ions

Sacch

aromyce

s

bipartit

ions

Supplementary Figure 9 | Selection of sites that contain a single rare but conserved amino acid substitution or indels has a large, negative effect on GSF and IC values of internodes of the yeast phylogeny. The X-axis shows the 20 bipartitions present in the yeast phylogeny suggested by concatenation analysis and the Y-axis the percent change in Internode Certainty (IC) observed for each bipartition between the treatment (selection of specific sites or indels) and the default analysis (all sites included). Only GSF changes ≥3% are shown. The red bars correspond to changes in IC when using only the 20,289 sites that contain single radical substitutions (defined as a substitution with a blosum62 matrix score ≤–3), the blue bars correspond to changes in IC when using only the 4,075 sites that contain a single substitution between amino acids that differ radically in their physicochemical properties, and the yellow bars correspond to changes in IC when using only the 2,474 characters which mark the presence / absence of a single indel that spans 7 or more aa among the 23 yeast species.



RESEARCH

c

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

Inte

rnod

e C

erta

inty

Internode Certainty values for all internodes of the Vertebrate species phylogeny

a

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400

600

800

1000

Num

ber o

f Gen

e Tr

ees

Normalized Robinson-Foulds Tree Distance

1,086 observed gene trees1,000 random gene trees

0 0.2 0.4 0.6 0.8 1

Distribution of vertebrate gene tree distancesfrom the Concatenation species phylogeny

0.30; Average distance between 1,086 gene trees and the concatenation phylogeny

0.42; Average distance between the 1,086 gene trees

X. tropicalisG. gallus

M. domesticaB. taurus

E. caballusC. familiaris

P. pygmaeusH. sapiensP. troglodytes

R. norvegicusM. musculus

C. porcellusD. rerio

O. latipesT. nigroviridis

T. rubripesG. aculeatus

*/87 */46

*/89

*/22

*/86

*/61*/71

*/34

*/52

*/94

*/91

*/46

*/95

M. mulatta

Vertebrate Concatenation phylogeny

0.2

b

*/98

*/80

Supplementary Figure 10 | High levels of incon-gruence in Vertebrate and Metazoan phyloge-nomic datasets despite the inference of highly supported phylogenies by concatenation analysis. a, The distribution of the agreement between the bipartitions present in the 1,086 individual gene trees (GTs) and the vertebrate concatenation phylogeny, as well as the distribution of the agreement between the bipartitions present in 1,000 randomly generated trees of equal taxon number and the concatenation phylogeny, measured using the normalized Robinson-Foulds tree distance. The average tree distances between the 1,086 GTs and the concatena-tion phylogeny as well as between the 1,086 GTs with each other are also shown. b, The vertebrate species phylogeny recovered from concatenation analysis of 1,086 genes using maximum likelihood. The extended majority rule consensus (eMRC) phylogeny is topologically identical to the concat-enation phylogeny. Values near internodes corre-spond to bootstrap support and gene support frequency (GSF), respectively. Asterisks (*) denote internodes that received 100% bootstrap support by the concatenation analysis. c, The distribution of Internode Certainty (IC) values for all internodes of the vertebrate species phylogeny.



0

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S. purpuratusB. floridae

C. intestinalisG. gallusM. musculusH. sapiens

X. tropicalisD. rerio

H. robustaL. gigantea

C. elegansS. mansoni

I. scapularisD. pulex

A. melliferaT. castaneum

D. melanogasterB. mori

N. vectensisT. adhaerens

M. brevicollis

*/1059/12

*/23

*/97*/67

*/76

*/94*/19

*/10

98/29

*/72

*/35

*/39 */59

92/05

*/23

95/25

*/50

Metazoan Concatenation phylogeny

0.3

Internode Certainty values for all internodes of the Metazoan species phylogeny

d

0

40

80

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160

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Num

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Normalized Robinson-Foulds Tree Distance

Distribution of metazoan gene tree distancesfrom the Concatenation species phylogeny

225 observed gene trees1,000 random gene trees

Average distance between 0.60225 gene trees and the

concatenation phylogeny

Average distance between 0.72the 225 gene trees

Supplementary Figure 10 | ...continued. d, The distribution of the agreement between the biparti-tions present in the 225 individual GTs and the metazoan concatenation phylogeny, as well as the distribution of the agreement between the biparti-tions present in 1,000 randomly generated trees of equal taxon number and the concatenation phylog-eny, measured using the normalized Robinson-Foulds tree distance. The average tree distances between the 225 GTs and the concatenation phylo-geny as well as between the 225 GTs with each other are also shown. e, The metazoan species phylogeny recovered from concatenation analysis of 225 genes using maximum likelihood. The eMRC phylogeny is topologically identical to the concatenation phylo-geny. Values near internodes correspond to bootstrap support and gene support frequency, respectively. Asterisks (*) denote internodes that received 100% bootstrap support by the concatenation analysis. f, The distribution of IC values for all internodes of the metazoan species phylogeny. Note that GSF and IC values indicate the existence of numerous internodes in the vertebrate and especially in the metazoan phylogeny that are supported by a small percentage of gene trees and have very small or zero IC values.



RESEARCH

a

b

Using only the 904 genes whose bootstrap consensus trees have average Bootstrap Support ≥60%

Using only the 545 genes whose bootstrap consensus trees have average Bootstrap Support ≥70%


0.3





















Candida lusitaniae (Clus)Candida dubliniensis (Cdub)



98/0.93

eMRC phylogeny





















100/0.99

38/0.09

43/0.3232/0.03

67/0.6225/0.02

32/0.1330/0.02

99/0.9555/0.07

63/0.3581/0.60

31/0.01 30/0.02

48/0.11

90/0.7793/0.80

99/0.97

92/0.80

0.3Candida tropicalis (Ctro)












Saccharomyces mikatae (Smik)Saccharomyces paradoxus (Spar)










7399/0.96

eMRC phylogeny





















100/1.0048/0.37

41/0.1034/0.02

75/0.6327/0.02

38/0.2131/0.02

100/0.9860/0.11

69/0.4288/0.68

33/0.02 31/0.02

55/0.1593/0.84

96/0.84

96/0.8399/0.97

Using only the 131 genes whose bootstrap consensus trees have average Bootstrap Support ≥80% c

0.3Candida albicans (Calb)















Kluyveromyces thermotolerans (Kthe)Saccharomyces kluyveri (Sklu)

Kluyveromyces polysporus (Kpol)Saccharomyces castellii (Scas)






98

95






















100/1.00

eMRC phylogeny

100/1.0051/0.36

52/0.1334/0.00

89/0.7931/0.01

49/0.2129/0.00

100/1.0073/0.30

85/0.6898/0.84

44/0.03

62/0.17

37/0.01

96/0.8896/0.84

98/0.89100/1.00

Supplementary Figure 11 | Selection of genes whose bootstrap consensus trees have high average Bootstrap Support (avBS) or Tree Certainty (TC) has a large, positive effect on GSF and IC values of internodes of the yeast phylogeny inferred by concatenation and eMRC approaches. Each panel shows the yeast species phylogeny inferred from concatenation analysis (left panel) and from extended majority rule consensus (eMRC) analysis (right panel) following the selection of genes whose trees have high average bootstrap support (BS) or Tree Certainty (TC). All internodes of phylogenies inferred by concatenation received 100% bootstrap support unless otherwise indicated. Values near internodes of phylogenies inferred by eMRC analysis correspond to gene support frequency and internode certainty, respectively. a, Concatena-tion (left) and eMRC (right) phylogenies of the 904 genes whose gene trees have average BS ≥60%. b, Concatenation (left) and eMRC (right) phylogenies of the 545 genes whose gene trees have average BS ≥70%. c, Concatenation (left) and eMRC (right) phylogenies of the 131 genes whose gene trees have average BS ≥80%.



Using only the 545 genes whose bootstrap consensus trees have highest Tree Certainty

Using only the 131 genes whose bootstrap consensus trees have highest Tree Certainty

e

f

0.3












Kluyveromyces thermotolerans (Kthe)Saccharomyces kluyveri (Sklu)









96

0.3







Candida albicans (Calb)Candida dubliniensis (Cdub)







Eremothecium gossypii (Egos)Zygosaccharomyces rouxii (Zrou)





Saccharomyces castellii (Scas)Candida glabrata (Cgla)



64






















98/0.94

eMRC phylogeny

100/0.9849/0.41

42/0.1033/0.01

74/0.6526/0.02

37/0.1833/0.03

99/0.9861/0.12

71/0.4488/0.70

34/0.02 31/0.02

55/0.1795/0.87

96/0.85

98/0.89100/0.98






















100/1.00

eMRC phylogeny

100/1.0051/0.41

50/0.0934/0.00

89/0.7930/0.02

47/0.1432/0.01

100/1.0075/0.32

84/0.6797/0.84

40/0.03

64/0.2198/0.93

37/0.01

97/0.88

98/0.93100/1.00

Using only the 904 genes whose bootstrap consensus trees have highest Tree Certaintyd

0.2














































97/0.92

eMRC phylogeny

100/0.9743/0.34

38/0.0932/0.03

66/0.6025/0.02

31/0.1330/0.02

100/0.9955/0.08

63/0.3582/0.62

32/0.01 30/0.02

48/0.11

90/0.7892/0.82

93/0.8299/0.98

Supplementary Figure 11 | ...continued. d, Concatenation (left) and eMRC (right) phylogenies of the 904 genes with the highest TC. e, Concat-enation (left) and eMRC (right) phylogenies of the 545 genes with the highest TC. f, Concatenation (left) and eMRC (right) phylogenies of the 131 genes with the highest TC.



RESEARCH

0.5

0.4

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0

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0.5

Cha

nge

in IC

com

pare

d to

def

ault

anal

ysis

Calb,C

dub

Calb,C

dub,C

tro

Cpar,L

elo

Calb,C

dub,C

par,C

tro,Le

lo

Calb,C

dub,C

par,C

tro,Le

lo,Psti

Cgui,D

han

Calb,C

dub,C

gui,C

par,C

tro,D

han,L

elo,Psti

Calb,C

dub,C

gui,C

lus,C

par,C

tro,D

han,L

elo,Psti

Egos,K

lac

Kthe,K

wal

Kthe,K

wal,Sklu

Egos,K

lac,K

the,K

wal,Sklu

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r,Zrou

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Cgla,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Sbay,S

cas,S

cer,S

kud,S

mik,Spa

r

Scer,S

kud,S

mik,Spa

r

Sbay,S

cer,S

kud,S

mik,Spa

r

Scer,S

mik,Spa

r

Scer,S

par

Candid

a

bipartit

ions

Sacch

aromyce

s

bipartit

ions

Using only the 131 genes with average BS ≥80%Using only the 131 genes with the highest TC

Using only the 100 slowest evolving genesUsing only bipartitions with BS ≥80%

Change in Internode Certainty for highly supported genes, bipartitions or slow evolving genes

-45

-35

-25

-15

-505

15

25

35

45

Using only the 131 genes with average BS ≥80%

Using only the 100 slowest evolving genesUsing only the 131 genes with the highest TC

Calb,C

dub

Calb,C

dub,C

tro

Cpar,L

elo

Calb,C

dub,C

par,C

tro,Le

lo

Calb,C

dub,C

par,C

tro,Le

lo,Psti

Cgui,D

han

Calb,C

dub,C

gui,C

par,C

tro,D

han,L

elo,Psti

Calb,C

dub,C

gui,C

lus,C

par,C

tro,D

han,L

elo,Psti

Egos,K

lac

Kthe,K

wal

Kthe,K

wal,Sklu

Egos,K

lac,K

the,K

wal,Sklu

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r,Zrou

Cgla,K

pol,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Cgla,S

bay,S

cas,S

cer,S

kud,S

mik,Spa

r

Sbay,S

cas,S

cer,S

kud,S

mik,Spa

r

Sbay,S

cer,S

kud,S

mik,Spa

r

Scer,S

kud,S

mik,Spa

r

Scer,S

mik,Spa

r

Scer,S

par

Candid

a

bipartit

ions

Sacch

aromyce

s

bipartit

ions

Cha

nge

in G

SF c

ompa

red

to d

efau

lt an

alys

is

b

Change in Gene Support Frequency for highly supported genes or slow evolving genes a

Supplementary Figure 12 | Selecting highly supported genes or bipartitions has a large, positive effect on GSF and IC values of internodes of the yeast phylogeny. The X-axis shows the 20 bipartitions present in the yeast phylogeny suggested by concat-enation analysis and the Y-axis the percent change in Gene Support Frequency (GSF) and Internode Certainty (IC) observed for each bipartition between the treatment (selection of highly supported genes or internodes) and the default analysis. Only GSF changes ≥3% and IC changes ≥0.03 are shown. The red bars correspond to changes in IC when using only the 131 genes with average bootstrap support ≥80%, the yellow bars correspond to changes in IC when using only the 131 genes with the highest Tree Certainty, the black bars correspond to changes in IC when using only those bipartitions found in the bootstrap consensus trees of individual genes that had bootstrap support ≥80%, and the blue bars correspond to changes in IC when using only the 100 slowest-evolving genes. a, Change in GSF for highly supported genes or slow evolving genes. b, Change in IC for highly supported genes, bipartitions or slow evolving genes.



Using only bipartitions that received ≥60 bootstrapsupport in individual gene tree analysesa

c

b Using only bipartitions that received ≥70 bootstrapsupport in individual gene tree analyses

Using only bipartitions that received ≥80 bootstrapsupport in individual gene tree analyses





















Candida lusitaniae (Clus)eMRCphylogeny






















eMRC phylogeny









Candida lusitaniae (Clus)eMRC

phylogeny

d

0

0.2

0.4

0.6

0.8

1

Defaultanalysis

Using bipartitions ≥60 BS in individualgene tree analyses

Kthe,KwalCalb,CdubSbay,Scer,Skud,Smik,SparCalb,Cdub,Cgui,Clus,Cpar,Ctro,Dhan,Lelo,PstiCalb,Cdub,CtroCpar,LeloCgla,Kpol,Sbay,Scas,Scer,Skud,Smik,Spar,Zrou

Calb,Cdub,Cpar,Ctro,LeloScer,Spar

Scer,Smik,SparScer,Skud,Smik,SparCalb,Cdub,Cpar,Ctro,Lelo,PstiKthe,Kwal,SkluEgos,Klac

Egos,Klac,Kthe,Kwal,SkluCgla,Sbay,Scas,Scer,Skud,Smik,SparSbay,Scas,Scer,Skud,Smik,SparCalb,Cdub,Cgui,Cpar,Ctro,Dhan,Lelo,PstiCgui,DhanCgla,Kpol,Sbay,Scas,Scer,Skud,Smik,Spar



Inte

rnod

e C

erta

inty

Change in Internode Certainty when using bipartitions thatwere highly supported in individual gene analyses

18/0.09

94/0.94

98/0.99

22/0.15

25/0.49

48/0.7410/0.02

18/0.3016/0.03

98/0.9936/0.08

37/0.4767/0.74

31/0.00

15/0.13

20/0.08

81/0.8883/0.87

85/0.8997/0.97

94/0.95

14/0.1117/0.23

18/0.5198/1.00

41/0.777/0.02

14/0.3311/0.01

97/0.9930/0.14

31/0.5459/0.80

12/0.01 15/0.10

27/0.17 96/0.8975/0.93

82/0.9396/0.99

94/0.96

96/1.0012/0.58

Eremothecium gossypii (Egos)Kluyveromyces lactis (Klac)13/0.31

10/0.13


Saccharomyces paradoxus (Spar)Saccharomyces cerevisiae (Scer)




Candida glabrata (Cgla)35/0.80

4/0.0110/0.39

6/0.0196/0.99

20/0.1922/0.69

49/0.85

7/0.00 10/0.12

20/0.20

70/0.9471/0.93

75/0.9694/0.99

Supplementary Figure 13 | Selection of highly supported bipartitions from the bootstrap consensus trees of individual genes has a large, positive effect on the IC values of internodes of the yeast phylogeny inferred by the eMRC approach. The first three panels show the yeast species phylogeny inferred from extended majority rule consensus (eMRC) analysis following the selection of bipartitions that had high bootstrap support (BS) in the bootstrap consensus trees of individual genes. Values near internodes correspond to the percentage of bootstrap consensus trees of individual genes in which this specific bipartition received high BS and to internode certainty (IC), respectively. a, The eMRC phylogeny inferred from selecting bipartitions that had BS ≥60% in individual gene analyses. b, The eMRC phylogeny inferred from selecting bipartitions that had BS ≥70% in individual gene analyses. c, The eMRC phylogeny inferred from selecting bipartitions that had BS ≥80% in individual gene analyses. d, Plot that illustrates the change in IC of internodes relative to the values obtained in the default analysis associated with the use of bipartitions that had high bootstrap support (BS) in the bootstrap consensus trees of individual genes. Each line of different color depicts the IC value obtained for a given internode in the default analysis (Fig. 1a), when using only bipartitions that had BS ≥60%, BS ≥70%, and BS ≥80%.



RESEARCH

0

0.2

0.4

0.6

0.8

1 Drer,Ggal,Hsap,Mmus,XtroHsap,MmusGgal,Hsap,MmusAmel,Bmor,Dmel,TcasGgal,Hsap,Mmus,XtroAmel,Bmor,Dmel,Dpul,TcasAmel,Bmor,Dmel,Dpul,Isca,TcasBmor,DmelNvec,TadhBmor,Dmel,TcasHrob,LgigCele,SmanCint,Drer,Ggal,Hsap,Mmus,XtroMbre,Nvec,TadhBflo,Cint,Drer,Ggal,Hsap,Mmus,XtroAmel,Bmor,Cele,Dmel,Dpul,Hrob,Isca,Lgig,Sman,Tcas

0

0.2

0.4

0.6

0.8

1 Drer,Gacu,Olat,Tnig,TrubTnig,TrubMmus,RnorGacu,Olat,Tnig,TrubDrer,Gacu,Ggal,Mdom,Olat,Tnig,Trub,XtroDrer,Gacu,Ggal,Olat,Tnig,Trub,XtroHsap,Mmul,Ppyg,PtroDrer,Gacu,Olat,Tnig,Trub,XtroHsap,PtroHsap,Ppyg,PtroCpor,Mmus,RnorGacu,Tnig,TrubBtau,Cfam,EcabCpor,Hsap,Mmul,Mmus,Ppyg,Ptro,Rnor

a

b

Inte

rnod

e C

erta

inty

Inte

rnod

e C

erta

inty

Defaultanalysis Using only bipartitions that received

≥XX bootstrap support (BS) inindividual gene tree analyses

≥60 BS ≥70 BS ≥80 BS≥60 BS ≥70 BS ≥80 BSUsing only those genes whose

bootstrap consensus trees had ≥XXaverage bootstrap support (BS)

Defaultanalysis Using only bipartitions that received

≥XX bootstrap support (BS) inindividual gene tree analyses

≥60 BS ≥70 BS ≥80 BS≥40 BS ≥50 BS ≥60 BSUsing only those genes whose

bootstrap consensus trees had ≥XXaverage bootstrap support (BS)

Change in Internode Certainty of the Vertebrate phylogenywhen using highly-supported genes and bipartitions

Change in Internode Certainty of the Metazoan phylogenywhen using highly-supported genes and bipartitions

Supplementary Figure 14 | Selection of highly supported genes and bipartitions has a large, positive effect on IC values of inter-nodes of the vertebrate and metazoan phylogenies. a, Plot that illustrates the change in IC of internodes of the vertebrate phylogeny relative to the values obtained in the default analysis associated with the use of genes whose bootstrap consensus trees have high average bootstrap support (BS) or with the use of bipartitions that had high BS in the bootstrap consensus trees of individual genes. Each line of different color depicts the IC value obtained for a given internode in the default analysis (Supplementary Fig. S10b), when using only genes with average BS ≥60%, BS ≥70%, and BS ≥80%, as well as when using only bipartitions that had BS ≥60%, BS ≥70%, and BS ≥80%. b, Plot that illustrates the change in IC of internodes of the metazoan phylogeny relative to the values obtained in the default analysis associated with the use of genes whose bootstrap consensus trees have high average bootstrap support (BS) or with the use of bipartitions that had high BS in the bootstrap consensus trees of individual genes. Each line of different color depicts the IC value obtained for a given internode in the default analysis (Supplementary Fig. S10e), when using only genes with average BS ≥40%, BS ≥50%, and BS ≥60%, as well as when using only bipartitions that had BS ≥60%, BS ≥70%, and BS ≥80%. The slight differences in the pattern of change of IC in the metazoan dataset relative to the other two datasets is likely to be due to the much smaller number of metazoan genes in the dataset and their lower average bootstrap support, which will result in smaller sets of genes and bipartitions with strong phylogenetic signal.



0.1

0.01




Zygosacharomycesrouxii (Zrou)

Kluyveromycespolysporus (Kpol)

S. bayanus (Sbay)S. kudriavzevii (Skud)

S. mikatae (Smik)

S. paradoxus (Spar) S.cerevisiae (Scer)



Candidaparapsilosis (Cpar)

Lodderomyceselongisporus (Lelo)

Candida albicans (Calb)Candida

dubliniensis (Cdub)Candida tropicalis (Ctro)



Saccharomycescastellii (Scas)

Candidaglabrata Cgla)



Saccharomyces sensu stricto clade

Supplementary Figure 15 | The phylogenetic consensus network that describes the 1,070 yeast gene histories. The consensus network inferred using the 1,070 maximum likeli-hood gene trees under the median network construction algorithm in the SplitsTree4 software. Boxes in the network denote internodes that harbor significant conflict, with the length of each branch in each box being proportional to the number of GTs that support it. Only branches that are present in at least 10% of the GTs are shown in the network.



RESEARCH

41/0.3299/0.96

36/0.09

62/0.59

31/0.04

95/0.90

24/0.0229/0.12

29/0.02

89/0.77

98/0.9590/0.78

86/0.76

45/0.11

29/0.01

29/0.02

52/0.0660/0.30

77/0.54

99/0.97

0.2

Kluyveromyces waltii (Kwal)Kluyveromyces thermotolerans (Kthe)

Saccharomyces kluyveri (Sklu)Kluyveromyces lactis (Klac)

Eremothecium gossypii (Egos)Zygosacharomyces rouxii (Zrou)

Kluyveromyces polysporus (Kpol) Candida glabrata (Cgla)

Saccharomyces castellii (Scas)Saccharomyces bayanus (Sbay)


Saccharomyces paradoxus (Spar)Saccharomyces cerevisiae (Scer)

Candida lusitaniae (Clus)Candida dubliniensis (Cdub)Candida albicans (Calb)Candida tropicalis (Ctro)




SupportedWeakly supportedUnresolved

Supplementary Figure 16 | Supported, weakly supported, and unresolved inter-nodes in the yeast phylogeny. Values near internodes correspond to gene support frequency and internode certainty, respectively calculated from the 1,070 yeast gene histories. Note that the validity of certain internodes marked as “unresolved” is supported by independent data (e.g., rare genomic changes).



STAR internode length versus GSF STAR internode length versus IC

0

0.5

1

1.5

2

2.5

0 20 40 60 80 1000

0.5

1

1.5

2

2.5

0 0.2 0.4 0.6 0.8 1

r = 0.83 r = 0.88

STA

R in

tern

ode

leng

th

Gene Support Frequency

STA

R in

tern

ode

leng

th

Internode Certainty

The yeast species phylogeny inferred using the STAR species tree methoda

b4.0






















100/1.4799/0.53

89/0.45

83/0.40

100/2.68

100/1.3667/0.22

89/0.4277/0.25

100/2.1358/0.29

96/0.5399/0.84

100/1.03100/0.98

100/1.25

100/0.9484/0.58

68/0.24

77/0.34

Supplementary Figure 17 | The yeast phylogeny inferred using a “species tree” method that accounts for variation between the 1,070 gene histories is highly supported and has extremely short internodes whose coalescent unit lengths are highly correlated with gene support frequency and internode certainty values. Using the 1,070 gene dataset, we inferred a yeast species phylogeny under the coalescent model and average ranks of gene coalescence times, as implemented in the STAR species tree method. a, The yeast species phylogeny under the coalescent. Values near internodes correspond to bootstrap support and internode length in coalescence units, respectively. The inferred topology is identical to the phylogeny shown in Figure 1a, except with respect to the placement of Candida lusitaniae. b, The lengths of internodes in the phylogeny inferred using the STAR species tree method, measured in average coalescent units, is highly correlated with internodes’ Gene Support Frequency (left panel) and Internode Certainty (right panel) values. The strength of each correlation is indicated by r, Pearson’s correlation coefficient.

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SUPPLEMENTARY INFORMATIONharvardphylogenetics.weebly.com/uploads/2/1/1/0/... · SUPPLEMENTARY INFORMATION 6 | RESEARCH 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0 10 20 30 40 50 60 70 80