supplementary information · micrognathozoa, cycliophora, orthonectida, and dicyemida. resolution...
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SUPPLEMENTAL DISCUSSION
Relationships within Spiralia and the position of Ctenophora
The inference of relationships within Spiralia is susceptible to parameter changes and
method of phylogenetic inference. Trochozoa, consisting of Mollusca, Annelida,
Nemertea, and Brachiopoda + Phoronida, is consistently recovered as in other
analyses2,11,25, although relationships among these taxa are poorly supported.
Lophophorata including Bryozoa is not recovered in any analyses, in contrast to
recent results30. A sister relationship between Bryozoa and Entoprocta is supported in
maximum likelihood analyses, but not Bayesian inference. Interestingly, Gastrotricha
is non-monophyletic in maximum likelihood analyses and in Bayesian analyses under
the GTR model, but is recovered monophyletic in Bayesian analyses under the
CAT+GTR+Γ model. We have not included several spiralian taxa for which genomic
data or deeply sequenced transcriptomes were not available, such as Gnathostomulida,
Micrognathozoa, Cycliophora, Orthonectida, and Dicyemida. Resolution of the
relationships within this clade will require broader taxon sampling than was feasible
within this study. Similarly, the first branch of metazoa is Ctenophora in our
maximum likelihood analyses, while Porifera holds this position in Bayesian analyses.
Further critical testing including broader taxon sampling within non-metazoans will
be required to identify the source of this intriguing discrepancy.
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SUPPLEMENTARY INFORMATIONdoi:10.1038/nature16520
Supplementary Data Table 1. Sources for sequence data used in phylogenomic analyses. New Illumina transcriptome data sequenced in this study indicated in bold.
Species Sequence Type Source or collection locality
Accession # or URL
Acoela
Childia submaculatum transcriptome N 58.2859, E 11.5265 SAMN04088540
Convolutriloba macropyga transcriptome USA SRX1343815
Diopisthoporus gymnopharyngeus transcriptome N 34.6969, W
76.7387 SAMN04088542
Diopisthoporus longitubus transcriptome N 58.2859, E
11.5265 SAMN04088543
Eumecynostomum macrobursalium transcriptome N 58.2519, E
11.4656 SAMN04088544
Hofstenia miamia transcriptome NCBI SRA SRS584107, SRS584110
Isodiametra pulchra transcriptome Austria SRX1343817
Annelida
Capitella teleta genome JGI http://genome.jgi-
psf.org/Capca1/Capca1.download.ftp.html
Helobdella robusta genome JGI http://genome.jgi-
psf.org/Helro1/Helro1.download.ftp.html
Pomatoceros lamarckii transcriptome NCBI SRA SRX156389
Arthropoda
Daphnia pulex genome JGI http://genome.jgi.doe.gov/Dappu1/Dappu1.download.ft
p.html
Drosophila melanogaster genome Ensembl ftp://ftp.ensemblgenomes.org/pub/metazoa/release-
24/fasta/drosophila_melanogaster/pep/
Ixodes scapularis genome Ensembl ftp://ftp.ensemblgenomes.org/pub/metazoa/release-
24/fasta/ixodes_scapularis/pep/
Strigamia maritima genome Ensembl ftp://ftp.ensemblgenomes.org/pub/metazoa/release-
24/fasta/strigamia_maritima/pep/
Brachiopoda
Hemithiris psittacea transcriptome NCBI SRA SRX731469
Novocrania anomala transcriptome 60.3377 N 5.1916 W SRX1343816
Terebratalia transversa transcriptome Friday Harbor, USA SRX1307070
Bryozoa Membranipora
membranacea transcriptome NCBI SRA SRX1121923
Choanoflagellata
Monosiga brevicollis genome NCBI ABFJ00000000,
http://www.ncbi.nlm.nih.gov/genome/713
Salpingoeca rosetta genome Broad
Institute www.broadinstitute.org/annotation/genome/
multicellularity_project/MultiHome.html
Chordata
Botryllus schlosseri genome Stanford
University http://botryllus.stanford.edu/botryllusgenome/download
/botznik-transcripts.fa
Branchiostoma floridae genome JGI http://genome.jgi-
psf.org/Brafl1/Brafl1.download.ftp.html
Ciona intestinalis genome Ensembl ftp://ftp.ensembl.org/pub/release-78/fasta/ciona_intestinalis/pep/
Gallus gallus genome NCBI http://www.ncbi.nlm.nih.gov/genome?term=gallus%20
gallus
Homo sapiens genome Ensembl ftp://ftp.ensembl.org/pub/release-
78/fasta/homo_sapiens/pep/
Petromyzon marinus genome Ensembl ftp://ftp.ensembl.org/pub/release-
78/fasta/petromyzon_marinus/pep/
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Cnidaria
Acropora digitifera genome NCBI BACK00000000,
http://www.ncbi.nlm.nih.gov/genome/10529
Agalma elegans transcriptome NCBI SRA SRR871526
Craspedacusta sowerbyi transcriptome NCBI SRA SRX315373
Eunicella cavolinii transcriptome NCBI SRA SRX565138
Nematostella vectensis genome NCBI ABAV00000000,
http://www.ncbi.nlm.nih.gov/genome/230
Stomolophus meleagris transcriptome NCBI SRA SRX470083
Ctenophora
Euplokamis dunlapae transcriptome NCBI SRA SRR777663
Mnemiopsis leidyi genome NCBI GCA_000226015,
http://www.ncbi.nlm.nih.gov/assembly/GCA_000226015.1/#/st
Pleurobrachia bachei genome Neurobase http://neurobase.rc.ufl.edu/pleurobrachia/download
Echinodermata
Astrotomma agassizi transcriptome NCBI SRA SAMN03012756
Dumetocrinus sp. transcriptome NCBI SRA SAMN03012750
Labidiaster annulatus transcriptome NCBI SRA SAMN03012748, SAMN03012747
Leptosynapta clarki transcriptome NCBI SRA SAMN03012745
Strongylocentrotus purpuratus genome SpBase http://www.spbase.org/SpBase/downloads.php
Entoprocta
Barentsia gracilis transcriptome NCBI SRA SRX731475
Loxosoma pectinaricola transcriptome NCBI SRA SRX731476
Gastrotricha
Lepidodermella squamata transcriptome NCBI SRA SRX1000997
Macrodasys sp. transcriptome NCBI SRA SRX534826, SRX533489-SRX533490
Megadasys sp. transcriptome NCBI SRA SRX534832, SRX534834-SRX534835
Hemichordata
Cephalodiscus gracilis transcriptome NCBI SRA SAMN03012629
Ptychodera bahamensis transcriptome NCBI SRA SAMN03012539
Saccoglossus mereschkowskii transcriptome NCBI SRA SAMN03012542
Schizocardium c.f. braziliense transcriptome NCBI SRA SAMN03012605, SAMN03012582
Mollusca
Crassostrea gigas genome Ensembl ftp://ftp.ensemblgenomes.org/pub/metazoa/release-
24/fasta/crassostrea_gigas/pep/
Leptochiton rugatus transcriptome NCBI SRA SRX731464
Lottia gigantea Genome JGI http://genome.jgi-
psf.org/Lotgi1/Lotgi1.download.ftp.html
Nemertea
Cephalothrix honkongiensis
transcriptome NCBI SRA SRX205320
Lineus longissimus transcriptome 60.2542 N 5.2197 E SRX1343823
Nemertodermatida
Ascoparia sp. transcriptome 29.5019 N 34.9174 E SRX1343822
Meara stichopi transcriptome 60.2649 N 5.1408 E SRX1343814
Nemertoderma westbladi transcriptome 58.2614 N, 11.4368 E SRX1343819
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Sterreria sp. transcriptome 29.5019 N 34.9174 E SRX1343821
Onychophora
Peripatopsis capensis transcriptome NCBI SRA SRX451023
Phoronida
Phoronis psammophila transcriptome NCBI SRA SRX731473
Placozoa
Trichoplax adhaerens genome JGI http://genome.jgi-
psf.org/Triad1/Triad1.download.ftp.html
Platyhelminthes
Macrostomum lignano transcriptome Switzerland SRX1343824
Prostheceraeus vittatus transcriptome NCBI SRA SRX999630
Schistosoma mansoni genome Ensembl ftp://ftp.ensemblgenomes.org/pub/metazoa/release-
28/fasta/schistosoma_mansoni/pep/
Schmidtea mediterranea genome NCBI http://www.ncbi.nlm.nih.gov/genome/232
Taenia pisiformes transcriptome SRA SRX113900
Porifera
Amphimedon queenslandica genome NCBI
ACUQ00000000, http://www.ncbi.nlm.nih.gov/genome/2698
Aphrocallistes vastus transcriptome NCBI SRA SRX386258
Cliona varians transcriptome NCBI SRA SRX333053
Leucosolenia complicata genome Data Dryad http://datadryad.org/resource/doi:10.5061/dryad.tn0f3
Oscarella carmela genome NCBI http://www.ncbi.nlm.nih.gov/genome/23321
Sycon ciliatum genome Data Dryad http://datadryad.org/resource/doi:10.5061/dryad.tn0f3
Priapulida
Halicryptus spinulosus transcriptome Askö, Sweden SRX1343820
Priapulus caudatus transcriptome Kristineberg,Sweden SRX507009
Rotifera
Adineta ricciae transcriptome NCBI SRA ERX083858, ERR106425
Adineta vaga genome Genoscope http://www.genoscope.cns.fr/adineta/data/Adineta_vaga
.v2.pep.fa.gz
Brachionus calyciflorus
NCBI SRA SRX203186, SRX203185
Xenoturbella
Xenoturbella bocki transcriptome 58.2759 N 11.4735 E SRX1343818
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Data Table 2. Translated unigenes per species, percent gene coverage, and leaf stability.
Species Translated Unigenes/ Proteins
% Genes in 212
Dataset
Leaf Stability
(212 dataset) Acropora digitifera 23677 61 0.991135
Adineta ricciae 19766 76 0.986535
Adineta vaga 49300 98 0.986535 Agalma elegans 82093 90 0.991135
Amphimedon queenslandica 29883 93 0.981013 Aphrocallistes vastus 51711 93 0.981013
Ascoparia sp. 20126 58 0.996956 Astrotomma agassizii 43982 35 0.991458
Barentsia gracilis 37823 41 0.995290 Botryllus schlosseri 47978 76 0.994392
Brachionus calyciflorus 22857 96 0.986535 Branchiostoma floridae 50817 98 0.993120
Capitella teleta 32415 97 0.992968 Cephalodiscus gracilis 20892 33 0.982668
Cephalothrix hongkongiensis 35897 59 0.984432 Childia submaculatum 38442 91 0.995635
Ciona intestinalis 16416 99 0.994392 Cliona varians 74687 84 0.981013
Convolutriloba macropyga 23870 98 0.995635 Craspedacusta sowerbyi 53373 96 0.991135
Crassostrea gigas 26089 85 0.990573 Daphnia pulex 30810 93 0.996093 Diopisthoporus
gymnopharyngeus 25511 55 0.994418
Diopisthoporus longitubus 48202 88 0.994418 Drosophila melanogaster 26822 100 0.996093
Dumetocrinus sp. 53419 80 0.991232 Eumecynostomum macrobursalium 11458 46 0.995635
Eunicella cavolinii 24780 61 0.991135
Euplokamis dunlapae 90267 64 0.986061 Gallus gallus 32134 88 0.994392
Halicryptus spinulosus 144017 98 0.996825 Helobdella robusta 23432 97 0.992968
Hemithiris psittacea 114624 92 0.991847 Homo sapiens 93859 100 0.994392
Hofstenia miamia 18155 94 0.991807 Isodiametra pulchra 22262 98 0.995724
Ixodes scapularis 20486 85 0.995251 Labidiaster annulatus 67857 46 0.991754
Lepidodermella squamata 43289 94 0.987511
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Leptochiton rugatus 68934 85 0.990573 Leptosynapta clarki 65607 67 0.991968
Leucosolenia complicata 92106 98 0.979833 Lineus longissimus 84854 98 0.984432
Lottia gigantea 23851 96 0.990573 Loxosoma pectinaricola 56046 43 0.995290
Macrodasys sp. 16565 77 0.980821 Macrostomum lignano 48968 95 0.990989
Meara stichopi 16255 96 0.996956 Megadasys sp. 23321 38 0.980821
Membranipora membranacea 18930 99 0.995483 Mnemiopsis leidyi 126790 77 0.986061
Monosiga brevicollis 10336 87 0.986061 Nematostella vectensis 27273 95 0.991135
Nemertoderma westbladi 104698 99 0.996956 Novocrania anomala 27566 99 0.991847
Oscarella carmela 29220 96 0.977712 Peripatopsis capensis 25233 58 0.996654
Petromyzon marinus 11442 56 0.994392 Phoronis psammophila 100408 95 0.991847
Pleurobrachia bachei 19524 64 0.986061 Pomatoceros lamarckii 19238 56 0.992968
Priapulus caudatus 55300 94 0.996825 Prostheceraeus vittatus 32908 98 0.990989
Ptychodera bahamensis 59573 85 0.992450 Saccoglossus mereschkowskii 89977 92 0.992450
Salpingoeca rosetta 11731 88 0.986061 Schistosoma mansoni 11751 90 0.991227
Schizocardium brasiliense 49006 38 0.992450 Schmidtea mediterranea 8977 54 0.991227
Sterreria sp. 4552 8 0.996956 Stomolophus meleagris 27815 82 0.991135
Strigamia maritima 15008 85 0.995251 Strongylocentrotus
purpuratus 22709 96 0.991924
Sycon ciliatum 50731 98 0.979833 Taenia pisiformis 26627 56 0.991227
Terebratalia transversa 18280 97 0.991847 Trichoplax adhaerens 11520 96 0.956911
Xenoturbella bocki 15427 98 0.996956
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Supplementary Table 3. Leaf stability indices for Philippe et al. (2011) EST data matrix, sorted lowest to highest.
Taxon Leaf Stability Taxon Leaf Stability Xenoturbella 0.796541 Cerebratulus 0.951684
Nemertoderma 0.870692 Bugula 0.953020
Meara 0.870692 Cristatella 0.953020 Isodiametra 0.888838 Scutigera 0.954323
Convolutriloba 0.888838 Spadella 0.956372 Symsagittifera 0.888838 Flaccisagitta 0.956372
Leucetta 0.930651 Philodina 0.957815 Trichoplax 0.932873 Brachionus 0.957815
Oscarella 0.934565 Capitella 0.960343 Amphimedon 0.935570 Alvinella 0.961516
Suberites 0.935570 Pomatoceros 0.962555 Holothuria 0.936431 Helobdella 0.962779
Strongylocentrotus 0.936431 Tubifex 0.962779 Patiria 0.936431 Macrostomum 0.964320
Saccoglossus 0.936970 Paraplanocera 0.964320 Ptychodera 0.936970 Anoplodactylus 0.964501
Acropora 0.937834 Euprymna 0.964588 Anemonia 0.937834 Crassostrea 0.964588
Nematostella 0.937834 Mytilus 0.964588 Cyanea 0.937834 Lottia 0.964588
Hydra 0.937834 Aplysia 0.964588 Hydractinia 0.937834 Ixodes 0.965631
Branchiostoma 0.946252 Acanthoscurria 0.965631 Molgula 0.946252 Pedicellina 0.966042
Halocynthia 0.946252 Symbion 0.966042 Ciona 0.946252 Daphnia 0.967906
Xenopus 0.946252 Litopenaeus 0.967962 Gallus 0.946252 Onychiurus 0.968353
Danio 0.946252 Gryllus 0.968382 Leucoraja 0.946252 Rhodnius 0.968382
Petromyzon 0.946252 Priapulus 0.971787 Eptatretus 0.946252 Echinoderes 0.971787
Carinoma 0.951684 Euperipatoides 0.971787
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Supplementary Figure 1. Maximum likelihood topology based on the primary 212-gene matrix with Xenoturbella bocki removed. The most likely tree sampled in RAxML using the LG+I+ Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 43510 AAs, and overall matrix completeness is 69 percent.
0.2
Megadasys sp.
Adineta ricciae
Agalma elegans
Hemithiris psittacea
Salpingoeca rosetta
Leptochiton rugatus
Ascoparia sp.
Barentsia gracilis
Prostheceraeus vittatus
Cephalodiscus gracilis
Trichoplax adhaerens
Gallus gallus
Amphimedon queenslandica
Ixodes scapularis
Daphnia pulex
Lineus longissimus
Leptosynapta clarki
Eumecynostomum macrobursalium
Drosophila melanogaster
Diopisthoporus gymnopharyngeus
Homo sapiens
Schistosoma mansoni
Branchiostoma floridae
Crassostrea gigas
Eunicella cavolinii
Halicryptus spinulosus
Helobdella robusta
Pleurobrachia bachei
Taenia pisiformes
Stomolophus meleagris
Oscarella carmelaEuplokamis dunlapae
Saccoglossus mereschkowskii
Astrotomma agassizi
Meara stichopi
Macrostomum lignano
Acropora digitifera
Sterreria sp.
Phoronis psammophila
Peripatopsis capensis
Lottia gigantea
Nemertoderma westbladi
Sycon ciliatum
Labidiaster annulatus
Pomatoceros lamarckii
Brachionus calyciflorus
Petromyzon marinus
Terebratalia transversa
Adineta vaga
Botryllus schlosseri
Schmidtea mediterranea
Cliona varians
Strongylocentrotus purpuratus
Hofstenia miamiaConvolutriloba macropyga
Aphrocallistes vastus
Ptychodera bahamensis
Monosiga brevicollis
Diopisthoporus longitubus
Lepidodermella squamata
Schizocardium c.f. braziliense
Novocrania anomala
Dumetocrinus sp.
Strigamia maritima
Macrodasys sp.
Craspedacusta sowerby
Leucosolenia complicata
Membranipora membranacea
Ciona intestinalis
Mnemiopsis leidyi
Priapulus caudatus
Capitella teleta
Nematostella vectensis
Childia submaculatum
Isodiametra pulchra
Cephalothrix hongkongiensis
Loxosoma pectinaricola
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 2a. Maximum likelihood topology based on the primary 212-gene matrix with Acoela excluded. The most likely tree sampled in RAxML using the LG+I+ Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 43451 AAs, and overall matrix completeness is 69 percent.
0.2
Cephalodiscus gracilis
Taenia pisiformes
Strongylocentrotus purpuratus
Novocrania anomala
Ascoparia sp.
Helobdella robusta
Pleurobrachia bachei
Euplokamis dunlapae
Ixodes scapularis
Phoronis psammophila
Labidiaster annulatus
Stomolophus meleagrisAgalma elegans
Brachionus calyciflorus
Lineus longissimus
Botryllus schlosseri
Halicryptus spinulosus
Sterreria sp.
Pomatoceros lamarckii
Homo sapiens
Peripatopsis capensis
Craspedacusta sowerby
Mnemiopsis leidyi
Hemithiris psittacea
Macrodasys sp.
Monosiga brevicollis
Leptochiton rugatus
Loxosoma pectinaricolaBarentsia gracilis
Oscarella carmela
Megadasys sp.
Astrotomma agassizi
Petromyzon marinus
Cliona varians
Meara stichopi
Schistosoma mansoni
Lottia gigantea
Saccoglossus mereschkowskii
Crassostrea gigas
Aphrocallistes vastus
Branchiostoma floridae
Adineta vaga
Trichoplax adhaerens
Acropora digitifera
Xenoturbella bocki
Sycon ciliatumLeucosolenia complicata
Ciona intestinalis
Daphnia pulex
Nematostella vectensis
Nemertoderma westbladi
Priapulus caudatus
Macrostomum lignano
Capitella teleta
Lepidodermella squamata
Membranipora membranacea
Drosophila melanogaster
Strigamia maritima
Ptychodera bahamensis
Prostheceraeus vittatusSchmidtea mediterranea
Gallus gallus
Cephalothrix hongkongiensis
Terebratalia transversa
Adineta ricciae
Amphimedon queenslandica
Dumetocrinus sp.
Leptosynapta clarki
Salpingoeca rosetta
Eunicella cavolinii
Schizocardium c.f. braziliense
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Supplementary Figure 2b. Bayesian inference tree based on the primary 212-gene matrix with Acoela excluded. Results are shown from MrBayes analyses of four independent Metropolis-coupled chains run for four million generations, with sampling every 500 generations. Amino acid data were back-translated to nucleotides and analysed under an independent substitution model.
0.1
Lottia gigantea
Adineta vaga
Nemertoderma westbladi
Barentsia gracilis
Saccoglossus mereschkowskii
Peripatopsis capensis
Acropora digitifera
Cephalodiscus gracilis
Nematostella vectensis
Daphnia pulex
Crassostrea gigas
Pomatoceros lamarckii
Sterreria sp.
Eunicella cavolinii
Taenia pisiformes
Halicryptus spinulosus
Cephalothrix hongkongiensis
Craspedacusta sowerby
Oscarella carmela
Ciona intestinalis
Trichoplax adhaerens
Phoronis psammophila
Cliona varians
Strigamia maritima
Pleurobrachia bachei
Meara stichopi
Botryllus schlosseri
Leptosynapta clarki
Prostheceraeus vittatus
Aphrocallistes vastus
Stomolophus meleagris
Capitella telata
Dumetocrinus sp.
Agalma elegans
Adineta ricciae
Mnemiopsis leidyi
Monosiga brevicollis
Euplokamis dunlapae
Homo sapiens
Schistosoma mansoni
Branchiostoma floridae
Megadasys sp.
Brachionus calyciflorus
Ascoparia sp.
Ixodes scapularis
Loxosoma pectinaricola
Priapulus caudatus
Gallus gallus
Amphimedon queenslandica
Ptychodera bahamensis
Hemithiris psittacea
Salpingoeca rosetta
Strongylocentrotus purpuratus
Leucosolenia complicata
Leptochiton rugatus
Lineus longissimus
Schizocardium c.f. brasiliense
Terebratalia transversa
Petromyzon marinus
Macrodasys sp.
Lepidodermella squamata
Drosophila melanogaster
Helobdella robusta
Xenoturbella bocki
Macrostomum lignano
Sycon ciliatum
Astrotomma agassizi
Membranipora membranacea
Novocrania anomala
Labidiaster annulatus
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Schmidtea mediterranea
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Supplementary Figure 3. Maximum likelihood topology based on the primary 212-gene matrix with Nemertodermatida excluded. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 45054 AAs, and overall matrix completeness is 70 percent.
0.2
Agalma elegans
Xenoturbella bocki
Schistosoma mansoni
Lottia gigantea
Oscarella carmela
Salpingoeca rosetta
Hemithiris psittacea
Isodiametra pulchra
Schizocardium c.f. braziliense
Diopisthoporus gymnopharyngeus
Taenia pisiformes
Petromyzon marinus
Lineus longissimus
Helobdella robusta
Lepidodermella squamata
Phoronis psammophila
Peripatopsis capensis
Macrostomum lignano
Astrotomma agassizi
Daphnia pulex
Novocrania anomala
Barentsia gracilis
Strongylocentrotus purpuratus
Childia submaculatum
Adineta ricciae
Brachionus calyciflorus
Cephalodiscus gracilis
Strigamia maritima
Nematostella vectensis
Ptychodera bahamensis
Leptosynapta clarki
Saccoglossus mereschkowskii
Craspedacusta sowerby
Macrodasys sp.
Crassostrea gigas
Convolutriloba macropyga
Terebratalia transversa
Amphimedon queenslandica
Homo sapiens
Acropora digitifera
Drosophila melanogaster
Gallus gallus
Euplokamis dunlapae
Halicryptus spinulosus
Capitella teleta
Monosiga brevicollis
Pomatoceros lamarckii
Eunicella cavolinii
Ixodes scapularis
Eumecynostomum macrobursalium
Hofstenia miamia
Leptochiton rugatus
Cliona varians
Labidiaster annulatus
Trichoplax adhaerens
Dumetocrinus sp.
Cephalothrix hongkongiensis
Pleurobrachia bachei
Adineta vaga
Ciona intestinalis
Branchiostoma floridae
Leucosolenia complicata
Prostheceraeus vittatus
Stomolophus meleagris
Diopisthoporus longitubus
Priapulus caudatus
Botryllus schlosseri
Schmidtea mediterranea
Megadasys sp.
Aphrocallistes vastus
Mnemiopsis leidyi
Membranipora membranacea
Sycon ciliatum
Loxosoma pectinaricola
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 4. Maximum likelihood topology based on the primary 212-gene matrix with Ctenophora excluded. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 47011 AAs, and overall matrix completeness is 70 percent.
0.2
Lepidodermella squamata
Membranipora membranacea
Diopisthoporus gymnopharyngeus
Cephalodiscus gracilis
Meara stichopi
Priapulus caudatus
Hemithiris psittacea
Xenoturbella bocki
Astrotomma agassizi
Leucosolenia complicataAphrocallistes vastus
Branchiostoma floridae
Nematostella vectensis
Schmidtea mediterranea
Brachionus calyciflorus
Oscarella carmela
Terebratalia transversa
Lineus longissimus
Leptosynapta clarki
Trichoplax adhaerens
Petromyzon marinus
Monosiga brevicollis
Pomatoceros lamarckii
Drosophila melanogaster
Salpingoeca rosetta
Ascoparia sp.
Crassostrea gigas
Isodiametra pulchra
Agalma elegans
Ixodes scapularis
Prostheceraeus vittatusMacrodasys sp.
Eunicella cavolinii
Novocrania anomala
Lottia gigantea
Labidiaster annulatus
Sterreria sp.
Halicryptus spinulosus
Botryllus schlosseri
Stomolophus meleagris
Adineta ricciae
Schistosoma mansoni
Childia submaculatum
Helobdella robusta
Saccoglossus mereschkowskii
Loxosoma pectinaricola
Strigamia maritima
Homo sapiens
Convolutriloba macropyga
Macrostomum lignano
Eumecynostomum macrobursalium
Peripatopsis capensis
Barentsia gracilis
Strongylocentrotus purpuratus
Cephalothrix hongkongiensis
Capitella teleta
Amphimedon queenslandica
Taenia pisiformes
Diopisthoporus longitubus
Gallus gallus
Schizocardium c.f. braziliensePtychodera bahamensis
Dumetocrinus sp.
Acropora digitifera
Nemertoderma westbladi
Phoronis psammophila
Cliona varians
Adineta vaga
Daphnia pulex
Ciona intestinalis
Hofstenia miamia
Craspedacusta sowerby
Leptochiton rugatus
Sycon ciliatum
Megadasys sp.
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 5. Maximum likelihood topology based on the primary 212-gene matrix with Cnidaria excluded. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 44990 AAs, and overall matrix completeness is 69 percent.
0.2
Astrotomma agassizi
Daphnia pulex
Oscarella carmela
Drosophila melanogaster
Adineta ricciae
Capitella teleta
Hemithiris psittacea
Amphimedon queenslandica
Schmidtea mediterranea
Euplokamis dunlapae
Strigamia maritima
Sycon ciliatum
Megadasys sp.
Pleurobrachia bachei
Sterreria sp.
Loxosoma pectinaricola
Isodiametra pulchra
Saccoglossus mereschkowskii
Lepidodermella squamata
Lineus longissimus
Trichoplax adhaerens
Branchiostoma floridae
Ixodes scapularis
Membranipora membranacea
Crassostrea gigas
Brachionus calyciflorus
Childia submaculatum
Adineta vaga
Ciona intestinalisBotryllus schlosseri
Convolutriloba macropyga
Labidiaster annulatus
Taenia pisiformes
Gallus gallus
Aphrocallistes vastus
Strongylocentrotus purpuratus
Schistosoma mansoni
Nemertoderma westbladi
Priapulus caudatus
Petromyzon marinus
Ascoparia sp.
Novocrania anomala
Eumecynostomum macrobursalium
Helobdella robusta
Hofstenia miamia
Phoronis psammophila
Lottia gigantea
Cephalodiscus gracilis
Ptychodera bahamensis
Diopisthoporus longitubusDiopisthoporus gymnopharyngeus
Macrostomum lignanoMacrodasys sp.
Dumetocrinus sp.
Monosiga brevicollis
Leptosynapta clarki
Salpingoeca rosetta
Xenoturbella bocki
Peripatopsis capensis
Terebratalia transversa
Mnemiopsis leidyi
Meara stichopi
Homo sapiens
Pomatoceros lamarckii
Barentsia gracilis
Schizocardium c.f. braziliense
Prostheceraeus vittatus
Halicryptus spinulosus
Cliona varians
Leptochiton rugatusCephalothrix hongkongiensis
Leucosolenia complicata
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 6. Maximum likelihood topology based on the primary 212-gene matrix with Porifera excluded. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 43829 AAs, and overall matrix completeness is 69 percent.
0.2
Xenoturbella bocki
Botryllus schlosseri
Diopisthoporus gymnopharyngeus
Leptochiton rugatus
Adineta ricciae
Schistosoma mansoni
Strongylocentrotus purpuratus
Craspedacusta sowerby
Childia submaculatum
Terebratalia transversa
Astrotomma agassizi
Loxosoma pectinaricola
Prostheceraeus vittatus
Macrostomum lignano
Diopisthoporus longitubus
Pomatoceros lamarckii
Priapulus caudatus
Crassostrea gigas
Cephalodiscus gracilis
Schizocardium c.f. braziliense
Phoronis psammophila
Branchiostoma floridae
Saccoglossus mereschkowskii
Barentsia gracilis
Ascoparia sp.
Lepidodermella squamata
Ptychodera bahamensis
Stomolophus meleagris
Monosiga brevicollis
Acropora digitifera
Macrodasys sp.
Petromyzon marinus
Agalma elegans
Daphnia pulexHalicryptus spinulosus
Trichoplax adhaerens
Convolutriloba macropyga
Hofstenia miamia
Mnemiopsis leidyi
Dumetocrinus sp.
Pleurobrachia bachei
Taenia pisiformes
Lottia gigantea
Membranipora membranacea
Nematostella vectensis
Labidiaster annulatus
Ciona intestinalis
Drosophila melanogaster
Novocrania anomala
Capitella teleta
Megadasys sp.
Ixodes scapularis
Euplokamis dunlapae
Sterreria sp.
Gallus gallus
Lineus longissimus
Eunicella cavolinii
Brachionus calyciflorus
Peripatopsis capensis
Eumecynostomum macrobursalium
Schmidtea mediterranea
Salpingoeca rosetta
Cephalothrix hongkongiensis
Meara stichopi
Leptosynapta clarki
Adineta vaga
Homo sapiens
Isodiametra pulchra
Nemertoderma westbladi
Helobdella robusta
Hemithiris psittacea
Strigamia maritima
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 7. Maximum likelihood topology based on the primary 212-gene matrix with Trichoplax adhaerens excluded. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 43940 AAs, and overall matrix completeness is 69 percent.
0.2
Diopisthoporus gymnopharyngeus
Labidiaster annulatus
Botryllus schlosseri
Ixodes scapularis
Taenia pisiformes
Convolutriloba macropyga
Leucosolenia complicata
Meara stichopi
Barentsia gracilis
Salpingoeca rosetta
Ptychodera bahamensis
Loxosoma pectinaricolaBrachionus calyciflorus
Terebratalia transversa
Saccoglossus mereschkowskii
Pomatoceros lamarckii
Crassostrea gigas
Pleurobrachia bachei
Novocrania anomala
Gallus gallus
Peripatopsis capensis
Schizocardium c.f. braziliense
Lottia gigantea
Agalma elegans
Ascoparia sp.
Ciona intestinalis
Acropora digitifera
Xenoturbella bocki
Branchiostoma floridae
Craspedacusta sowerby
Helobdella robusta
Amphimedon queenslandica
Dumetocrinus sp.
Daphnia pulex
Strigamia maritima
Priapulus caudatus
Macrostomum lignano
Sterreria sp.
Astrotomma agassizi
Macrodasys sp.
Prostheceraeus vittatus
Childia submaculatum
Schistosoma mansoni
Diopisthoporus longitubus
Monosiga brevicollis
Eunicella cavolinii
Isodiametra pulchra
Drosophila melanogaster
Eumecynostomum macrobursalium
Schmidtea mediterranea
Phoronis psammophila
Adineta vaga
Lepidodermella squamata
Petromyzon marinus
Megadasys sp.
Cephalothrix hongkongiensis
Strongylocentrotus purpuratus
Lineus longissimus
Stomolophus meleagris
Hemithiris psittacea
Cephalodiscus gracilis
Hofstenia miamia
Capitella teleta
Leptochiton rugatus
Euplokamis dunlapae
Nemertoderma westbladi
Mnemiopsis leidyi
Membranipora membranacea
Aphrocallistes vastusOscarella carmela
Leptosynapta clarki
Homo sapiens
Nematostella vectensis
Halicryptus spinulosus
Adineta ricciae
Sycon ciliatum
Cliona varians
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 8. Maximum likelihood topology based on the primary 212-gene matrix with Ctenophora, Cnidaria and Trichoplax adhaerens removed. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 47115 AAs, and overall matrix completeness is 70 percent.
0.2
Terebratalia transversa
Labidiaster annulatus
Cliona varians
Gallus gallus
Diopisthoporus longitubus
Leptochiton rugatus
Strigamia maritima
Lineus longissimus
Taenia pisiformes
Xenoturbella bocki
Megadasys sp.
Botryllus schlosseri
Barentsia gracilis
Amphimedon queenslandica
Cephalothrix hongkongiensis
Convolutriloba macropyga
Pomatoceros lamarckii
Schmidtea mediterranea
Helobdella robusta
Schizocardium c.f. braziliense
Brachionus calyciflorus
Dumetocrinus sp.
Isodiametra pulchraEumecynostomum macrobursalium
Monosiga brevicollis
Petromyzon marinus
Ascoparia sp.
Drosophila melanogaster
Homo sapiens
Adineta ricciae
Lottia gigantea
Cephalodiscus gracilis
Novocrania anomala
Membranipora membranacea
Daphnia pulex
Branchiostoma floridae
Leucosolenia complicata
Leptosynapta clarki
Nemertoderma westbladi
Macrodasys sp.
Macrostomum lignano
Halicryptus spinulosus
Oscarella carmela
Saccoglossus mereschkowskii
Adineta vaga
Crassostrea gigas
Astrotomma agassizi
Meara stichopi
Diopisthoporus gymnopharyngeus
Childia submaculatum
Hofstenia miamia
Hemithiris psittacea
Loxosoma pectinaricola
Ixodes scapularis
Priapulus caudatus
Ptychodera bahamensis
Strongylocentrotus purpuratus
Peripatopsis capensis
Prostheceraeus vittatus
Ciona intestinalis
Sycon ciliatum
Lepidodermella squamata
Salpingoeca rosetta
Sterreria sp.
Aphrocallistes vastus
Phoronis psammophila
Capitella teleta
Schistosoma mansoni100
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9359
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 9. Maximum likelihood topology based on the primary 212-gene matrix with non-metazoan outgroups removed. Tree is rooted on Ctenophora. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 43764 AAs, and overall matrix completeness is 69 percent.
0.2
Stomolophus meleagris
Crassostrea gigas
Ciona intestinalis
Cephalothrix hongkongiensis
Gallus gallus
Acropora digitifera
Schizocardium c.f. brazilienseSaccoglossus mereschkowskii
Sycon ciliatum
Astrotomma agassizi
Megadasys sp.
Agalma elegans
Botryllus schlosseri
Aphrocallistes vastus
Petromyzon marinus
Peripatopsis capensis
Novocrania anomala
Cliona varians
Labidiaster annulatus
Leucosolenia complicata
Homo sapiens
Strongylocentrotus purpuratus
Adineta ricciae
Schmidtea mediterranea
Halicryptus spinulosus
Branchiostoma floridae
Membranipora membranacea
Craspedacusta sowerby
Drosophila melanogasterDaphnia pulex
Diopisthoporus gymnopharyngeus
Strigamia maritima
Dumetocrinus sp.
Pomatoceros lamarckii
Leptochiton rugatus
Phoronis psammophila
Xenoturbella bocki
Oscarella carmela
Nematostella vectensis
Loxosoma pectinaricola
Ixodes scapularis
Eunicella cavolinii
Mnemiopsis leidyi
Capitella teleta
Ptychodera bahamensis
Trichoplax adhaerens
Terebratalia transversa
Nemertoderma westbladi
Taenia pisiformes
Diopisthoporus longitubus
Amphimedon queenslandica
Prostheceraeus vittatus
Convolutriloba macropyga
Macrostomum lignano
Schistosoma mansoni
Sterreria sp.
Leptosynapta clarki
Brachionus calyciflorus
Lineus longissimus
Euplokamis dunlapae
Lottia gigantea
Helobdella robusta
Eumecynostomum macrobursalium
Barentsia gracilis
Pleurobrachia bachei
Hofstenia miamiaChildia submaculatum
Lepidodermella squamata
Isodiametra pulchra
Ascoparia sp.
Meara stichopi
Adineta vaga
Cephalodiscus gracilis
Macrodasys sp.
Priapulus caudatus
Hemithiris psittacea
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 10. Maximum likelihood topology based on the primary 212-gene matrix with taxon sampling for Deuterostomia reduced. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 46101 AAs, and overall matrix completeness is 71 percent.
0.2
Oscarella carmela
Daphnia pulex
Strongylocentrotus purpuratus
Ptychodera bahamensis
Schmidtea mediterranea
Meara stichopi
Lineus longissimusCephalothrix hongkongiensis
Drosophila melanogaster
Eunicella cavolinii
Monosiga brevicollis
Ascoparia sp.
Prostheceraeus vittatus
Salpingoeca rosetta
Botryllus schlosseriCiona intestinalis
Acropora digitifera
Petromyzon marinus
Eumecynostomum macrobursalium
Sycon ciliatum
Branchiostoma floridae
Crassostrea gigas
Phoronis psammophila
Agalma elegans
Mnemiopsis leidyiPleurobrachia bachei
Sterreria sp.
Diopisthoporus gymnopharyngeus
Helobdella robustaIxodes scapularis
Adineta ricciae
Hofstenia miamia
Pomatoceros lamarckii
Xenoturbella bocki
Halicryptus spinulosus
Nematostella vectensis
Macrodasys sp.
Capitella teleta
Lottia gigantea
Leucosolenia complicata
Barentsia gracilis
Lepidodermella squamata
Taenia pisiformes
Brachionus calyciflorus
Novocrania anomala
Leptochiton rugatus
Diopisthoporus longitubus
Stomolophus meleagris
Nemertoderma westbladi
Labidiaster annulatus
Schistosoma mansoni
Saccoglossus mereschkowskii
Convolutriloba macropyga
Hemithiris psittacea
Priapulus caudatus
Megadasys sp.
Loxosoma pectinaricolaMembranipora membranacea
Terebratalia transversa
Childia submaculatum
Amphimedon queenslandica
Craspedacusta sowerby
Gallus gallus
Adineta vaga
Strigamia maritima
Homo sapiens
Leptosynapta clarki
Trichoplax adhaerens
Isodiametra pulchra
Cliona varians
Macrostomum lignano
Aphrocallistes vastusEuplokamis dunlapae
Peripatopsis capensis
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 11. Bayesian inference topology of metazoan relationships inferred from 212 genes under the GTR+ Γ model. Filled circles indicate posterior probabilities of 1.0. Shown is the majority rule consensus tree of three independent chains of >14,000 cycles each and burnin of 4,000 cycles. Convergence of the three chains was indicated by a “maxdiff” value of 0.07.
0.2
Adineta ricciae
Botryllus schlosseri
Astrotomma agassizi
Euplokamis dunlapae
Nematostella vectensis
Lottia gigantea
Strongylocentrotus purpuratus
Barentsia gracilisMegadasys sp.
Halicryptus spinulosus
Mnemiopsis leidyi
Cephalothrix hongkongiensis
Homo sapiens
Diopisthoporus gymnopharyngeus
Terebratalia transversa
Helobdella robusta
Lineus longissimus
Craspedacusta sowerbyAgalma elegans
Crassostrea gigas
Cephalodiscus gracilis
Amphimedon queenslandica
Convolutriloba macropyga
Pomatoceros lamarckii
Prostheceraeus vittatus
Hofstenia miamia
Xenoturbella bocki
Isodiametra pulchra
Loxosoma pectinaricola
Sterreria sp.
Oscarella carmela
Membranipora membranacea
Eumecynostomum macrobursalium
Daphnia pulex
Childia submaculatum
Sycon ciliatum
Saccoglossus mereschkowskii
Gallus gallus
Capitella teleta
Labidiaster annulatus
Drosophila melanogaster
Monosiga brevicollis
Leptosynapta clarki
Cliona varians
Nemertoderma westbladi
Phoronis psammophila
Peripatopsis capensis
Ptychodera bahamensis
Leucosolenia complicata
Macrostomum lignano
Macrodasys sp.
Petromyzon marinus
Pleurobrachia bachei
Schizocardium brazilienseBranchiostoma floridae
Lepidodermella squamata
Dumetocrinus sp.
Stomolophus meleagris
Ciona intestinalis
Hemithiris psittacea
Leptochiton rugatus
Adineta vagaBrachionus calyciflorus
Acropora digitifera
Taenia pisiformes
Novocrania anomala
Eunicella cavolinii
Trichoplax adhaerens
Meara stichopi
Strigamia maritimaIxodes scapularis
Ascoparia sp.
Schistosoma mansoni
Salpingoeca rosetta
Aphrocallistes vastus
Diopisthoporus longitubus
Priapulus caudatus
Schmidtea mediterranea
0.88
WWW.NATURE.COM/NATURE | 19
SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 12. Maximum likelihood topology based on the primary 212-gene matrix with only the 52 taxa with >80% gene occupancy. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 43868 AAs, and overall matrix completeness is 16 percent.
0.2
Drosophila melanogaster
Trichoplax adhaerens
Lottia gigantea
Stomolophus meleagris
Amphimedon queenslandica
Macrostomum lignano
Strigamia maritima
Adineta vaga
Schistosoma mansoni
Ptychodera bahamensis
Halicryptus spinulosus
Leptochiton rugatus
Ciona intestinalis
Nemertoderma westbladi
Convolutriloba macropygaIsodiametra pulchra
Childia submaculatum
Brachionus calyciflorus
Dumetocrinus sp.
Nematostella vectensis
Crassostrea gigas
Membranipora membranacea
Monosiga brevicollis
Daphnia pulex
Lepidodermella squamata
Terebratalia transversa
Hofstenia miamia
Saccoglossus mereschkowskii
Branchiostoma floridae
Leucosolenia complicataAphrocallistes vastus
Novocrania anomala
Prostheceraeus vittatus
Priapulus caudatus
Hemithiris psittacea
Capitella teleta
Gallus gallus
Agalma elegans
Diopisthoporus longitubus
Lineus longissimus
Homo sapiens
Ixodes scapularis
Xenoturbella bocki
Salpingoeca rosetta
Meara stichopi
Oscarella carmela
Craspedacusta sowerby
Sycon ciliatum
Helobdella robusta
Phoronis psammophila
Strongylocentrotus purpuratus
Cliona varians
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 13. Maximum likelihood topology based on the primary 212-gene matrix with only the 40 taxa with >90% gene occupancy. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 42840 AAs, and overall matrix completeness is 11 percent.
0.2
Childia submaculatum
Schistosoma mansoni
Amphimedon queenslandica
Homo sapiens
Prostheceraeus vittatus
Sycon ciliatum
Priapulus caudatus
Craspedacusta sowerby
Oscarella carmela
Hemithiris psittacea
Lepidodermella squamata
Lineus longissimus
Convolutriloba macropyga
Agalma elegans
Phoronis psammophila
Membranipora membranacea
Adineta vaga
Aphrocallistes vastus
Hofstenia miamia
Strongylocentrotus purpuratus
Leucosolenia complicata
Novocrania anomala
Nematostella vectensis
Nemertoderma westbladi
Macrostomum lignano
Trichoplax adhaerens
Xenoturbella bocki
Capitella teleta
Branchiostoma floridae
Ciona intestinalis
Terebratalia transversa
Brachionus calyciflorus
Helobdella robusta
Daphnia pulex
Lottia gigantea
Saccoglossus mereschkowskii
Drosophila melanogaster
Meara stichopi
Halicryptus spinulosus
Isodiametra pulchra
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 14. Maximum likelihood topology based on the primary 212-gene matrix with taxa with LB scores (calculated using TreSpex) over 13 excluded. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 43247 AAs, and overall matrix completeness is 70 percent.
0.2
Diopisthoporus gymnopharyngeus
Eunicella cavolinii
Drosophila melanogaster
Labidiaster annulatus
Nematostella vectensis
Macrodasys sp.Megadasys sp.
Ixodes scapularis
Petromyzon marinus
Membranipora membranacea
Cephalothrix hongkongiensis
Sycon ciliatum
Branchiostoma floridae
Homo sapiens
Brachionus calyciflorus
Loxosoma pectinaricola
Amphimedon queenslandicaMonosiga brevicollis
Pomatoceros lamarckii
Strigamia maritima
Gallus gallus
Novocrania anomala
Lottia gigantea
Ciona intestinalis
Capitella teletaHelobdella robusta
Saccoglossus mereschkowskii
Peripatopsis capensis
Barentsia gracilis
Cephalodiscus gracilis
Botryllus schlosseri
Daphnia pulex
Ptychodera bahamensis
Terebratalia transversa
Halicryptus spinulosus
Cliona varians
Meara stichopi
Leptosynapta clarki
Craspedacusta sowerby
Strongylocentrotus purpuratus
Hemithiris psittacea
Oscarella carmela
Stomolophus meleagrisTrichoplax adhaerens
Salpingoeca rosetta
Prostheceraeus vittatus
Leptochiton rugatus
Priapulus caudatus
Lineus longissimus
Xenoturbella bocki
Crassostrea gigas
Nemertoderma westbladi
Schizocardium c.f. braziliense
Phoronis psammophila
Leucosolenia complicata
Acropora digitifera
Astrotomma agassizi
Dumetocrinus sp.
Agalma elegans
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 15. Maximum likelihood topology based on the primary 212-gene matrix with taxa with LB scores (calculated using TreSpex) over 30 excluded. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 44260 AAs, and overall matrix completeness is 70 percent.
0.2
Pomatoceros lamarckii
Astrotomma agassizi
Leptochiton rugatus
Amphimedon queenslandica
Homo sapiens
Leucosolenia complicata
Ptychodera bahamensis
Adineta ricciae
Xenoturbella bocki
Euplokamis dunlapae
Megadasys sp.
Strongylocentrotus purpuratus
Oscarella carmela
Cliona varians
Daphnia pulex
Sterreria sp.
Novocrania anomala
Adineta vaga
Salpingoeca rosetta
Nematostella vectensis
Craspedacusta sowerby
Monosiga brevicollis
Stomolophus meleagris
Isodiametra pulchra
Strigamia maritima
Capitella teleta
Agalma elegans
Lepidodermella squamataLoxosoma pectinaricola
Cephalothrix hongkongiensis
Brachionus calyciflorus
Schizocardium c.f. braziliense
Eumecynostomum macrobursalium
Prostheceraeus vittatus
Priapulus caudatus
Helobdella robusta
Dumetocrinus sp.
Botryllus schlosseri
Ixodes scapularis
Hemithiris psittacea
Cephalodiscus gracilis
Diopisthoporus longitubus
Crassostrea gigas
Macrostomum lignano
Acropora digitifera
Meara stichopiPeripatopsis capensis
Halicryptus spinulosus
Hofstenia miamia
Barentsia gracilis
Lottia giganteaLabidiaster annulatus
Mnemiopsis leidyi
Eunicella cavolinii
Trichoplax adhaerens
Terebratalia transversa
Branchiostoma floridae
Leptosynapta clarki
Phoronis psammophila
Ciona intestinalis
Drosophila melanogaster
Saccoglossus mereschkowskii
Gallus gallus
Petromyzon marinus
Sycon ciliatum
Lineus longissimus
Aphrocallistes vastus
Diopisthoporus gymnopharyngeus
Membranipora membranacea
Convolutriloba macropyga
Macrodasys sp.
Nemertoderma westbladiAscoparia sp.
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 16. Maximum likelihood topology of the 106-genes with the best LB scores as calculated by TreSpeX. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 22295 AAs, and overall matrix completeness is 71 percent.
0.2
Branchiostoma floridae
Stomolophus meleagris
Euplokamis dunlapae
Trichoplax adhaerens
Oscarella carmela
Macrodasys sp.
Lepidodermella squamata
Isodiametra pulchra
Homo sapiens
Leucosolenia complicata
Pleurobrachia bachei
Halicryptus spinulosus
Adineta ricciae
Leptochiton rugatus
Crassostrea gigas
Ixodes scapularis
Lottia gigantea
Gallus gallus
Diopisthoporus gymnopharyngeus
Taenia pisiformes
Leptosynapta clarki
Nemertoderma westbladi
Sycon ciliatum
Sterreria sp.
Acropora digitifera
Hemithiris psittacea
Megadasys sp.
Diopisthoporus longitubus
Novocrania anomala
Childia submaculatum
Nematostella vectensis
Mnemiopsis leidyi
Adineta vaga
Cephalodiscus gracilis
Craspedacusta sowerby
Eumecynostomum macrobursalium
Meara stichopi
Loxosoma pectinaricola
Agalma elegans
Cliona varians
Macrostomum lignano
Ascoparia sp.
Convolutriloba macropyga
Aphrocallistes vastus
Monosiga brevicollis
Daphnia pulexDrosophila melanogaster
Terebratalia transversa
Petromyzon marinusDumetocrinus sp.
Saccoglossus mereschkowskii
Prostheceraeus vittatus
Strongylocentrotus purpuratus
Botryllus schlosseri
Helobdella robusta
Eunicella cavolinii
Ptychodera bahamensis
Xenoturbella bocki
Astrotomma agassizi
Peripatopsis capensis
Labidiaster annulatus
Lineus longissimus
Priapulus caudatus
Phoronis psammophila
Schmidtea mediterranea
Capitella teleta
Salpingoeca rosetta
Strigamia maritima
Schistosoma mansoni
Hofstenia miamia
Brachionus calyciflorus
Ciona intestinalis
Schizocardium c.f. braziliense
Amphimedon queenslandica
Membranipora membranacea
Cephalothrix hongkongiensis
Pomatoceros lamarckii
Barentsia gracilis100
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 17. Maximum likelihood topology of the 106-genes with the worst LB scores as calculated by TreSpeX The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 22601 AAs, and overall matrix completeness is 68 percent.
0.2
Eunicella cavolinii
Mnemiopsis leidyi
Ixodes scapularis
Ptychodera bahamensis
Nematostella vectensis
Macrodasys sp.
Ciona intestinalis
Helobdella robusta
Adineta vaga
Acropora digitifera
Gallus gallus
Macrostomum lignano
Loxosoma pectinaricola
Dumetocrinus sp.
Cephalothrix hongkongiensis
Amphimedon queenslandica
Barentsia gracilis
Meara stichopi
Phoronis psammophila
Membranipora membranacea
Hofstenia miamia
Lineus longissimus
Diopisthoporus gymnopharyngeus
Pomatoceros lamarckii
Sycon ciliatum
Oscarella carmela
Diopisthoporus longitubus
Cephalodiscus gracilis
Drosophila melanogaster
Crassostrea gigas
Terebratalia transversa
Branchiostoma floridae
Schistosoma mansoniSchmidtea mediterranea
Agalma elegans
Astrotomma agassizi
Prostheceraeus vittatus
Leptosynapta clarki
Capitella teleta
Xenoturbella bocki
Peripatopsis capensis
Novocrania anomala
Botryllus schlosseri
Strigamia maritima
Lepidodermella squamata
Trichoplax adhaerens
Childia submaculatum
Adineta ricciae
Homo sapiens
Petromyzon marinus
Stomolophus meleagris
Lottia gigantea
Nemertoderma westbladi
Halicryptus spinulosus
Megadasys sp.
Schizocardium c.f. braziliense
Aphrocallistes vastus
Brachionus calyciflorus
Taenia pisiformes
Strongylocentrotus purpuratus
Eumecynostomum macrobursalium
Ascoparia sp.
Priapulus caudatus
Labidiaster annulatus
Monosiga brevicollis
Sterreria sp.
Saccoglossus mereschkowskii
Daphnia pulex
Hemithiris psittacea
Leptochiton rugatus
Cliona varians
Leucosolenia complicata
Convolutriloba macropygaIsodiametra pulchra
Craspedacusta sowerby
Salpingoeca rosettaPleurobrachia bachei
Euplokamis dunlapae
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 18. Maximum likelihood topology of the 106 least saturated genes as calculated by TreSpeX The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 23414 AAs, and overall matrix completeness is 71 percent.
0.2
Macrodasys sp.
Eumecynostomum macrobursaliumIsodiametra pulchra
Euplokamis dunlapae
Leucosolenia complicata
Mnemiopsis leidyi
Terebratalia transversa
Ixodes scapularis
Megadasys sp.
Daphnia pulex
Meara stichopi
Petromyzon marinus
Schmidtea mediterranea
Priapulus caudatus
Ascoparia sp.
Barentsia gracilis
Crassostrea gigas
Sycon ciliatum
Nematostella vectensis
Eunicella cavolinii
Childia submaculatumConvolutriloba macropyga
Saccoglossus mereschkowskii
Botryllus schlosseri
Ptychodera bahamensis
Novocrania anomala
Labidiaster annulatus
Strigamia maritima
Capitella teleta
Pleurobrachia bachei
Drosophila melanogaster
Leptochiton rugatus
Cephalodiscus gracilis
Hemithiris psittacea
Membranipora membranacea
Oscarella carmela
Pomatoceros lamarckii
Cliona varians
Brachionus calyciflorus
Peripatopsis capensis
Adineta vaga
Schizocardium c.f. braziliense
Diopisthoporus longitubusDiopisthoporus gymnopharyngeus
Sterreria sp.
Lottia gigantea
Lepidodermella squamataMacrostomum lignano
Homo sapiensBranchiostoma floridae
Agalma elegans
Cephalothrix hongkongiensis
Schistosoma mansoni
Trichoplax adhaerens
Amphimedon queenslandica
Dumetocrinus sp.
Salpingoeca rosetta
Adineta ricciae
Gallus gallus
Craspedacusta sowerby
Aphrocallistes vastus
Xenoturbella bocki
Acropora digitifera
Lineus longissimus
Monosiga brevicollis
Loxosoma pectinaricola
Ciona intestinalis
Halicryptus spinulosus
Phoronis psammophila
Nemertoderma westbladi
Hofstenia miamia
Helobdella robusta
Prostheceraeus vittatus
Leptosynapta clarki
Astrotomma agassizi
Taenia pisiformes
Stomolophus meleagris
Strongylocentrotus purpuratus
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 19. Maximum likelihood topology of the 106 most saturated genes as calculated by TreSpeX. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 21482 AAs, and overall matrix completeness is 66 percent.
0.2
Helobdella robusta
Priapulus caudatus
Lepidodermella squamata
Lineus longissimus
Craspedacusta sowerby
Convolutriloba macropyga
Macrostomum lignano
Acropora digitifera
Membranipora membranacea
Eumecynostomum macrobursalium
Nematostella vectensis
Ixodes scapularis
Petromyzon marinus
Nemertoderma westbladi
Crassostrea gigas
Adineta ricciae
Megadasys sp.
Salpingoeca rosetta
Daphnia pulex
Barentsia gracilis
Peripatopsis capensis
Hofstenia miamia
Agalma elegans
Diopisthoporus gymnopharyngeus
Phoronis psammophila
Mnemiopsis leidyiPleurobrachia bachei
Prostheceraeus vittatus
Branchiostoma floridae
Schizocardium c.f. braziliense
Stomolophus meleagris
Loxosoma pectinaricola
Dumetocrinus sp.
Leucosolenia complicata
Oscarella carmela
Isodiametra pulchra
Cephalodiscus gracilis
Sycon ciliatum
Amphimedon queenslandica
Ascoparia sp.
Hemithiris psittacea
Schmidtea mediterranea
Adineta vaga
Aphrocallistes vastus
Cliona varians
Trichoplax adhaerens
Drosophila melanogaster
Saccoglossus mereschkowskii
Euplokamis dunlapae
Novocrania anomala
Halicryptus spinulosus
Gallus gallus
Astrotomma agassizi
Terebratalia transversa
Ciona intestinalis
Meara stichopi
Labidiaster annulatus
Childia submaculatum
Strongylocentrotus purpuratus
Capitella teleta
Sterreria sp.
Diopisthoporus longitubus
Macrodasys sp.
Leptosynapta clarki
Cephalothrix hongkongiensis
Ptychodera bahamensis
Botryllus schlosseri
Pomatoceros lamarckii
Leptochiton rugatus
Schistosoma mansoni
Eunicella cavolinii
Monosiga brevicollis
Strigamia maritima
Lottia gigantea
Xenoturbella bocki
Brachionus calyciflorus
Homo sapiens
Taenia pisiformes
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 20. Maximum likelihood topology of 207 non-ribosomal protein coding genes. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 44715 AAs, and overall matrix completeness is 68 percent.
0.2
Ciona intestinalis
Craspedacusta sowerby
Megadasys sp.
Ixodes scapularis
Diopisthoporus longitubus
Branchiostoma floridae
Eunicella cavolinii
Isodiametra pulchra
Euplokamis dunlapae
Helobdella robusta
Pomatoceros lamarckii
Daphnia pulex
Schistosoma mansoni
Cephalodiscus gracilis
Lottia gigantea
Schizocardium braziliense
Trichoplax adhaerens
Priapulus caudatus
Stomolophus meleagris
Membranipora membranacea
Novocrania anomala
Lineus longissimus
Saccoglossus mereschkowskii
Ascoparia sp.
Amphimedon queenslandica
Loxosoma pectinaricola
Hofstenia miamia
Capitella teleta
Nemertoderma westbladi
Lepidodermella squamata
Cephalothrix hongkongiensis
Childia submaculatumConvolutriloba macropyga
Macrodasys sp.
Gallus gallus
Astrotomma agassizi
Salpingoeca rosetta
Prostheceraeus vittatus
Leptosynapta clarki
Acropora digitifera
Dumetocrinus sp.
Leucosolenia complicata
Peripatopsis capensis
Strongylocentrotus purpuratus
Terebratalia transversa
Brachionus calyciflorus
Sterreria sp.Meara stichopi
Botryllus schlosseri
Sycon ciliatum
Hemithiris psittacea
Ptychodera bahamensis
Monosiga brevicollis
Drosophila melanogaster
Phoronis psammophila
Pleurobrachia bachei
Leptochiton rugatus
Macrostomum lignano
Agalma elegans
Adineta vaga
Taenia pisiformes
Xenoturbella bocki
Strigamia maritima
Homo sapiens
Aphrocallistes vastus
Cliona varians
Eumecynostomum macrobursalium
Halicryptus spinulosus
Nematostella vectensis
Adineta ricciae
Schmidtea mediterranea
Mnemiopsis leidyi
Diopisthoporus gymnopharyngeus
Petromyzon marinus
Labidiaster annulatus
Crassostrea gigas
Barentsia gracilis
Oscarella carmela
100
100
94
100
100
100
100
72100
100
100
48
100
75
100
100
71
79
100
100
97
97
71
100
100
100
100
100
100
97
100
95
74
100
44
100
100
63
100
100
100
100
100
100
100100
100
100
100
41
100
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100
99
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90
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100
86
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60
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98
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 21. Maximum likelihood topology of 53 ribosomal protein genes. The most likely tree sampled in RAxML using the LG+I+Γ substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 9010 AAs, and overall matrix completeness is 81 percent.
0.2
Mnemiopsis leidyi
Acropora digitifera
Schizocardium c.f. braziliense
Lineus longissimus
Convolutriloba macropyga
Halicryptus spinulosus
Meara stichopi
Prostheceraeus vittatus
Barentsia gracilis
Amphimedon queenslandica
Pomatoceros lamarckii
Crassostrea gigas
Eunicella cavolinii
Sterreria sp.
Labidiaster annulatus
Petromyzon marinus
Adineta vaga
Cliona varians
Schistosoma mansoni
Hofstenia miamia
Childia submaculatum
Oscarella carmela
Brachionus calyciflorus
Saccoglossus mereschkowskii
Peripatopsis capensis
Leptosynapta clarki
Trichoplax adhaerens
Macrostomum lignano
Lottia gigantea
Nematostella vectensis
Branchiostoma floridae
Strigamia maritima
Diopisthoporus gymnopharyngeus
Strongylocentrotus purpuratus
Priapulus caudatus
Gallus gallus
Eumecynostomum macrobursaliumIsodiametra pulchra
Astrotomma agassizi
Taenia pisiformes
Helobdella robusta
Leptochiton rugatus
Ixodes scapularis
Ptychodera bahamensis
Ascoparia sp.
Daphnia pulex
Botryllus schlosseri
Adineta ricciaeMacrodasys sp.
Cephalodiscus gracilis
Membranipora membranacea
Lepidodermella squamata
Euplokamis dunlapae
Homo sapiens
Aphrocallistes vastus
Cephalothrix hongkongiensis
Megadasys sp.
Ciona intestinalis
Monosiga brevicollis
Terebratalia transversa
Salpingoeca rosetta
Loxosoma pectinaricola
Agalma elegans
Pleurobrachia bachei
Dumetocrinus sp.
Xenoturbella bocki
Novocrania anomala
Capitella teleta
Stomolophus meleagris
Nemertoderma westbladi
Phoronis psammophila
Craspedacusta sowerby
Diopisthoporus longitubis
Leucosolenia complicata
Sycon ciliatum
Drosophila melanogaster
Hemithiris psittacea
Schmidtea mediterranea
88
92
79
52
62
100
26
34
9
100
100
66
24100
100
94
97
21
32
100
82
36
45
82
94
100
42
98
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20
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95
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13
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24
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93
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45
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34
98
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87
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44
95
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55
75
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39
67
100
100
8197
100
100
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520
Supplementary Figure 22. Maximum likelihood topology of BMGE-trimmed data matrix. The most likely tree sampled in RAxML using the LG4X substitution model for each gene is shown with ML bootstrap (bs) support values from 100 replicates indicated at each node. The length of the matrix is 33323 AAs, and overall matrix completeness is 66 percent.
Xenoturbella bockiDiopisthoporus longitubus
Diopisthoporus gymnopharyngeus100
Hofstenia miamia53
Isodiametra pulchraEumecynostomum macrobursalium
Childia submaculatumConvolutriloba macropyga54
100100
100
Meara stichopiNemertoderma westbladi
75
Sterreria sp.94
Ascoparia sp.100
100
100
Priapulus caudatusHalicryptus spinulosus100
Peripatopsis capensisStrigamia maritima
Drosophila melanogasterDaphnia pulex
10071
Ixodes scapularis100
100
100
Crassostrea gigasLottia gigantea100
Leptochiton rugatus100
Hemithiris psittaceaTerebratalia transversa100
Novocrania anomala84
Phoronis psammophila97
Lineus longissimusCephalothrix hongkongiensis
10035
66
Capitella teletaPomatoceros lamarckii95
Helobdella robusta
100
Taenia pisiformesSchistosoma mansoni100
Schmidtea mediterranea100
Prostheceraeus vittatus97
Macrostomum lignano100
Lepidodermella squamataMegadasys sp.
Macrodasys sp.10056
47
Brachionus calyciflorusAdineta vaga
Adineta ricciae100100
97
Loxosoma pectinaricolaBarentsia gracilis
100
Membranipora membranacea98
99
98
100
Labidiaster annulatusAstrotomma agassizi
Strongylocentrotus purpuratus48
Leptosynapta clarki51
100
Dumetocrinus sp.Cephalodiscus gracilis97
98
Saccoglossus mereschkowskiiSchizocardium c.f. braziliense
Ptychodera bahamensis100100
100
Homo sapiensGallus gallus
100
Petromyzon marinus100
Ciona intestinalisBotryllus schlosseri
100100
Branchiostoma floridae
90
99
100
100
Eunicella cavoliniiAcropora digitifera
Nematostella vectensis100
100
Agalma elegansCraspedacusta sowerby
100
Stomolophus meleagris100
100
Trichoplax adhaerens
56
100
Sycon ciliatumLeucosolenia complicata
100
Oscarella carmela87
Amphimedon queenslandicaCliona varians
100
Aphrocallistes vastus100
66
82
Euplokamis dunlapaeMnemiopsis leidyi
Pleurobrachia bachei100100
99
Salpingoeca rosettaMonosiga brevicollis
0.01
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SUPPLEMENTARY INFORMATIONRESEARCHdoi:10.1038/nature16520