Data from: Phylotranscriptomic consolidation of the jawed vertebrate timetree

Irisarri I, Baurain D, Brinkmann H, Delsuc F, Sire J, Kupfer A, Petersen J, Jarek M, Meyer A, Vences M, Philippe H

Date Published: July 24, 2017

DOI: http://dx.doi.org/10.5061/dryad.r2n70

 

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Title Supplementary Methods, Tables and Figures
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Description Supplementary Methods, Tables, and Figures
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Title Custom scripts
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Description detect-divergent-seq-ali.c detect-problems-arb-3-9-15.c ParalogDetector_V4-sort.sh split-out-paralog.c
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Title Nuclear datasets
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Description 0DP gene set – 4593 gene alignments; 1DP gene set – 1162 gene alignments; 2DP gene set – 1434 gene alignments; nuclear test dataset
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Title ML tree NoDP dataset, RAxML GTR+G
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Description ML tree NoDP dataset, RAxML GTR+G, 100 non-parametric rapid bootstrap
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Title ML tree 0DP dataset, LG+G+F
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Description ML tree 0DP dataset, RAxML LG+G+F, 100 non-parametric rapid bootstrap
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Title Mitochondrial datasets
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Description Concatenated mitochondrial proteins of jawed vertebrate (except ND6), either containing the total set of 106 taxa or a reduced set of 95 taxa after removing fastest-evolving taxa.
Download mtP-Gnatho-ND6_datasets.tgz (3.130 Mb)
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Title BI tree, mitochondrial dataset 95 taxa, PhyloBayes CAT+G
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Title BI tree, mitochondrial dataset 95 taxa, PhyloBayes CATGTR+G
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Title BI tree, mitochondrial dataset 106 taxa, PhyloBayes CAT+G
Downloaded 1 time
Download mtP-Gnatho-ND6_strh04_R106_V2086-CAT_25_1...nn.tre (4.223 Kb)
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Title BI tree, mitochondrial dataset 106 taxa, PhyloBayes CATGTR+G
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Title Species tree of the 0DP dataset, ASTRAL
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Description Species tree of the 0DP dataset, ASTRAL tree estimated on 4593 gene trees, branch support is measured by local posterior probabilities
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Title Species tree of the 1DP dataset, ASTRAL
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Description Species tree of the 1DP dataset, ASTRAL tree estimated on 1162 gene trees, branch support is measured by local posterior probabilities
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Title Species tree of the 2DP dataset, ASTRAL
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Description Species tree of the 2DP dataset, ASTRAL tree estimated on 1434 gene trees, branch support is measured by local posterior probabilities
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Title BI tree, NoDP dataset, PhyloBayes CAT+G
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Description Majority rule consensus from 100 BI analyses of 100 gene jackknife replicates (alignments with ~50,000 amino acid position each). PhyloBayes, CAT+G model
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Title BI tree, 1DP dataset, PhyloBayes CAT+G
Downloaded 1 time
Description Majority rule consensus from 100 BI analyses of 100 gene jackknife replicates (alignments with ~50,000 amino acid position each). PhyloBayes, CAT+G model
Download jack50000-1DP-all-CATG-A.con.ann.tre (4.063 Kb)
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Title BI tree, 2DP dataset, PhyloBayes CAT+G
Downloaded 1 time
Description Majority rule consensus from 100 BI analyses of 100 gene jackknife replicates (alignments with ~50,000 amino acid position each). PhyloBayes, CAT+G model
Download jack50000-2DP-all-CATG-A.con.ann.tre (4.111 Kb)
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Title Genome-averaged timetree, PhyloBayes
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Description Timetree showing averaged dates across 100 timetrees, each estimated in PhyloBayes from 100 independent gene jackknife replicates. CATGTR+G substitution model, autocorrelated log-normal clock model, 16 cross-validated calibration points with soft bounds and birth-death tree prior
Download CATGTR-LN-BD-SB_100jacks.chronogram_mean_...rI.tre (4.529 Kb)
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Title Timetree with 30 calibrations, nuclear test dataset, PhyloBayes
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Description Timetree estimated in PhyloBayes under CATGTR+G substitution model, autocorrelated log-normal clock model, 30 calibration points with soft bounds and birth-death tree prior
Download 14K_CATGTR-LN-BD-SB_all30.ch2_sample.chro...am.tre (4.3 Kb)
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Title Timetree with 16 calibrations, nuclear test dataset, PhyloBayes
Downloaded 2 times
Description Timetree estimated in PhyloBayes under CATGTR+G substitution model, autocorrelated log-normal clock model, 16 cross-validated calibration points with soft bounds and birth-death tree prior
Download 14K_CATGTR-LN-BD-SB_CVed16b.ch2_sample.chronogram (4.299 Kb)
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Title Neoceratodus forsteri transcriptome
Downloaded 4 times
Download Neoceratodus_forsteri_transcriptome_trinit...fa.gz (309.6 Mb)
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Title Megophrys nasuta transcriptome
Downloaded 8 times
Download Megophrys_nasuta_transcriptome_JP25.fasta.gz (15.97 Mb)
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Title Discoglossus pictus transcriptome
Downloaded 3 times
Download Discoglossus_pictus_transcriptome_JP15.fasta.gz (16.15 Mb)
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Title Andrias davidianus transcriptome
Downloaded 5 times
Download Andrias_davidianus_transcriptome_JP19.fasta.gz (14.27 Mb)
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Title Calotriton asper transcriptome
Downloaded 4 times
Download Calotriton_asper_transcriptome_JP21.fasta.gz (14.49 Mb)
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Title Lepidosiren paradoxa transcriptome
Downloaded 3 times
Download Lepidosiren_paradoxa_transcriptome_trinity...fa.gz (312.1 Mb)
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Title Protopterus annectens transcriptome
Downloaded 3 times
Download Protopterus_annectens_transcriptome_trinit...fa.gz (185.6 Mb)
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Title Geotrypetes seraphini transcriptome
Downloaded 5 times
Download Geotrypetes_seraphini_transcriptome_JP24.fasta.gz (15.25 Mb)
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Title Hymenochirus curtipes transcriptome
Downloaded 5 times
Download Hymenochirus_curtipes_transcriptome_JP17.fasta.gz (21.87 Mb)
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Title Pipa pipa transcriptome
Downloaded 3 times
Download Pipa_pipa_transcriptome_JP18.fasta.gz (10.87 Mb)
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Title Proteus anguinus transcriptome
Downloaded 4 times
Download Proteus_anguinus_transcriptome_JP22.fasta.gz (15.27 Mb)
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Title Siren lacertina transcriptome
Downloaded 5 times
Download Siren_lacertina_transcriptome_JP16.fasta.gz (14.49 Mb)
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Title Typhlonectes natans transcriptome
Downloaded 6 times
Download Typhlonectes_natans_transcriptome_JP23.fasta.gz (10.62 Mb)
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Title Acipenser baerii transcriptome
Downloaded 4 times
Download Acipenser_baerii_transcriptome.fasta.bz2 (49.04 Mb)
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Title Amia calva transcriptome
Downloaded 3 times
Download Amia_calva_transcriptome.fasta.bz2 (35.27 Mb)
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Title Lepisosteus platyrhincus transcriptome
Downloaded 4 times
Download Lepisosteus_platyrhincus_transcriptome.fasta.bz2 (55.62 Mb)
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Title Pleurodeles waltl transcriptome
Downloaded 4 times
Download Pleurodeles_waltl_transcriptome.fasta.bz2 (35.44 Mb)
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Title Polypterus senegalus transcriptome
Downloaded 4 times
Download Polypterus_senegalus_transcriptome.fasta.bz2 (36.69 Mb)
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Title Protopterus aethiopicus transcriptome
Downloaded 4 times
Download Protopterus_aethiopicus_transcriptome.fasta.bz2 (21.95 Mb)
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Title Raja clavata transcriptome
Downloaded 3 times
Download Raja_clavata_transcriptome.fasta.bz2 (36.85 Mb)
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Title Rhinatrema bivittatum transcriptome
Downloaded 5 times
Download Rhinatrema_bivittatum_transcriptome.fasta.bz2 (31.10 Mb)
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Title Scyliorhinus canicula transcriptome
Downloaded 3 times
Download Scyliorhinus_canicula_transcriptome.fasta.bz2 (28.93 Mb)
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Title Tarentola mauritanica transcriptome
Downloaded 5 times
Download Tarentola_mauritanica_transcriptome.fasta.bz2 (60.27 Mb)
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Title Typhlonectes compressicauda transcriptome
Downloaded 3 times
Download Typhlonectes_compressicauda_transcriptome...ta.bz2 (27.87 Mb)
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Title ML tree, mitochondrial dataset 106 taxa, RAxML GTR+G
Downloaded 2 times
Download mtP-Gnatho-ND6_strh04_R106_2773_RaxGTR4g_...ng.tre (5.248 Kb)
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Title ML tree, mitochondrial dataset 106 taxa, RAxML MTREV+G
Downloaded 2 times
Download mtP-Gnatho-ND6_strh04_R106_2773_RaxMtRevF...ng.tre (5.248 Kb)
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Title ML tree, mitochondrial dataset 95 taxa, RAxML GTR+G
Downloaded 3 times
Download mtP-Gnatho_mi11F-ND6_strh04_R95_2866_RaxG...ng.tre (4.717 Kb)
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Title ML tree, mitochondrial dataset 95 taxa, RAxML MTREV+G
Downloaded 2 times
Download mtP-Gnatho_mi11F-ND6_strh04_R95_2866_RaxM...ng.tre (4.717 Kb)
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When using this data, please cite the original publication:

Irisarri I, Baurain D, Brinkmann H, Delsuc F, Sire J, Kupfer A, Petersen J, Jarek M, Meyer A, Vences M, Philippe H (2017) Phylotranscriptomic consolidation of the jawed vertebrate timetree. Nature Ecology & Evolution 1(9): 1370-1378. http://dx.doi.org/10.1038/s41559-017-0240-5

Additionally, please cite the Dryad data package:

Irisarri I, Baurain D, Brinkmann H, Delsuc F, Sire J, Kupfer A, Petersen J, Jarek M, Meyer A, Vences M, Philippe H (2017) Data from: Phylotranscriptomic consolidation of the jawed vertebrate timetree. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.r2n70
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