Data from: Phylogenomic resolution of the cetacean tree of life using target sequence capture
Data files
Oct 16, 2019 version files 4.15 GB
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10_genes_SortaDate_10parts.phy
7.48 MB
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10_genes_SortaDate_3parts.phy
4.98 MB
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10_genes_SortaDate_6parts.phy
7.48 MB
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ASTRAL_species_tree.txt
18.29 KB
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Bayes_tree.nex
46.10 KB
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Cetacea_ExaBayes.phy
652.76 MB
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Cetacea_gene_partition.txt
101.23 KB
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Cetacea_partition_mcmctree_3.aln
310.69 MB
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Cetacea_partition_mcmctree_6.aln
466.04 MB
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config.nex
2.68 KB
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DATASET_A.phylip.txt
652.76 MB
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DATASET_B.phylip
639.71 MB
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ExaBayes_parameters.run-0.Cetacea_1
632.25 KB
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ExaBayes_parameters.run-0.Cetacea_2
632.25 KB
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ExaBayes_topologies.run-0.Cetacea_1
9.72 MB
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ExaBayes_topologies.run-0.Cetacea_2
9.72 MB
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FigTree_parts_10_mcmctree_AR_mcmc.txt
107.79 MB
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FigTree_parts_10_mcmctree_AR_mcmc2.txt
21.14 MB
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FigTree_parts_10_mcmctree_AR.tre
4.96 KB
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FigTree_parts_10_mcmctree_AR2.tre
2.60 KB
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FigTree_parts_10_mcmctree_IR_2.tree
2.57 KB
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FigTree_parts_10_mcmctree_IR.tre
4.96 KB
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FigTree_parts_3_mcmctree_AR_1.tre
4.95 KB
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FigTree_parts_3_mcmctree_IR_2.tre
4.96 KB
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FigTree_parts_3_mcmctree_IR.tre
4.95 KB
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FigTree_parts_6_mcmctree_AR.tre
4.96 KB
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FigTree_parts_6_mcmctree_IR_2.tre
4.96 KB
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FigTree_parts_6_mcmctree_IR.tre
4.96 KB
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FigTree_SortaDate_parts10_mcmctree_AR.tre
4.96 KB
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FigTree_SortaDate_parts10_mcmctree_IR.tre
4.96 KB
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FigTree_SortaDate_parts3_mcmctree_AR.tree
2.61 KB
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FigTree_SortaDate_parts3_mcmctree_IR.tree
2.58 KB
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FigTree_SortaDate_parts6_mcmctree_AR.tree
2.59 KB
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FigTreeparts_3_mcmctree_AR_2.tre
4.95 KB
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Figure_S1.pdf
187.01 KB
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Figure_S10.pdf
765.30 KB
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Figure_S11.pdf
1.10 MB
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Figure_S12.pdf
166.20 KB
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Figure_S13.pdf
222.23 KB
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Figure_S14.pdf
210.54 KB
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Figure_S15.pdf
333.18 KB
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Figure_S2.pdf
26.27 KB
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Figure_S3.pdf
142.95 KB
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Figure_S4_Tracer_3_AR.pdf
978.33 KB
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Figure_S5_Tracer_3_IR.pdf
489.43 KB
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Figure_S6_Tracer_6_AR.pdf
977.51 KB
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Figure_S7_Tracer_6_IR.pdf
981.85 KB
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Figure_S8_Tracer_10_AR.pdf
51.39 KB
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Figure_S9_Tracer_10_IR.pdf
51.89 KB
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GENE_LIST3.phylip
158.19 MB
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mcmctree_3p_AR.ctl
1.30 KB
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mcmctree_3p_IR.ctl
1.30 KB
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mcmctree_6p_AR.ctl
1.30 KB
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mcmctree_6p_IR.ctl
1.30 KB
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partitionfindersets
78.75 KB
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parts_10_mcmctree_IR_2mcmc.txt
21.14 MB
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parts_10_mcmctree_IR_mcmc.txt
107.69 MB
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parts_3_mcmctree_AR_2_mcmc.txt
93.69 MB
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parts_3_mcmctree_AR_mcmc.txt
91.69 MB
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parts_3_mcmctree_IR_2_mcmc.txt
93.69 MB
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parts_3_mcmctree_IR_mcmc.txt
91.69 MB
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parts_6_mcmctree_AR_mcmc.txt
97.69 MB
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parts_6_mcmctree_IR_2_mcmc.txt
99.69 MB
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parts_6_mcmctree_IR_mcmc.txt
97.69 MB
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RAXML_boostrap_by_gene_result.txt
904.30 KB
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RAxML_bootstrap_partition_by_gene.result
1.21 MB
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RAxML_bootstrap_partitionfinder.result.txt
873.95 KB
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RAxML_bootstrap_unpartitioned.result.txt
873.95 KB
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RAxML_DATASET_B_all_genes_bestTree.result
5.35 KB
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RAxML_DATASET_B_partitionfinder_bestTree.result
5.32 KB
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RAxML_DATASET_B_unpartitioned_bestTree.result
5.32 KB
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RAXML_gene_trees_ASTRAL_input
16.74 MB
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RAxML_partition_by_gene_best_tree.tre
5.46 KB
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RAxML_partitionfinder_bootstrap.result.txt
891.09 KB
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RAxML_unpartitioned_best_tree.tree
5.46 KB
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RAxML_unpartitioned_bootstrap.result
891.09 KB
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RAxMLpartitionfinder_best_tree.tre
5.46 KB
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README_for_Figure_S1.pdf
187.01 KB
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SortaDate_parts10_mcmctree_AR_mcmc.txt
107.79 MB
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SortaDate_parts10_mcmctree_IR_mcmc.txt
107.69 MB
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SortaDate_parts3_mcmctree_AR_mcmc.txt
18.34 MB
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SortaDate_parts3_mcmctree_IR_mcmc.txt
18.34 MB
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SortaDate_parts6_mcmctree_AR_mcmc.txt
19.54 MB
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Supplemental_Figure_Captions.docx
14.17 KB
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Table_S1.xlsx
20.57 KB
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Table_S2.docx
21.73 KB
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Table_S3.xlsx
38.02 KB
Abstract
The evolution of the cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, while the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for ~3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from >38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic dataset for cetaceans, spanning 6,527,596 aligned base pairs and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among ocean dolphins, especially the problematic subfamily Delphininae, which includes the common and bottlenose dolphins. We performed Bayesian estimation of species divergence times using MCMCtree, integrating recently described fossils as calibration points (e.g., Mystacodon selenensis) that have not been used before. Integration of new fossil dates in the context of autocorrelated rates indicate that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene.