Data from: Restructuring higher taxonomy using broad-scale phylogenomics: the living Ophiuroidea

The power and throughput of next-generation sequencing is instigating a major transformation in our understanding of evolution and classification of life on our planet. The new trees of life are robust and comprehensive. Here we provide a landmark phylogeny of the living ophiuroids and use it as the basis for a major revision of the higher classification of this class of marine invertebrates. We used an exon-capture system to generate a 1484 exon (273 kbp) data-matrix from DNA extracted from ethanol-preserved museum samples. We successfully obtained an average of 90% of our target sequence from 576 species spread across the known taxonomic diversity. The topology of the major lineages was robust to taxon sampling, exon-sampling, models and methods. However, estimates of node age were much less precise, varying by about a quarter of mean age. We used a combination of phylogenetic distinctiveness and temporal-banding to guide our revision of the family-level classification. Empirically, we determined that limiting family crown age to 110 ± 10 Ma (mid Cretaceous) selected phylogenetically distinct nodes while minimising disruption to the existing taxonomy. The resulting scheme of 32 families and six orders considerably expands the number of higher taxa. The families are generally longitudinally widespread across the world's oceans, although 17 are largely confined to temperate and equatorial latitudes and six to relatively shallow water (less than 1000 m depth).OphiuroidHC_TableS1S1. Table of information on samples, exons and genes.OphiuroidHC_Table S2S2. Calibrations and fossil evidence used to date the molecular phylogeny.OphiuroidHC_576taxa_treesNexus format RAxML tree with bootstrap values, and PLRS version.OphiuroidHC_185taxa_RAxMLtreesOphiuroidHC_185taxa_BEASTtreesOphiuroidHC_576taxa_1484exonNexus format 416 gene, 1484 exon, 272,952 site, 576 taxa data-matrix.OphiuroidHC_S7_revised_classificationSupplementary material S7, Revised classification of the recent Ophiuroidea.OphiuroidHC_FigS3S3. 576 taxa all-sites RAxML phylogeny with bootstrap (BS) support.OphiuroidHC_FigS4S4. 185 taxa all-sites nucleotide RAxML with BS support.OphiuroidHC_FigS5S5. 185 taxa all-sites amino acid RAxML tree with BS support.OphiuroidHC_FigS6S6. 185 taxa ASTRAL species tree, with local posterior probability support.OphiuroidHC_DRYAD_readme_fileWord document with information on constituents of this Dryad packageOphiuroidHC_distribution_summaryExcel file of family latitude, longitude and depth distribution summary histogram values, with ggplot script, used to generate Figure 4