Data from: A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans

Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic–Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.READMEDescription of all files associated with this paper, in all subfolders in this repository.dryad_readme.txtBC_Transcriptome_dataThis file contains the assembled transcriptome reads for 4 species (across multiple life stages) used to develop anchored enrichment probes.D_Probe_designThis file contains the probe sequences for each of 6 infraorders (Achelata, Anomura, Astacidea, Brachyura, Caridea, Dendrobranchiata) that were ordered from Agilent, and supporting files related to how the probe sets were constructed.EF_AHE_dataThis file contains the exon-based reference loci from the E. sinensis genome, and the key mapping the final 410 exon-based loci (folder GHI_Data_matrices) to the 352 AHE targets.GHI_Data_matricesThis file contains data matrices used in this study.J_Phylogenetic_treesThis file contains all the phylogenetic trees associated with this study.L_Divergence_time_resultsThis package contains the results of divergence time analyses.Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-155605