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.