Phylogenomic analyses recover a clade of large-bodied decapodiform cephalopods.

Phylogenetic relationships among the squids and cuttlefishes (Cephalopoda:Decapodiformes) have resisted clarification for decades, despite multiple analyses of morphological, molecular and combined data sets. More recently, analyses of complete mitochondrial genomes and hundreds of nuclear loci have yielded similarly ambiguous results. In this study, we re-evaluate hypotheses of decapodiform relationships by increasing taxonomic breadth and utilizing higher-quality genome and transcriptome data for several taxa. We also employ analytical approaches to (1) identify contamination in transcriptome data, (2) better assess model adequacy, and (3) account for potential biases. Using this larger data set, we consistently recover a clade comprising Myopsida (closed-eye squid), Sepiida (cuttlefishes), and Oegopsida (open-eye squid) that is sister to a Sepiolida (bobtail and bottletail squid) clade. Idiosepiida (pygmy squid) is consistently recovered as the sister group to all sampled decapodiform lineages. Further, a weighted Shimodaira-Hasegawa test applied to one of our larger data matrices rejects all alternatives to these ordinal-level relationships. At present, available nuclear genome-scale data support nested clades of relatively large-bodied decapodiform cephalopods to the exclusion of pygmy squids, but improved taxon sampling and additional genomic data will be needed to test these novel hypotheses rigorously.