Data from: Phylogenomic resolution of the Hemichordate and Echinoderm clade

Ambulacraria, comprising Hemichordata and Echinodermata, is closely
related to Chordata, making it integral to understanding chordate origins
and polarizing chordate molecular and morphological characters.
Unfortunately, relationships within Hemichordata and Echinodermata have
remained unresolved, compromising our ability to extrapolate findings from
the most closely related molecular and developmental models outside of
Chordata (e.g., the acorn worms Saccoglossus kowalevskii and Ptychodera
flava and the sea urchin Strongylocentrotus purpuratus). To resolve
long-standing phylogenetic issues within Ambulacraria, we sequenced
transcriptomes for 14 hemichordates as well as 8 echinoderms and
complemented these with existing data for a total of 33 ambulacrarian
operational taxonomic units (OTUs). Examination of leaf stability values
revealed rhabdopleurid pterobranchs and the enteropneust Stereobalanus
canadensis were unstable in placement; therefore, analyses were also run
without these taxa. Analyses of 185 genes resulted in reciprocal monophyly
of Enteropneusta and Pterobranchia, placed the deep-sea family
Torquaratoridae within Ptychoderidae, and confirmed the position of
ophiuroid brittle stars as sister to asteroid sea stars (the Asterozoa
hypothesis). These results are consistent with earlier perspectives
concerning plesiomorphies of Ambulacraria, including pharyngeal gill
slits, a single axocoel, and paired hydrocoels and somatocoels. The
resolved ambulacrarian phylogeny will help clarify the early evolution of
chordate characteristics and has implications for our understanding of
major fossil groups, including graptolites and somasteroideans.