Data from: Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms

Background: Earthworms (Crassiclitellata) are a diverse group of annelids
of substantial ecological and economic importance. Earthworms are
primarily terrestrial infaunal animals, and as such are probably rather
poor natural dispersers. Therefore, the near global distribution of
earthworms reflects an old and likely complex evolutionary history.
Despite a long-standing interest in Crassiclitellata, relationships among
and within major clades remain unresolved. Methods: In this study, we
evaluate crassiclitellate phylogenetic relationships using 38 new
transcriptomes in combination with publicly available transcriptome data.
Our data include representatives of nearly all extant earthworm families
and a representative of Moniligastridae, another terrestrial annelid group
thought to be closely related to Crassiclitellata. We use a series of
differentially filtered data matrices and analyses to examine the effects
of data partitioning, missing data, compositional and branch-length
heterogeneity, and outgroup inclusion. Results and discussion: We recover
a consistent, strongly supported ingroup topology irrespective of
differences in methodology. The topology supports two major earthworm
clades, each of which consists of a Northern Hemisphere subclade and a
Southern Hemisphere subclade. Divergence time analysis results are
concordant with the hypothesis that these north-south splits are the
result of the breakup of the supercontinent Pangaea. Conclusions: These
results support several recently proposed revisions to the classical
understanding of earthworm phylogeny, reveal two major clades that seem to
reflect Pangaean distributions, and raise new questions about earthworm
evolutionary relationships.