Investigating sources of conflict in deep phylogenomics of vetigastropod snails

Phylogenetic analyses may suffer from multiple sources of error leading to
conflict between genes and methods of inference. The evolutionary history
of the mollusc clade Vetigastropoda makes them susceptible to these
conflicts, their higher level phylogeny remaining largely unresolved.
Originating over 350 million years ago, vetigastropods were the dominant
marine snails in the Paleozoic. Multiple extinction events and new
radiations have resulted in both very long and very short branches and a
large extant diversity of over 4000 species. This is the perfect setting
of a hard phylogenetic question in which sources of conflict can be
explored. We present 41 new transcriptomes across the diversity of
vetigastropods (62 terminals total), and provide the first genomic-scale
phylogeny for the group. We find that deep divergences differ from
previous studies in which long branch attraction was likely pervasive.
Robust results leading to changes in taxonomy include the paraphyly of the
order Lepetellida and the family Tegulidae. Tectinae subfam.
nov. is designated for the clade
comprising Tectus, Cittarium and Rochia. For two early divergences, topologies disagreed between concatenated analyses using site heterogeneous models vs. concatenated partitioned analyses and summary coalescent methods. We investigated rate and composition heterogeneity among genes, as well as missing data by locus and by taxon, none of which had an impact on the inferred topologies. We also found no evidence for ancient introgression throughout the phylogeny. We further tested whether uninformative genes and over-partitioning were responsible for this discordance by evaluating the phylogenetic signal of individual genes using likelihood mapping, and by analyzing the most informative genes with a full multispecies coalescent model. We find that most genes are not informative at the two conflicting nodes, but neither this nor gene-wise partitioning are the cause of discordant results. New method implementations that simultaneously integrate amino acid profile mixture models and the multispecies coalescent might be necessary to resolve these and other recalcitrant nodes in the Tree of Life.