Integrating host use and dispersal ability with species delimitation to unravel a cryptic radiation of photosynthetic sea slugs

Species delimitation models are important quantitative tools for
facilitating the discovery of cryptic species and clarifying the
boundaries between focal taxa. However, distinct evolutionary processes
may promote diversification at different points in a radiation,
complicating efforts to identify speciation processes and diagnostic
characters. Moreover, traits like dispersal ability can have opposing
effects on diversification rate versus population subdivision, which
causes coalescent models to oversplit samples. In this study, we examined
the effects of larval dispersal and host use on population structure and
diversity in a Caribbean radiation of photosynthetic herbivores, sea slugs
in the genus Elysia. We applied five species delimitation models (SDMs) to
molecular datasets, and also performed phylogenetic analyses of
evolutionary relationships and population-genetic structure within
species. We further modeled ancestral use of host algae using Bayesian
Inference methods. Datafiles archived here include input files for
analyses such as DNA sequence alignments and Arlequin input files, and
also output files generated by the
program BayesTraits during ancestral state
reconstruction of host use. The findings broadly supported six
described taxa as well as a 7th, previously unrecognized taxon. However,
species with less dispersive offspring were often oversplit by SDMs based
on the multispecies coalescent. Surprisingly, species that spanned a major
phylogeographic break were also likely to be split into multiple taxa by
coalescent models, regardless of their dispersal ability. Some host shifts
may have contributed to divergence, but others predated speciation,
suggesting ecological specialization can promote reproductive isolation
but often acted at deeper timescales; recent speciation was more often
driven by sea level fluctuations and changes in reproductive anatomy,
potentially reinforced by dispersal limitation.