Supplementary data for the thesis Reconstructing the Demographic History of the Pacific Nudibranch Genus Hermissenda

The Pacific nudibranch Hermissenda crassicornis (sensu lato) is a well-known model organism in neuroscience. This species was recently split into three pseudocryptic species based on differences in genetics, morphology, and behaviour. We used ddRADSeq data from 33 individuals (2354 loci) and coalescent isolation-with-migration models to estimate the demographic history of the clade. We inferred (1) a novel phylogenetic tree topology, (2) relatively old divergence times (0.55 and 1.29 mya), (3) a much larger population size in the southern species H. opalescens, and (4) no gene flow between the sympatric species H. crassicornis and H. opalescens. We then used forward simulations to investigate the plausibility of these results. Preliminary simulations suggest the inference approach applied to the Hermissenda data may be incorrectly estimating the older split, an observation needing further study. Overall, our results support the need to reassess previous studies that used H. crassicornis (sensu lato) as a model organism.