Testing a mitochondrial species radiation with exon capture data - The Antarctic sea slug Doris 'kerguelenensis'

The Southern Ocean sea slug Doris 'kerguelenensis' is now recognised as a large endemic radiation in Antarctica, revealed through nuclear and mitochondrial DNA sequencing and metabolomics. Sanger sequencing of cytochrome c oxidase subunit I has suggested at least 59 putative species exist. This radiation is thought to result from a unique combination of selection and allopatry over millions of years of glacial cycles. To achieve phylogenetic resolution among species, large-scale genomic data were required. We employed an exon capture approach, targeting thousands of exons from hundreds of genes across 130 individuals representing the 59 putative species. Our goals were to i) test a newly designed bait set spanning Doridida, ii) objectively assess mitochondrial species hypotheses, and iii) evaluate species delimitation and phylogenetic reconstruction methods for resolving this Antarctic sea slug complex. Maximum likelihood and ASTRAL tree topologies were largely congruent with mitochondrial hypotheses but revealed some mito-nuclear discordance. Despite this, we resolved a robust phylogeny of the Doris 'kerguelenensis' complex. Species boundaries were further assessed using multiple delimitation tools, with the unconstrained SODA algorithm emerging as the most practical and balanced. It detected more species (n = 75) than mitochondrial data, and high levels of hybridization were detected. The baits developed here span the full taxonomic breadth of Doridida nudibranchs. By generating a universal set of genetic markers beyond the scope of this study, these resources will help standardise future data collection and enable comparative studies across a range of questions, scales, and disciplines.