Assessing the phylogenetic relationships of softnose skates (Bathyraja) based on RADseq and mtDNA data

Abstract

Despite their high species diversity, skates (Rajidae) exhibit morphological conservatism which may hamper identification and assessment efforts. Bathyraja, the most species-rich genus of skate, is known to have particularly unclear systematics and several ambiguous species boundaries. To elucidate these phylogenetic relationships, I assessed RADseq data from 139 specimens across 17 species of Bathyraja available in the University of Washington Fish Collection. I compared these results to a phylogenetic tree generated from COI sequences available on GenBank to evaluate whether genome-wide sequencing can provide greater resolution than a single gene approach. Both trees demonstrated possible instances of incomplete lineage sorting, resolving B. panthera as paraphyletic in the RADseq tree and B. parmifera as paraphyletic in the COI tree. Incomplete lineage sorting was also possible for B. mariposa and B. violacea, sister species that exhibited reciprocal monophyly within the B. interrupta clade. The COI tree failed to separate B. maculata and B. lindbergi into genetically isolated groups, as has been observed previously. Conversely, the RADseq tree resolved B. maculata and B. lindbergi into distinct lineages. Neither phylogenetic tree showed clear genetic divergence between B. kincaidii and B. interrupta, a species pair with particularly uncertain boundaries. The species pair did exhibit population structure in the Salish Sea, a pattern that has not yet been observed for either species. Morphological and genetic assessments of samples throughout the entire B. interrupta/B. kincaidii range is needed to resolve whether B. kincaidii is a junior synonym of B. interrupta.