Phylogeography of a salmonid fish, white-spotted charr (Salvelinus leucomaenis), in a historically non-glaciated region in the northwestern North Pacific

Abstract The area around the Sea of Okhotsk and the Sea of Japan in the north-western North Pacific provides opportunities for studying the impact of climate oscillations on the evolutionary history of cold-temperate species independent of direct ice sheet development. We conducted a range-wide collection survey of white-spotted charr, Salvelinus leucomaenis, and integrated nuclear DNA and mitochondrial DNA (mtDNA) data to reveal the evolutionary history of this species. Phylogeographic analyses using genome-wide SNP data revealed the presence of five geographically distinct groups with slightly overlapping ranges. Of these, a northern group was widely distributed along the coast of the Sea of Okhotsk, the Sea of Japan and the northern region of Honshu Island, whereas the other four groups were only found on Honshu Island. The population structure of Honshu Island was largely divided into the Sea of Japan and Pacific Ocean groups by the mountain ranges running through the centre of Honshu Island, and was further subdivided by many geological factors, such as river capture and other vicariance processes. There was a discrepancy in the phylogeographic patterns between nuclear DNA and mtDNA, which was likely influenced by a complex population history that involved multiple dispersal and secondary contact events during several glacial-interglacial cycles.