Phylogeography of the stonefly Kamimuria tibialis: multiple glacial refugia and sympatric occurrence of different lineages in the southern islands of Japan

To elucidate the effect of Pleistocene climatic fluctuations on the historical distribution and geographical genetic structure of temperate Japanese species, we performed phylogeographical and demographic analyses using mitochondrial gene sequences obtained from the stonefly species Kamimuria tibialis, sampled from four main islands of the Japanese Archipelago (i.e. Hokkaido, Honshu, Shikoku and Kyushu) and Tsushima Island. We detected three main clades with distinct geographical distributions, including the Tsushima, Kyushu and Hokkaido–Honshu–Shikoku phylogroups. These groups were estimated to have diverged from one another 0.54–2.02 Mya, suggesting they have undergone several glacial cycles in different refugia. Our results showed that during the glacial epochs and with a fall in sea-level, gene flow was limited among Tsushima and Kyushu, and among Hokkaido and Honshu, probably because the straits between these islands are deep. The population in Kyushu and Shikoku, the southernmost islands, exhibited high genetic diversity, with two distinct haplotype lineages occurring sympatrically. These results suggest that the population division into multiple refugia and the existence of stable southern refugia have contributed to the high genetic diversity of the species in this region.