Abstract
The Japanese Archipelago hosts a diverse group of mammalian species, including subterranean moles, whose migratory and dispersion patterns are believed to have been significantly influenced by environmental fluctuations during the Quaternary period. However, the genetic structure of these species has not been extensively studied using large-scale molecular data. In this study, we explored the population structure of 2 widely distributed mole species in Japan: the Lesser Japanese Mole (Mogera imaizumii), found mainly in eastern Honshu with a few isolated patches in western Honshu, and the Large Japanese Mole (M. wogura), distributed in western Honshu, Shikoku, and Kyushu. We constructed a genome sequence for M. wogura using the Chromium system and conducted a reduced genome representation analysis using multiplexed inter-simple sequence repeat genotyping by sequencing on M. imaizumii and M. wogura. Our findings indicate that M. imaizumii comprises 3 major genetic clusters (ncMim- 1 to 3) that are strongly differentiated (fixation index ranging from 0.376 to 0.478). We discovered genetic connections between populations in the southern Kinki area and isolated populations in western Japan. Mogera wogura consists of 5 main genetic clusters (ncMwo- 1 to 5). Evidence of introgression between 2 genetic clusters (ncMwo-2/ncMwo-3) was found among individuals from the Chugoku area, indicating secondary contact between the 2 differentiated populations. Both species shared a similar population boundary within the Kinki area, which may be associated with current and past geographic barriers. We confirmed that the Kinki region serves as an important site for the diversification of moles, where multiple factors (topographic barriers, interspecific interactions, and/or isolation related to vegetation) may have shaped their population genetic structures.