Quaternary environmental changes fundamentally influenced genetic diversity of the temperate-zone terrestrial animals, including those on the Japanese Archipelago. The genetic diversity of present-day populations are taxon and region specific, but its determinants are poorly understood. Here, we analyzed cytochrome b gene (Cytb) sequences (1,140 bp) of mitochondrial DNA (mtDNA) to elucidate factors determining the genetic variation in three species of large moles: Mogera imaizumii and Mogera wogura occur in Northern and Southern mainland Japan (Honshu, Shikoku, and Kyushu), and Mogera robusta occurs on the nearby Asian continent. Network construction with the Cytb sequences revealed 10 star-shaped clusters with apparent geographic affinity. Mismatch distribution analysis showed that modes of pairwise nucleotide differences (t values) were grouped into five classes in terms of the level, implying the occurrence of five stages for the rapid expansion. It is conceivable that a severe cold periods and a subsequent warm periods during the late Quaternary are responsible for the population expansion events. The first and third oldest events include island-derived haplotypes, indicative of involvement of land bridge formation between remote islands, hence suggesting association of the ends of the penultimate (PGM, ca. 130,000 years ago) and last (LGM, ca. 15,000 years ago) glacial maxima, respectively. Since the third one is followed by the fourth one, it is plausible that the termination of Younger Dryas and subsequent abrupt warming at ca. 11,500 years ago facilitated the fourth expansion event. The second is most likely corresponding to the early marine isotope stage (MIS) 3 (ca. 53,000 years ago) when the glaciation and subsequent warming period are predicted to have influenced biodiversity. Utilization of the critical times of 130,000, 53,000, 15,000, and 11,500, years ago as calibration points yielded evolutionary rates of 0.03, 0.045, 0.10 and 0.10 substitutions/site/million years, respectively, showing the time-dependent manner whose pattern is similar to that seen in small rodents reported in our previous studies. The age of the fifth expansion event was calculated to be 5,800 years ago with the rate of 0.10 substitutions/site/million years ago, during the mid-Holocene, suggestive of influence of humans or other unspecified reason, such as the Jomon marine transgression. 

We used mitochondrial cytochrome b gene sequenxes (1140 bp) of four mole species (the genus Mogera) in this study. Mogera imaizumii specimens (n = 77) used for molecular phylogenetic analyses (Supplementary Table S1, Fig. 1) consisted of 40 newly collected individuals and 37 obtained from the nucleotide database GenBank/EMBLE/DDBJ. Mogera wogura specimens (n = 131; Supplementary Table S1) consisted of 101 newly collected individuals and 30 from the database. M. robusta (n = 14) samples included two newly collected individuals from Russia and 12 from the database.