DOI: 10.5061/dryad.cjsxksn51
title: Influence of Quaternary environmental changes on mole populations inferred from mitochondrial sequences and evolutionary rate estimation

description: 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. 
description: We used mitochondrial cytochrome <em>b</em> gene sequenxes (1140 bp) of four mole species (the genus <em>Mogera</em>) in this study. <i>Mogera imaizumii</i> 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. <i>Mogera wogura</i> specimens (n = 131; Supplementary Table S1) consisted of 101 newly collected individuals and 30 from the database. <i>M. robusta </i>(n = 14) samples included two newly collected individuals from Russia and 12 from the database.