We examined the sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 286 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges of northern Eurasia (musculus, MUS), India and Southeast Asia (castaneus, CAS), Nepal (unspecified, NEP), western Europe (domesticus, DOM) and Yemen (gentilulus). Our results confirm previous suggestions of Southwestern Asia as the likely place of origin of M. musculus and the region of Iran, Afghanistan, Pakistan, and northern India, specifically as the ancestral homeland of CAS. The divergence of the subspecies lineages and of internal sublineage differentiation within CAS were estimated to be 0.37-0.47 and 0.14-0.23 million years ago (mya), respectively, assuming a split of M. musculus and Mus spretus at 1.7 mya. Of the four CAS sublineages detected, only one extends to eastern parts of India, Southeast Asia, Indonesia, Philippines, South China, Northeast China, Primorye, Sakhalin and Japan, implying a dramatic range expansion of CAS out of its homeland during an evolutionary short time, perhaps associated with the spread of agricultural practices. Multiple and non-coincident eastward dispersal events of MUS sublineages to distant geographic areas, such as northern China, Russia and Korea, are inferred, with the possibility of several different routes.

Reliable estimates of evolutionary rates of mitochondrial DNA might allow us to build realistic evolutionary scenarios covering broad time scales based on phylogenetic inferences. In the present study, we sought to obtain estimates of evolutionary rates in murine rodents using calibrations against historical biogeographic events. We first assumed that land-bridge-like structures that appeared intermittently at glacial maxima with 100,000-year intervals shaped the divergence patterns of cytochrome b (Cytb) sequences (1140 bp) of the larger Japanese wood mouse Apodemus speciosus. The comparison of sequences from peripheral remote islands that are separated from one another by deep straits allowed us to estimate mitochondrial DNA evolutionary rates (substitutions/site/million years) to be 0.027 to 0.036, with presumed calibrations from 140,000, 250,000, 350,000, and 440,000 years ago. Second, we addressed rapid expansion events inferred from analyses of the Cytb sequences of the lesser Japanese wood mouse A. argenteus. We detected five expansion signals in the dataset and established three categories based on the expansion parameter tau values: 3.9, 5.6-5.7, and 7.8-8.1. Considering that the climate became warmer 15,000, 53,000, and 115,000 years ago after preceding periods of rapid cooling, we calculated evolutionary rates to be 0.114, 0.047, and 0.031, respectively. This preliminary concept of the evolutionary rates on a time scale from 15,000 to 440,000 years ago for the wood mouse should be refined and tested in other species of murine rodents, including mice and rats.

The Japanese archipelago is comprised of four main islands—Hokkaido, Honshu, Shikoku, and Kyushu—which contain high mountainous areas that likely allowed for lineage differentiation and population genetic structuring during the climatic changes of the late Pleistocene. Here, we assess the historical background of the evolutionary dynamics of herbivorous red-backed voles (Myodes) in Japan, examining the evolutionary trends of mitochondrial cytochrome b gene (Cytb) sequence variation. Four apparent signals from rapid expansion events were detected in three species, M. rufocanus and M. rutilus from Hokkaido and M. smithii from central Honshu. Taken together with results from previous studies on Japanese wood mice (Apodemus spp.), three of the expansion events were considered to be associated with predicted bottleneck events at the marine isotope stage (MIS) 4 period, in which glaciers are thought to have expanded extensively, especially at higher elevations. In the late Pleistocene, the possible candidates are transitions MIS 6/5, MIS 4/3, and MIS 2/1, which can be characterized by the cold periods of the penultimate glacial maximum, MIS 4, and the last glacial maximum, respectively. Our data further reveal the genetic footprints of repeated range expansion and contraction in the northern and southern lineages of the vole species currently found in central Honshu, namely M. andersoni and M. smithii, in response to climatic oscillation during the late Pleistocene. The time-dependent evolutionary rates of the mitochondrial Cytb presented here would provide a possible way for assessing population dynamics of cricetid rodents responding to the late Pleistocene environmental fluctuation.

Current phylogenetic analyses of relatively long sequences of mitochondrial DNA (4,225 bp) in the Japanese house mouse Mus musculus provided the first evidence that both southern Asian subspecies of Mus musculus castaneus (CAS) and northern Asian subspecies of M. m. musculus (MUS) arrived in Japan through rapid population expansion events, from Southern China ~4,000 years ago and the Korean Peninsula ~2,000 years ago, respectively. Nuclear DNA haplotype structure analyses targeted a chromosome region with two different tract sizes, 1 Mb and 5 Mb, consisting of nine and six tandemly arranged markers, respectively, yielding a possible average fragment length of 170 kb of CAS haplotypes in the MUS background genome in northern Japan, providing a rough estimate of its elapsed time of 815 generations under an assumption of continued backcrossing. Less frequent and shortened CAS-like haplotypes specific to Japan were detected, suggestive of ancient introduction prior to the appearance of the South Chinese CAS in Japan. Our analyses also showed sporadic appearance of long fragments (2-5 Mb) from the west European subspecies M. m. domesticus, indicating contemporary stowaway introduction. Overall, multiple overseas introductions, and the time-lagged inter-subspecies genetic admixture, likely resulted in the heterogeneous state of Japanese wild mice.

We examined the nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 2 gene (976 base pairs) for 279 individuals of the sable Martes zibellina (Carnivora, Mustelidae), derived from diverse areas throughout the regions of the Ural Mountains to the Russian Far East on the Eurasian continent and the peripheral peninsula (Kamchatka) and islands (Sakhalin, Hokkaido, and southern Kurils). The demographic history of the sable and its migration history to the eastern peripheral peninsula and islands were inferred using phylogeographic approaches. The analyses confirmed the previously found major lineages for the examined sables and further identified novel sublineages. Our data also support that a lineage, which is endemic to the eastern marginal islands (Sakhalin, Hokkaido, and southern Kurils), was produced by the demographic expansion of an ancestral lineage in the Eurasian continent. The most recent common ancestor of the Sakhalin, Hokkaido, and southern Kuril sables was estimated to exist during the Late Pleistocene. We also determined that another lineage exists on Sakhalin and is shared by the Far East Primorsky population. Our results indicate multiple migration events onto Sakhalin from the continent and suggest the importance of the formation of several straits to the distribution of sable lineages. Meanwhile, Kamchatka is dominated by a sole lineage which would also have followed the demographic expansion on the Eurasian continent. The Russian Far East was indicated as the source area for lineage diversifications; in this region, genetic diversity was relatively high, which is consistent with previous studies.