Gohta Kinoshita

Evolutionary and dispersal history of Eurasian house mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA.

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.

The Influence of Pleistocene Refugia on the Evolutionary History of the Japanese Hare, Lepus brachyurus

We performed a phylogeographic analysis of the Japanese hare, Lepus brachyurus, using the mitochondrial cytochrome b gene (1140 bp). In total, 119 haplotypes were recovered from 197 samples isolated from 82 localities on three main islands of the Japanese archipelago: Honshu, Sikoku, Kyushu, Sado Island and the Oki Islands. Results showed two distinct clades at a genetic distance of 3.5%, equivalent to an estimated 1.2 million years. The two clades, encompassing seven subclades, showed an apparent geographic affinity to Kyushu, Shikoku and the nearby area of Honshu (southern group) by one clade, whereas the other clade covered the remaining area of Honshu (northern group). The landscape shape interpolation analysis exhibited a higher genetic diversity in the southern parts of central Honshu (northern group) and Shikoku and Kyushu regions (southern group), suggesting the existence of multiple geographical origins of population expansion in each clade. The Bayesian skyline plot analysis showed that lineage diversifications occurred about 0.35, 0.20 and 0.05 million years ago (Mya), which coincide closely with the glacial—interglacial cycles during the Pleistocene. Therefore, we suggest that the Japanese hare population once inhabited northern and southern refugia, and subsequently developed several populations through local demographic fluctuations. The present day demarcation in the northern and southern geographic groups is considered to be a temporal remnant of Pleistocene population dynamics and the geographic boundary between them could move or fade away in time.

Colonization history of the sable Martes zibellina (Mammalia, Carnivora) on the marginal peninsula and islands of northeastern Eurasia

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.

Ancient Colonization and Within-Island Vicariance Revealed by Mitochondrial DNA Phylogeography of the Mountain Hare (Lepus timidus) in Hokkaido, Japan

We examined the phylogenetic status and history of the mountain hare Lepus timidus in and around Hokkaido using mitochondrial cytochrome b (cyt b) sequences from 158 samples from Hokkaido and 14 from Sakhalin, as well as four samples from the Korean hare, L. coreanus. The phylogenetic analysis of the cyt b sequences generated in this study and obtained from DNA databases showed the clear genetic specificity of the Hokkaido lineage as a clade. The Hokkaido lineage was estimated to have diverged from the other conspecific and L. coreanus lineages 0.46 and 0.30 million years ago (Mya), respectively. These results suggest that the common ancestor of the mitochondrial lineage in Hokkaido and Korea inhabited Far East Asia before colonization by the present continental lineages of L. timidus, including the Sakhalin population. We estimated the time of the most recent common ancestor of the Hokkaido population to be 0.17 Mya, and found two distinct haplogroups within the island. One group had greater genetic diversity (mean number of pairwise differences: &pgr; = 0.0188 ± 0.0108) and appears to have expanded from the west to the entire island of Hokkaido. The other had lower genetic diversity (&pgr; = 0.0038 ± 0.0037) and its distribution was concentrated in the east. These contrasting west/east trends indicate that the Hokkaido population was fragmented in the past, and then subsequently expanded. Our study suggests that Hokkaido was an important refugium for boreal species in the far eastern region, and allowed the formation of various population genetic structures within the island.

Estimation of Evolutionary Rates of Mitochondrial DNA in Two Japanese Wood Mouse Species Based on Calibrations with Quaternary Environmental Changes

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.

Variation in the Coat-Color-Controlling Genes, Mc1r and Asip, in the House Mouse Mus musculus from Madagascar

Abstract. Variability in the coat color of the house mouse, Mus musculus, provides an opportunity to study the evolution of phenotypes in this species. Here we associated genetic variations with coat color in seven mice from Madagascar that had identical M. m. gentilulus mitochondrial DNA sequences. The entire coding region of the 948-base pair (bp) coat-color-related gene, Mc1r, was shown to have no nonsynonymous changes. However, analyses of the two exon-1 promoter regions—termed 1A (317 bp) and 1B (499 bp)—from a second gene, Asip, which is also involved in the evolution of coat color, revealed two distinct haplotypes in each region. Associations between Asip promoter regions and dorsal color were ambiguous; however, two ventral color types—light and dark gray—were associated with the haplotypes of 1A, as determined by clustering analysis. Notably, the haplotype of the light gray animals was identical to the Asip Aw allele that is associated with white bellies.

Intraspecific phylogeny of the house shrews, Suncus murinus-S. montanus species complex, based on the mitochondrial cytochrome b gene

Abstract. A phylogenetic tree was reconstructed based on the mitochondrial cytochrome b gene nucleotide sequences of 169 individuals of house shrews (Suncus murinus and S. montanus) from 44 localities in East Asia, Southeast Asia, West Asia, and islands in the western Indian Ocean. Shrews from China (Zhejiang), Japan (Okinawa), Vietnam, and Indonesia (Java) formed a monophyletic group with less genetic variation. Therefore, the shrews of these regions appeared to have originated from one or a few localities. Contrary to this, shrews from Sri Lanka, Myanmar, and Pakistan consisted of several haplogroups. This finding suggests immigration movements to these areas. Fascinating findings were also obtained concerning the islands in the western Indian Ocean. First, shrews on Zanzibar Island (Tanzania) had almost the same haplotype as those in southwestern Iran. Therefore, the house shrew in Zanzibar may have immigrated from Iran (or vice versa). Second, shrews from Madagascar and Grande Comore Island shared the same haplotype, whereas the shrews on Réunion Island were clearly different from those of Madagascar and Comoros. Thus, there appears to have been several immigration routes to the islands of the western Indian Ocean.