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The present phylogeographic pattern of red deer in Eurasia is not only a result of the contraction of their distribution range into glacial refugia and postglacial expansion, but probably also an effect of replacement of some red deer s.l. mtDNA lineages by others during the last 50 000 years. To better recognize this process, we analysed 501 sequences of mtDNA cytochrome b , including 194 ancient and 75 contemporary samples newly obtained for this study. The inclusion of 161 radiocarbon-dated samples enabled us to study the phylogeny in a temporal context and conduct divergence-time estimation and molecular dating. Depending on methodology, our estimate of divergence between Cervus elaphus and Cervus canadensis varied considerably (370 000 or 1.37 million years BP, respectively). The divergence times of genetic lineages and haplogroups corresponded to large environmental changes associated with stadials and interstadials of the Late Pleistocene. Due to the climatic oscillations, the distribution of C. elaphus and C. canadensis fluctuated in north–south and east–west directions. Some haplotypes dated to pre-Last Glacial Maximum periods were not detected afterwards, representing possibly extinct populations. We indicated with a high probability the presence of red deer sensu lato in south-eastern Europe and western Asia during the Last Glacial Maximum. [ABSTRACT FROM AUTHOR]

Although the present-day distributional boundary between the European badger (Meles meles) and the Asian badger (Meles leucurus) is around the Volga River, studies of ancient bone remains have indicated changes in the distribution of M. meles and M. leucurus in the Urals–Volga region during the Holocene. To examine past changes in distribution using genetic data, changes in genetic diversity, and the relationships of Holocene to modern populations, we sequenced ~150 bp of the mitochondrial DNA control region from the 44 ancient badger remains excavated from European Russian, Ural and Western Siberian sites, and we detected 12 haplotypes. Our study revealed Holocene changes in the distributional boundary between these badger species. Meles meles inhabited the Ural Mountains east of the Volga River in the Early Holocene, whereas M. leucurus expanded its distribution westwards, starting ~2500 years ago. Thereafter, M. leucurus rapidly replaced M. meles in the region between the Urals and the Volga, resulting in the present-day boundary in the Volga–Kama region. Among the 12 haplotypes detected, three for M. leucurus and four for M. meles were identical to partial sequences of haplotypes detected in modern populations, indicating considerable genetic continuity between Holocene and modern populations. [ABSTRACT FROM AUTHOR]

Major histocompatibility complex (MHC) genes encode proteins that play a key role in the adaptive immune system of vertebrates and are generally highly polymorphic for defence against various pathogens. To understand the diversity and evolution of MHC variation in badgers in the genus Meles (Carnivora, Mustelidae), we analysed sequence variation of the MHC class II DRB gene exon 2 in the Japanese (Meles anakuma), Asian (Meles leucurus), European (Meles meles) and Southwest Asian (Meles canescens) badgers. Variation was higher in the Meles species than in other species in Mustelidae, and altogether 60 alleles were isolated from 28 individuals. The variable number of three to eight putative alleles per individual was observed, indicating the presence of two to four DRB loci per haploid genome. Non-synonymous substitutions exceeded synonymous substitutions at putative antigen-binding sites. Selection analyses of PAML models, fixed-effect likelihood and mixed-effect model evolution, together with the single breakpoint recombination, indicated that recombination and selection could be responsible for driving and maintaining the diversity of Meles DRBs. In a phylogenetic analysis, the DRB sequences from Meles were distributed in several clusters, which were dispersed among sequences of other mustelid family, even five alleles comprised a monophyletic group of Meles DRBs within a canid clade. The data demonstrate trans-species polymorphisms at different taxonomic and temporal scales, transgressing family-, genus- and species-level splits. Some allele sequences were shared by two to four of the Meles species, in line with a close phylogenetic relationship among these species. [ABSTRACT FROM AUTHOR]

Mustela nivalis, the smallest member of the family Mustelidae, is widely distributed in the Holarctic region and shows high geographical variation. To further understand the molecular evolution of major histocompatibility complex (MHC), we sequenced part of MHC class II DRB gene exon 2, including codons encoding the antigen binding site (ABS), from 35 individuals from Finland, Bulgaria, Russia, and Japan. We detected 27 species-specific alleles (Muni- DRBs), some of which were broadly distributed and others geographically restricted. The ratio of nonsynonymous to synonymous substitution rates for predicted ABS codons exceeded 1, though not statistically significant. In addition, the single break point recombination (SBP) and mixed-effects model evolution (MEME) analyses demonstrated a recombination site and positive selection sites that could be committed to maintain the diversity of Muni-DRBs. In a Bayesian phylogenetic tree, all Muni-DRBs grouped within a Mustelidae clade. The Muni-DRBs showed transspecies polymorphism in related Mustela species that could have appeared to be evolved under long-lasting balancing selection. However, the sister-group patterns suggested that Mustela itatsi and Mustela sibirica alleles are much more closely related to one another than either are to M. nivalis alleles. This result correlates with the large genetic distance separating M. nivalis from M. itatsi or M. sibirica, data for which we have previously reported. [ABSTRACT FROM AUTHOR]

We analyzed the complete mitochondrial genome for 26 individuals of the endemic Japanese weasel (Mustela itatsi) and 20 individuals of its continental sister species, the Siberian weasel (Mustela sibirica). These species diverged an estimated 1.19 Mya, in the Early Pleistocene. Mustela itatsi comprised two haplotype clades that diverged an estimated 0.93 Mya, in the Middle Pleistocene: a northern (Honshu) clade comprising geographically distinct basal, northern, and eastern subclades, and a western paraphyletic group, as well as a southern clade comprising geographically distinct subclades on Kyushu, Shikoku, and adjacent small islands. Our results indicate a single migration of an ancestral population from the Korean Peninsula to southern Japan across an Early Pleistocene land bridge, followed by allopatric speciation of M. itatsi in Japan. The southern lineage appears to have remained in place, whereas the range of the northern lineage expanded stepwise from southwestern to northern Honshu between 0.31 and 0.11 Mya. Mustela sibirica also comprised two main clades that diverged an estimated 0.67 Mya; one containing haplotypes from continental Russia and Tsushima Island (Japan), and the other containing haplotypes from Korea, China, and Taiwan. The M. sibirica population on Tsushima Island is likely a relict from the continental Russian population. [ABSTRACT FROM AUTHOR]

To further elucidate the migration history of the brown bears (Ursus arctos) on Hokkaido Island, Japan, we analyzed the complete mitochondrial DNA (mtDNA) sequences of 35 brown bears from Hokkaido, the southern Kuril Islands (Etorofu and Kunashiri), Sakhalin Island, and the Eurasian Continent (continental Russia, Bulgaria, and Tibet), and those of four polar bears. Based on these sequences, we reconstructed the maternal phylogeny of the brown bear and estimated divergence times to investigate the timing of brown bear migrations, especially in northeastern Eurasia. Our gene tree showed the mtDNA haplotypes of all 73 brown and polar bears to be divided into eight divergent lineages. The brown bear on Hokkaido was divided into three lineages (central, eastern, and southern). The Sakhalin brown bear grouped with eastern European and western Alaskan brown bears. Etorofu and Kunashiri brown bears were closely related to eastern Hokkaido brown bears and could have diverged from the eastern Hokkaido lineage after formation of the channel between Hokkaido and the southern Kuril Islands. Tibetan brown bears diverged early in the eastern lineage. Southern Hokkaido brown bears were closely related to North American brown bears. [ABSTRACT FROM PUBLISHER]