Researcher Database

Ryuichi Masuda
Faculty of Science Biological Sciences Biodiversity

Researcher Profile and Settings


  • Faculty of Science Biological Sciences Biodiversity

Job Title

  • Professor


  • Doctor of Science(Hokkaido University)

Research funding number

  • 80192748

J-Global ID

Research Interests

  • 進化遺伝学   分子系統学   Evolutionary genetics   Molecular phylogenetics   

Research Areas

  • Life sciences / Biodiversity and systematics
  • Life sciences / Evolutionary biology

Academic & Professional Experience

  • 2012 - Today Hokkaido University Faculty of Science Professor
  • 2007 - 2012 Hokkaido University Associate Professor
  • 2001 - 2007 Hokkaido University Associate Professor
  • 1991 - 2001 Hokkaido University Assistant Professor
  • 1989 - 1991 National Cancer Institute, U.S.A Postdoctoral Fellow

Association Memberships

  • 日本哺乳類学会   日本動物学会   

Research Activities

Published Papers

  • Sho Hosotani, Yoshinori Nishita, Ryuichi Masuda
    Mammal Research 65 (3) 573 - 582 2199-2401 2020/07 [Refereed][Not invited]
  • Yu Endo, Liang-Kong Lin, Koji Yamazaki, Kurtis Jai-Chyi Pei, Shih-Wei Chang, Yen-Jean Chen, Keiji Ochiai, Shuuji Yachimori, Tomoko Anezaki, Yayoi Kaneko, Ryuichi Masuda
    Mammal Study 45 (3) 243 - 243 1343-4152 2020/06/26 [Refereed][Not invited]
  • Mizumachi, K., Spassov, N., Kostov D., Raichev E.G., Peeva S., Hirata D., Nishita Y., Kaneko Y., Masuda R.
    Mammal Research 65 (2) 413 - 421 2020/04 [Refereed][Not invited]
  • Kinoshita E., Kosintsev P.A., Abramov A.V., Solovyev V.A., Saveljev A.P., Nishita Y., Masuda R.
    Biological Journal of the Linnean Society 129 (3) 594 - 602 2020/03 [Refereed][Not invited]
  • Ishikawa, K, Abramov, A.V, Amaike, Y, Nishita, Y, Masuda, R
    Biological Journal of the Linnean Society 129 (3) 587 - 593 2020/03 [Refereed][Not invited]
  • Sato, T., Abramov, A.V., Raichev, E.G., Kosintsev, P.A., Väinölä, R., Murakami, T., Kaneko, Y., Masuda, R.
    Journal of Zoological Systematics and Evolutionary Research 58 (1) 408 - 426 2020/02 [Refereed][Not invited]
  • Bartocillo, A.M, Nishita, Y, Abramov, A.V, Masuda, R
    Biological Journal of the Linnean Society 129 (1) 61 - 73 2020/01 [Refereed][Not invited]
  • S. Abduriyim, Y. Nishita, A. V. Abramov, V. A. Solovyev, A. P. Saveljev, P. A. Kosintsev, A. P. Kryukov, E. Raichev, R. Väinölä, Y. Kaneko, R. Masuda
    Journal of Zoology 308 28 - 36 0952-8369 2019/05 [Refereed][Not invited]
  • Shamshidin Abduriyim, Yoshinori Nishita, Pavel A Kosintsev, Evgeniy Raichev, Risto Väinölä, Alexey P Kryukov, Alexei V Abramov, Yayoi Kaneko, Ryuichi Masuda
    Heredity 122 (2) 205 - 218 0018-067X 2019/02 [Refereed][Not invited]
    Because of their role in immune defense against pathogens, major histocompatibility complex (MHC) genes are useful in evolutionary studies on how wild vertebrates adapt to their environments. We investigated the molecular evolution of MHC class I (MHCI) genes in four closely related species of Eurasian badgers, genus Meles. All four species of badgers showed similarly high variation in MHCI sequences compared to other Carnivora. We identified 7-21 putatively functional MHCI sequences in each of the badger species, and 2-7 sequences per individual, indicating the existence of 1-4 loci. MHCI exon 2 and 3 sequences encoding domains α1 and α2 exhibited different clade topologies in phylogenetic networks. Non-synonymous nucleotide substitutions at codons for antigen-binding sites exceeded synonymous substitutions for domain α1 but not for domain α2, suggesting that the domains α1 and α2 likely had different evolutionary histories in these species. Positive selection and recombination seem to have shaped the variation in domain α2, whereas positive selection was dominant in shaping the variation in domain α1. In the separate phylogenetic analyses for exon 2, exon 3, and intron 2, each showed three clades of Meles alleles, with rampant trans-species polymorphism, indicative of the long-term maintenance of ancestral MHCI polymorphism by balancing selection.
  • Nishita Yoshinori, Spassov Nikolai, Peeva Stanislava, Raichev Evgeniy G, Kaneko Yayoi, Masuda Ryuichi
    ETHOLOGY ECOLOGY & EVOLUTION 31 (1) 59 - 72 0394-9370 2019/01/02 [Refereed][Not invited]
  • Andrey Yu Puzachenko, Ryuichi Masuda, Alexei V. Abramov
    Russian Journal of Theriology 18 12 - 19 1682-3559 2019/01 [Refereed][Not invited]
  • Shirane Yuri, Shimozuru Michito, Yamanaka Masami, Tsuruga Hifumi, Hirano Saiko, Nagano Natsuo, Moriwaki Jun, Nakanishi Masanao, Ishinazaka Tsuyoshi, Nose Takane, Kasai Shinsuke, Shirayanagi Masataka, Masuda Yasushi, Fujimoto Yasushi, Osada Masahiro, Akaishi Masao, Mano Tsutomu, Masuda Ryuichi, Sashika Mariko, Tsubota Toshio
    EUROPEAN JOURNAL OF WILDLIFE RESEARCH 64 (6) 65  1612-4642 2018/12 [Refereed][Not invited]
  • Yosuke Amaike, Yoshinori Nishita, Kohji Uraguchi, Ryuichi Masuda
    Zoological science 35 (5) 402 - 410 0289-0003 2018/10 [Refereed][Not invited]
    To assess the genetic diversity of the red fox (Vulpes vulpes) population on Hokkaido Island, northern Japan, we examined genotypes of exon 2 of the major histocompatibility complex (MHC) class II DRB1 gene for 232 individuals and identified 17 novel alleles. The subpopulation in the Southern area was genetically differentiated from those in all other areas on Hokkaido, suggesting isolation in southern Hokkaido. In addition, the Southern subpopulation is lower in genetic diversity than the other subpopulations, possibly resulting from purifying selection and/or a recent bottleneck. The non-synonymous substitutions exceeded the synonymous substitutions for codons encoding antigen-binding sites (ABSs) in exon 2, indicating that the red fox DRB1 alleles have evolved under positive selection. In a Bayesian phylogenetic tree, although most of the DRB1 alleles from the Hokkaido red fox were contained within a red fox-like canid (Vulpes) clade, some belonged to another canid clade. This means trans-species polymorphism maintained by balancing selection. Our results showed the local variability and the presence of selection on the MHC gene in this population, which contributes to the understanding of the historical background and the molecular evolution.
  • Amaike Yosuke, Murakami Takahiro, Masuda Ryuichi
    MAMMAL STUDY 43 (3) 141 - 152 1343-4152 2018/09 [Refereed][Not invited]
  • Yoshinori Nishita, Alexei V. Abramov, Takahiro Murakami, Ryuichi Masuda
    Mammal Research 63 (3) 369 - 378 2199-241X 2018/07/01 [Refereed][Not invited]
    The sable (Martes zibellina) is a medium-sized mustelid inhabiting forest environments in Siberia, northern China, the Korean Peninsula, and Hokkaido Island, Japan. To further understand the molecular evolution of the major histocompatibility complex (MHC), we sequenced part of exon 2 in MHC class II DRB genes, including codons encoding the antigen binding site, from 33 individuals from continental Eurasia and Japan. We identified 16 MHC class II DRB alleles (Mazi-DRBs), some of which were geographically restricted and others broadly distributed, and eight putative pseudogenes. A single-breakpoint recombination analysis detected a recombination site in the middle of exon 2. A mixed effects model of evolution analysis identified five amino acid sites presumably under positive selection. These sites were all located in the region 3′ to the recombination site, suggesting that positive selection and recombination could be committed to the diversity of the M. zibellina DRB gene. In a Bayesian phylogenetic tree, all Mazi-DRBs and the presumed pseudogenes grouped within a Mustelidae clade. The Mazi-DRBs showed trans-species polymorphism, with some alleles most closely related to alleles from other mustelid species. This result suggests that the sable DRBs have evolved under long-lasting balancing selection.
  • Keita Omote, Sergei G. Surmach, Tetsuo I. Kohyama, Takeshi Takenaka, Chizuko Nishida, Ryuichi Masuda
    Journal of Raptor Research 52 (1) 31 - 41 0892-1016 2018/03/01 [Refereed][Not invited]
    The endangered Blakiston's Fish-Owl (Bubo blakistoni) has a fragmented distribution in the northeastern Eurasian continent, as well as on Hokkaido, southern Kuril, and Sakhalin islands. To examine the phylogeography of this species, we analyzed mitochondrial sequences. The whole mitochondrial genome, which included duplicated genes, was the largest (> 21 kbp) in vertebrates to date. A Bayesian phylogenetic analysis of mitochondrial gene sequences revealed a clear separation between two clades. The insular clade comprised the mitochondrial haplotypes from Hokkaido, southern Kuril, and Sakhalin islands, whereas the continental clade consisted of those from the Eurasian continent, including the Primorye, Amur, and Magadan areas. Analyses based on whole mitochondrial sequences suggested that the level of genetic differentiation between the two subspecies, B. b. blakistoni on the islands and B. b. doerriesi on the continent, was enough to recognize them as separate species. The estimated divergence time between the clades was at least 500,000 yr before present. In contrast, the divergence times within the clades were less than 10,000 yr before present, indicating that the haplotypes within the clades diverged after the last glacial maximum (LGM). Information on the distribution of vegetation suggests that the main areas currently inhabited by B. blakistoni were unsuitable as habitats during the LGM. Lower diversities, higher growth rate, and the pattern of haplotype distribution in the continental population suggest a severe bottleneck and rapid dispersion through the last glacial period. In contrast, the insular population retains a higher haplotype variation. Because southern Hokkaido Island was covered with forests in the LGM, the area could have acted as a refugia for this species.
  • Toshinori Saka, Yoshinori Nishita, Ryuichi Masuda
    Immunogenetics 70 (2) 115 - 124 0093-7711 2018/02 [Refereed][Not invited]
    Isolated populations of the leopard cat (Prionailurus bengalensis) on Tsushima and Iriomote islands in Japan are classified as subspecies P. b. euptilurus and P. b. iriomotensis, respectively. Because both populations have decreased to roughly 100, an understanding of their genetic diversity is essential for conservation. We genotyped MHC class II DRB exon 2 and MHC-linked microsatellite loci to evaluate the diversity of MHC genes in the Tsushima and Iriomote cat populations. We detected ten and four DRB alleles in these populations, respectively. A phylogenetic analysis showed DRB alleles from both populations to be closely related to those in other felid DRB lineages, indicating trans-species polymorphism. The MHC-linked microsatellites were more polymorphic in the Tsushima than in the Iriomote population. The MHC diversity of both leopard cat populations is much lower than in the domestic cat populations on these islands, probably due to inbreeding associated with founder effects, geographical isolation, or genetic drift. Our results predict low resistance of the two endangered populations to new pathogens introduced to the islands.
  • Emi Kinoshita, Alexei V. Abramov, Vyacheslav A. Soloviev, Alexander P. Saveljev, Yoshinori Nishita, Yayoi Kaneko, Ryuichi Masuda
    Mammalian Biology 94 140 - 148 1618-1476 2018 [Refereed][Not invited]
    Two closely related species of Meles (Carnivora), the European badger (M. meles) and the Asian badger (M. leucurus), are distributed allopatrically in continental Eurasia but show a narrow contact zone around the Volga and Kama Rivers, Russia. We analyzed maternally (mitochondrial DNA), paternally (SRY gene and CAN-SINEs on the Y chromosome), and biparentally (CFTR gene and nine microsatellite loci) inherited genes for evidence of hybridization between the two species in the contact zone. Of 71 badgers examined, we identified 17 individuals as hybrids with mixed genotypes for the first time. Some hybrids appeared to have resulted from repeated backcrossing with the parental species. In addition, the hybridization was symmetric between the two species. Compared with previous palaeontological data, the hybridization between the two species could have resulted from secondary contact due to western expansion in distribution by the Asian badgers.
  • Alexei V. Abramov, Andrey Yu. Puzachenko, Ryuichi Masuda
    Zoological Studies 57 : 14  1810-522X 2018 [Refereed][Not invited]
    Morphometric variation in 23 cranial characters of 555 Siberian weasels (Mustela sibirica) was studied across its whole distribution range. Most of the distribution range in Siberia and China is occupied by medium-sized weasels, whereas the eastern part of the species range-including the Russian Far East, Korea and eastern China-is occupied by the larger form. Specimens from the Pacific islands (Jeju and Tsushima) were morphologically closely related to the western form of M. sibirica than to the neighboring continental weasels. The western form can be treated as nominotypical subspecies M. s. sibirica Pallas, 1773, whereas the eastern form can be treated as M. s. manchurica Brass, 1911. Small-sized weasels from the eastern Himalayan area (Myanmar and southwestern China) form a distinct group within M. sibirica, and they were treated as a subspecies M. s. moupinensis (Milne-Edwards, 1874). Specimens from the western Himalayas (Kashmir, Nepal and Sikkim) are morphologically distinct from all other populations of Mustela sibirica and can be treated as a separate species Mustela subhemachalana Hodgson, 1837.
  • Keita Omote, Tetsuo I. Kohyama, Chizuko Nishida, Keisuke Saito, Satoshi Fujimoto, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 34 (6) 484 - 489 0289-0003 2017/12 [Refereed][Not invited]
    The major histocompatibility complex (MHC) includes many genes that are essential for the adaptive immune system, and variation in the antigen binding site (ABS) is related to resistance against pathogens. In the present study, quantitative real-time PCR indicated a larger number of MHC gene copies in the endangered population of Blakiston's fish owl (Bubo blakistoni) than in five other owl species, and massively parallel pyrosequencing detected more MHC class II beta per individual alleles in B. blakistoni than in the other species. A chromosomal fluorescence in situ hybridization (FISH) analysis showed that the MHC class I and class II beta loci are closely linked on a single pair of micro-chromosomes, indicating that the MHC genes were tandemly duplicated in a limited chromosomal region. Because B. blakistoni has twice as many MHC genes as its sister species, the tawny fish owl (Bubo flavipes), the duplication of MHC genes occurred after these species diverged by speciation. A Bayesian molecular phylogenetic analysis showed that the DAB1 and DAB2 lineages of MHC class II beta alleles from various strigid species each formed a separate clade, indicating that the two allelic lineages preceded the radiation of Strigidae and evolved as paralogs. By contrast, the ABS sequences did not form distinct clades between DAB1 and DAB2 alleles but were intermixed, presumably due to gene conversion. Despite the low diversity of alleles per locus, B. blakistoni had many lineages of MHC class II beta alleles. Gene duplication increases variation in the MHC genes in this species, and could have facilitated adaptation in small populations.
  • Daisuke Hirata, Tsutomu Mano, Alexei V. Abramov, Gennady F. Baryshnikov, Pavel A. Kosintsev, Koichi Murata, Ryuichi Masuda
    ZOOLOGICAL LETTERS 3 21  2056-306X 2017/11 [Refereed][Not invited]
    Background: Sex-biased dispersal is widespread among mammals, including the brown bear (Ursus arctos). Previous phylogeographic studies of the brown bear based on maternally inherited mitochondrial DNA have shown intraspecific genetic structuring around the northern hemisphere. The brown bears on Hokkaido Island, northern Japan, comprise three distinct maternal lineages that presumably immigrated to the island from the continent in three different periods. Here, we investigate the paternal genetic structure across northeastern Asia and assess the connectivity among and within intraspecific populations in terms of male-mediated gene flow. Results: We analyzed paternally inherited Y-chromosomal DNA sequence data and Y-linked microsatellite data of 124 brown bears from Hokkaido, the southern Kuril Islands (Kunashiri and Etorofu), Sakhalin, and continental Eurasia (Kamchatka Peninsula, Ural Mountains, European Russia, and Tibet). The Hokkaido brown bear population is paternally differentiated from, and lacked recent genetic connectivity with, the continental Eurasian and North American populations. We detected weak spatial genetic structuring of the paternal lineages on Hokkaido, which may have arisen through male-mediated gene flow among natal populations. In addition, our results suggest that the different dispersal patterns between male and female brown bears, combined with the founder effect and subsequent genetic drift, contributed to the makeup of the Etorofu Island population, in which the maternal and paternal lineages show different origins. Conclusions: Brown bears on Hokkaido and the adjacent southern Kuril Islands experienced different maternal and paternal evolutionary histories. Our results indicate that sex-biased dispersal has played a significant role in the evolutionary history of the brown bear in continental populations and in peripheral insular populations, such as on Hokkaido, the southern Kuril Islands, and Sakhalin.
  • Shamshidin Abduriyim, Yoshinori Nishita, Pavel A. Kosintsev, Evgeniy Raichev, Risto Vainola, Alexey P. Kryukov, Alexei V. Abramov, Yayoi Kaneko, Ryuichi Masuda
    BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 122 (2) 258 - 273 0024-4066 2017/10 [Refereed][Not invited]
    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.
  • H. Tsunoda, E. G. Raichev, C. Newman, R. Masuda, D. M. Georgiev, Y. Kaneko
    JOURNAL OF ZOOLOGY 303 (1) 64 - 71 0952-8369 2017/09 [Refereed][Not invited]
    In Europe, the range of the golden jackal (Canis aureus) has expanded since the mid-twentieth century, but little is known about how it interacts with other sympatric carnivores. Among European countries, Bulgaria has the largest population of golden jackals and jackal numbers have increased around two-fold during the past two decades, particularly in lowland habitats. Larger canids often competitively exclude, or even kill, smaller sympatric ones, especially when guild dynamics are in flux due to population re-establishment. We therefore investigate whether trophic niche segregation occurs between golden jackals and red foxes (Vulpes vulpes) in central Bulgaria, where both species are sympatric. Because jackals are more abundant in lowland than in upland Bulgaria, we further investigate whether habitat elevation affects the strength of trophic competition. From the analysis of stomach contents of both species, collected from lowland and upland areas during hunting seasons between 1997 and 2009, we found no significant food niche overlap, and no effect of elevation on trophic interactions. In lowland habitat, golden jackals mainly scavenged carcasses of domestic animals, whereas in upland habitat they consumed mostly carcasses of wild ungulates. In contrast, red foxes predominantly and consistently predated rodents in both habitats. This suggests that trophic segregation facilitates the coexistence of these canids under these prevailing population conditions. Nevertheless, we stress that as golden jackals colonize Eastern Europe, impacts on red foxes, and consequences for ecological communities, should be monitored carefully, especially in regions with less carrion available to support jackals.
  • Takuya Akiyama, Tetsuo I. Kohyama, Chizuko Nishida, Manabu Onuma, Kunikazu Momose, Ryuichi Masuda
    IMMUNOGENETICS 69 (7) 451 - 462 0093-7711 2017/07 [Refereed][Not invited]
    Populations that have drastically decreased in the past often have low genetic variation, which may increase the risk of extinction. The genes of major histocompatibility complex (MHC) play an important role in the adaptive immune response of jawed vertebrates. Maintenance of adaptive genetic diversity such as that of MHC genes is important for wildlife conservation. Here, we determined genotypes of exon 3 of MHC class IA genes (MHCIA) and exon 2 of MHC class IIB genes (MHCIIB) to evaluate genetic variation of the endangered red-crowned crane population on Hokkaido Island, Japan, which experienced severe population decline in the past. We identified 16 and 6 alleles of MHCIA and MHCIIB, respectively, from 152 individuals. We found evidence of a positive selection at the antigen-binding sites in MHCIA exon 3 and MHCIIB exon 2. The phylogenetic analyses indicated evidence of trans-species polymorphism among the crane MHC genes. The genetic variability in both classes of MHC genes at the population level was low. No geographic structure was found based on the genetic diversity of microsatellite and MHC genes. Our study provides useful data for the optimal management of the red-crowned crane population in Hokkaido and can contribute to future studies on MHC genes of the continental populations of the red-crowned crane and other crane species.
  • Takuya Akiyama, Kunikazu Momose, Manabu Onuma, Fumio Matsumoto, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 34 (3) 211 - 216 0289-0003 2017/06 [Refereed][Not invited]
    The red-crowned crane (Grus japonensis) is recognized internationally as an endangered species. Migratory populations breed in eastern Russia and northeastern China, whereas the resident population inhabits the island of Hokkaido, Japan. Although the population inhabiting Hokkaido had experienced a severe bottleneck by the end of the 19th century, the population size has recovered to about 1500 and continues to increase now thanks to conservation efforts. A previous study reported that no marked genetic differences were seen in the island population, and that the genetic variation of the whole population on Hokkaido was lower than that of the continental population. However, the precise genetic structure of the island population in the past or near present remains unclear. To better understand the spatiotemporal changes in the genetic structure of the island population, we performed mitochondrial DNA (mtDNA) analyses using stuffed specimens (years 1878-2001) and tissue or blood samples (years 1970-2014). We found three haplotypes in the island population, one of which was a novel mtDNA haplotype in 1997 and 2007 samples. In addition, there was no clear difference in the haplotype frequency through the time span. These results suggest that the low genetic variation of the island population persisted for the last hundred years. It is thus nearly impossible for the island population to recover its genetic variation in isolation. Conservation plans for this species should therefore include the promotion of genetic exchanges between the continental and island populations, such as through artificial introduction to Hokkaido.
  • Yoshinori Nishita, Pavel A. Kosintsev, Voitto Haukisalmi, Risto Vainola, Evgeniy G. Raichev, Takahiro Murakami, Alexei V. Abramov, Yayoi Kaneko, Ryuichi Masuda
    BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 121 (1) 28 - 37 0024-4066 2017/05 [Refereed][Not invited]
    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 trans-species 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.
  • Masumi Hisano, Lisa Hoshino, Shouko Kamada, Ryuichi Masuda, Chris Newman, Yayoi Kaneko
    ZOOLOGICAL SCIENCE 34 (2) 137 - 146 0289-0003 2017/04 [Refereed][Not invited]
    We compared the reliability of visual diagnostic criteria to DNA diagnostic techniques, including newly designed primers, to discriminate Japanese marten (Martes melampus) feces from those of other sympatric carnivore species. Visual criteria proved > 95% reliable for fresh, odoriferous scats in good condition. Based upon this verification, we then examined if and how Japanese marten diet differs among seasons at high elevation study site (1500-2026 m). We also considered how intra-specific competition with the Japanese red fox (Vulpes vulpes japonica) may shape marten feeding ecology. From 120 Japanese marten fecal samples, high elevation diet comprised (frequency of occurrence) 30.6-66.0% mammals, 41.0-72.2% insects and 10.6-46.2% fruits, subject to seasonal variation, with a Shannon-Weaver index value of 2.77. These findings contrast substantially to seasonal marten diet reported in adjacent lowland regions (700-900 m), particularly in terms of fruit consumption, showing the trophic adaptability of the Japanese marten. We also noted a substantial dietary overlap with the red fox (n = 26 scats) with a Shannon-Weaver index of 2.61, inferring little trophic niche mutual exclusion (trophic niche overlap: 0.95), although some specific seasonal prey selection differences were likely related to relative differences in body size between foxes and martens. This additional information on the feeding ecology of the Japanese marten enables a better assessment of the specific risks populations face in mountainous regions.
  • Emi Kinoshita, Pavel A. Kosintsev, Evgeniy G. Raichev, Voitto K. Haukisalmi, Alexey P. Kryukov, Oystein Wiig, Alexei V. Abramov, Yayoi Kaneko, Ryuichi Masuda
    BIOCHEMICAL SYSTEMATICS AND ECOLOGY 71 121 - 130 0305-1978 2017/04 [Refereed][Not invited]
    Based on previous molecular and morphological analyses, Eurasian badgers are currently classified into Metes metes distributed in Europe, M. canescens in the Caucasus and Middle East, M. leucurus in continental Asia and M. anakuma in Japan. The precise locations of their distribution boundaries are still unclear. Therefore, in the present study, we clarified the phylogenetic relationships in the genus Metes around its distribution boundaries, based on mitochondrial DNA (mtDNA) and Y-chromosomal genes. From 71 badgers examined, 29 mtDNA haplotypes were identified, including new 26 types. Multiple haplotypes of SRY and CAN-SINEs were identified from 23 males, including two new haplotypes of SRY. The mtDNA phylogeny showed that the Ural Mountains were not a current distribution boundary between M metes and M. leucurus. In addition, our results supported the hypothesis that the Bosphorus Strait is a geographical barrier between M. metes and M. canescens. The badgers from Bulgaria north of the Bosphorus Strait shared haplotypes with M. metes. On the other hand, badgers from Far Eastern Russia distributed in the eastern peripheral region of the Asian Continent had haplotypes of M. leucurus. The badgers from Norway and Finland shared haplotypes with M. metes. (C) 2017 Elsevier Ltd. All rights reserved.
  • Y. Kato, Y. Amaike, T. Tomioka, T. Oishi, K. Uraguchi, R. Masuda
    JOURNAL OF ZOOLOGY 301 (2) 118 - 124 0952-8369 2017/02 [Refereed][Not invited]
    In some countries, the red fox Vulpes vulpes has been rapidly expanding its range into urban and suburban areas, where it is referred to as the urban fox'. In the city of Sapporo, northern Japan, the population of urban foxes has been increasing since the 1990s. Because the red fox carries several zoonoses, it is important to understand its population structure and migration status in urban areas, for not only basic biology but also public health. In this study, to clarify population genetic structure and gene flow, we examined the genotypes of nine microsatellite loci for 578 road-killed foxes collected in and around residential areas of Sapporo from 2002 to 2014 (except for 2009 and 2010). Based on the genotype data and spatial information for the sampled animals, we detected three subpopulations within the urban fox population. Boundaries separating the three subpopulations were a river and a railway crossing in central Sapporo. The subpopulations separated by the railway were more genetically differentiated than those separated by the river, and the railway, which is surrounded by crowded roads, may have had a greater effect on gene flow and genetic differentiation. Levels of genetic differentiation among the subpopulations in Sapporo, however, were lower than those of urban fox populations studied in other countries. Our results suggest that there is weak gene flow among the subpopulations in Sapporo.
  • Mohammed A. Shalabi, Alexei V. Abramov, Pavel A. Kosintsev, Liang-Kong Lin, Sang-Hoon Han, Shigeki Watanabe, Koji Yamazaki, Yayoi Kaneko, Ryuichi Masuda
    BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 120 (2) 333 - 348 0024-4066 2017/02 [Refereed][Not invited]
    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. (C) 2016 The Linnean Society of London,
  • Kaito Mizumachi, Yoshinori Nishita, Nikolai Spassov, Evgeniy G. Raichev, Stanislava Peeva, Yayoi Kaneko, Ryuichi Masuda
    BIOCHEMICAL SYSTEMATICS AND ECOLOGY 70 99 - 107 0305-1978 2017/02 [Refereed][Not invited]
    In this study, we investigated molecular phylogenetic status of the marbled polecat (Vormela peregusna) from Bulgaria, using sequences of two Y-chromosomal genes (SRY and ZFY). The phylogenetic tree inferred using combined sequences of both genes indicated that the marbled polecat was split from genera Lutra, Neovison and Mustela after genus Martes was diverged in family Mustelidae. In addition, we analyzed molecular phyla geography of the Bulgarian population of the marbled polecat, using cytochrome b and control region sequences of mitochondrial DNA (mtDNA). The phylogenetic tree of cytochrome b indicated that the haplotypes of the Bulgarian population comprised two haplogroups, which were the most ancestral clades. Additionally, the control region phylogeny showed that the haplotypes of Bulgaria formed two haplogroups: one was the most ancestral Glade, and the other was the derivative Glade. One individual with the most ancestral cytochrome b Glade had a control region haplotype of the derivative Glade. Thus, this study revealed that the most ancestral lineages of the marbled polecat are included in the population of Bulgaria. The Bulgarian population could be a remnant lineage from a basal for the species, which in Pleistocene occupied a relatively large area related to the Balkan-Caucasian. (C) 2016 Elsevier Ltd. All rights reserved.
  • Raichev, E, Peeva, S, Masuda, R, Kaneko, Y, Tsunoda, H, Georgiev, D, Georgiev, D
    Trakia Journal of Sciences 15 135 - 140 2017 [Refereed][Not invited]
  • Takuya Akiyama, Chizuko Nishida, Kunikazu Momose, Manabu Onuma, Kazutoshi Takami, Ryuichi Masuda
    MOLECULAR PHYLOGENETICS AND EVOLUTION 106 158 - 163 1055-7903 2017/01 [Refereed][Not invited]
    The gene duplication in mitochondrial DNA (mtDNA) has been reported in diverse bird taxa so far. Although many phylogenetic and population genetic analyses of cranes were carried out based on mtDNA diversity, whether mtDNA contains duplicated regions is unknown. To address the presence or absence of gene duplication in cranes and investigate the molecular evolutionary features of crane mtDNA, we analyzed the gene organization and the molecular phylogeny of mtDNA from 13 crane species. We found that the mtDNA in 13 crane species shared a tandem duplicated region, which consists of duplicated sequence sets including cytochrome b (Cytb), NADH6, control region (CR) and three genes of tRNA. The gene order in the duplicated region was identical among all the 13 crane species, and the nucleotide sequences found within each individual showed high similarities. In addition, phylogenetic trees based on homologous sequences of CR and Cytb indicated the possibility of concerted evolution among the duplicated genes. The results suggested that the duplication event occurred in the common ancestor of crane species or some older ancestors. (C) 2016 Elsevier Inc. All rights reserved.
  • Wataru Saito, Yosuke Amaike, Takako Sako, Yayoi Kaneko, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 33 (5) 485 - 490 0289-0003 2016/10 [Refereed][Not invited]
    The raccoon dog (Nyctereutes procyonoides, Canidae, Carnivora) is highly adaptable to urban environments. Populations of carnivorans inhabiting urban areas sometimes differ ecologically and genetically from those in rural areas. However, there is little information on urban raccoon dogs. This study focused on raccoon dog populations in Tokyo, one of the most highly urbanized cities in the world. We examined the genotypes of 10 microsatellites for 101 fecal samples from raccoon dogs inhabiting the grounds of the Imperial Palace, a green space in central Tokyo. We successfully genotyped 58 samples originating from 31 individuals. We also analyzed muscle tissue samples from raccoon dogs from the grounds of the Imperial Palace, the Akasaka Imperial Grounds (a green space close to the Imperial Palace), and the surrounding urban area, and then investigated the genetic structure and diversity of these populations, and the genetic differentiation among them. The population on the grounds of the Imperial Palace was genetically differentiated from that in the Akasaka Imperial Grounds, suggesting that the roads and buildings act as barriers to gene flow. In addition, the population on the grounds of the Imperial Palace showed greater genetic difference from that in the surrounding area than that in the Akasaka Imperial Grounds. We speculate that the moats around the Imperial Palace restrict individual ranges within the palace grounds and limit migration and gene flow to other areas.
  • Ryuichi Masuda, Robert J. Losey, Vladimir I. Bazaliiskii, Bair Badmaev
    QUATERNARY INTERNATIONAL 419 133 - 139 1040-6182 2016/10 [Refereed][Not invited]
    We analyzed mitochondrial DNA (mtDNA) from ancient marmot teeth (similar to 7550-6800 cal. BP), which were recovered during archaeological excavations of two contemporary cemeteries near Lake Baikal, Russia: one archaeological site is the Shamanka II cemetery located on the southwest shoreline of Lake Baikal, and the other is the Lokomotiv-Raisovet cemetery located about 77 km to northwest and within the modern city of Irkutsk. Although the teeth had not been identified to species based on their morphology, our ancient DNA analysis revealed that all incisors from ten individuals were of the tarbagan marmot (Marmota sibirica), which is currently not distributed around those archaeological sites. In contrast, the black-capped marmot (Marmota camtschatica), which also has a dominant distribution in Eastern Siberia and whose incisors are morphologically similar to M. sibirica, was not identified from our ancient tooth samples. In addition, the mtDNA sequence variation showed that the genealogy of marmots in the Shamanka II cemetery could have been different from that of the Lokomotiv-Raisovet cemetery. These data indicate that the ancient people at the Shamanka II cemetery could have used M. sibirica from different regions than those utilized at the Lokomotiv-Raisovet site. This suggests non-overlapping marmot hunting ranges for the people buried at the two Middle Holocene cemeteries. (C) 2015 Elsevier Ltd and INQUA. All rights reserved.
  • M. Hisano, E. G. Raichev, S. Peeva, H. Tsunoda, C. Newman, R. Masuda, D. M. Georgiev, Y. Kaneko
    ETHOLOGY ECOLOGY & EVOLUTION 28 (3) 295 - 311 0394-9370 2016/07 [Refereed][Not invited]
    Understanding whether and how carnivores can adapt to urbanised environments is becoming increasingly important, as human populations grow and undeveloped landscape is lost. The stone marten (Martes foina) is often found in urban habitats across continental Europe, due to its flexible foraging behaviour. We compare the utilisation of food types for martens living in villages in a more populated region with that of martens living in a less populated mountainous forest region, over the summer fruiting season (May-July) of 2013, inferred from the analysis of 310 faecal samples. Fruits were the primary food for martens in both regions, but comprised a significantly greater proportion of the diet in villages. Invertebrates and rodents were utilised significantly more in the natural habitat. Garbage and domestic animals were rarely exploited in either region; however, village-dwelling martens appeared to rely heavily on being subsidised by cultivated fruits grown in gardens and orchards, and along the streets. We conclude that the stone marten is able to succeed in urbanised regions of Central Bulgaria by exploiting cultivated food resources, attributable to its flexible and adaptable generalist diet.
  • Maiko Noda, Tatsuo Oshida, Alexei V. Abramov, Galina Baranova, Gennady Baryshinikov, Hideo Ichikawa, Ryuichi Masuda
    JOURNAL OF NATURAL HISTORY 50 (11-12) 771 - 786 0022-2933 2016/03 [Refereed][Not invited]
    To test postglacial population expansion in small arboreal mammals dependent on boreal and subboreal forests, we used complete mitochondrial cytochrome b gene sequences (1140 bases) to investigate the phylogeography of the Eurasian red squirrel (Sciurus vulgaris orientis) on the Hokkaido Island of Japan. This subspecies is common in the boreal and subboreal forests of Hokkaido. We examined 61 specimens from 27 localities in Hokkaido. Phylogenetic relationships among 29 haplotypes found in the Hokkaido populations were not associated with geographic distribution of sampling localities. There were four mitochondrial DNA phylogroups. Phylogeographic analyses support sudden expansion of S. vulgaris orientis from restricted refugium in the southern part of Hokkaido during the last glacial period. The phylogeographic structure of this subspecies directly reflects the boreal and subboreal forest dynamics occurring in Hokkaido.
  • Y. Nishita, A. V. Abramov, P. A. Kosintsev, L. -K. Lin, S. Watanabe, K. Yamazaki, Y. Kaneko, R. Masuda
    TISSUE ANTIGENS 86 (6) 431 - 442 0001-2815 2015/12 [Refereed][Not invited]
    Major histocompatibility complex (MHC) genes encode proteins that play a critical role in vertebrate immune system and are highly polymorphic. To further understand the molecular evolution of the MHC genes, we compared MHC class II DRB genes between the Japanese weasel (Mustela itatsi), a species endemic to Japan, and the Siberian weasel (Mustela sibirica), a closely related species on the continent. We sequenced a 242-bp region of DRB exon 2, which encodes antigen-binding sites (ABS), and found 24 alleles from 31 M. itatsi individuals and 17 alleles from 21 M. sibirica individuals, including broadly distributed, species-specific and/or geographically restricted alleles. Our results suggest that pathogen-driven balancing selection have acted to maintain the diversity in the DRB genes. For predicted ABS, nonsynonymous substitutions exceeded synonymous substitutions, also indicating positive selection, which was not seen at non-ABS. In a Bayesian phylogenetic tree, two M. sibirica DRB alleles were basal to the rest of the sequences from mustelid species and may represent ancestral alleles. Trans-species polymorphism was evident between many mustelid DRB alleles, especially between M. itatsi and M. sibirica. These two Mustela species divided about 1.7 million years ago, but still share many MHC alleles, indicative of their close phylogenetic relationship.
  • Yosuke Amaike, Takuya Oishi, Kohji Uraguchi, Alexei V. Abramov, Ryuichi Masuda
    MAMMAL STUDY 40 (4) 245 - 256 1343-4152 2015/12 [Refereed][Not invited]
    To investigate the morphological variation in an island population of the red fox (Vulpes vulpes), we measured 25 cranial and 24 dental characters for 225 specimens (137 males and 88 females) from Hokkaido Island, Japan. A Bayesian principal component analysis found only small differences among three groups identified genetically in previous studies. Concretely, analyses of variance and post-hoc tests detected clear differences in two functionally important measurements: postorbital constriction-and upper fourth premolar length. In the postorbital constriction, relating to size of the temporal muscle, a difference with a gradient of increase from west to east on Hokkaido Island was found in both sexes. In the upper fourth premolar length, relating to body size, a difference between the Southern and Central groups was found in both sexes. Additionally, in differences in four measurements of skull width, skull height, mastoid width, and occipital condyle width, relating to braincase, were detected in only male. Subsequently, a correlation analysis showed that the postorbital constriction might be related to climatic conditions (e.g., minimum mean monthly temperature and snowfall). Endemic climate conditions and food habits appeared to contribute to the observed geographical variation in skull morphology.
  • Tetsuo I. Kohyama, Takuya Akiyama, Chizuko Nishida, Kazutoshi Takami, Manabu Onuma, Kunikazu Momose, Ryuichi Masuda
    IMMUNOGENETICS 67 (11-12) 705 - 710 0093-7711 2015/11 [Refereed][Not invited]
    In this study, we isolated and characterized the major histocompatibility complex (MHC) class II B genes in cranes. Genomic sequences spanning exons 1 to 4 were amplified and determined in 13 crane species and three other species closely related to cranes. In all, 55 unique sequences were identified, and at least two polymorphic MHC class II B loci were found in most species. An analysis of sequence polymorphisms showed the signature of positive selection and recombination. A phylogenetic reconstruction based on exon 2 sequences indicated that trans-species polymorphism has persisted for at least 10 million years, whereas phylogenetic analyses of the sequences flanking exon 2 revealed a pattern of concerted evolution. These results suggest that both balancing selection and recombination play important roles in the crane MHC evolution.
  • Wenwen Chen, Chris Newman, Zhijin Liu, Yayoi Kaneko, Keita Omote, Ryuichi Masuda, Christina D. Buesching, David W. Macdonald, Zongqiang Xie, Youbing Zhou
    CONSERVATION GENETICS RESOURCES 7 (3) 697 - 704 1877-7252 2015/09 [Refereed][Not invited]
    Although the impacts of the legal and illegal wildlife trade are broadly recognised for flagship species (e.g., elephant, rhino and tiger), less is known about how exploitation affects more common, and less charismatic species. This is of especial concern in Asia in general, and particularly in China, where demands for wild game species, and derived products are increasing, but a lack of data on illegal bushmeat hunting limits the development of effective species and ecosystem conservation measures. Genetic monitoring provides an informative tool to assess the pressures on regional populations, particularly for species that are difficult to monitor, for example, using arboreal or subterranean refugia. Here, using microsatellite markers, we investigated the effect of hunting on the genetic diversity of a regional population of the hog badger. Samples were collected from hog badgers confiscated from illegal traffickers and local hunters by forest authorities in the market towns of Wufeng and Yuguan, which lie 40 km apart in Hubei Province, China. To isolate novel hog badger microsatellite loci, we constructed a biotin-enriched microsatellite DNA library. Furthermore, we also tested the suitability of microsatellite loci designed for the European badger in the hog badger. Using these microsatellite markers, we found that these seized hog badgers exhibited a high level of genetic diversity-mean alleles per locus (A) were 8.33 and mean expected heterozygosities (H (E)) were 0.77. Despite 40 km separation between sample sites, spatial segregation was not apparent from genetics. This suggests that our confiscated hog badgers belong to the same meta-population. Although limited by a lack of geographical data on the source of these hog badgers, preventing the analysis of isolation by distance effects, hunting likely eroded hog badger population social structure, promoting gene flow among demes. We conclude that the exploitation of this wild source population seems unsustainable.
  • Ryuichi Masuda, Takao Sato
    ANTHROPOLOGICAL SCIENCE 123 (2) 95 - 98 0918-7960 2015/08 [Refereed][Not invited]
    To investigate the genetic variation of Jomon dogs (Canis familiaris) in Japan, partial sequences of the mitochondrial DNA (mtDNA) control region were determined from dog bone remains, which were excavated from two Jomon-period archaeological sites, the Kamikuroiwa Rock Shelter site in Ehime Prefecture (Shikoku Island) and the Higashimyo site in Saga Prefecture (Kyushu Island), Japan. Of seven individuals from the Kamikuroiwa Rock Shelter site, the mtDNA sequences from two individuals were successfully determined. Comparison of the resultant 215 base pair sequences with previously reported sequences showed that one of these two individuals had a new haplotype, named KRA1, and that the other had the previously reported M1 haplotype. For the Higashimyo site, three of 11 individuals yielded successful sequences. Two of these three individuals shared M1 and the other one had M20, both of which are haplotypes previously reported in modem Japanese dogs, but had not been found in any Jomon dogs. The success rate in the present study was 27.8% (5/18 samples). It is noticed that the three mtDNA haplotypes (M1, M20 and KRA1) were found in Jomon dogs for the first time. In addition, sequence data were obtained from Jomon dogs in Shikoku for the first time. The results suggest that the genetic lineages in the Jomon dog populations were more polymorphic than previously reported, and that at least some maternal lineages shared in the Jomon period descended to modern dogs on the Japanese islands.
  • D. Hirata, V. D. Doichev, E. G. Raichev, N. A. Palova, J. L. Nakev, Y. M. Yordanov, Y. Kaneko, R. Masuda
    ANIMAL GENETICS 46 (2) 209 - 212 0268-9146 2015/04 [Refereed][Not invited]
    East Balkan Swine (EBS) Sus scrofa is the only aboriginal domesticated pig breed in Bulgaria and is distributed on the western coast of the Black Sea in Bulgaria. To reveal the breed's genetic characteristics, we analysed mitochondrial DNA (mtDNA) and Y chromosomal DNA sequences of EBS in Bulgaria. Nucleotide diversity ((n)) of the mtDNA control region, including two newly found haplotypes, in 54 EBS was higher (0.014 +/- 0.007) compared with that of European (0.005 +/- 0.003) and Asian (0.006 +/- 0.003) domestic pigs and wild boar. The median-joining network based on the mtDNA control region showed that the EBS and wild boar in Bulgaria comprised mainly two major mtDNA clades, European clade E1 (61.3%) and Asian clade A (38.7%). The coexistence of two mtDNA clades in EBS in Bulgaria may be the relict of historical pig translocation. Among the Bulgarian EBS colonies, the geographical differences in distribution of two mtDNA clades (E1 and A) could be attributed to the source pig populations and/or historical crossbreeding with imported pigs. In addition, analysis of the Y chromosomal DNA sequences for the EBS revealed that all of the EBS had haplotype HY1, which is dominant in European domestic pigs.
  • Omote, K, Nishida, C, Takenaka, T, Saito, K, Shimura, R, Fujimoto, S, Sato, T, Masuda, R
    Zoological Letters 1 16  2015 [Refereed][Not invited]
  • Kohyama, T.I, Omote, K, Nishida, C, Takenaka, T, Saito, K, Fujimoto, S, Masuda, R
    Zoological Letters 1 13  2015 [Refereed][Not invited]
  • Tomoko Nagai, Takahiro Murakami, Ryuichi Masuda
    MAMMAL STUDY 39 (2) 99 - 104 1343-4152 2014/06 [Refereed][Not invited]
    In order to assess importance of isolated forests as the wintering habitat of the sable (Martes zibellina) in eastern Hokkaido, Japan, we performed DNA analyses on 59 samples noninvasively collected in field (54 fecal, 3 urine and 2 hair samples). Consequently, 46 (41 fecal, 3 urine and 2 hair samples) of the 59 samples were recognized to have dropped from the sable. In addition, we successfully identified the individuality on 36 (35 fecal and 1 urine samples) of the 46 samples, and they consisted of at least 23 individuals. Our new method using sex chromosomal DNA markers showed that the 23 individuals comprised 12 males, 9 females and 2 with unknown sex. In 2010 and 2011, the minimum number of individuals in the study area was 21 (11 males, 8 females and 2 with unknown sex) and 5 (1 male and 4 females), respectively. In addition, we found the sexual difference in fidelity to their home range. Thus, our noninvasive DNA technique provided promising information on estimating and monitoring ecological features about the regional sable population.
  • Yayoi Kaneko, Em Kanda, Sara Tashima, Ryuich Masuda, Christopher Newman, David W. Macdonald
    JOURNAL OF MAMMALOGY 95 (2) 290 - 300 0022-2372 2014/04 [Refereed][Not invited]
    We investigated the social interactions and spatial organization of the Japanese badger (Meles anakuma) using radiotelemetry. Fifty-two individuals (29 males and 23 females) were trapped and marked (tattooed) between 1990 and 1997 from a population with a density of 4 individuals/km(2). Twenty-one of these individuals were subsequently radiotracked. The average home-range size of males expanded from an average of X= 33.0 ha +/- 18.1 SD in the nonmating season to 62.6 +/- 48.2 ha in the mating season, and was significantly larger than the home-range size of females (15.2 +/- 6.3 ha in the mating season; with a lack of data on individual female home-range-size change between seasons). We posit that this range expansion by males occurred to encompass the key resource of estrous females during the breeding season; thus, males exhibited a flexible home-range strategy. Females with cubs had home ranges exclusive of other adult females, configured around areas rich in food resources, indicative of intrasex territoriality. This obstinate strategy, under the constant territory size hypothesis, likely serves to ensure a reliable supply of food resources (as determined by resource dispersion) for cub rearing. Eleven of 36 cubs born during the study remained in their natal range until the next spring and we observed 1 of 5 instances of matriarchal territory inheritance. Microsatellite DNA analysis indicated that the basic social unit was composed of the mother and cub(s), with less-related males providing gene flow. This mother-cub unit, with the retention of nonbreeding juveniles or young adults, or both, along with the loose affiliation of breeding males, informs understanding of the development of group-living, subject to ecological circumstances, in the genus Meles and broadens understanding of the evolution of carnivore sociality.
  • Wei Ou, Satomi Takekawa, Toshiya Yamada, Chisato Terada, Hiroyuki Uno, Junco Nagata, Ryuichi Masuda, Koichi Kaji, Takashi Saitoh
    POPULATION ECOLOGY 56 (2) 311 - 325 1438-3896 2014/04 [Refereed][Not invited]
    Since the 1980s, the sika deer (Cervus nippon Temminck, 1838) population of Hokkaido, Japan, has grown, resulting in range expansion. To assess the effects of this range expansion on the spatial genetic structure of the population, we compared subpopulation structures during 2 different periods (168 samples for 1991-1996, and 169 samples for 2008-2010), using mitochondrial DNA (mtDNA; D-loop) and microsatellites (9 loci). The number of gene-based subpopulations decreased across the 15-year period; specifically from four to three subpopulations based on mtDNA, and from two to one subpopulation based on microsatellite DNA. The fusion of the two northern subpopulations caused the change to the mtDNA-based structure, which might be explained by the dispersal of females from higher to lower density subpopulations. In comparison, the reason for the change in the microsatellite DNA-based structure was unclear, because no significant genetic differentiation was observed between the two study periods. A stable mtDNA-based structure was maintained in the north and central population separated by a west-to-east boundary, while a north-to-south boundary in eastern Hokkaido maintained stability in the eastern subpopulation versus all other subpopulations. The findings of this study demonstrate the importance of understanding gene flow within a structured population to implement effective management efforts; for instance, the culling of one subpopulation might not affect an adjacent subpopulation, because deer movement is limited between the subpopulations.
  • Daisuke Hirata, Alexei V. Abramov, Gennady F. Baryshnikov, Ryuichi Masuda
    BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 111 (3) 627 - 635 0024-4066 2014/03 [Refereed][Not invited]
    Sequence analyses of the complete brown bear, Ursus arctos, mitochondrial DNA (mtDNA) genome have detected scattered single nucleotide polymorphisms (SNPs) that define distinct mtDNA haplogroups in phylogeographical studies. The degraded DNA in historical samples, such as stuffed or excavated specimens, however, is often not suitable for sequence analyses. To address this problem, we developed an amplified product length polymorphism (APLP) analysis for mtDNA-haplogrouping U. arctos specimens by detecting haplogroup-specific SNPs. We verified the validity and utility of this method by analysing up to 170-year-old skin samples from U. arctos specimens collected widely across continental Eurasia. We detected some of the same haplogroups as those occurring in eastern Hokkaido (Japan) and eastern Alaska in continental Eurasia (the Altai and the Caucasus). Our results show that U. arctos in eastern Hokkaido and eastern Alaska descended from a common ancestor in continental Eurasia, and suggest that U. arctos occupied several refugia in southern Asia during the Last Glacial Maximum. (c) 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 627-635.
  • Notes on autumn-winter stomach contents of the stone marten (Martes foina) in the Balkan Mountains, Central Bulgaria
    Hisano, M, Raichev, E, Peeva, S, Georgiev, D, Tsunoda, H, Masuda, R, Kaneko, Y
    Zoo Notes 56 1 - 6 1313-9916 2014 [Refereed][Not invited]
  • Shouko Kamada, Takahiro Murakami, Ryuichi Masuda
    MAMMAL STUDY 38 (4) 261 - 267 1343-4152 2013/12 [Refereed][Not invited]
    The Japanese marten Martes melampus occurring on Hokkaido Island, Japan, is a domestic alien species, artificially introduced from their native distributional range. To reveal the genetic variation within the Hokkaido marten population and their relationships with native populations, we genotyped 14 individuals from Hokkaido using 10 microsatellite loci, and compared the genotype data with those of native populations reported previously. The Hokkaido population showed the highest number of private alleles and loci with private alleles. Relatively high levels of observed (Ho = 0.514) and expected (He = 0.724) heterozygosities and allelic richness (R = 5.290) suggested that the Hokkaido population maintains polymorphisms in microsatellites. These genetic characteristics in the Hokkaido population could have resulted from random mating in fur farms and/or multiple releases from them. Genetic distances among populations showed that the Hokkaido population is closely related to the Chubu and Kitakyushu populations. Bayesian clustering and assignment tests indicated that the Hokkaido population consists of two genetically distinct lineages. These results suggest that the founders were introduced to Hokkaido from multiple locations in the native distributional range in Japan, and that the descendants still maintain genetic polymorphisms.
  • Hisano Masumi, Raichev Evgeniy G, Tsunoda Hiroshi, Masuda Ryuichi, Kaneko Yayoi
    MAMMAL STUDY 38 (4) 293 - 298 1343-4152 2013/12 [Refereed][Not invited]
  • Daisuke Hirata, Tsutomu Mano, Alexei V. Abramov, Gennady F. Baryshnikov, Pavel A. Kosintsev, Alexandr A. Vorobiev, Evgeny G. Raichev, Hiroshi Tsunoda, Yayoi Kaneko, Koichi Murata, Daisuke Fukui, Ryuichi Masuda
    MOLECULAR BIOLOGY AND EVOLUTION 30 (7) 1644 - 1652 0737-4038 2013/07 [Refereed][Not invited]
    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.
  • Evgeniy G. Raichev, Hiroshi Tsunoda, Chris Newman, Ryuichi Masuda, Dian M. Georgiev, Yayoi Kaneko
    Mammal Study 38 (1) 19 - 27 1343-4152 2013/03 [Refereed][Not invited]
    Abstract. Wild canid foraging behaviour and regional abundance are often affected by the availability of anthropogenic food, supplementing natural diet. The feeding habitats of the golden jackal (Canis aureus) were compared between two populations in central Bulgaria, for which food availability and the extent of anthropogenic-modified habitat differed. Stomach contents were collected from hunting bags during winters from 1997 to 2009 and compared between an agriculturalhilly region (Region 1) and a forested-mountainous region (Region 2). Although mammalian prey predominated in the jackal's diet in the two regions, diets differed significantly between the regions: in Region 1 the main foods were domestic animals (30.2%), while in Region 2 wild ungulates proved to be the dominant food type (47.9%). We propose that although regional differences in jackal foraging habits were apparent between the two regions, foods originating from human activities were important in both regions. In Bulgaria, the golden jackal is regarded as a nuisance pest, requiring population control. Managing the availability of anthropogenic food sources to jackals, e.g., carcasses of wild and domestic animals, may implicitly reduce jackal abundance and/or discourage jackals from foraging around sites occupied by people. © The Mammal Society of Japan.
  • Keita Omote, Chizuko Nishida, Matthew H. Dick, Ryuichi Masuda
    Molecular Phylogenetics and Evolution 66 (3) 889 - 897 1055-7903 2013/03 [Refereed][Not invited]
    To investigate the phylogenetic position of Blakiston's fish owl (Bubo blakistoni), we sequenced the mitochondrial (mt) DNA control region and cytochrome b (cyt b) for nine Bubo species. Maximum-likelihood analyses of combined control region and cyt b sequences, and cyt b sequences alone, showed that species formerly placed in genus Ketupa comprise a monophyletic group. Unexpectedly, we discovered a long cluster of 20-25 tandem repeat units 77 or 78. bp long in the third control region domain in four of the nine Bubo species for which the control region was sequenced (B. blakistoni, B. flavipes, and B. ketupu in the Ketupa clade B. lacteus), leading to overall control region lengths of 3.0-3.8. kpb estimated from agarose gel electrophoresis. The control region in B. lacteus is the longest (3.8. kbp) reported to date in vertebrates. Sequencing of eight repeat units at each end of the cluster in 20 B. blakistoni individuals detected several types of repeat units 77 or 78. bp long, and six patterns in the order of unit types. The occurrence of a repeat cluster in all three species examined in the Ketupa clade suggests their common ancestor also had a cluster, whereas a maximum parsimony tree showed repeat-unit types grouping by species, rather than by paralog groups, suggesting independent origins of the clusters. We reconcile these results with a turnover model, in which the range in cluster-length variation and unit types at the 5' end are hypothetically functionally constrained by the protein-binding function of the control region, but otherwise there is a continual turnover of units in evolutionary time, with new unit types arising through mutations, proliferating by duplication of single and double repeat blocks, and being lost through deletion. Estimated free energies for reconstructed secondary structures of single and especially pairs of repeat units were higher than for homologous single-unit blocks in species lacking a repeat cluster, supporting slipped-strand mispairing as the mechanism of cluster turnover. © 2012 Elsevier Inc.
  • Tomoko Nagai, Evgeniy G. Raichev, Hiroshi Tsunoda, Yayoi Kaneko, Ryuichi Masuda
    MAMMAL STUDY 37 (4) 353 - 358 1343-4152 2012/12 [Refereed][Not invited]
  • Tomoko Nagai, Takahiro Murakami, Ryuichi Masuda
    MAMMAL STUDY 37 (4) 323 - 330 1343-4152 2012/12 [Refereed][Not invited]
    To assess the genetic variation and population structure of the sable Martes zibellina on eastern Hokkaido, Japan, we analyzed genotypes of 12 microsatellite loci on 48 individuals. Genotypes for all individuals examined were found to be different from each other. Mean observed and expected heterozygosites and allelic richness were calculated to be 0.52 (0.02-0.80), 0.58 (0.02-0.79) and 5.49, respectively. The genetic diversity of the eastern Hokkaido population was similar to those of farm-bred sables in Russia and other mustelids. STRUCTURE analysis showed that the sables of eastern Hokkaido were grouped into two genetic clusters. Eighty-nine percent (24/27) of individuals assigned to cluster 1 were distributed around Shiretoko Peninsula, whereas 81% (17/21) assigned to cluster 2 were distributed in the inner side of Hokkaido (Tokachi District). The two subpopulations could have been genetically differentiated due to geographic barriers such as higher mountains, lakes, rivers and solfatara areas, although the geographic isolation did not seem to be complete.
  • Shouko Kamada, Shusaku Moteki, Minoru Baba, Keiji Ochiai, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 29 (12) 827 - 833 0289-0003 2012/12 [Refereed][Not invited]
    A carnivoran mammal endemic to Japan, the Japanese marten (Martes melampus) is native in forested regions on Honshu, Shikoku, Kyushu (main islands of Japan), and the Tsushima Islands. The Tsushima population is classified as a different subspecies (M. m. tsuensis) from populations on the main islands (M. m. melampus). To elucidate the genetic structure of the Tsushima population, we genotyped 101 individuals from the Tsushima Islands and 43 individuals from Honshu and Kyushu using 10 microsatellite loci, and performed population genetic analyses on the genotype data. Genetic diversity was lower in the Tsushima population than in three geographic populations on the main islands: heterozygosity was 0.189-0.364 in the former, compared to 0.457-0.747 in the latter. In addition, high pairwise Fst values (0.485-0.682) and Nei's standard distance (0.550-1.183) between the Tsushima and main-island populations indicated a high degree of genetic differentiation. Finally, a Bayesian clustering analysis showed that the Tsushima population is apparently differentiated from the main-island populations and comprises two genetic clusters. A factorial correspondence analysis corroborated these results. Our results suggest that restricted gene flow or inbreeding may have reduced genetic diversity in the Tsushima population, which has been geographically isolated from the main-island populations since the formation of Tsushima Strait.
  • Ryuichi Masuda, Naoko Kurose, Shigeki Watanabe, Alexei V. Abramov, Sang-Hoon Han, Liang-Kong Lin, Tatsuo Oshida
    BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 107 (2) 307 - 321 0024-4066 2012/10 [Refereed][Not invited]
    To investigate the process of the population divergence of mammalian species endemic to continental islands, we studied the phylogeography of the Japanese weasel, Mustela itatsi, compared with its closely related continental species, the Siberian weasel M.?sibirica, using mitochondrial DNA control region sequences. Mustela itatsi is endemic to the main Japanese islands (Honshu, Shikoku and Kyushu Islands), except Hokkaido Island, whereas M.?sibirica is widespread in eastern Asia, southern Siberia, Taiwan and Tsushima Island. Fifty individuals of M.?itatsi collected from 19 localities in Japan were examined. For M.?sibirica, 27 individuals were analysed: 12 specimens from five localities within native habitats and 15 individuals (from the population introduced to Japan) from eight localities in western Japan. We identified 32 haplotypes for M.?itatsi, which were clustered into two main clades (Honshu and KyushuShikoku clades), whereas there were 11 haplotypes for M.?sibirica, all of which were clustered into one clade. The grade of genetic differentiation within each clade of M.?itatsi was similar to each other and to that of M.?sibirica from samples distributed widely across northern Eurasia. The two clades in M.?itatsi could have been established as a result of alternative zoogeographical events: geographical isolation of Honshu and KyushuShikoku Islands or independent migration of the two lineages from the continent to Japan at different times. The molecular phylogeographical and demographic analyses indicated that the population of M.?itatsi of Honshu Island expanded more recently than those of Kyushu and Shikoku Islands, which could have been refugia in the middle Pleistocene. In addition, the genetic differentiation and population expansion of M.?itatsi on the Japanese islands could have occurred earlier than for other mammalian species endemic to Japan. However, the phylogeographical results for M.?sibirica showed much less genetic variation through Eurasia, and that the introduced population in western Japan originated from a small founder population from the Korean Peninsula. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, , .
  • Fumiya Kobayashi, Dai Fukui, Eisuke Kojima, Ryuichi Masuda
    MAMMAL STUDY 37 (3) 227 - 235 1343-4152 2012/09 [Refereed][Not invited]
    Rivers are habitats favored by insectivorous bats. The Japanese large-footed bat (Myotis macrodactylus) is one of such species strongly associated with rivers. To clarify the population structure and migration pattern of M. macrodactylus, mitochondrial DNA (mtDNA) phylogeography was investigated in 15 subpopulations along three rivers (Tokachi, Ishikari and Teshio Rivers) on Hokkaido Island, northern Japan. Of 267 bats examined, nine mtDNA cytochrome b haplotypes were identified and separated into two major genetic clades, which did not reflect geographic distributions within and among the river regions. Principal component analysis of mtDNA haplotypes showed that most subpopulations in Ishikari and Teshio of the three river regions were grouped into one genetically related group, whereas those in the Tokachi river region were remotely related to those of the other two river regions. The results could be ascribed to no geographic barriers preventing bats' migration between the former two river regions. By contrast, it is possible that the Daisetsuzan and Hidaka mountain ranges play a role as effective geographic barriers against migrations of this species between the Tokachi and Ishikari/Teshio river regions.
  • Tomo Inoue, Yayoi Kaneko, Koji Yamazaki, Tomoko Anezaki, Shuuji Yachimori, Keiji Ochiai, Liang-Kong Lin, Kurtis Jai-Chyi Pei, Yen-Jean Chen, Shih-Wei Chang, Ryuichi Masuda
    CONSERVATION GENETICS 13 (4) 1095 - 1107 1566-0621 2012/08 [Refereed][Not invited]
    The masked palm civet Paguma larvata (Carnivora: Viverridae) in Japan has been phylogeographically considered an introduced species from Taiwan. To reveal the population structures and relationships among the P. larvata populations in Japan, seven compound microsatellite loci were isolated from the genome and genotyped for 287 individuals collected from the field. STRUCTURE analysis and factorial correspondence analysis of genotyping data revealed that animals from Japan were divided into four genetic clusters. Geographic distribution of the genetic clusters partly referred to sampling areas, indicating multiple introductions into distinct areas of Japan or independent founding events leading to the generation of different genetic clusters within introduced populations in Japan. The large genetic differentiation of populations in the Shikoku District from those in other areas within Japan suggests that there were at least two introduction routes into Japan, and a possibility that some founders from areas other than Taiwan were also involved in the introduction into Japan. The genetic variation within Japanese populations were not markedly reduced compared with that of Taiwan. The results indicated that the Japanese populations of P. larvata could have retained moderate genetic diversity during founding events, because of multiple introductions, or a large number or high genetic diversity of founders. Although some individuals in Japan showed a sign of admixture between different clusters, there is no evidence that such an admixture markedly increased the genetic diversity within Japanese populations.
  • Keita Omote, Chizuko Nishida, Takeshi Takenaka, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 29 (5) 299 - 304 0289-0003 2012/05 [Refereed][Not invited]
    The Blakiston's fish owl (Bubo blakistoni) population on Hokkaido Island, Japan, decreased to less than one hundred individuals over the last century due to habitat disruption by human activity. Although the ongoing conservation management has slightly restored the population, it remains endangered. In order to assess the genetic variation and population structure of the Blakiston's fish owl in Hokkaido, we genotyped eight microsatellite loci on 120 individuals sampled over the past three decades. The genotype data set showed low levels of genetic variation and gene flow among the geographically isolated five subpopulations. Comparative analysis of past and current populations indicated that some alleles shared by past individuals had been lost, and that genetic variation had declined over the last three decades. The result suggests that the genetic decline may have resulted from inbreeding and/or genetic drift due to bottlenecks in the Hokkaido population. The present study provides invaluable genetic information for the conservation and management of the endangered Blakiston's fish owl in Hokkaido.
  • Ayako Tsubouchi, Daisuke Fukui, Miya Ueda, Kazumi Tada, Shouji Toyoshima, Kazutoshi Takami, Tsunenori Tsujimoto, Kohji Uraguchi, Evgeniy Raichev, Yayoi Kaneko, Hiroshi Tsunoda, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 29 (3) 151 - 161 0289-0003 2012/03 [Refereed][Not invited]
    To investigate the molecular phylogeny and evolution of the family Canidae, nucleotide sequences of the zinc-finger-protein gene on the Y chromosome (ZFY, 924-1146 bp) and its homologous gene on the X chromosome (ZFX, 834-839 bp) for twelve canid species were determined. The phylogenetic relationships among species reconstructed by the paternal ZFY sequences closely agreed with those by mtDNA and autosomal DNA trees in previous reports, and strongly supported the phylogenetic affinity between the wolf-like canids clade and the South American canids clade. However, the branching order of some species differed between phylogenies of ZFY and ZFX genes: Cuon alpinus and Canis mesomelas were included in the wolf-like canid clades in the ZFY tree, whereas both species were clustered in a group of Chrysocyon brachyurus and Speothos venaticus in the ZFX tree. The topology difference between ZFY and ZFX trees may have resulted from the two-times higher substitution rate of the former than the latter, which was clarified in the present study. In addition, two types of transposable element sequence (SINE-I and SINE-II) were found to occur in the ZFY final intron of the twelve canid species examined. Because the SINE-I sequences were shared by all the species, they may have been inserted into the ZFY of the common ancestor before species radiation in Canidae. By contract, SINE-II found in only Canis aureus could have been inserted into ZFY independently after the speciation. The molecular diversity of SINE sequences of Canidae reflects evolutionary history of the species radiation.
  • Itsuro Koizumi, Nisikawa Usio, Tadashi Kawai, Noriko Azuma, Ryuichi Masuda
    PLOS ONE 7 (3) 1932-6203 2012/03 [Refereed][Not invited]
    Intra-specific genetic diversity is important not only because it influences population persistence and evolutionary potential, but also because it contains past geological, climatic and environmental information. In this paper, we show unusually clear genetic structure of the endangered Japanese crayfish that, as a sedentary species, provides many insights into lesser-known past environments in northern Japan. Over the native range, most populations consisted of unique 16S mtDNA haplotypes, resulting in significant genetic divergence (overall F-ST = 0.96). Owing to the simple and clear structure, a new graphic approach unraveled a detailed evolutionary history; regional crayfish populations were comprised of two distinct lineages that had experienced contrasting demographic processes (i.e. rapid expansion vs. slow stepwise range expansion) following differential drainage topologies and past climate events. Nuclear DNA sequences also showed deep separation between the lineages. Current ocean barriers to dispersal did not significantly affect the genetic structure of the freshwater crayfish, indicating the formation of relatively recent land bridges. This study provides one of the best examples of how phylogeographic analysis can unravel a detailed evolutionary history of a species and how this history contributes to the understanding of the past environment in the region. Ongoing local extinctions of the crayfish lead not only to loss of biodiversity but also to the loss of a significant information regarding past geological and climatic events.
  • Katerina Tsytsulina, Matthew H. Dick, Kishio Maeda, Ryuichi Masuda
    Russian Journal of Theriology 11 (1) 1 - 20 1682-3559 2012 [Refereed][Not invited]
    Phylogenetic relationships were examined among specimens identified as Myotis aurascens Kuzyakin, 1935 from across their distribution (Europe to the Korean Peninsula), and also among M. aurascens and other Myotis species. Phylogenetic reconstructions were based upon sequences of the mitochondrial cytochrome b and ND1 genes. In the cytochrome b analysis, the specimens identified as M. aurascens on the basis of morphology emerged as a polyphyletic group (referred to as clades A, B and C). Genetic data supported the status of clade A, which comprised most of the sequences, as a species distinct from M. mystacinus and the other species analysed. A paratype specimen of the form sogdianus Kuzyakin, 1934 appeared in the clade A of Myotis aurascens, which suggested clearly that they belong to the same species. However, despite that sogdianus Kuzyakin, 1934 should be considered a senior synonym of aurascens Kuzyakin, 1935, taking into consideration that a paratype does not have a name-baring function, we do not suggest to make any changes in the species name Myotis aurascens till further studies. In the morphometric analysis, M. aurascens showed a clinal pattern of variation in cranial length and most correlated measurements, which appears to be mostly independent from the mitochondrial gene patterns. Myotis nipalensis przewalskii appeared separately, with large genetic distances from M. mystacinus and the main M. aurascens clade. Our analysis suggests that because of the morphological similarity between M. aurascens, M. nipalensis, and the light coloured M. mystacinus throughout most of their distribution, identification of M. aurascens should be made on the basis of morphological characters, while in Europe and the Tien Shan Mountains region identifications should be made based on genetic data. © Russian Journal of Theriology, 2012.
  • Takehiro Sato, Dmitry Razhev, Tetsuya Amano, Ryuichi Masuda
    JOURNAL OF HUMAN GENETICS 56 (8) 602 - 608 1434-5161 2011/08 [Refereed][Not invited]
    In order to investigate the genetic features of ancient West Siberian people of the Middle Ages, we studied ancient DNA from bone remains excavated from two archeological sites in West Siberia: Saigatinsky 6 (eighth to eleventh centuries) and Zeleny Yar (thirteenth century). Polymerase chain reaction amplification and nucleotide sequencing of mitochondrial DNA (mtDNA) succeeded for 9 of 67 specimens examined, and the sequences were assigned to mtDNA haplogroups B4, C4, G2, H and U. This distribution pattern of mtDNA haplogroups in medieval West Siberian people was similar to those previously reported in modern populations living in West Siberia, such as the Mansi, Ket and Nganasan. Exact tests of population differentiation showed no significant differences between the medieval people and modern populations in West Siberia. The findings suggest that some medieval West Siberian people analyzed in the present study are included in direct ancestral lineages of modern populations native to West Siberia. Journal of Human Genetics (2011) 56, 602-608; doi:10.1038/jhg.2011.68; published online 14 July 2011
  • Hoshino Buho, Z. Jiang, C. Liu, T. Yoshida, Halik Mahamut, M. Kaneko, M. Asakawa, M. Motokawa, K. Kaji, X. Wu, N. Otaishi, Sumiya Ganzorig, R. Masuda
    ADVANCES IN SPACE RESEARCH 48 (1) 43 - 48 0273-1177 2011/07 [Refereed][Not invited]
    The spatial and temporal patterns of the endangered Tibetan antelope or chiru (Pantholops hodgsonii) have been studied using satellite-based ARGOS platform transmitter terminal (PTT) tracking data. The data was obtained from the satellite tracking of two female Tibetan antelopes that were collared with satellite transmitters and have been tracked from August 2007 to April 2009. Analysis of the locality data (LC) obtained, shows that both antelopes were migrant individuals, they shared the same calving ground surrounding lake Huiten (or Zhuonai lake), but different wintering pastures. Each antelope covered 250-300 km from the wintering to summer pastures. Annual range consisted of a core area that was used for at least 9 months; a calving ground used for a short time (from 820 days); and temporal pastures used during migration to and from the calving ground. Seasonal migration cycle was about 3 months, 27-30 days to reach the calving ground; 8-20 days staying there; and 36-40 days returning to the core area. Examination of the spatial distribution during migration showed that both chiru crossed the Qinghai-Tibetan railway (QTR) and the Golmud-Lhasa highway (GLH) at least two times, and reached calving ground (118-120 km from there) in 8 days, maintaining an average speed of 15 km per day. However, the return migration took twice as long (from 14 to 16 days). Each time, after reaching the QTR and GLH, the antelopes spent 20-40 days in that area, probably looking for passages and waiting. So far, we suppose that the QTR and the GLH have become a hindrance to the migration of the Tibetan antelopes and seriously delay their movement to and from the calving area. Extended aggregation of the herds of Tibetan antelopes along the QTR and the GLH may impact negatively with increased mortality among offspring, the spread of various diseases and overgrazing of pastures. (C) 2011 COSPAR. Published by Elsevier Ltd. All rights reserved.
  • Sara Tashima, Yayoi Kaneko, Tomoko Anezaki, Minoru Baba, Shuuji Yachimori, Alexei V. Abramov, Alexander P. Saveljev, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 28 (4) 293 - 303 0289-0003 2011/04 [Refereed][Not invited]
    In the present study, to further understand the phylogenetic relationships among the Eurasian badgers (Meles, Mustelidae, Carnivora), which are distributed widely in the Palearctic, partial sequences of the mitochondrial DNA (mtDNA) control region (539-545 base-pairs) as a maternal genetic marker, and the sex-determining region on the Y-chromosome gene (SRY: 1052-1058 base-pairs), as a paternal genetic marker, were examined. The present study revealed ten SRY haplotypes from 47 males of 112 individuals of the Eurasian Continent and Japan. In addition, 39 mtDNA haplotypes were identified from those animals. From the phylogeography of both the uniparentally inherited genes, four lineages were recognized as Japanese, eastern Eurasian, Caucasian, and western Eurasian. The distribution patterns of the mtDNA lineages showed the existence of a sympatric zone between the eastern and western Eurasian lineages around the Volga River in western Russia. Furthermore, the present study suggested that in the Japanese badgers, the larger genetic differentiation of the Shikoku population was attributable to geographic history in the Japanese islands.
  • Hisako Kazuta, Takehiro Sato, Yukio Dodo, Hirofumi Matsumura, Tetsuya Amano, Hajime Ishida, Ryuichi Masuda
    ANTHROPOLOGICAL SCIENCE 119 (1) 81 - 86 0918-7960 2011/04 [Refereed][Not invited]
    In order to investigate further the allele frequencies of the adenosine triphosphate-binding cassette sub-family C11 (ABCC11) gene, which determines earwax phenotypes, among ancient populations in Hokkaido, Japan, the single-nucleotide polymorphism and the 27 bp deletion in the ABCC11 gene were analyzed in ancient DNA extracted from 38 Epi-Jomon, 24 Jomon, and one Satsumon specimens excavated from various archaeological sites in Hokkaido. Of the specimens analyzed, 10 Epi-Jomon and three Jomon specimens were successfully genotyped. One homozygote for the 27 bp deletion was found first in one Epi-Jomon specimen. Including previously reported data on the Okhotsk people and modern Ainu, exact tests of population differentiation showed that allele frequencies of the ABCC11 gene between the Jomon people and Ainu were statistically significantly different, whereas those between the Jomon and Epi-Jomon people and those between the Epi-Jomon people and Ainu were not significantly different. This result indicates that the Ainu, direct descendants of the Jomon people, were genetically affected by populations who possessed high frequencies of allele A (recessive dry allele) of the ABCC11 locus after the Jomon period.
  • Sara Tashima, Yayoi Kaneko, Tomoko Anezaki, Minoru Baba, Shuuji Yachimori, Alexei V. Abramov, Alexander P. Saveljev, Ryuichi Masuda
    MAMMAL STUDY 36 (1) 41 - 48 1343-4152 2011/03 [Refereed][Not invited]
    The short interspersed nucleotide elements (SINEs) are specific to the taxa and thought to be one of powerful phylogenetic gene markers. Especially, the SINE sequences, which exist uniquely in genome of order Carnivora, are named CAN-SINEs. Among the Eurasian badgers (genus Aides), a member of the family Mustelidae in order Carnivora, the Japanese badger (M anakuma) was previously reported to have an insertion of CAN-SINE in the final intron of the zinc finger protein gene on Y chromosome (ZFY). In the present study, we examined occurrence of the CAN-SINE of the ZFY final intron in the Eurasian badgers, and three continental and four Japanese haplotypes were identified from a total of 40 male badgers. Among the Eurasian badger CAN-SINEs, a 12-bp deletion specific to the Japanese haplotypes was found, whereas the 12-bp region (non-deletion) in the continental haplotypes consisted of one 6-bp direct repeat and 6-bp microsatellite-like sequences. Moreover, the continental haplotypes were phylogenetically divided into three lineages: eastern Eurasia, Caucasus and western Eurasia. These genetic differentiations supported the classification recently proposing that genus Aides are grouped into the European badger (M. meles), the Southwest Asian badger (M canescens), the Northwest & Central Asian badger (M. leucurus) and the Japanese badger (M. anakuna). In addition, the number of adenines in the poly A/T rich tails was polymorphic among all lineages of Eurasian badgers, and geographically variable within the Japanese badgers.
  • Takuya Oishi, Kohji Uraguchi, Kenichi Takahashi, Ryuichi Masuda
    JOURNAL OF HEREDITY 102 (1) 38 - 46 0022-1503 2011/01 [Refereed][Not invited]
    In order to examine the population structures of the red fox (Vulpes vulpes) on the Hokkaido Island in Japan, we conducted analysis on 250 foxes from all over the island for 12 microsatellite loci. Assignment tests using the genotype data set showed that they were divided into 6 subpopulations. Of the 6, one was geographically isolated in the southern region and considered definitive subpopulation, whereas the other 5 were not. The slight differences among the latter 5 subpopulations were explained by the high adaptability and long dispersal of the red fox on the Hokkaido Island. Although there are few ecological data to explain the genetic differentiation of the southern population, we have proposed some hypotheses from the present ecological and geohistorical viewpoints. One convincing reason from the ecological viewpoint is the restriction of gene flow to southern Hokkaido from other areas due to geographical isolation resulting from the land shape. The other explanation is the geohistorical division of southern Hokkaido from other regions on the island during the last interglacial age, resulting in the isolation of the fox population.
  • Takuya Oishi, Kohji Uraguchi, Alexei V. Abramov, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 27 (12) 939 - 945 0289-0003 2010/12 [Refereed][Not invited]
    In order to clarify the morphological differences between two subspecies of the red fox (Vulpes vulpes) on the Japanese Islands and test the validity of Bergmann's rule, we examined geographical variations in 25 cranial and 24 dental characters in V. v. schrencki from Hokkaido and V. v. japonica from the other main islands of Japan (Honshu, Shikoku, and Kyushu). Many skull measurements, including the male greatest length, condylobasal length, and the length of upper and lower tooth rows, were significantly larger for V. v. japonica than for V. v. schrencki, whereas most tooth measurements, especially the length of molars and premolars, in V. v. schrencki were larger than those in V. v. japonica. Although the two subspecies were morphologically well-differentiated from each other, the results did not support that they have evolved following Bergmann's rule of adaptation to cold climates. Based on consideration of the relatively large differences of their tooth sizes, which are not easily influenced by food abundance, and previous genetic research on the different migration histories of the two subspecies, the morphological differences detected in the present study may have resulted not only from the present ecological differences between the two subspecies, but also from the difference of migration history and evolutionary constraints.
  • Sara Tashima, Yayoi Kaneko, Tomoko Anezaki, Minoru Baba, Shuuji Yachimori, Ryuichi Masuda
    MAMMAL STUDY 35 (4) 221 - 226 1343-4152 2010/12 [Refereed][Not invited]
    To further understand the population structures of the Japanese badgers (Meles anakuma) on the Japanese islands, we analyzed their bi-parentally inherited microsatellites. Based on genotypes of nine microsatellite loci, the badgers were divided into five discrete clusters: three clusters from the Honshu Island, one from Kyushu and one from Shikoku. We propose that this genetic differentiation among badgers from the Honshu, Shikoku and Kyushu Islands is as a consequence of geographical isolation caused by the Seto Inland Sea. Furthermore, the cluster containing individuals from Shikoku was more differentiated from the other clusters, plausibly attributable to the earlier geological separation of the Shikoku Island from the Honshu and Kyushu Islands. The three clusters in Honshu, however, did not correspond precisely with geographical locations. As indicated in previous studies, based on mitochondrial DNA analysis, the genetic relationships within the Japanese badgers might reflect recent population expansion, occurring over a relatively short evolutionary time-scale. The findings preliminarily indicate that the Japanese badgers do not possess the high levels of philopatry seen in the European badger (Meles meles), a closely related species, although further analyses using balanced sample sizes from a wider range is required.
  • N. Goda, T. Mano, P. Kosintsev, A. Vorobiev, R. Masuda
    TISSUE ANTIGENS 76 (5) 404 - 410 0001-2815 2010/11 [Refereed][Not invited]
    The allelic diversity of the DRB locus in major histocompatibility complex (MHC) genes was analyzed in the brown bear (Ursus arctos) from the Hokkaido Island of Japan, Siberia, and Kodiak of Alaska. Nineteen alleles of the DRB exon 2 were identified from a total of 38 individuals of U. arctos and were highly polymorphic. Comparisons of non-synonymous and synonymous substitutions in the antigen-binding sites of deduced amino acid sequences indicated evidence for balancing selection on the bear DRB locus. The phylogenetic analysis of the DRB alleles among three genera (Ursus, Tremarctos, and Ailuropoda) in the family Ursidae revealed that DRB allelic lineages were not separated according to species. This strongly shows trans-species persistence of DRB alleles within the Ursidae.
  • Takehiro Sato, Hisako Kazuta, Tetsuya Amano, Hiroko Ono, Hajime Ishida, Haruto Kodera, Hirofumi Matsumura, Minoru Yoneda, Yukio Dodo, Ryuichi Masuda
    JOURNAL OF HUMAN GENETICS 55 (10) 691 - 696 1434-5161 2010/10 [Refereed][Not invited]
    To investigate the genetic characteristics of the ancient populations of Hokkaido, northern Japan, polymorphisms of the ABO blood group gene were analyzed for 17 Jomon/Epi-Jomon specimens and 15 Okhotsk specimens using amplified product-length polymorphism and restriction fragment length polymorphism analyses. Five ABO alleles were identified from the Jomon/Epi-Jomon and Okhotsk people. Allele frequencies of the Jomon/Epi-Jomon and Okhotsk people were compared with those of the modern Asian, European and Oceanic populations. The genetic relationships inferred from principal component analyses indicated that both Jomon/Epi-Jomon and Okhotsk people are included in the same group as modern Asian populations. However, the genetic characteristics of these ancient populations in Hokkaido were significantly different from each other, which is in agreement with the conclusions from mitochondrial DNA and ABCC11 gene analyses that were previously reported. Journal of Human Genetics (2010) 55, 691-696; doi:10.1038/jhg.2010.90; published online 12 August 2010
  • Tomo Inoue, Takahiro Murakami, Alexei V. Abramov, Ryuiehi Masuda
    MAMMAL STUDY 35 (3) 145 - 155 1343-4152 2010/09 [Refereed][Not invited]
    To reveal phylogeographical features of the sable Martes zibellina on Hokkaido Island, northern Japan, we analyzed the 5'-portion sequences of the mitochondrial DNA control region (535 537 base pairs), and compared their sequence variations with those in Russia. Genetic differences between the Hokkaido and Russian individuals, revealed by the present study, indicated that the Hokkaido population has not been well-differentiated after the immigration into Hokkaido from the Eurasian Continent The intraspecific variations of M zibellina showed interpopulation-differentiations due to 'isolation by distance' within Hokkaido, and they were smaller than those of the Japanese marten M melampus, endemic to Honshu, Kyushu and Sikoku Islands of Japan The genetic diversit, in melampus populations introduced to Hokkaido was lower than that of 114 melampus native on Honshu and Kyushu, and the two mitochondrial DNA haplotypes were distributed at restricted areas in southern Hokkaido These findings suggest founder effects in introduced populations of melampus on Hokkaido. In addition, the clear phylogenetic separation between M zibellma and M melampus indicates that no hybridization between them have occurred on Hokkaido so far, although further studies using paternally and biparentally inherited genetic markers are necessary.
  • Takuya Oishi, Kohji Uraguchi, Ryuichi Masuda
    MAMMAL STUDY 35 (3) 201 - 207 1343-4152 2010/09 [Refereed][Not invited]
    In order to assess the genetic usefulness of feces that were obtained from field, we conducted genetic identification by microsatellite analysis on fecal samples of the red fox (Vulpes vulpes) collected in the Shiretoko National Park, Hokkaido Consequently, 59 fecal samples resulted in 22 as the minimum number of individuals The cumulative P-(ID)sibs in the 22 samples was less than 0 01 Two pairs of fecal samples having the identical genotypes (P-(ID)sibs< 0 01) were considered to be dropped by the same foxes, and the distribution of these feces was almost overlapped with the home ranee of one fox, revealed by a previous study Although few reports had revealed the absolute number of red foxes in field, the present study showed that the genetic analysis of their feces is useful for estimating. a presumable number of individuals in the area However, the lower genotyping success rates (23 3-69 8%) and genotyping reproducibility (53 5-88 4%) indicate the difficulty of genetic analysis by using. these fecal samples. In order to improve the efficiency of the analysis, it may be effective to select and use a marker set which has smaller allele sizes, because the genotyping success rates and reproducibility increased when the average allele size decreased.
  • Ryuichi Masuda, Liang-Kong Lin, Kurtis Jai-Chyi Pei, Yen-Jean Chen, Shih-Wei Chang, Yayoi Kaneko, Koji Yamazaki, Tomoko Anezaki, Shuuji Yachimori, Tatsuo Oshida
    ZOOLOGICAL SCIENCE 27 (6) 499 - 505 0289-0003 2010/06 [Refereed][Not invited]
    The source areas of the Japanese populations of the masked palm civet Paguma larvata (Viverridae, Carnivora), an alien species in Japan, have not been identified. In the present study, to reveal their origins and genetic features, we determined the full mitochondrial DNA cytochrome b sequences (1,140 base-pairs) of a total of 206 individuals of P. larvata from the Honshu and Shikoku islands of Japan (186 animals) and Taiwan (20 animals), and investigated their molecular phylogeography and the genetic relationships between populations in these countries. We found that each animal from Japan exhibited one of four haplotypes (JA1, JA2, JA4, and JA5), and that JA1 and JA4 were more frequent in eastern Honshu and Shikoku-central Honshu, respectively. By contrast, six haplotypes consisting of four new types (TW1, TW2, TW3, and TW4) and the previously reported two types (JA1 and JA4) were identified from 20 animals from native populations in Taiwan. Within Taiwan, one haplotype set (JA1, TW1, and TW2) was distributed in the western region, while a second (JA4, TW3, and TW4) was found in the eastern region; these regions are separated by high mountain ranges. Our comparison of haplotype distributions strongly demonstrated that the eastern Japanese populations originated from animals of western Taiwan, and that the western Japanese populations originated from those of eastern Taiwan. In addition, the lower genetic variability and particular distribution patterns of haplotypes in Japan showed founder effects, which may have resulted from multiple introductions of P. larvata to Japan from Taiwan.
  • Chiemi Yamada, Ryuichi Masuda
    MAMMAL STUDY 35 (1) 17 - 30 1343-4152 2010/03 [Refereed][Not invited]
    In the present study, we determined nucleotide sequences of three sex-chromosomal genes (SRY, ZFY and ZFX) for nine species of the family Mustelidae distributed around Japan, and constructed molecular phylogenetic trees, compared with previously reported phylogenies which were examined based on maternally and biparentally inherited genes. The tree topologies by combined sequence data (about 1,800 bp) of two genes (SRY and ZFY) on Y chromosome were almost the same as those by maternal and biparental genes: the mustelid species were basically divided into five genus lineages (Mustela group, Martes group, Neovison, Lutra and Metes). The branching order of Neovison vison and Mustela erminea was different between sex-chromosomal DNA trees. The higher substitution ratio of Y-chromosomal DNA (926-1143 bp of ZFY) than X-chromosomal DNA (848 869 bp of ZFX), revealed by the present study, could be responsible for the topological difference. Meanwhile, in the ZFY final introns of Mustela erminea and Metes anakuma, insertions of carnivore-specific SINEs (CAN-SINEs) were found. This indicates that the two homologous SINEs evolved in the mustelid genome and that they were inserted to the ZFY final introns lineage-independently after species radiation of Mustelidae.
  • Yukari Shimatani, Tsuyoshi Takeshita, Shirow Tatsuzawa, Tohru Ikeda, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 27 (3) 243 - 247 0289-0003 2010/03 [Refereed][Not invited]
    To determine the sex and identity of individual American minks (Neovison vsion), a species introduced into Japan, molecular genetic methods were employed on fecal samples collected from the Kushiro Wetland, eastern Hokkaido. We examined the sex chromosome-linked genes ZFX and ZFY and 11 microsatellite loci to identify individuals. From microsatellite genotypes, the probability of identity was calculated to distinguish between individuals with 99% certainty. To evaluate the accuracy of the genotyping results, we used two approaches for several randomly selected samples. In the first approach, we genotyped all samples from the results of a maximum of three independent polymerase chain reactions (PCRs). In the second approach, we genotyped 10% of the samples from the results of five independent PCRs. Samples subsequent genotypings disagreed with the first genotype were counted as one of three categories of error. The results indicated that genotyping more than 10 microsatellite loci was required to reduce the probability of error in identity to less than 0.01. Twenty of 72 fecal samples were genotyped at 10 or 11 microsatellite loci and sex-determined by ZFX/ZFY genes, resulting in identification of five males and nine females. In assessing the accuracy of the results, genotyping errors were found to have occurred in 20% of the first genotypes. The main type of error was 'missing data', which can be prevented by increasing the number of replicate PCRs.
  • Yukari Shimatani, Yuko Fukue, Ryosuke Kishimoto, Ryuichi Masuda
    MAMMAL STUDY 35 (1) 1 - 7 1343-4152 2010/03 [Refereed][Not invited]
    The American mink (Neovison vison) as invasive alien species has spread along the Chikuma River in Nagano Prefecture, central Honshu, Japan, through naturalization of animals escaped from fur farms in the past. To clarify genetic structures of the naturalized populations, we genotyped ten microsatellite loci on 126 wild-caught animals from this region. Consequently, the genetic variations of American minks in Nagano were relatively low, and no correlations between genetic distances and geographical distances were observed. Based on the genotype data, animals examined were divided to four genetically different clusters. The results suggest that the genetic characters of the American mink populations around the Chikuma River were not formed after naturalization, but during or before breeding in fur farms. In addition, the present study indicated their migration between localities which may bring gene flow and promote random mating, resulting in genetic structure change in the future populations.
  • Takehiro Sato, Tetsuya Amano, Hiroko Ono, Hajime Ishida, Haruto Kodera, Hirofumi Matsumura, Minoru Yoneda, Ryuichi Masuda
    ANTHROPOLOGICAL SCIENCE 117 (3) 171 - 180 0918-7960 2009/12 [Refereed][Not invited]
    In order to further understand the genetic status of the Okhotsk people, who were distributed in southern coastal regions of the Okhotsk Sea during the 5th-13th centuries, nucleotide variations in the hypervariable region (HVR) and the coding regions of mitochondrial DNA (mtDNA) were analyzed. Targeting the coding regions provides reliable genetic information even from ancient DNAs that may have suffered post-mortem damage. MtDNA haplogroups of 38 individuals were classified according to mtDNA lineages known in northeastern Asian people. Comparisons of mtDNA haplogroup frequencies between the Okhotsk people and other Asian populations revealed that the genetic structures of the Okhotsk people are very similar to those of populations currently living around lower regions of the Amur River and the Ainu of Hokkaido. The results support our previous Study on molecular phylogeny of mtDNA HVR I sequences, and strongly suggest that the Okhotsk people originated around the lower regions of the Amur River and became an intermediate of gene flow from the continental Sakhalin people to the Ainu.
  • Tatsuo Oshida, Ryuichi Masuda, Koichi Ikeda
    BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 98 (1) 47 - 60 0024-4066 2009/09 [Refereed][Not invited]
    To test the association between temperate forest dynamics and glacial refugia for arboreal small mammals, we studied the phylogeography of the Japanese giant flying squirrel (Petaurista leucogenys) using complete mitochondrial cytochrome b gene sequences (1140 bp). This squirrel is endemic to three of Japan's main islands: Honshu, Shikoku, and Kyushu. We examined 58 specimens of P. leucogenys collected from 40 localities in Japan. Additionally, two individuals with unknown sampling localities were included in phylogenetic analyses. There were 54 haplotypes of P. leucogenys. We found five major phylogroups (Northern, Central, South-eastern, South-western, and Southern). These phylogroups may have originated from glacial refugia during the Late Pleistocene. After the last glaciation, the Northern phylogroup, widely distributed in eastern Japan, could have extensively expanded northward from its refugia. By contrast, in western Japan, population expansion was restricted to western Japan. All members of four phylogroups existed in western Japan during glaciations. The complicated phylogeographical pattern of P. leucogenys populations originating from western Japan may have resulted from the long history. (C) 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 47-60.
  • Naoki Goda, Tsutomu Mano, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 26 (8) 530 - 535 0289-0003 2009/08 [Refereed][Not invited]
    To investigate genetic diversity of a major histocompatibility complex (MHC) gene in the brown bear (Ursus arctos) population on Hokkaido Island, northern Japan, we cloned and sequenced parts of exon 2 and intron 2 of the MHC class-II DQA gene from 32 brown bears. According to strict criteria for allele identification established by mammalian MHC nomenclature committees, four DQA types (Urar-DQA*01 to Urar-DQA*04) were identified. Of the four, however, Urar-DQA*04 had a 12-bp deletion not detected in a cDNA analysis, indicating that this is a pseudogene at a distinct locus generated by gene duplication. The nucleotide sequences of the other three DQA alleles, which were expressed (because detected from cDNA), were very similar, indicating lower DQA variation in the Hokkaido brown bear population than in other mammals. We attribute this low genetic diversity to (1) some limited effect of possible balancing selection; (2) bottlenecks and inbreeding after migration and isolation of the Hokkaido brown bear population from the Eurasian Continent; (3) a much slower evolutionary rate in DQA than in other MHC genes in the Hokkaido brown bear population.
  • Takehiro Sato, Tetsuya Amano, Hiroko Ono, Hajime Ishida, Haruto Kodera, Hirofumi Matsumura, Minoru Yoneda, Ryuichi Masuda
    JOURNAL OF HUMAN GENETICS 54 (7) 409 - 413 1434-5161 2009/07 [Refereed][Not invited]
    Human earwax is classified into wet and dry types, which are determined by a single-nucleotide polymorphism in the adenosine triphosphate-binding cassette, sub-family C11 (ABCC11) gene locus. To investigate the allele frequencies of the ABCC11 locus within ancient populations on the Northern Japanese island of Hokkaido, amplified product-length polymorphisms were analyzed for 50 specimens of the Okhotsk people and 35 specimens of the Jomon and Epi-Jomon people excavated from various archaeological sites of Hokkaido. Of these specimens, 31 Okhotsk and 19 Jomon/Epi-Jomon samples were genotyped successfully. Frequencies of the wet-type allele in the Jomon/Epi-Jomon people, considered a major ancestor of the Ainu, were higher than those of other Northeastern Asian populations, including the modern Ainu. By contrast, in the Okhotsk people, believed to originate from East Siberia, frequencies of the dry-type allele were relatively higher than those in the Ainu and Jomon/Epi-Jomon people. These results suggest that gene flow from the Northeastern Asian Continent to descendants of the Jomon/Epi-Jomon people of Hokkaido through the Okhotsk people occurred, resulting in the establishment of the Ainu. Journal of Human Genetics (2009) 54, 409-413; doi: 10.1038/jhg.2009.56; published online 26 June 2009
  • Shigeki Nakagome, Jill Pecon-Slattery, Ryuichi Masuda
    MOLECULAR BIOLOGY AND EVOLUTION 25 (7) 1344 - 1356 0737-4038 2008/07 [Refereed][Not invited]
    Evolution of the bear family Ursidae is well investigated in terms of morphological, paleontological, and genetic features. However, several phylogenetic ambiguities occur within the subfamily Ursinae (the family Ursidae excluding the giant panda and spectacled bear), which may correlate with behavioral traits of female philopatry and male-biased dispersal which form the basis of the observed matriarchal population structure in these species. In the process of bear evolution, we investigate the premise that such behavioral traits may be reflected in patterns of variation among genes with different modes of inheritance: matrilineal mitochondrial DNA (mtDNA), patrilineal Y chromosome, biparentally inherited autosomes, and the X chromosome. In the present study, we sequenced 3 Y-linked genes (3,453 bp) and 4 X-linked genes (4,960 bp) and reanalyzed previously published sequences from autosome genes (2,347 bp) in ursid species to investigate differences in evolutionary rates associated with patterns of inheritance. The results describe topological incongruence between sex-linked genes and autosome genes and between nuclear DNA and mtDNA. In more ancestral branches within the bear phylogeny, Y-linked genes evolved faster than autosome and X-linked genes, consistent with expectations based on male-driven evolution. However, this pattern changes among branches leading to each species within the lineage of Ursinae whereby the evolutionary rates of Y-linked genes have fewer than expected substitutions. This inconsistency between more recent nodes of the bear phylogeny with more ancestral nodes may reflect the influences of sex-biased dispersal as well as molecular evolutionary characteristics of the Y chromosome, and stochastic events in species natural history, and phylogeography unique to ursine bears.
  • Yukari Shimatani, Tsuyoshi Takeshita, Shirow Tatsuzawa, Tohru Ikeda, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 25 (7) 714 - 720 0289-0003 2008/07 [Refereed][Not invited]
    To identify mammalian carnivore species distributed in the Kushiro Wetland, eastern Hokkaido, Japan, we developed molecular-genetic methods for identification of the species from fecal samples collected from the field. Species-specific primers and PCR programs were established for five native and six alien species of carnivores: Martes zibellina, Mustela nivalis, Mustela erminea, Vulpes vulpes, and Nyctereutes procyonoides as native species, and Neovison vison, Martes melampus, Mustela itatsi, Canis familiaris, Felis catus, and Procyon lotor as alien species in Hokkaido. Touch-down PCR, in which the annealing temperature is decreased 1 degrees C every cycle, was more effective for some species from which fecal DNA was not amplified species-specifically with standard PCR programs. Of 405 fecal samples collected from the Kushiro Wetland, the species of origin of 246 samples were successfully identified: 88 samples for N. vison, 140 for M. zibellina, 13 for V vulpes, four for C. familiaris and one for E catus. The results show the particular applicability of this method to monitoring M. zibellina and N. vison. In addition, methods to PCR-amplify DNA from two crayfish species (Pacifastacus leniusculus and Cambaroides japonicus) were developed to determine whether the carnivore fecal samples contained detectable DNA from the prey crayfishes. DNA from P leniusculus was amplified from feces of N. vison identified in the present study, but no DNA from C. japonicus was detected. This indicates that N. vison preys on the alien species P leniusculus.
  • Tsutomu Tamada, Boripat Siriaroonrat, Vellayan Subramaniam, Masaharu Hamachi, Liang-Kong Lin, Tatsuo Oshida, Worawut Rerkamnuaychoke, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 25 (2) 154 - 163 0289-0003 2008/02 [Refereed][Not invited]
    To investigate genetic diversity and phylogeography of the Asian leopard cat (Felis bengalensis), mitochondrial DNA (mtDNA) sequences were determined for 39 individuals from various areas. Sequences combining the complete cytochrome b gene (1,140 bp) with the partial control region (646-810 bp) were classified into 24 haplotypes: 21 types from 21 animals, one from eight animals from Tsushima Islands, one from eight animals from Iriomote Island, and one from two animals from Southeast Asia. Phylogenetic trees of the 24 haplotypes clearly showed three clades: a Northern Lineage and Southern Lineages. 1 and 2. The Northern Lineage consisted of animals from Tsushima Islands, the Korean Peninsula, the continental Far East, Taiwan, and Iriomote Island. Within the Northern Lineage, genetic contacts could have occurred between geographically neighboring populations before isolation by straits. Southern Lineage 1, comprising Southeast Asian animals, showed higher genetic diversity. Southern Lineage 2 had large genetic distances from other lineages. Within the control region, the Asian leopard cats shared two to four repetitive motifs, and the number of motifs and their constitution were highly variable among individuals. The motifs were polymorphic even within individuals and could be classified into 31 types. Finally, males of mtDNA Southern Lineage 1 had either of two types of the Y-chromosomal gene ZFY, whereas all males of Northern Lineage shared only one type. Our results indicate that the diversity of southern populations is higher and that genetic differentiation among northern local populations reflects past geographical isolation.
  • Naoko Kurose, Alexei V. Abramov, Ryuichi Masuda
    Mammal Study 33 (1) 25 - 33 1343-4152 2008 [Refereed][Not invited]
    To further understand the phylogenetic relationships among the mustelid genus Mustela, we newly determined nucleotide sequences of the mitochondrial 12S rRNA gene from 11 Eurasian species of Mustela, including the domestic ferret and the American mink. Phylogenetic relationships inferred from the 12S rRNA sequences were similar to those based on previously reported mitochondrial cytochrome b data. Combined analyses of the two genes demonstrated that species of Mustela were divided into two primary clades, named "the small weasel group" and "the large weasel group", and others. The Japanese weasel (Mustela itatsi) formerly classified as a subspecies of the Siberian weasel (M. sibirica), was genetically well-differentiated from M. sibirica, and the two species clustered with each other. The European mink (M. lutreola) was closely related to "the ferret group" (M. furo, M. putorius, and M. eversmanii). Both the American mink of North America and the back-striped weasel (M. strigidorsa) of Southeast Asia were more closely related to each other than to other species of Mustela, indicating that M. strigidorsa originated from an independent lineage that differs from other Eurasian weasels. Based on biochemical, cytogenetic, and molecular differences as well as morphological evidence, it is proposed that the American mink be elevated to a distinct mustelid genus, Neovison. © the Mammalogical Society of Japan.
  • Ryuichi Masuda, Yayoi Kaneko, Boripat Siriaroonrat, Vellayan Subramaniam, Masaharu Hamachi
    Mammal Study 33 (1) 19 - 24 1343-4152 2008 [Refereed][Not invited]
    It is still unclear whether the masked palm civet (Paguma larvata) is native to the Japanese islands or introduced from the outside via human activities. In the present study, we sequenced the whole region (1,140 base-pairs) of the mitochondrial cytochrome b gene for 29 masked palm civets from Japan and Southeast Asia, and investigated their molecular phylogeography. Nine haplotypes were identified from the animals. Five halpotypes identified from 24 animals of Japan were clustered and separated from four haplotypes from five animals of Southeast Asia, showing clear differentiation between Japanese and Southeast Asian lineages. Sequence differences within Japanese haplotypes were smaller than those within Southeast Asian haplotypes and those between Japanese and Southeast Asian haplotypes. Within Japanese animals, all haplotypes found in eastern Honshu (Kanto district) were different from those of central Honshu (Chubu district). The present study highlighted the problem whether the Japanese Paguma larvata is an introduced species showing multiple original routes, or whether it is a native species genetically differentiated from Southeast Asian populations and even within Japan. © the Mammalogical Society of Japan.
  • Takehiro Sato, Tetsuya Amano, Hiroko Ono, Hajime Ishida, Haruto Kodera, Hirofumi Matsumura, Minoru Yoneda, Ryuichi Masuda
    JOURNAL OF HUMAN GENETICS 52 (7) 618 - 627 1434-5161 2007/06 [Refereed][Not invited]
    In order to investigate the phylogenetic status of the Okhotsk people that were distributed in northern and eastern Hokkaido as well as southern Sakhalin during the fifth to the thirteenth centuries, DNA was carefully extracted from human bone and tooth remains excavated from archaeological sites. The hypervariable region 1 sequences of the mitochondrial DNA (mtDNA) control region were successfully amplified and 16 mtDNA haplotypes were identified from 37 individuals of the Okhotsk people. Of the 16 haplotypes found, 6 were unique to the Okhotsk people, whereas the other 10 were shared by northeastern Asian people that are currently distributed around Sakhalin and downstream of the Amur River. The phylogenetic relationships inferred from mtDNA sequences showed that the Okhotsk people were more closely related to the Nivkhi and Ulchi people among populations of northeastern Asia. In addition, the Okhotsk people had a relatively closer genetic affinity with the Ainu people of Hokkaido, and were likely intermediates of gene flow from the northeastern Asian people to the Ainu people. These findings support the hypothesis that the Okhotsk culture joined the Satsumon culture (direct descendants of the Jomon people) resulting in the Ainu culture, as suggested by previous archaeological and anthropological studies.
  • T. Sato, H. Ono, T. Amano, H. Ishida, H. Kodera, H. Matsumura, M. Yoneda, R. Masuda
    ANTHROPOLOGICAL SCIENCE 114 (3) 236 - 236 0918-7960 2006/12 [Refereed][Not invited]
  • Ryuichi Masuda, Toshiyuki Tamura, Osamu Takahashi
    ANTHROPOLOGICAL SCIENCE 114 (3) 211 - 215 0918-7960 2006/12 [Refereed][Not invited]
    Ancient DNA, sampled from ten brown bear (Ursus arctos) skulls excavated from a rock shelter site of the Ainu culture at Bihue, central Hokkaido, Japan, was analyzed. This ritual site (iwaya or siratcise), located in a mountainous area near the western coast of Lake Shikotsu, is considered to have been used for bear-sending ceremonies by the Ainu people at least until about 70 years ago. We identified four mitochondrial DNA (mtDNA) haplotypes at Bilme, all of which were shared by the modem brown bears of Hokkaido. A previous study showed that three mtDNA lineages (groups A, B, and C) of modem brown bears are allopatrically distributed: group A in north-central Hokkaido, group B in eastern Hokkaido, and group C in southern Hokkaido. The ritual site of Bihue is located in the group C area. While one haplotype of group C was recovered from four of the Bihue skulls, three haplotypes of group A were recovered from six skulls. No haplotype of group B was found. The distribution of the four identified haplotypes at Bilme overlaps extensively with the area of the Ainu community called Shumukuru. These results indicate that, at the Bihue ritual site, the Ainu people probably performed bear-sending ceremonies that included skulls of bears that lived far from the Bihue area. This suggests that, earlier in the Ainu culture period (after the 17th century), the Bihue ritual site could have been used by multiple villages within an Ainu community, such as the Shumukuru, and/or that bear-hunting areas may have expanded from Bihue. This might have led to the promotion of cultural communication and unity among local villages via bear-sending ceremonies.
  • N Kurose, R Masuda, M Tatara
    JOURNAL OF HEREDITY 96 (6) 688 - 697 0022-1503 2005/11 [Refereed][Not invited]
    Fecal analysis is a useful tool for the investigation of food habits and species identity in mammals. However, it is generally difficult to identify the species based on the morphological features and contents of feces deposited by mammals of similar body size. Therefore we developed noninvasive DNA analysis methods using fecal samples for identification of the species and sex of four small sympatric carnivores living on the Tsushima Islands of Japan: the leopard cat (Felis bengalensis), Japanese marten (Martes melampus), Siberian weasel (Mustela sibirica), and feral cat (Felis catus). Based on DNA sequence data from previous phylogenetic studies, we designed species-specific primers for polymerase chain reaction (PCR) amplification of the partial mitochondrial cytochrome b gene (112-347 bp) to identify the species and primers for the partial SRY gene (135 bp) to determine the sex. Due to the adjustment of PCR conditions, those specific DNA fragments were successfully amplified and then applied for species and sex identification. Nucleotide sequences obtained from the PCR products corresponded with cytochrome b sequences of the carnivore species expected. The protocol developed could be a valuable tool in the management and conservation of the four carnivore species occurring on the Tsushima Islands.
  • N Kurose, AV Abramov, R Masuda
    ZOOLOGICAL SCIENCE 22 (10) 1069 - 1078 0289-0003 2005/10 [Refereed][Not invited]
    Phylogeography of the ermine Mustela erminea and the least weasel M. nivalis from Palaearctic and Nearctic regions were investigated based on mitochondrial DNA control region sequences. Mustela erminea exhibited a very low level of genetic variation, and geographic structures among populations were unclear. This may indicate that M. erminea recently reoccupied a wide territory in Eurasia following the last glacial retreat. In comparison with M. erminea, genetic variations within and among populations of M. nivalis were much greater. Molecular phylogenetic relationships showed that two lineages of M. nivalis occurred in the Holarctic region: one spread from the Eurasian region to North America, and the other occurred in south-eastern Europe, the Caucasus and Central Asia. The results suggest either mitochondrial DNA introgression among populations of south-eastern Europe, the Caucasus and Central Asia, or ancestral polymorphisms remaining in those populations. Contrastive phylogeographic patterns between the two mustelid species could reflect differences of their migration histories in Eurasia after the last glacial age.
  • Tsutomu Tamada, Naoko Kurosel, Ryuichi Masuda
    ZOOLOGICAL SCIENCE 22 (6) 627 - 633 0289-0003 2005/06 [Refereed][Not invited]
    Nucleotide sequences of mitochondrial DNA (mtDNA) of 50 domestic cats (Felis catus) obtained from the Tsushima Islands were determined and the genetic diversity was analyzed. In the cats, six haplotypes of the complete cytochrome b sequences (1, 140 base-pairs, bp) and ten haplotypes of the partial control region sequences (350 bp) were identified. Haplotypes obtained from both genes showed existence of at least 11 maternal lineages of domestic cats in Tsushima. Mean values of polymorphic site numbers and sequences differences in the control region were 2.4 times and 1.8 times higher than those in the cytochrome b gene, respectively. Our results support the idea that the evolutionary rate of the control region was faster than that of the cytochrome b as reported in other mammals. Molecular phylogenetic trees showed the similar clustering of haplotypes for both genes. Meanwhile, no individual variations within the Tsushima leopard cat (Felis bengalensis euptilura), which is native to Tsushima, were observed, possibly as a result of genetic drift in the small ancestral population by geographical isolation. In contrast, the diversity of the domestic cat population was higher than that of the leopard cats, because the genetic variability of the former's founders, which were repeatedly brought to Tsushima in the past, still remains. In addition, no sequences of the leopard cat mtDNA were detected in any domestic cats. However, because the possibility that the domestic cat would crossbreed with the leopard cat cannot be denied, genetic monitoring of two species is necessary to biological conservation in Tsushima.
  • T Oshida, A Abramov, H Yanagawa, R Masuda
    MOLECULAR ECOLOGY 14 (4) 1191 - 1196 0962-1083 2005/04 [Refereed][Not invited]
    A phylogeographical study of the Russian (Siberian) flying squirrel (Pteromys volans) was carried out using the complete mitochondrial (mt) cytochrome b gene sequences with special reference to the refugia theory for the arboreal traits of this species. We examined 31 specimens from 24 localities, resulting in 28 haplotypes. One breeding specimen with a unique haplotype from Hokkaido, Japan was included in the phylogenetic analysis. There were three mtDNA lineages: Hokkaido, Far Eastern, and northern Eurasia. Divergence data among lineages demonstrated that the Hokkaido group separated from the other groups during the Holsteinian interglacial. The phylogeographical pattern of P. volans is different from that previously reported for terrestrial rodents associated with treeless habitats. Unlike grasslands, forests decreased during glaciation and moved southward because of the cold and arid environmental conditions. The glacial refugia of P. volans would have been associated with forest dynamics in the Pleistocene.
  • O Tatsuo, S Ohdachi, SH Han, R Masuda
    CARYOLOGIA 58 (1) 52 - 55 0008-7114 2005/01 [Refereed][Not invited]
    Karyotypes of Sorex caecutiens from Cheju Island of Korea were examined with conventional staining and G-banding by trypsin treatment stained with Giemsa (GTG). The diploid and fundamental autosomal arm numbers were 42 and 66, respectively. The autosomal complement in the karyotype comprised six pairs of metacentrics, seven pairs of submetacentrics or subtelocentrics, and seven pairs of acrocentrics. The X was a largest acrocentric chromosome, and the Y was a small subtelocentric chromosome. Chromosomal constitutions and G-banding partern of S. caecutiens from Cheju Island were essentially identical to those reported for S. shinto from Honshu Island, Japan. This similarity may indicate the ancestral character of the monophyletic S. caecutiens/shinto group.
  • T Oshida, CM Shafique, S Barkati, M Yasuda, NA Hussein, H Endo, H Yanagawa, R Masuda
    CANADIAN JOURNAL OF ZOOLOGY-REVUE CANADIENNE DE ZOOLOGIE 82 (8) 1336 - 1342 0008-4301 2004/08 [Refereed][Not invited]
    The phylogenetic relationships of flying squirrels (Pteromyinae) were studied by obtaining complete sequence data from the mitochondrial cytochrome b gene of eight Old World and two New World flying squirrel species, with special reference to the systematic and phylogenetic status among Hylopetes fimbriatus (Gray, 1837) (= Eoglaucomys fimbriatus (Gray, 1837)) from Pakistan, two Glaucomys Thomas, 1908 species from North America, and two Hylopetes Thomas, 1908 species from Southeast Asia. Phylogenctic trees supported clustering of (i) Belomys pearsonii (Gray, 1842), (ii) H. fimbriatus, the Glaucomys species, Hylopetes lepidus (Horsfield, 1823), and Hylopetes phayrei (Blyth, 1859), (iii) species of Pteromys G. Cuvier, 1800, and (iv) species of Petaurista Link, 1795. Early polytomic divergence among the flying squirrel genera could have taken place in the northern part of the Eurasian continent. The unclear divergence between the Old and New World flying squirrels shows that divergence among flying squirrel genera could have occurred before the formation of the Bering Strait. Hylopetes fimbriatus was more closely related to the two Glaucomys species than to H. lepidus or H. phayrei, supporting placement of the species fimbriatus in the monotypic genus Eoglaucomys Howell, 1915.
  • SD Ohdachi, MA Iwasa, VA Nesterenko, H Abe, R Masuda, W Haberl
    JOURNAL OF MAMMALOGY 85 (3) 396 - 403 0022-2372 2004/06 [Refereed][Not invited]
    Phylogenetic relationships among 8 species of white-toothed shrews (Crocidurinae, Mammalia) in East and Central Asia were evaluated based on mitochondrial cytochrome-b gene sequences. The taxon formerly regarded as Crocidura suaveolens in East Asia phylogenetically is distinct from that of true C. suaveolens in Europe, suggesting that specimens in East Asia should be considered a distinct species, C. shantungensis. All shrews from Central Asia were regarded as C. sibirica, although phylogenetic comparison with the unsampled C. gmelini is needed to confirm its taxonomic status. C. shantungensis, C. suaveolens, and C. sibirica formed a well-supported monophyletic group. C. dsinezumi, C. lasiura, C. kurodai, and C. watasei also formed a well-supported monophyletic group. Within C. dsinezumi, there were 2 clusters, referable to western and eastern Japan. Based on low genetic divergence, C. dsinezumi on Cheju and Hokkaido islands appear to be the result of a recent introduction from western Japan and northern-eastern Honshu, respectively.
  • Bottleneck effects on the sika deer Cervus nippon population in Hokkaido, revealed by ancient DNA analysis
    D Nabata, R Masuda, O Takahashi, J Nagata
    ZOOLOGICAL SCIENCE 21 (4) 473 - 481 0289-0003 2004/04 [Refereed][Not invited]
    The population size of the sika deer Cervus nippon on Hokkaido Island of Japan had been remarkably reduced because of heavy hunting pressure since the beginning of Meiji Period and effects of heavy snow in 1879 and 1881. After that, the number of sika deer in Hokkaido has increased gradually due to the protection by the Hokkaido government. In the present study, in order to investigate the bottleneck effects, we analyzed ancient mitochondrial DNA (mtDNA) on sika deer bones excavated from archaeological sites just before Meiji Period. On 86 of 113 bones from 13 archaeological sites of Ainu Culture Period (17-19th centuries), 602 base-pair fragments of the mtDNA control region were successfully sequenced. Consequently, we found three new haplotypes (g-, h- and i-types) which had not been identified in modern sika deer. In addition, four haplotypes (a-, b-, c- and d-types) identified from modern sika deer were also found in the archaeological deer. The new haplotypes and previously reported hapoltypes from sika deer of Hokkaido were phylogenetically much closer to each other, compared with those of modern sika deer from Honshu, Kyushu and the Chinese continent. Geographical distribution patterns of haplotypes of the ancient population were different from those of the modern population in Hokkaido. Our findings indicated that their genetic diversity was reduced through the bottleneck and that population structures of sika deer were changed widely in Hokkaido due to genetic drift.
  • Baryshnikov, G.F, Mano, T, Masuda, R
    Russian Journal of Theriology 3 77 - 88 2004 [Refereed][Not invited]
  • Oshida, T, Shafique, C.M, Barkati, S, Fujita, Y, Lin, L.-K, Masuda R
    Russian Journal of Theriology 3 15 - 24 2004 [Refereed][Not invited]
  • T Oshida, SD Ohdachi, R Masuda
    CARYOLOGIA 56 (4) 447 - 451 0008-7114 2003/10 [Refereed][Not invited]
    Chromosomes of the short-tailed shrew Blarina brevicauda, which display the numerical polymorphism arisen from Robertsonian rearrangements, were analyzed with conventional and silver staining and G- and C-banding techniques. With respect to all specimens examined in the present study, the diploid chromosome number (2n) and fundamental autosomal arm number (FN) were 50 and 48, respectively. The karyotype consisted of 24 pairs of acrocentric autosomes, a large-sized metacentric X chromosome, and a small-sized submetacentric Y chromosome. The comparison with previous findings suggested the geographic polymorphism of Y chromosome in this species. All autosomes and the X chromosome carried slight centromeric constitutive heterochromatin, whereas the Y chromosome was entirely heterochromatic. On the satellites of short arms of two autosomal pairs, the nucleolus organizer regions (NORs) were recognized. The G- and C-banded and Ag-NOR-stained karyotypes presented in the present study could be useful cytogenetic characteristics for specification of chromosomes participating in Robertsonian rearrangements within this species and for karyo-systematic study of genus Blarina.
  • M Li, HB Tamate, FW Wei, XM Wang, R Masuda, HL Sheng, N Ohtaishi
    ACTA THERIOLOGICA 48 (2) 207 - 219 0001-7051 2003/06 [Refereed][Not invited]
    The phylogenetic relationships of Cervidae and Moschidae were examined using partial sequence data of mitochondrial DNA (mtDNA) cytochrome b. Ten new sequences were obtained for six species of Cervidae and Moschidae, and aligned with those previously reported for other deer species. Our results demonstrated that the phylogenetic status of the taxa inferred from molecular data was congruent with taxonomy based on morphological studies. Cervidae formed a monophyletic group that consists of four subfamilies: Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. Moschidae occurred at the base of the Cervidae clade. On the basis of molecular clocks for genetic distance, the divergence time of mtDNA haplotypes within the subfamily Cervinae, among subfamilies in Cervidae, and between Moschidae and Cervidae was estimated to date 2-7 MYA, 6-10 MYA and 8-13 MYA, respectively.The phylogenetic relationships of Cervidae and Moschidae were examined using partial sequence data of mitochondrial DNA (mtDNA) cytochrome b. Ten new sequences were obtained for six species of Cervidae and Moschidae, and aligned with those previously reported for other deer species. Our results demonstrated that the phylogenetic status of the taxa inferred from molecular data was congruent with taxonomy based on morphological studies. Cervidae formed a monophyletic group that consists of four subfamilies: Cervinae, Muntiacinae, Hydropotinae, and Odocoileinae. Moschidae occurred at the base of the Cervidae clade. On the basis of molecular clocks for genetic distance, the divergence time of mtDNA haplotypes within the subfamily Cervinae, among subfamilies in Cervidae, and between Moschidae and Cervidae was estimated to date 2-7 MYA, 6-10 MYA and 8-13 MYA, respectively.
  • Y Satoh, T Mano, H Tsuruga, R Masuda, T Matsuhashi, M Onuma, M Suzuki, N Ohtaishi
    JAPANESE JOURNAL OF VETERINARY RESEARCH 50 (4) 195 - 199 0047-1917 2003/02 [Refereed][Not invited]
    To develop an easy method of typing of mitochondrial DNA (mtDNA) in Hokkaido brown bears (Ursus arctos yesoensis), the PCR-RFLP technique was improved using four restriction enzymes : Mbo 1, Cfr 13 I, TspE 1, and Fok 1. This approach identified seven groups of mtDNA haplotypes, HB1/2/5-7, HB 3, HB4, HB8/9, HB10/11, HB12 and HB13 from 102 brown bears of northern, central and eastern Hokkaido.
  • H Mahmut, R Masuda, M Onuma, M Takahashi, J Nagata, M Suzuki, N Ohtaishi
    ZOOLOGICAL SCIENCE 19 (4) 485 - 495 0289-0003 2002/04 [Refereed][Not invited]
    To illustrate phylogeography of red deer (Cervus elaphus) populations of Xinjiang, we determined their mitochondrial DNA (mtDNA) control region sequences, and then investigated geographic variations and phylogenetic relationships between Xinjiang populations and other populations from Asia, Europe, and North America. The C. elaphus mtDNA control region shared different copy numbers of tandem repeats of 38 to 43-bp motifs which clearly distinguished the Western lineage from the Eastern lineage of this species in Eurasia. The western lineage comprised the Tarim populations from southern Xinjiang and the European populations, all of which had four copies of the motifs. By contrast, the Eastern lineage consisted of populations from northern Xinjiang (Tianshan and Altai Mountains), other Asian areas (Alashan, Gansu, Tibet, Mongolia, and northeastern China), and North America, all of which shared six copies of the motifs. MtDNA phylogenetic trees showed that there are two major clusters of haplotypes which referred to the Western and Eastern lineages, and that subgroupings of haplotypes in each cluster were congruent with their geographic distributions. The present study revealed that a boundary separating the Western lineage from the Eastern lineage occurs between Tarim Basin and Tianshan Mountains in Xinjiang. Meanwhile, North American populations were genetically closer to those of northern Xinjiang, northeastern China, and Mongolia, supporting that C. elaphus immigrated from northeastern Eurasia to North America through the glacier-induced land-bridge (Beringia) which had formed between the two continents after Late Pleistocene.
  • Masuda, R, Noro, M, Nishida-Umehara, C, Yamazaki, T
    Japanese Journal of Zoo and Wildlife Medicine 7 75 - 80 2002 [Refereed][Not invited]
  • N Kurose, Y Kaneko, AV Abramov, B Siriaroonrat, R Masuda
    ZOOLOGICAL SCIENCE 18 (8) 1145 - 1151 0289-0003 2001/11 [Refereed][Not invited]
    To assess the level of genetic variations of the Eurasian badger Meles metes in Japan, the entire sequences (1,140 base pairs) of the mitochondrial cytochrome b gene were phylogenetically examined. Most of substitutions between haplotypes were transitions resulting in synonymous mutations. A phylogenetic tree reconstructed by sequence differences clearly showed that Japanese populations of Metes meles were differentiated from continental populations (from the Baikal area and eastern Europe) of M. meles. By contrast, genetic distances among Japanese populations were much smaller, and their geographic structures did not reflect geographic distances between sampling localities. The results indicate that polymorphisms of the ancestral populations still remain via loss of haplotypes by population size changes. In addition, M. metes could have occupied the present habitats in Japanese main islands (Honshu, Shikoku, and Kyushu) in a short period, possibly after the last glacial age.
  • T Matsuhashi, R Masuda, T Mano, K Murata, A Aiurzaniin
    ZOOLOGICAL SCIENCE 18 (8) 1137 - 1143 0289-0003 2001/11 [Refereed][Not invited]
    Previous phylogenetic studies using mitochondrial DNA sequences of the brown bear Ursus arctos have separately defined two major lineages in Europe, three in Alaska, and three in Hokkaido Island of Japan. To reconstruct phylogenetic relationships among worldwide populations of the species, nucleotide sequences of the mitochondrial DNA control region and cytochrome b were determined for some additional subpopulations of Asia (Gobi and Tibetan), and then all the data including previously reported sequences were compared. The resultant phylogenetic trees showed that the worldwide populations could be grouped into at least five lineages. One of the five lineages had a wide distributional range covering Eurasia, Alaska, and central Hokkaido. Moreover, it is likely that populations from eastern Hokkaido and eastern Alaska are the direct derivatives of a single lineage. These results suggest that brown bears may have widely colonized Eurasia and North America from their original areas somewhere in Eurasia more than once.
  • H Mahmut, S Ganzorig, M Onuma, R Masuda, M Suzuki, N Ohtaishi
    JAPANESE JOURNAL OF VETERINARY RESEARCH 49 (3) 231 - 237 0047-1917 2001/11 [Refereed][Not invited]
    To evaluate the genetic diversity of the Xinjiang Tarim red deer (Cervus elaphus yarkandensis) population, we analyzed the frequencies of microsatellite alleles. Samples were collected from 3 isolated populations in Xaya, Lopnur and Qarqan of Xinjiang. Although 10 microsatellite loci were examined, alleles of 133 to 190 base-pairs were detected for only 3 loci: BM5004, BM4208 and BM888. The average observed multilocus heterozygosity was 0.08 +/-0.04 for the Xaya, 0 for the Lopnur, and 0.17 +/-0.08 for the Qarqan population. The average beterozygosity of all populations was 0.08 +/-0.02. The observed heterozygosities were significantly lower than the expected values. The present results suggest that the bottleneck effect has occurred in the populations of the Xinjiang Tarim red deer.
  • S Ohdachi, NE Dokuchaev, M Hasegawa, R Masuda
    MOLECULAR ECOLOGY 10 (9) 2199 - 2213 0962-1083 2001/09 [Refereed][Not invited]
    Intraspecific phylogeny and genetic variation were investigated based on nucleotide sequences of the mitochondrial cytochrome b gene in six soricine shrew species, Sorex unguiculatus, S. caecutiens, S. shinto, S. gracillimus, S. minutissimus and S. hosonoi, collected primarily from northeastern Asia. Maximum likelihood trees and a phylogenetic network were generated to estimate intraspecific phylogenies. S. minutissimus showed high congruence between phylogenetic position and geographical origin and S. gracillimus showed low congruence. In contrast, there was no congruence between phylogeny and geography in S. unguiculatus and the S. caecutiens from Sakhalin-Eurasia. Positive correlation between genetic and geographical distances was found in S. minutissimus and S. gracillimus, but not in the other species (or regional populations). The results of the phylogenetic and genetic analyses suggest that S. minutissimus and S. gracillimus have occupied their present ranges for a longer time than the other species if we assume a stepping-stone model of population structure. In addition, there was no contradiction between the present investigations and the hypotheses of multiple immigration by S. gracillimus and a single immigration by S. unguiculatus into Hokkaido Island. It is proposed that these six northeastern Asian species experienced different historical processes of range expansion and dispersal despite the fact that some of them currently show similar patterns of distribution.
  • R Masuda, T Amano, H Ono
    ZOOLOGICAL SCIENCE 18 (5) 741 - 751 0289-0003 2001/07 [Refereed][Not invited]
    Ancient DNA was analyzed from skull remains of 12 brown bears (Ursus arctos) excavated from the archeological site of the Okhotsk Culture on Rebun Island of Hokkaido, where no natural populations of brown bears currently occur, in order to trace their original habitats. The Okhotsk Culture developed around southern coastal regions of the Okhotsk Sea (southern Sakhalin, Rebun and Rishiri Islands, northern and eastern Hokkaido, and southern Kuril Islands) during 6-11 th centuries, A.D. The ancient people of those days are considered to have involved brown bears for traditional ceremonies and rituals. From the skull remains, partial fragments (approximately 250-360 base pairs) of the mitochondrial DNA (mtDNA) control region were successfully sequenced. Compared with sequence data of modern brown bears of the Hokkaido main land, ancient mtDNAs of Rebun Island were phylogenetically classified into either of two lineages of modern mtDNA: the north-central Hokkaido lineage and southern Hokkaido lineage. The southern Hokkaido lineage was identified from three juvenile (less than one year old) ancient bears, while the north-central Hokkaido lineage was mainly from adults (more than three years old). Our findings demonstrated that juvenile ancient bears of Rebun Island were originated from southern Hokkaido, which was an outside area of the Okhotsk Culture and belonged to the Epi-Jomon Culture with a close relation to a northern part of the Tohoku district. The molecular phylogeographic study on ancient and modern brown bears provides an insight to further understanding zooarcheology and ancient people's cultures around Hokkaido.
  • T Oshida, M Yasuda, H Endo, NA Hussein, R Masuda
    MAMMALIA 65 (4) 473 - 482 0025-1461 2001 [Refereed][Not invited]
    Phylogeographic relationship among five Callosciurus species (C. caniceps, C. erythraeus, C. finlaysonii and C. nigrovittatus, and C. prevostii) from Southeast Asia were inferred from partial mitochondrial cytochrome b gene sequences (1,080 bases-pairs). Maximum parsimony (MP), neighbor-joining (NJ), and maximum likelihood (ML) trees showed very similar branching patterns, although the phylogenetic position of C. caniceps in NJ tree was different from those in MP and ML trees. The five Callosciurus species were clustered in two lineages : one cluster consisting of C. caniceps, C. erythraeus, and C. finlaysonii (79 % bootstrap value in MP tree and 57 % support value in ML tree) and the other cluster consisting of C. nigrovittatus and C. prevostii (100 % bootstrap values in MP and NJ trees and 100 % support value). Based on morphological and zoogeographical data, Callosciurus was previously categorized into two groups : the mainland unit and the Sundaland unit. The present work seems to support this hypothesis. Phylogenetic relationship and divergence times estimated from molecular data suggested that early divergences between the two lineages might have occurred during the Miocene, and that subsequent divergence in each lineage might have taken place during the Pliocene.
  • T Oshida, K Ikeda, K Yamada, R Masuda
    ZOOLOGICAL SCIENCE 18 (1) 107 - 114 0289-0003 2001/01 [Refereed][Not invited]
    To investigate genetic diversity among populations of the Japanese giant flying squirrel Petaurista leucogenys, the mitochondrial DNA control region sequences (1,052-1,054 bases) were determined in 37 specimens from 17 localities on the Honshu, Shikoku, and Kyushu Islands of Japan. Of the 37 animals examined, 24 haplotypes were identified. All haplotypes from Kyushu consisted of 1,052 bases, whereas those from Honshu and Shikoku consisted of 1,054 bases including two insertions, except for three haplotypes (which had 1,052 or 1,053 bases). Phylogenetic relationships reconstructed using neighbor-joining and maximum parsimony methods indicated that P. leucogenys is essentially separated into three major lineages: Group A consisting of a single haplotype from Kyushu, Group B consisting of some haplotypes from Kyushu and one haplotype from Honshu, and Group C consisting mostly of haplotypes from Honshu and Shikoku. Animals with the Kyushu haplotypes were split into two lineages (Groups A and B), suggesting that Group A diverged at an earlier point from the other groups. Genetic distances in Group C were not related to geographic distances between sampling localities, indicating that ancestral populations of this group recently expanded their distribution in a short time, possibly after the last glacial stage.
  • N Kurose, R Masuda, T Aoi, S Watanabe
    CARYOLOGIA 53 (3-4) 269 - 275 0008-7114 2000/07 [Refereed][Not invited]
    Chromosomes of the Japanese weasel Mustela itatsi endemic to Japanese main islands except Hokkaido were examined by conventional, G-, and C-stainings, and compared with those of the Siberian weasel M. sibirica which is widespread in eastern Asia and Siberia. The two species shared the same diploid chromosome number (2n=38). However, their fundamental numbers and G- and C-banding patterns were largely differentiated from each other. Judging from the karyological features as well as mitochondrial DNA data and morphological characters previously reported, M. itatsi should be regarded as an independent species from M. sibirica, in agreement with the first description.
  • N Kurose, AV Abramov, R Masuda
    ZOOLOGICAL SCIENCE 17 (5) 673 - 679 0289-0003 2000/07 [Refereed][Not invited]
    To illuminate molecular phylogenetic relationships among Eurasian species of the genus Mustela (Mustelidae, Carnivora), we determined nucleotide sequences of the complete mitochondrial cytochrome b gene region (1,140 base pairs). Molecular phylogenetic trees, constructed using the neighbor-joining and the maximum likelihood methods, showed the common topology of species relationships to each other. The American mink M. vison first branched off and was positioned very remotely from the other species of Mustela. Excluding M. vison, the ermine M. erminea first split from the rest of the species. Two small body-sized weasels, the least weasel M. nivalis and the mountain weasel M, altaica, comprised one cluster (named "the small weasel group"). The other species formed another cluster, where the remarkably close relationships among the domestic ferret M. furo, the European polecat M. putorius, and the steppe polecat nn. eversmanni were noticed with 87-94% bootstrap values (named "the ferret group"), supporting the history that the ferret was domesticated from IM. putorius and/or M. eversmanni The European mink M. lutreola was the closest to the ferret group. The genetic distance between the Siberian weasel M. sibirica and the Japanese weasel M. itatsi corresponded to differences of interspecific level, while the two species were relatively close to M. lutreola and the ferret group. These results provide invaluable insight for understanding the evolution of Mustela as well as for investigating the hybridization status between native and introduced species for conservation.
  • T Oshida, LK Lin, H Yanagawa, H Endo, R Masuda
    ZOOLOGICAL SCIENCE 17 (4) 485 - 489 0289-0003 2000/05 [Refereed][Not invited]
    Petauristinae (flying squirrels) consists of 44 extant species in 14 recent genera, and their phylogenetic relationships and taxonomy are unsettled questions. We analyzed partial mitochondrial cytochrome b gene sequences (1,068 base pairs) to investigate the phylogenetic relationships among six flying squirrel genera (Belomys, Hylopetes, Petaurista, Petinomys, and Pteromys from Asia and Glaucomys from North America). Molecular phylogenetic trees, constructed by neighbor-joining and maximum likelihood methods, strongly indicated the closer relationship between Hylopetes and Petinomys with 100% bootstrap values. Belomys early split from other flying squirrels. Petaurista was closely related to Pteromys, and Glaucomys was most closely related to the cluster consisting of Hylopetes and Petinomys. The bootstrap values supporting branching at the deeper nodes were not always so high, suggesting the early radiation in the evolution of flying squirrels.
  • T Oshida, R Masuda
    ZOOLOGICAL SCIENCE 17 (3) 405 - 409 0289-0003 2000/04 [Refereed][Not invited]
    To investigate the phylogenetic relationships between the New World Sciurus and the Old World Sciurus and their biogeographic history, the partial mitochondrial cytochrome b gene sequences (1,040 base pairs) were analyzed on six Sciurus species: S. aberti, S. carolinensis, S. lis, S. niger, S. stramineus, and S. vulgaris. Phylogenetic trees (maximum parsimony, neighbor-joining, and maximum likelihood methods) commonly showed two groups with high bootstrap values (73-100%): one consisting of the New World Sciurus and the other consisting of the Old World Sciurus. Genetic distances among the New World Sciurus species were remarkably larger than that between two Sciurus species of the Old World, suggesting the earlier radiation of the New World Sciurus than the Old World Sciurus.
  • T Oshida, LK Lin, R Masuda, MC Yoshida
    ZOOLOGICAL SCIENCE 17 (1) 123 - 128 0289-0003 2000/01 [Refereed][Not invited]
    To elucidate the phylogenetic relationships among four species belonging to the genus Petaurista (P. alborufus castaneus, P. alborufus lena, P. leucogenys leucogenys, P. leucogenys nikkonis, P. petaurista melanotus, and P. philippensis grandis), we investigated the partial sequences (1,068 bp) of the mitochondrial cytochrome b gene for these giant flying squirrels. Phylogenetic trees (NJ, MP, and ML trees) constructed from cytochrome b sequences indicated that P. leucogenys was grouped independently with other species, and that P. philippensis was most closely related to P, petaurista with 99-100% bootstrap values. In addition, two subspecies of P. alborufus did not form a single clade: P. alborufus castaneus from China was most distantly related to the other species, whereas P. alborufus lena from Taiwan was closely related to P. petaurista and P. philippensis with 82-90% bootstrap values. This result suggests that it is reasonable to regard P. alborufus lena as a distinct species from P. alborufus castaneus.
  • N Kurose, R Masuda, MC Yoshida
    ZOOLOGICAL SCIENCE 16 (6) 971 - 977 0289-0003 1999/12 [Refereed][Not invited]
    The least weasel Mustela nivalis and the ermine M. erminea of Japan are considered relicts of the last glacial period. To study phylogeographic variation in these mustelines, fragments of the mitochondrial DNA control region were sequenced. In both species, the control region included tandem repeats of 10-base motifs at the 3' portion specific to the genus Mustela. Phylogenetic trees of the 5' portion (581-584 bases) of M. nivalis indicated that haplotypes in the Hokkaido population clearly diverged from those in the Honshu population. Geographic pattern of intraspecific variations illustrated by this result is concordant with that by the result of a previous cytogenetic study, which revealed the karyotypic differentiation between the two populations. These findings might suggest that the Hokkaido and Honshu populations of M. nivalis were geographically isolated in advance of the formation of the Tsugaru strait between Hokkaido and Honshu. Distribution pattern of the mitochondrial DNA haplotypes within Hokkaido suggests that M. nivalis experienced the repeated changes of environments during glacial and inter-glacial periods of the Quaternary, or that this species immigrated from Sakhalin/Siberia into Hokkaido so recently. On the other hand, M. erminea exhibited a smaller sequence divergence between the Hokkaido and Honshu populations, suggesting a shorter geographic isolation than in M. nivalis.
  • J Nagata, R Masuda, HB Tamate, S Hamasaki, K Ochiai, M Asada, S Tatsuzawa, K Suda, H Tado, MC Yoshida
    MOLECULAR PHYLOGENETICS AND EVOLUTION 13 (3) 511 - 519 1055-7903 1999/12 [Refereed][Not invited]
    To investigate genetic diversity among populations of the sika deer, Cervus nippon, nucleotide sequences (705-824 bases) of the mitochondrial D-loop regions were determined in animals from 13 localities in the Japanese islands. Phylogenetic trees constructed by the sequences indicated that the Japanese sika deer is separated into two distinct lineages: the northern Japan group (the Hokkaido island and most of the Honshu mainland) and the southern Japan group (a part of the southern Honshu mainland, the Kyushu island, and small islands around the Kyushu island). All sika deer examined in this study shared four to seven units of repetitive sequences (37 to 40 bases each) within the D-loop sequences. The number of tandem repeats was different among the populations, and it was specific to each population. Six or seven repeats occurred in populations of the northern Japan group, while four or five repeats occurred in populations of the southern Japan group. Each repeat unit included several nucleotide substitutions, compared with others, and 26 types were identified from 31 animals. Sequences of the first, second, and third units in arrays were clearly different between the northern and the southern groups. Based on these D-loop data, colonization and separation of the sika deer populations in the Japanese islands were estimated to have occurred less than 0.5 million years before present. Our results provide an invaluable insight into better understanding the evolutionary history, phylogeny, taxonomy, and population genetics of the sika deer. (C) 1999 Academic Press.
  • N Kurose, R Masuda, B Siriaroonrat, MC Yoshida
    ZOOLOGICAL SCIENCE 16 (4) 693 - 700 0289-0003 1999/08 [Refereed][Not invited]
    To assess genetic variations of two Japanese species of the genus Martes, the Japanese marten M. melampus and the sable M. zibellina, the whole regions (1,140 base pairs) of the mitochondrial cytochrome b gene were sequenced. Intraspecific variable sites were different between these two species, and most substitutions were transitions resulting in synonymous mutations. Molecular phylogenetic trees exhibited genetic differentiation between the two species. Genetic variations among M. melampus from Honshu, Shikoku, and Kyushu were larger than those among M. zibellina from Hokkaido. Genetic distance between cytochrome b haplotypes did not correlate to geographic distance between sampling localities. This result suggests the introgression of mitochondrial DNA haplotypes between local populations, probably resulting from incomplete geographic isolation, and/or their recent expansion on each island during a short period.
  • T Matsuhashi, R Masuda, T Mano, MC Yoshida
    MOLECULAR BIOLOGY AND EVOLUTION 16 (5) 676 - 684 0737-4038 1999/05 [Refereed][Not invited]
    We investigated nucleotide sequences of the mitochondrial DNA control region to describe natural genetic variations and to assess the relationships between subpopulations of the brown bear Ursus arctos on Hokkaido Island, Japan. Using the polymerase chain reaction product-direct sequencing technique, partial sequences (about 930 bases) of the control region were determined for 56 brown bears sampled throughout Hokkaido Island. A sequence alignment revealed that the brown bear control region included a variable sequence on the 5' side and a repetitive region on the 3' side. Phylogenetic trees reconstructed from the 5' variable region (696-702 bases) exhibited 17 haplotypes, which were clustered into three groups (Clusters A, B, and C). The distribution of each group did not overlap with those of the others, and the three different areas were located in separate mountainous forests of Hokkaido Island. Furthermore, most of the phylogenetically close haplotypes within each group were distributed geographically close to each other. In addition, the 3' repetitive region (arrays of 10 bases) exhibited a much faster mutation rate than the 5' variable region, resulting in heteroplasmy. Such mitochondrial DNA divergence in each group could have occurred after the brown bears migrated from the continent to Hokkaido and became fixed in the different areas.
  • The taxonomic status of Moschus moschiferus anhuiensis
    M Li, YG Li, HL Sheng, H Tamate, R Masuda, J Nagata, N Ohtaishi
    CHINESE SCIENCE BULLETIN 44 (8) 719 - 723 1001-6538 1999/04 [Refereed][Not invited]
    Since the musk deer distributed in the Dabie Mountains, Anhui was defined as Moschus moschiferus anhuiensis, its status has been disputed based on researches of morphology and ecology. This study further probed into its taxonomic status with principal components analysis (PCA) on skull measurements and mtDNA cytochrome b sequences (367 bp) analysis so as to clear its status. It is concluded that the figure and skull in Anhui musk deer are different from other species, and DNA divergence between it and other species is 6.24%-7.90%, which belongs to inter-specific difference. Thus, the study defines this musk deer as one distinct species, Moschus anhuiensis (Wang, Hu et al.).
  • Lungka, G, Siriaroonrat, B, Kangwanpong, D, Masuda, R
    Japanese Journal of Zoo and Wildlife Medicine 4 39 - 43 1999 [Refereed][Not invited]
  • Siriaroonrat, B, Angkawanish, T, Kangwanpong, D, Masuda, R
    Japanese Journal of Zoo and Wildlife Medicine 4 65 - 71 1999 [Refereed][Not invited]
  • J Nagata, R Masuda, K Kaji, M Kaneko, MC Yoshida
    MOLECULAR ECOLOGY 7 (7) 871 - 877 0962-1083 1998/07 [Refereed][Not invited]
    Mitochondrial DNA (mtDNA) D-loop region sequences (602 bp) from 141 samples of the sika deer Cervus nippon collected from Hokkaido Island of Japan were investigated to elucidate population genetic structure. All animals possessed seven repeat units (38 or 39 by each) in the sequences. Comparison of the 602-bp sequences showed four sites of transitional mutations (A <----> G or C <----> T). Based on combination of the substitutions, six D-loop haplotypes (a-f types) were identified in the Hokkaido population, suggesting the occurrence of at least six maternal lineages. Distribution maps of the haplotypes constructed using the Geographic Information System showed that the distribution patterns differed from haplotype to haplotype. In particular, distribution of the major three types (a-, b-, and c-types) almost overlapped with three main areas of coniferous forests in Hokkaido. These results suggest that expansion of the sika deer population could have occurred through the habitat of coniferous forests after the historical bottleneck in Hokkaido.
  • M Takahashi, R Masuda, H Uno, M Yokoyama, M Suzuki, MC Yoshida, N Ohtaishi
    JOURNAL OF VETERINARY MEDICAL SCIENCE 60 (6) 713 - 716 0916-7250 1998/06 [Refereed][Not invited]
    In Order to determine the sex of carcass remains of the Sika deer (Cervus nippon), we improved a polymerase chain reaction (PCR) technique for amplification of the Sika deer Sry, a male-specific DNA region on the mammalian Y chromosome. From the nucleotide sequence of the Sry region obtained here, PCR primers, MT1 and MT2, capable of amplifying a shorter Sry region were newly designed, and a microsatellite locus was used as a positive control. Using these primers, 96 of 109 sex-unknown fawns (88%, 96/109) were successfully sexed (46 males and 50 females) regardless of the conditions of carcasses found in the field. The results and the methodology could greatly contribute to the study of the mortality pattern of the Sika deer population.
  • M Noro, R Masuda, IA Dubrovo, MC Yoshida, M Kato
    JOURNAL OF MOLECULAR EVOLUTION 46 (3) 314 - 326 0022-2844 1998/03 [Refereed][Not invited]
    Complete sequences of cytochrome b (1,137 bases) and 12S ribosomal RNA (961 bases) genes in mitochondrial DNA were successfully determined from the woolly mammoth (Mammuthus primigenius), African elephant (Loxodonta africana), and Asian elephant (Elephas maximus). From these sequence data, phylogenetic relationships among three genera were examined. Molecular phylogenetic trees reconstructed by the neighbor-joining and the maximum parsimony methods provided an identical topology both for cytochrome b and 12S rRNA genes. These results support the "Mammuthus-Loxodonta" clade, which is contrary to some previous morphological reports that Mammuthus is more closely related to Elephas than to Loxodonta.
    Mammal Study 23 (2) 95 - 101 1343-4152 1998 [Refereed][Not invited]
  • R Masuda, M Noro, N Kurose, C Nishida-Umehara, H Takechi, T Yamazaki, M Kosuge, MC Yoshida
    ZOO BIOLOGY 17 (2) 111 - 121 0733-3188 1998 [Refereed][Not invited]
  • R Masuda, K Murata, A Aiurzaniin, MC Yoshida
    HEREDITAS 128 (3) 277 - 280 0018-0661 1998 [Refereed][Not invited]
    The brown bear Ursus arctos is widely distributed in the Northern Hemisphere including Eurasia and North America, its breeding range being the largest among seven bear species in the world. Recent phylogeographic studies of mitochondrial DNA (mtDNA) sequences have revealed the evolutionary history of brown bear populations in Europe and North America (HANNI et al. 1994; RANDI et al. 1994; TABERLET and BOUVET 1994; TALBOT and SHIELDS 1996). In contrast, genetic characteristics of Asian brown bears are poorly known. Such information would be essential for a better understanding of the evolution of the brown bear. For instance, the evolutionary origin of the brown bear may either be in Asia or Europe or both, a question associated with some controversy (KURTEN 1976; MAZZA and RUSTIONI 1994). In addition, some Asian brown bear populations have experienced habitat fragmentation, environmental changes, and intense hunting by human, so there is a need for clarifying their genetics for conservation purposes. In this report, we present partial sequences of the mtDNA control region of some Asian brown bears. Based on these mtDNA data and a comparison with those of European brown bears, we discuss the phylogenetic status of the brown bears of Asia. Our results offer an important information on the genetics of Asian brown bears.
  • S Ohdachi, R Masuda, H Abe, NE Dokuchaev
    RESEARCHES ON POPULATION ECOLOGY 39 (2) 157 - 162 0034-5466 1997/12 [Refereed][Not invited]
    A hypothetical biogeographical history of northeastern Asiatic soricine shrews in the late Quaternary was developed by integrating their present distributions, fossil records, a hypothetical phylogeny, and geological investigations. First, a biological area cladogram of the northeastern Asiatic region was constructed by applying the vicariance hypothesis to the phylogeny of the caecutiens/shinto group, a monophyletic group proposed by Ohdachi et al. (1997). Comparing the biological area cladogram with a geological hypothesis by Ohshima(1990, 1991, 1992), we hypothesized a geographical history of northeastern Asia. Species were then located on the dendrogram of the geographical history, referring to the present distributions, fossil records, and phylogeny of shrews. According to our hypothesis, higher species diversity of the northern region of northeastern Asia (Hokkaido, Sakhalin, and Eastern Siberia) was achieved by several series of colonizations and habitat expansion. On the other hand, the shrew communities of the southern region (Honshu, Sado, Shikoku, and Kyushu) were created by extinction and isolation followed by speciation.
  • S Ohdachi, R Masuda, H Abe, J Adachi, NE Dokuchaev, Haukisalmi, V, MC Yoshida
    ZOOLOGICAL SCIENCE 14 (3) 527 - 532 0289-0003 1997/06 [Refereed][Not invited]
    Phylogenetic relationships among 31 operational taxonomic units of shrews (Soricidae, Mammalia), mainly from eastern Eurasia, were inferred from partial nucleotide sequences of the mitochondrial cytochrome b gene by maximum likelihood !ML! and neighbor joining (NJ) methods, Eleven monophyletic groups were recognized among the soricine shrews examined in the ML tree. However, branching orders of the groups were obscure judging from the local bootstrap values, and two out of the 11 groups were not monophyletic in the NJ tree. The phylogenetic relationships among Sorer caecutiens, S. shinto, and S. sadonis in the Japanese and Sakhalin islands, whose taxonomy was controversial, were clarified. S. shinto in the Honshu and Shikoku Islands is genetically differentiated enough to be considered a separate species from S. caecutiens, while S. sadonis could be treated as a subspecies of S. shinto. Some other taxonomic problems are also discussed.
  • K Murata, R Masuda
    JOURNAL OF VETERINARY MEDICAL SCIENCE 58 (12) 1157 - 1159 0916-7250 1996/12 [Refereed][Not invited]
    Polymerase chain reaction (PCR) amplification of a partial fragment of the sex determining region Y (SRY) gene was used for sexing a young Linne's two-toed sloth (Choloepus didactylus), a species in which gender determination from the external genitalia is difficult. DNA was extracted from hairs of a 5-month-old sloth as well as the dam and sire as external controls. A SRY fragment (216 bases) was PCR-amplified both from the offspring and the sire, but not amplified from the dam. The DNA sequence (166 bases without primers) of the sloth PCR product was determined and compared with SRY sequences of other mammals previously reported. High homology of their nucleotide (74.1-86.8%) and deduced amino acid (63.6-85.5%) sequences indicates that the PCR product of the sloth was amplified from a region of the SRY gene, and that SRY sequences are conserved throughout mammalian orders. From the result the sex of the young sloth was determined as a male. The PCR method using hairs for sexing the sloth provides an advantageous tool for captive propagation plan in toes. To the authors' knowledge, no report regarding SRY sequences in the order Xenarthra (Edentata) has been published.
  • R Masuda, JV Lopez, JP Slattery, N Yuhki, SJ OBrien
    MOLECULAR PHYLOGENETICS AND EVOLUTION 6 (3) 351 - 365 1055-7903 1996/12 [Refereed][Not invited]
    Molecular phylogeny of the cat family Felidae is derived using two mitochondrial genes, cytochrome b and 12S rRNA. Phylogenetic methods of weighted maximum parsimony and minimum evolution estimated by neighbor-joining are employed to reconstruct topologies among 20 extant felid species. Sequence analyses of 363 bp of cytochrome b and 376 bp of the 12S rRNA genes yielded average pair-wise similarity values between felids ranging from 94 to 99% and from 85 to 99%, respectively. Phylogenetic reconstruction supports more recent, intralineage associations but fails to completely resolve interlineage relationships. Both genes produce a monophyletic group of Felis species but vary in the placement of the pallas cat. The ocelot lineage represents an early divergence within the Felidae, with strong associations between ocelot and margay, Geoffroy's cat and kodkod, and pampas cat and tigrina. Implications of the relative recency of felid evolution, presence of ancestral polymorphisms, and influence of outgroups in placement of the topological root are discussed. (C) 1996 Academic Press, Inc.
  • T Oshida, R Masuda, MC Yoshida
    ZOOLOGICAL SCIENCE 13 (4) 615 - 620 0289-0003 1996/08 [Refereed][Not invited]
    In order to investigate phylogenetic relationships of the family Sciuridae living in Japan, we sequenced partial regions (379 bases) of mitochondrial 12S rRNA genes in six species of Japanese and other Asian squirrels. Phylogenetic trees constructed by sequence data indicated that two genera of flying squirrels (Petaurista and Pteromys) were clustered in a group distinct from non-flying squirrels, suggesting a possible monophyletic relationships of these flying squirrels. The evolutionary distance between the Japanese squirrel (Sciurus lis) from Honshu island and the Eurasian red squirrel (Sciurus vulgaris) from Hokkaido island was comparable to intraspecific distances of the remaining species examined.
    ZOOLOGICAL SCIENCE 12 (5) 655 - 659 0289-0003 1995/10 [Refereed][Not invited]
    We previously revealed, based on mitochondrial DNA sequence analysis, that the Iriomote cat is very closely related to the leopard cat Felis bengalensis, which is widespread in Asia [24]. In this study, in order to understand the phylogenetic status of the Tsushima cat which is the other wildcat in Japan, partial sequences (402 bases) of the mitochondrial cytochrome b region were determined and compared with those of the Iriomote cat and other feline species. The phylogenetic tree of the cytochrome b sequences indicated that the Tsushima cat and the Iriomote cat have the same mitochondrial DNA lineage as the leopard cat. One or two transitional substitutions were observed among the two Japanese wildcats and the leopard cat. The divergence time (approximately 100,000 years ago) of the Tsushima cat and the leopard cat, estimated by sequence data, was in concordance with the formation date of the Tsushima Island. These results suggest that genetic drift after geographic isolation has brought fixation of some genetic and morphological characters to the Tsushima cat and the Iriomote cat, while these two Japanese wildcats are still genetically close to the continental leopard cat. Considering morphological differences and molecular phylogeny, it is reasonable for the two Japanese wildcats to be classified as two subspecies of F. bengalensis.
  • Nagata, J, Masuda, R, Yoshida, M
    Journal of the Mammalogical Society of Japan 20 (1) 1 - 8 0914-1855 1995 [Refereed][Not invited]
    JOURNAL OF MOLECULAR EVOLUTION 39 (5) 544 - 544 0022-2844 1994/11 [Refereed][Not invited]
    ZOOLOGICAL SCIENCE 11 (4) 605 - 612 0289-0003 1994/08 [Refereed][Not invited]
    To study the phylogenetic relationships between the species of the family Mustelidae, by using the improved polymerase chain reaction-product direct sequencing technique, nucleotide sequences (375 bases) of the mitochondrial cytochrome b gene were determined on ten species from five genera of the Mustelidae and three species of other carnivore families, all of which are distributed in or around Japan. The molecular phylogenetic tree indicated a clear separation of five genera: Mustela and Martes from the subfamily Mustelinae, Lutra and Enhydra from the subfamily Lutrinae, and Meles from the subfamily Melinae. This clustering agreed with the previously reported morphological and karyological taxonomy. Furthermore, the relationships between the intrageneric species were discussed in more detail. This is the first report on the molecular phylogeny throughout the Japanese species of the Mustelidae, inferred from the mitochondrial DNA sequences.
    ZOOLOGICAL SCIENCE 11 (4) 597 - 604 0289-0003 1994/08 [Refereed][Not invited]
    To investigate the molecular phylogenetic status of the Iriomote cat Felis iriomotensis, partial sequences of the mitochondrial 12S rRNA gene (373 bases) and the cytochrome b gene (402 bases) were determined by using the polymerase chain reaction-product direct sequencing technique and then compared with those of seven other feline species. Six Iriomote cats examined in this study showed no intraspecific variation for both genes. The sequence comparisons and the molecular phylogenetic trees indicated that the Iriomote cat is very closely related to the leopard cat Felis bengalensis, which is a widespread species throughout southern and eastern Asia, and that it is reasonable for these two felines to be classified to the same genus. Based on sequence data, the Iriomote cat was estimated to have diverged from the leopard cat arround or less than 0.2 million years ago, and this concurs with the previously reported geological isolation date of the Ryukyu Arc from the Chinese continent. Our results suggest that the geographic barrier has led the fixation of some unique morphological characters into the Iriomote cat population while both the Iriomote cat and the leopard cat still retain very close genetic characters.
    JOURNAL OF MOLECULAR EVOLUTION 39 (2) 174 - 190 0022-2844 1994/08 [Refereed][Not invited]
    The mitochondrial DNA of plant and animal cells is a transcriptionally active genome that traces its origins to a symbiotic infection of eucaryotic cells by bacterial progenitors. As prescribed by the Serial Endosymbiosis Theory, symbiotic organelles have gradually transferred their genes to the eucaryotic genome, producing a functional interaction of nuclear and mitochondrial chondrial genes in organelle function. We report there a recent remarkable transposition of 7.9 kb of a typically 17.0-kb mitochondrial genome to a specific nuclear chromosomal position in the domestic cat. The integrated segment has subsequently become amplified 38-76 times and now occurs as a tandem repeat macrosatellite with multiple-length alleles resolved by pulse-field gel electrophoresis (PFGE) segregating in cat populations. Sequence determination of the nuclear mitochondrial DNA segment, Numt, revealed a d(CA)-rich 8-bp motif [ACACACGT] repeated imperfectly five times at the deletion junction that is a likely target for recombination. The extent and pattern of sequence divergence of Numt genes from the cytoplasmic mtDNA homologues plus the occurrence of Numt in other species of the family Felidae allowed an estimate for the origins of Numt at 1.8-2.0 million years ago in an ancestor of four modern species in the genus Felis. Numt genes do not function in cats; rather, the locus combines properties of nuclear minisatellites and pseudogenes. These observations provide an empirical glimpse of historic genomic events that may parallel the accommodation of organelles in eucaryotes.
    GENOMICS 11 (4) 1007 - 1013 0888-7543 1991/12 [Refereed][Not invited]
    MUTATION RESEARCH 244 (4) 309 - 316 0921-8262 1990/08 [Refereed][Not invited]
    JAPANESE JOURNAL OF CANCER RESEARCH 80 (11) 1024 - 1027 0910-5050 1989/11 [Refereed][Not invited]
    JAPANESE JOURNAL OF CANCER RESEARCH 79 (7) 821 - 827 0910-5050 1988/07 [Refereed][Not invited]
    JAPANESE JOURNAL OF CANCER RESEARCH 79 (7) 828 - 835 0910-5050 1988/07 [Refereed][Not invited]
    LABORATORY ANIMALS 22 (2) 166 - 169 0023-6772 1988/04 [Refereed][Not invited]
    JAPANESE JOURNAL OF CANCER RESEARCH 79 (2) 250 - 254 0910-5050 1988/02 [Refereed][Not invited]
    JAPANESE JOURNAL OF CANCER RESEARCH 79 (1) 5 - 8 0910-5050 1988/01 [Refereed][Not invited]
    INTERNATIONAL JOURNAL OF BIOCHEMISTRY 20 (10) 1171 - & 0020-711X 1988 [Refereed][Not invited]
    JOURNAL OF HEREDITY 78 (6) 361 - 365 0022-1503 1987/11 [Refereed][Not invited]
    JAPANESE JOURNAL OF CANCER RESEARCH 77 (11) 1055 - 1058 0910-5050 1986/11 [Refereed][Not invited]

Books etc

  • ヒグマ学への招待 〜 自然と文化で考える
    増田隆一 (Editor)
    北海道大学出版会 2020/03 (ISBN: 9784832974159)
  • ユーラシア動物紀行
    増田 隆一 (Single work)
    岩波新書 2019/01 (ISBN: 9784004317579)
  • 日本の食肉類 〜 生態系の頂点に立つ哺乳類
    増田 隆一 (Editor)
    東京大学出版会 2018/08 (ISBN: 9784130602372)
  • 動物学の百科事典(分担執筆)
    丸善 2018 (ISBN: 9784621303092)
  • Biodiversity Conservation Using Umbrella Species: Blakiston's Fish Owl and the Red-crowned Crane (Ecological Research Monographs)(分担執筆)
    Springer-Verlag 2018 (ISBN: 9811072027)
  • 増田 隆一 (Single work)
    東京大学出版会 2017/06 (ISBN: 9784130602525)
  • 高畑 雅一, 増田 隆一, 北田 一博 (Joint work)
    医学書院 2013/02 (ISBN: 9784260031882)
  • The Wild Mammals of Japan(分担執筆)
    Shoukadoh 2009 (ISBN: 4879746266)
  • (Contributor)
    北海道大学出版会 2008 (ISBN: 4832981838) 272
  • (Contributor)
    同成社 2007 (ISBN: 9784886213907)
  • 天野 哲也, 増田 隆一, 間野 勉 (Joint editor)
    北海道大学出版会 2006/10 (ISBN: 4832973916)
  • 増田 隆一, 阿部 永, 阿部 永, 増田 隆一 (Joint editor)
    北海道大学出版会 2005/05 (ISBN: 4832981013) 288
  • 保全遺伝学(分担執筆)
    東京大学出版会 2003 (ISBN: 9784130602136)
  • 琉球弧の成立と生物の渡来(分担執筆)
    沖縄タイムス社 2002 (ISBN: 487127151X)
  • 希少猛禽類保護の現状と新しい調査法(分担執筆)
    技術情報協会 2001 (ISBN: 4906317375)
  • 地球・人間・環境シリーズ 環境保全・創出のための生態工学(分担執筆)
    丸善 1999 (ISBN: 462104639X)
  • 動物の自然史(分担執筆)
    北海道大学図書刊行会 1995 (ISBN: 9784832996014)
  • The LEC Rat (分担執筆)
    Springer-Verlag 1991 (ISBN: 9784431681557)

Conference Activities & Talks

  • 哺乳類食肉目の種多様性と生物地理的歴史  [Invited]
    増田 隆一
    第65回日本生態学会・シンポジウム「系統地理学と地質学からせまる日本列島の生物多様性形成史」  2018/03
  • Molecular phylogeography of mustelid species endemic to the Japanese islands and closely related species  [Invited]
    MASUDA Ryuichi
    Symposium “Diversity among Mustelidae: evolution, genetics, socio-ecology inform conservation in Asia and Far East”: 12th International Mammalogical Congress (IMC12)  2017/07
  • ヒグマの遺伝的多様性と移動の歴史  [Invited]
    増田 隆一
    北海道自然保護協会講演会  2017/05
  • ヒグマの多様性と北海道への渡来の歴史  [Invited]
    増田 隆一
    第23回氷海の民シンポジウム(第32回北方圏国際シンポジウム市民公開講座)(道民カレッジ連携講座)  2017/02
  • 動物の進化をひもとく〜都会に暮らす動物たちの遺伝的多様性〜  [Invited]
    増田 隆一
    井の頭自然文化園開園記念日講演会  2016/05
  • Collaborations of biogeographic studies between Japan and Finland  [Invited]
    MASUDA Ryuichi
    The Annual ACF (Alumni Club of Finland) General Assembly and the All Alumni Meeting “Academic Links between Finland and Japan”  2015/10
  • Founder effects on the Japanese populations of the masked palm civet Paguma larvata, revealed by molecular phylogeny and population genetics  [Invited]
    MASUDA Ryuichi
    Symposium “Genetics on Isolated Populations”, 5th International Wildlife Management Congress 2015  2015/07
  • Historical changes of genetic diversity in the Blakiston's fish owl and red crowned crane populations on Hokkaido  [Invited]
    MASUDA Ryuichi
    Symposium “Biodiversity conservation using Blakiston's fish owl and red crowned crane as umbrella species”, 5th International Wildlife Management Congress 2015  2015/07
  • DNAからみたヒグマの系譜:世界へ発信 考古学と分子系統学のコラボレーション  [Invited]
    増田 隆一
    北海道立埋蔵文化財センター・夏期講演会  2015/06
  • シマフクロウとタンチョウにおける遺伝的多様性の歴史と将来  [Invited]
    増田 隆一
    市民向けシンポジウム「シマフクロウ・タンチョウを指標とした生物多様性保全 北海道の過去・現在・未来」  2015/02


  • 哺乳類を主な対象とした分子系統進化学および生物地理学


  • Ryuichi Masuda  Mammalian Science  60-  (2)  377  -384  2020/08  [Not refereed][Invited]
  • 増田隆一  野鳥  83-  (7)  6‐9  2018/08  [Not refereed][Invited]
  • 遺伝子が解き明かす北海道の生物地理
    増田隆一  ビオヒストリー  30-  12  -15  2018  [Not refereed][Invited]
  • ハクビシンの起源をたどる
    増田隆一  東京大学出版会 UP  (539)  25  -30  2017/09  [Not refereed][Invited]
  • ヒグマの遺伝的多様性と移動の歴史
    増田隆一  北海道自然保護協会誌 NC Hokkaido  (173)  12  -13  2017/08  [Not refereed][Invited]
  • 斎藤昌幸, 斎藤昌幸, 金子弥生, 増田隆一, 園田陽一, 保坂哲朗  哺乳類科学  57-  (1)  157‐158(J‐STAGE)  2017  [Not refereed][Not invited]
  • Kaneko, Y, Masuda, R, Abramov, A. V  The IUCN Red List of Threatened Species 2016-2  --  (-)  2016  [Refereed][Not invited]
  • ミトコンドリアDNAからみた縄文犬
    増田隆一  東名遺跡群IV – 東名遺跡群総括報告 第1分冊【堆積層・遺構編】(佐賀市教育委員会)  167  -168  2016  [Not refereed][Invited]
  • 夏期講演会DNAからみたヒグマの系譜—世界に発信!考古学と分子系統学のコラボレーション
    増田隆一  北海道立埋蔵文化財センター年報  17-  38  -45  2016  [Not refereed][Invited]
  • 動物の進化をひもとく 〜 都会でくらす動物たちの遺伝的多様性
    増田隆一  どうぶつと動物園  Autumn-  32-33  -(Vol.68: 194-195)  2016  [Not refereed][Invited]
  • Abramov, A. V, Kaneko, Y, Masuda, R  The IUCN Red List of Threatened Species 2016-2  --  (-)  2015  [Not refereed][Not invited]
  • DNAから見たヒグマの進化と歴史
    増田隆一  モーリー (Hokkaido Nature Magazine MALLY)  35-  8  -11  2014  [Not refereed][Invited]
  • 遺伝的特徴から見たオホーツク人——大陸と北海道の間の交流
    増田隆一  北海道大学総合博物館研究報告  6-  103  -108  2013  [Not refereed][Not invited]
  • アイヌ民族とオホーツク文化人集団
    石田肇, 増田隆一  季刊考古学  118-  85  -87  2012  [Not refereed][Not invited]
  • 遺伝子の流れから見たオホーツク文化人と北海道への影響
    増田隆一  新しいアイヌ史の構築 プロジェクト報告書2012:新しいアイヌ史の構築 先史編 古代編 中世編(北海道大学アイヌ・先住民研究センター)  32  -36  2012  [Not refereed][Invited]
  • トコロチャシ跡遺跡オホーツク地点出土ヒグマ骨のミトコンドリアDNA分析
    増田隆一, 坂絵利  トコロチャシ跡遺跡 オホーツク地点,東京大学大学院人文社会系研究科考古学研究室・常呂実習施設編  360  -366  2012  [Not refereed][Invited]
  • 日本のハクビシンは台湾からやってきた〜遺伝子から探る起源と多様性
    増田隆一  どうぶつと動物園  63-  26  -29  2011  [Not refereed][Invited]
  • 増田隆一  哺乳類科学  51-  205  2011  [Not refereed][Not invited]
  • 阿部豪, 平川浩文, 増田隆一, 佐鹿万里子, 中井真理子, 島田健一郎  哺乳類科学  51-  (2)  321-325 (J-STAGE)  2011  [Refereed][Not invited]
  • 増田隆一  哺乳類科学  51-  (1)  188-191 (J-STAGE)  2011  [Not refereed][Not invited]
  • 分子系統地理から見た日本と台湾の食肉類(日本台湾共同国際シンポジウム記録)
    増田隆一  哺乳類科学  50-  217  -219  2010  [Not refereed][Invited]
  • Asiatic wild cat (Felis silvestris ornata) is no more a ‘Least Concern’ species in Xinjiang, China
    Abdukadir, A, Khan B, Masuda, R, Ohdachi, S  Pakistan Journal of Wildlife  1-  57  -63  2010  [Refereed][Not invited]
  • 増田隆一, 福江佑子, 谷地森秀二, 浦口宏二  哺乳類科学  49-  137  -141  2009/06  [Not refereed][Not invited]
  • ハクビシンはどこから来たか〜ハクビシンの遺伝的変異
    増田隆一  どうぶつと動物園  61-  22  -25  2009  [Not refereed][Invited]
  • 増田隆一  哺乳類科学  49-  157  2009  [Not refereed][Not invited]
  • 増田隆一, 嶋谷ゆかり, 大石琢也, 合田直樹, 田島沙羅, 佐藤丈寛  哺乳類科学  49-  (2)  283-302 (J-STAGE)  2009  [Not refereed][Not invited]
  • Bird and mammal specimens in the Swedish Museum of Natural History originating from Hokkaido University: Bergman’s collection and a specimen gifted from Professor Saburo Hatta
    Masuda, R, Sato, T, Grönwall, O, Kato, M  Bulletin of Botanic Garden Hokkaido University  8-  1  -8  2008  [Refereed][Not invited]
  • エゾヒグマの自然史とヒトの文化の変遷
    増田隆一  Bears Japan (日本クマネットワークニュースレター)  7-  93  -95  2007  [Not refereed][Invited]
  • ヒグマとエゾシカ
    増田隆一  沙流川歴史館年報  7-  19  -35  2006  [Not refereed][Invited]
  • Molecular Phylogeny and Genetics: The Status of Brown Bears in Japan, Biology
    Masuda, R  Understanding Asian Bears to Secure Their Future (compiled by Japan Bear Network)  114  2006  [Not refereed][Invited]
  • クマのDNAが語るオホーツク人の交流
    増田隆一  日本文化財科学会会報  49-  16  -21  2005  [Not refereed][Invited]
  • 古代DNA分析から見る北方文化の起源と変遷
    増田隆一  歴史読本  (12)  233  -235  2004  [Not refereed][Invited]
  • Molecular phylogeny of whiskered bats (Myotis, Vespretilionidae, Chiroptera) in Palaearctic region
    Tsytsulina, K, Masuda, R  Proceedings of International Symposium on “Dawn of a New Natural History – Integration of Geoscience and Biodiversity Studies"  85  -89  2004  [Not refereed][Not invited]
  • マハムト・ハリク, 増田隆一, アブリミト・アブダカディル, 大泰司紀之  哺乳類科学  43-  1  -17  2003  [Not refereed][Not invited]
  • 青苗砂丘遺跡から発掘されたヒグマ遺存体のDNA分析
    増田隆一  奥尻町青苗砂丘遺跡2(北海道立埋蔵文化財センター)  74  -77  2003  [Not refereed][Invited]
  • 遺伝子から探るヒグマの渡来史と古代文化との関係
    増田隆一  東北学  (7)  170  -182  2002  [Not refereed][Invited]
  • Ancient DNA analysis of brown bear remains from the Kafukai site on Rebun Island, Hokkaido: On the origin of "bear-sending ceremony" from the Okhotsk Culture
    Masuda, R, Amano, T, Ono, H  Report of the 5th Open Symposium of the Hokkaido University Museum: Okhotsk Culture -- Formation, Metamorphosis and Ending  154  -159  2002  [Not refereed][Not invited]
  • 動物学と古代DNA分析 – マンモスとヒグマ考古遺物の遺伝子解析 --
    増田隆一  歴博  115-  9  -13  2002  [Not refereed][Invited]
  • 古代DNA分析による礼文島香深井A遺跡出土ヒグマ遺存体の起源-- オホーツク文化における飼育型クマ送り儀礼の成立と異文化交流 --
    増田隆一, 天野哲也, 小野裕子  動物考古学  19-  1  -14  2002  [Not refereed][Not invited]
  • 増田隆一  生物の科学 遺伝  56-  47  -52  2002  [Not refereed][Invited]
  • 環オホーツク海地域におけるヒグマの遺伝的多様性、古環境の変遷およびクマ送り文化の考察
    増田隆一, 天野哲也  日本人と日本文化・その起源をさぐる  (15)  8  2001  [Not refereed][Invited]
  • 遥かなる新彊シルクロードと動物調査談
    増田隆一  Arctic Circle (北海道立北方民族博物館友の会・季刊誌)  38-  12  -14  2001  [Not refereed][Invited]
  • エゾヒグマの渡来史を探る:遺伝子からのアプローチ
    増田隆一  Bears Japan (日本クマネットワークニュースレター)  2-  55  -56  2001  [Not refereed][Invited]
  • Molecular phylogeographic patterns and migration history of brown bear (Ursus arctos) populations around Okhotsk Sea
    Masuda, R  Proceeding of the 16th International Symposium on Okhotsk Sea & Sea Ice  255  -261  2001  [Not refereed][Not invited]
  • 増田隆一  月刊海洋  32-  (4)  214  -218  2000/04  [Not refereed][Invited]
  • Genetic diversity and biogeographic history of the Japanese population of the brown bear (Ursus arctos)
    Masuda, R  Report of IIAS International Symposium on Biodiversity (International Institute for Advanced Studies)  33  -41  2000  [Not refereed][Invited]
  • 増田隆一  哺乳類科学  39-  351  -358  1999  [Not refereed][Not invited]
  • 増田隆一, ABDUKADIR A, HALIK M, 大舘智志, 高橋学察  哺乳類科学  39-  307  -321  1999  [Not refereed][Not invited]
  • ツシマヤマネコの過去・現在・未来
    増田隆一  とらやまの森(環境省対馬野生生物保護センター発行誌)  (4)  4  -5  1999  [Not refereed][Invited]
  • DNAから探るヒグマの渡来ルート
    増田隆一  北海道の自然  37-  17  -20  1999  [Not refereed][Invited]
  • 増田隆一  哺乳類科学  39-  323  -328  1999  [Not refereed][Not invited]
  • イエネコ・ヤマネコの過去・未来
    増田隆一  Biohistory 生命誌  21-  12  -13  1998  [Not refereed][Invited]
  • Molecular genetic study on diversity and evolution of mammals in Asia
    Masuda, R  Environmental Conservation and Land Use Management of Wetland Ecosystem in Southeast Asia: Annual Report and Proceedings for International Workshop, Core University Program between Hokkaido University, Japan and R & D Center of Biology, LIPI  64  -66  1998  [Not refereed][Not invited]
  • 増田隆一, 茂原信生  哺乳類科学  37-  87  -93  1997/10  [Not refereed][Not invited]
  • 動物園でのDNA利用--できること、できないこと--
    増田隆一, 村田浩一  どうぶつと動物園  49-  182  -187  1997  [Not refereed][Invited]
  • 増田隆一  生物の科学 遺伝  50-  (3)  11  -12  1996/03  [Not refereed][Invited]
  • 増田隆一  化学  51-  (2)  74  -76  1996/02  [Not refereed][Invited]
  • 遺伝子からみたネコ類の近縁関係
    増田隆一  どうぶつと動物園  48-  112  -115  1996  [Not refereed][Invited]
  • ラッコ新生仔の胎盤および臍帯DNAからのSRY遺伝子検出による性判別
    村田浩一, 滝導博, 増田隆一  動物園水族館雑誌  38-  48  -51  1996  [Refereed][Not invited]
  • 遺伝子から見た動物の進化 --イタチ科の分子系統--
    増田隆一  山と博物館  40-  (11)  2  -3  1995  [Not refereed][Invited]
  • 肝炎ラットLECの遺伝子の探索
    吉田廸弘, 小野教夫, 増田隆一  アニテックス  6-  128  -130  1994  [Not refereed][Invited]
  • 米国留学記
    増田隆一  北海道分子生物学研究会会報  25-  4  -6  1992  [Not refereed][Invited]
  • 米国NCI留学記
    増田隆一  SHINKA  2-  (2)  37  -38  1992  [Not refereed][Invited]
  • 増田隆一  Biomedica  6-  (7)  734  -738  1991/06  [Not refereed][Invited]
  • 幸田弘信, 上出利光, 伝法公磨, 森道夫, 菊地浩吉, 増田隆一, 吉田廸弘, 関谷千尋  医学のあゆみ  144-  (6)  569  -570  1988/02  [Refereed][Not invited]
  • 伝法公麿, 小山田正人, 藤本佳範, 高橋秀俊, 佐藤睦, 服部淳夫, 森道夫, 増田隆一, 吉田廸弘  Journal of Toxicologic Pathology  1-  53  -60  1988  [Refereed][Not invited]
  • Yoshinori Fujimoto, Ryuichi Masuda, Masahito Oyamada, Atsuo Hattori, Hidetoshi Takahashi, Masaaki Satoh, Kimimaro Dempo, Michio Mori  Acta Hepatologica Japonica  29-  (7)  967  -968  1988  [Refereed][Not invited]

Awards & Honors

  • 2019 日本哺乳類学会賞
    受賞者: 増田 隆一「分子系統進化学に基づく哺乳類の生物地理学への寄与」
  • 2019 日本動物学会賞
    受賞者: 増田 隆一「北ユーラシアにおける大型哺乳類・鳥類の遺伝的多様性と動物地理学的歴史の解明」
  • 2002 日本動物学会論文賞(Zoological Science Award)
    Masuda, R., Amano, T., and Ono, H. (2001) Ancient DNA analysis of brown bear (Ursus arctos) remains from the archeological site of Rebun Island, Hokkaido, Japan. Zoological Science 18: 741-751.

Research Grants & Projects

  • 遺伝学と形態学的アプローチによる北ユーラシアにおける食肉類の多様性と進化の解明
    Date (from‐to) : 2019/04 -2021/03 
    Author : 増田 隆一
  • ブルガリアの生物地理とトラキア文化の起源に関する分子系統・動物考古学的研究
    Date (from‐to) : 2017/04 -2019/03 
    Author : 増田 隆一
  • ユーラシア中央部・南部でのヒグマ多様性変遷の探求と北海道ヒグマ三系統の起源解明
    Date (from‐to) : 2015/04 -2019/03 
    Author : 増田 隆一
  • 北方ユーラシアにおける食肉類の遺伝的多様性および形態的多様性の比較研究
    Date (from‐to) : 2016/04 -2018/03 
    Author : 増田 隆一
  • ウラル地方と北海道での古代から現代へのヒグマの系統地理、形態、文化変遷の比較研究
    Date (from‐to) : 2014/04 -2016/03 
    Author : 増田 隆一
  • 絶滅危惧種シマフクロウの遺伝的多様性評価と遺伝子資源保存の基盤形成
    Date (from‐to) : 2011/04 -2015/03 
    Author : 増田 隆一
  • 北海道および北方域の希少種・固有集団の進化起源と多様性に関する保全遺伝学的研究
    Date (from‐to) : 2015 
    Author : 増田 隆一
  • ツシマヤマネコをモデルとした糞からの生物多様性情報の抽出と種保全への展開
    Date (from‐to) : 2011/04 -2013/03 
    Author : 増田 隆一
  • 氷河期から現代にいたるシベリア・日本哺乳類相の系統地理と移動史の比較研究
    Date (from‐to) : 2007/04 -2009/03 
    Author : 増田 隆一
  • 更新世の動物遺存体の古代ゲノム解析法の開発と系統地理学研究の新しい展開
    Date (from‐to) : 2007/04 -2009/03 
    Author : 増田 隆一
  • 古代DNA分析を導入したシベリア・マンモス動物群から現代動物相の多様性変遷の解明
    日本学術振興会:科研費・基盤研究(B) (海外学術調査)
    Date (from‐to) : 2005/04 -2009/03 
    Author : 増田 隆一
  • 古代DNA分析を導入したエゾシカ集団の系統地理の変遷と多様性成立機構の解明
    日本学術振興会:科研費・基盤研究(B) (一般)
    Date (from‐to) : 2003/04 -2007/03 
    Author : 増田 隆一
  • 中央アジアおよびザバイカルにおけるヒグマ集団の分子系統地理と進化起源の探索
    日本学術振興会:科研費・基盤研究(B) (海外学術調査)
    Date (from‐to) : 2002/04 -2005/03 
    Author : 増田 隆一
  • 北海道・環オホーツク海地域におけるヒグマ集団の遺伝的多様性の起源と成立機構の解明
    Date (from‐to) : 2001/04 -2003/03 
    Author : 増田 隆一

Educational Activities

Teaching Experience

  • Inter-Graduate School Classes(General Subject):Natural and Applied Sciences
    開講年度 : 2018
    課程区分 : 修士課程
    開講学部 : 大学院共通科目
    キーワード : 地球生命史, 生物進化, 地球環境変化, 気候変動, 生物大量絶滅, 生物多様性, 古生物科学, 地質年代
  • Inter-Graduate School Classes(Educational Program):Museology
    開講年度 : 2018
    課程区分 : 修士課程
    開講学部 : 大学院共通科目
    キーワード : 学術標本・資料、博物館、学芸員、アドバンストコース
  • Biodiversity
    開講年度 : 2018
    課程区分 : 修士課程
    開講学部 : 理学院
    キーワード : 生物多様性,進化,絶滅,種分化,動物,植物,統計モデリング
  • Methods in Biodiversity Studies
    開講年度 : 2018
    課程区分 : 修士課程
    開講学部 : 理学院
    キーワード : 生物多様性,分類,系統,古生物,進化発生学,動物,植物,海藻,原生生物,系統地理学
  • Advanced Biodiversity Study I
    開講年度 : 2018
    課程区分 : 修士課程
    開講学部 : 理学院
    キーワード : 分子系統、動物地理、進化、集団遺伝
  • Laboratory Course in Systematic Zoology
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 理学部
    キーワード : 分類学 系統学
  • Biodiversity Studies I
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 理学部
    キーワード : 分類学、系統学、生態学、種分化学、原核生物、菌類
  • Biodiversity Studies II
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 理学部
    キーワード : 藻類,陸上植物,無脊椎動物,脊椎動物,分類,系統,進化
  • Environment and People
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 全学教育
    キーワード : ヒグマ,自然環境,生態系,文化,クマ送り,地域社会,共存
  • Biology II
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 全学教育
    キーワード : 生物の多様性,系統,進化,生物の形態,生命活動の多様性
  • Systematics and Evolution
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 理学部
    キーワード : 哺乳類 形態進化 分子進化 生物地理学 鳥類 島 生態 固有種

Campus Position History

  • 2013年4月1日 
  • 2015年4月1日 
  • 2017年4月1日 

Position History

  • 2013年4月1日 
  • 2015年4月1日 
  • 2017年4月1日 

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