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Kim HJ, Han B, Lee HI, Ju JW, Shin HI. Current Status of Trypanosoma grosi and Babesia microti in Small Mammals in the Republic of Korea. Animals (Basel) 2024; 14:989. [PMID: 38612228 PMCID: PMC11010837 DOI: 10.3390/ani14070989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/13/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Small mammals, such as rodents and shrews, are natural reservoir hosts of zoonotic diseases, including parasitic protozoa. To assess the risk of rodent-borne parasitic protozoa in the Republic of Korea (ROK), this study investigated the status of parasitic protozoa, namely Trypanosoma, Babesia, and Theileria, in small mammals. In total, 331 blood samples from small mammals were analyzed for parasites using PCR and sequenced. Samples were positive for Trypanosoma grosi (23.9%; n = 79) and Babesia microti (10%; n = 33) but not Theileria. Small mammals from Seogwipo-si showed the highest infection rate of T. grosi (48.4%), while the highest B. microti infection rate was observed in those from Gangneung-si (25.6%). Sequence data revealed T. grosi to be of the AKHA strain. Phylogenetic analysis of B. microti revealed the US and Kobe genotypes. B. microti US-type-infected small mammals were detected throughout the country, but the Kobe type was only detected in Seogwipo-si. To our knowledge, this is the first nationwide survey that confirmed T. grosi and B. microti infections at the species level in small mammals in the ROK and identified the Kobe type of B. microti. These results provide valuable information for further molecular epidemiological studies on these parasites.
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Affiliation(s)
| | | | | | | | - Hyun-Il Shin
- Division of Vectors and Parasitic Diseases, Korea Disease Control and Prevention Agency, 187 Osongsaenmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju 28159, Republic of Korea; (H.J.K.); (B.H.); (H.-I.L.); (J.-W.J.)
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2
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Kim YR, Kim HR, Kim JY, Myeong HH, Kang JH, Kim BJ, Lee HJ. Spatio-temporal genetic structure of the striped field mouse (Apodemus agrarius) populations inhabiting national parks in South Korea: Implications for conservation and management of protected areas. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1038058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Population or habitat connectivity is a key component in maintaining species and community-level regional biodiversity as well as intraspecific genetic diversity. Ongoing human activities cause habitat destruction and fragmentation, which exacerbate the connectivity due to restricted animal movements across local habitats, eventually resulting in the loss of biodiversity. The Baekdudaegan Mountain Range (BMR) on the Korean Peninsula represents “biodiversity hotspots” and eight of the 22 Korean national parks are located within the BMR. Given the striped field mouse (Apodemus agrarius) is the most common and ecologically important small mammals in these protected areas, the population genetic assessment of this species will allow for identifying “genetic diversity hotspots” and also “genetic barriers” that may hinder gene flow, and will therefore inform on effective conservation and management efforts for the national park habitats. We collected samples from hair, tail, or buccal swabs for 252 A. agrarius individuals in 2015 and 2019. By using mitochondrial DNA cytochrome b (cyt b) sequences and nine microsatellite loci, we determined levels of genetic diversity, genetic differentiation, and gene flow among eight national park populations of A. agrarius along the BMR. We found high levels of genetic diversity but the occurrences of inbreeding for all the nine samples analyzed. Our results also indicated that there was detectable temporal genetic variation between the 2015 and 2019 populations in the Jirisan National Park, which is probably due to a short-term decline in genetic diversity caused by reduced population sizes. We also found a well-admixed shared gene pool among the national park populations. However, a significant positive correlation between geographic and genetic distances was detected only in mtDNA but not microsatellites, which might be attributed to different dispersal patterns between sexes. There was a genetic barrier to animal movements around the Woraksan National Park areas. The poor habitat connectivity surrounding these areas can be improved by establishing an ecological corridor. Our findings of the presence of genetic barriers in some protected areas provide insights into the conservation and management efforts to improve the population or habitat connectivity among the national parks.
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Yalkovskaya L, Sibiryakov P, Borodin A. Phylogeography of the striped field mouse (Apodemus agrarius Pallas, 1771) in light of new data from central part of Northern Eurasia. PLoS One 2022; 17:e0276466. [PMID: 36264913 PMCID: PMC9584417 DOI: 10.1371/journal.pone.0276466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022] Open
Abstract
A phylogeographic analysis of A. agrarius based on the complete mtDNA cytochrome b and control region sequences has been performed using data obtained for the first time for the species from large regions of the central part of Northern Eurasia (23 localities of Altai, Western Siberia, and the Urals). The obtained results have demonstrated a complex intraspecific differentiation of A. agrarius, which has manifested not only in the isolation of the isles populations in Southeast Asia (Jeju and Taiwan), but also in the genetic heterogeneity of mainland populations, which has reflected the history of the modern intraspecific genetic diversity formation against the background of changing physiographic conditions of Eurasia in the Quaternary. The divergence of genetic lineages has taken place apparently simultaneously (in mid-Pleistocene) on the territory of the Eastern part of the modern disjunctive range, where all the identified lineages are present today. The demographic history and possible evolutionary scenarios for A. agrarius in the Western part of the range have been considered. TMRC reconstructions have shown that the lifetime of the common ancestor of the lineage that expanded in the Western Palearctic is about 17.7 [95% HPD 13.2–22.5] kyr. This suggests that the transcontinental expansion of A. agrarius is a relatively recent event that has occurred after the LGM.
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Affiliation(s)
- Lidia Yalkovskaya
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
- * E-mail:
| | - Petr Sibiryakov
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Aleksandr Borodin
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
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Inoue Y, Suzuki Y, Hanazaki K, Suzuki H. Quaternary Environmental Changes Shaped Mitochondrial DNA Diversity in the Large Japanese Wood Mouse Apodemus speciosus in Hokkaido, Japan. MAMMAL STUDY 2022. [DOI: 10.3106/ms2021-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Yuta Inoue
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yutaro Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kaori Hanazaki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
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Li K, Sommer S, Yang Z, Guo Y, Yue Y, Ozgul A, Wang D. Distinct body-size responses to warming climate in three rodent species. Proc Biol Sci 2022; 289:20220015. [PMID: 35414239 PMCID: PMC9006008 DOI: 10.1098/rspb.2022.0015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In mammals, body-size responses to warming climates are diverse, and the mechanisms underlying these different responses have been little investigated. Using temporal and spatial datasets of three rodent species distributed across different climatic zones in China, we investigated temporal and spatial trends of body size (length and mass), identified the critical drivers of these trends, and inferred the potential causes underlying the distinct body-size responses to the critical drivers. We found that body mass of all species remained stable over time and across space. Body length, however, increased in one species over time and in two species across space. Generally, body-length variation was predicted best by minimum ambient temperature. Moreover, in two species, body length changed linearly with temperature differences between ancestral and colonization areas. These distinct temperature-length patterns may jointly be caused by species-specific temperature sensitivities and experienced magnitudes of warming. We hypothesize that species or populations distributed across distinct temperature gradients evolved different intrinsic temperature sensitivities, which affect how their body sizes respond to warming climates. Our results suggest that size trends associated with climate change should be explored at higher temporal and spatial resolutions, and include clades of species with similar distributions.
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Affiliation(s)
- Ke Li
- College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, People's Republic of China.,College of Grassland Science and Technology, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, People's Republic of China
| | - Stefan Sommer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Zaixue Yang
- Yuqing Plant Protection and Quarantine Station, Yuqing County, Guizhou 564400, People's Republic of China
| | - Yongwang Guo
- National Agro-tech Extension and Service Center, 20 Maizidian Avenue, Chaoyang District, Beijing 100026, People's Republic of China
| | - Yaxian Yue
- College of Grassland Science and Technology, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, People's Republic of China
| | - Arpat Ozgul
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Deng Wang
- College of Grassland Science and Technology, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, People's Republic of China
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Lee C, Fong JJ, Jiang JP, Li PP, Waldman B, Chong JR, Lee H, Min MS. Phylogeographic study of the Bufo gargarizans species complex, with emphasis on Northeast Asia. Anim Cells Syst (Seoul) 2021; 25:434-444. [PMID: 35059143 PMCID: PMC8765247 DOI: 10.1080/19768354.2021.2015438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We conduct a phylogeographic and population genetic study of the Asiatic toad (Bufo gargarizans) to understand its evolutionary history, and the influence of geology and climate. A total of 292 individuals from 94 locations were genotyped for two mitochondrial loci (cytb, ND2) and five nuclear introns (Sox9-2, Rho-3, CCNB2-3, UCH-2, and DBI-2), and we performed a suite of phylogenetic, population genetic, and divergence dating analyses. The phylogenetic trees constructed using mitochondrial loci inferred B. gargarizans being divided into two major groups: China mainland and Northeast Asia (Northeast China, Russia, and Korean Peninsula). As with previous studies of this species, we recover population genetic structure not tied to geographic region. Additionally, we discover a new genetic clade restricted to Northeast Asia that points towards the Korean Peninsula being a glacial refugium during the Pleistocene. The weak phylogeographic pattern of B. gargarizans is likely the result of multiple biological, anthropogenic, and historical factors – robust dispersal abilities as a consequence of physiological adaptations, human translocation, geologic activity, and glacial cycles of the Pleistocene. We highlight the complex geologic and climatic history of Northeast Asia and encourage further research to understand its impact on the biodiversity in the region.
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Affiliation(s)
- Changhoon Lee
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, South Korea
- Team of Climate Change Research, National Institute of Ecology, Seocheon-gun, South Korea
| | - Jonathan J. Fong
- Science Unit, Lingnan University, Tuen Mun, Hong Kong, People’s Republic of China
| | - Jian-Ping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, People’s Republic of China
| | - Pi-Peng Li
- Center for Chinese Endemic Herp-Breeding and Conservation Research and Liaoning Key Laboratory of Evolution and Biodiversity, Shenyang Normal University, Shenyang, People’s Republic of China
| | - Bruce Waldman
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
| | | | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, South Korea
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7
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Late Pleistocene Expansion of Small Murid Rodents across the Palearctic in Relation to the Past Environmental Changes. Genes (Basel) 2021; 12:genes12050642. [PMID: 33925980 PMCID: PMC8145813 DOI: 10.3390/genes12050642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022] Open
Abstract
We investigated the evolutionary history of the striped field mouse to identify factors that initiated its past demographic changes and to shed light on the causes of its current genetic structure and trans-Eurasian distribution. We sequenced mitochondrial cyt b from 184 individuals, obtained from 35 sites in central Europe and eastern Mongolia. We compared genetic analyses with previously published historical distribution models and data on environmental and climatic changes. The past demographic changes displayed similar population trends in the case of recently expanded clades C1 and C3, with the glacial (MIS 3–4) expansion and postglacial bottleneck preceding the recent expansion initiated in the late Holocene and were related to environmental changes during the upper Pleistocene and Holocene. The past demographic trends of the eastern Asian clade C3 were correlated with changes in sea level and the formation of new land bridges formed by the exposed sea shelf during the glaciations. These data were supported by reconstructed historical distribution models. The results of our genetic analyses, supported by the reconstruction of the historical spatial distributions of the distinct clades, confirm that over time the local populations mixed as a consequence of environmental and climatic changes resulting from cyclical glaciation and the interglacial period during the Pleistocene.
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Wang Y, Feijó A, Cheng J, Xia L, Wen Z, Ge D, Sun J, Lu L, Li S, Yang Q. Ring distribution patterns-diversification or speciation? Comparative phylogeography of two small mammals in the mountains surrounding the Sichuan Basin. Mol Ecol 2021; 30:2641-2658. [PMID: 33817880 DOI: 10.1111/mec.15913] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 03/15/2021] [Accepted: 03/24/2021] [Indexed: 01/26/2023]
Abstract
Studying the genetic differentiation in a unique geographical area contributes to understanding the process of speciation. Here, we explore the spatial genetic structure and underlying formation mechanism of two congeneric small mammal species (Apodemus draco and A. chevrieri), which are mainly distributed in the mountains surrounding the lowland Sichuan Basin, southwest China. We applied a set of comparative phylogeographical analyses to determine their genetic diversification patterns, combining mitochondrial (Cytb and COI) and nuclear (microsatellite loci) markers, with dense sampling throughout the range (411 A. draco from 21 sites and 191 A. chevrieri from 22 sites). Moreover, we performed three complementary statistical methods to investigate the correlation between genotype and geographical and environmental components, and predicted the potential suitable distributional range under the present and historical climate conditions. Our results suggest that both species have experienced allopatric differentiation and admixture in historical periods, resulting in a ring-shape diversification, under the barrier effect of the Sichuan Basin. We infer that the tectonic events of the Qinghai-Tibetan Plateau and climatic oscillations during the Quaternary played an important role on the genetic divergence of the two species by providing environmental heterogeneity and geographical variation. Our study reveals a case of two sympatric small mammals following a ring-shaped diversification pattern and provides insight into the process of differentiation.
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Affiliation(s)
- Yanqun Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,School of Animal Science, Xichang College, Xichang, Sichuan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jian Sun
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Liang Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Centre for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Song Li
- Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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9
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Li B, Lu J, Monakhov V, Kang H, Xu Y, An B, Ghani MU, Li M, Peng W, Ma X. Phylogeography of subspecies of the sable (Martes zibellina L.) based on mitochondrial genomes: implications for evolutionary history. Mamm Biol 2021. [DOI: 10.1007/s42991-020-00092-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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Phylogeography of the striped field mouse, Apodemus agrarius (Rodentia: Muridae), throughout its distribution range in the Palaearctic region. Mamm Biol 2020. [DOI: 10.1007/s42991-019-00001-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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11
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Kinoshita G, Nunome M, Kryukov AP, Kartavtseva IV, Han SH, Yamada F, Suzuki H. Contrasting phylogeographic histories between the continent and islands of East Asia: Massive mitochondrial introgression and long-term isolation of hares (Lagomorpha: Lepus). Mol Phylogenet Evol 2019; 136:65-75. [PMID: 30951923 DOI: 10.1016/j.ympev.2019.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 03/19/2019] [Accepted: 04/01/2019] [Indexed: 01/16/2023]
Abstract
Hares of the genus Lepus are distributed worldwide, and introgressive hybridization is thought to be pervasive among species, leading to reticulate evolution and taxonomic confusion. Here, we performed phylogeographic analyses of the following species of hare across East Asia: L. timidus, L. mandshuricus, L. coreanus, and L. brachyurus collected from far-eastern Russia, South Korea, and Japan. Nucleotide sequences of one mitochondrial DNA and eight nuclear gene loci were examined, adding sequences of hares in China from databases. All nuclear DNA analyses supported the clear separation of three phylogroups: L. timidus, L. brachyurus, and the L. mandshuricus complex containing L. coreanus. On the other hand, massive mitochondrial introgression from two L. timidus lineages to the L. mandshuricus complex was suggested in continental East Asia. The northern population of the L. mandshuricus complex was mainly associated with introgression from the continental lineage of L. timidus, possibly since the last glacial period, whereas the southern population of the L. mandshuricus complex experienced introgression from another L. timidus lineage related to the Hokkaido population, possibly before the last glacial period. In contrast to continental hares, no evidence of introgression was found in L. brachyurus in the Japanese Archipelago, which showed the oldest divergence amongst East Asian hare lineages. Our findings suggest that glacial-interglacial climate changes in the circum-Japan Sea region promoted distribution shifts and introgressive hybridization among continental hare species, while the geographic structure of the region contributed to long-term isolation of hares on the islands, preventing inter-species gene flow.
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Affiliation(s)
- Gohta Kinoshita
- Course in Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo 060-0810, Japan; Laboratory of Forest Biology Division of Forest & Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake, Sakyoku, Kyoto 606-8502, Japan.
| | - Mitsuo Nunome
- Laboratory of Animal Genetics, Graduate School of Bioagricultural Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Alexey P Kryukov
- Laboratory of Evolutionary Zoology and Genetics, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Irina V Kartavtseva
- Laboratory of Evolutionary Zoology and Genetics, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - San-Hoon Han
- Inter-Korea Wildlife Institute, Namtong-dong, Gumi-si, Kyeongsang-Bukdo 39301, Republic of Korea
| | - Fumio Yamada
- Laboratory of Wildlife Ecology, Forestry and Forest Products Research Institute (FFPRI), Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Hitoshi Suzuki
- Course in Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo 060-0810, Japan
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Biogeography of Korea's top predator, the yellow-throated Marten: evolutionary history and population dynamics. BMC Evol Biol 2019; 19:23. [PMID: 30642240 PMCID: PMC6332909 DOI: 10.1186/s12862-019-1347-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/02/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Peninsulas often harvest high genetic diversity through repeated southward migrations of species during glacial maxima. Studies addressing within-species evolutionary responses to climate fluctuations in northeast Asia are limited compared to other regions of the world, and more so in the Korean Peninsula. In this study, we conducted the first population-level study of the yellow-throated marten, Martes flavigula, from the Korean Peninsula, Russian, Taiwanese and Chinese localities in a biogeographic framework using mitochondrial (cyt-b, nd2, cr) and nuclear gene sequencing (ghr). RESULTS Bayesian analyses revealed a rather young population, with a split from the most recent common ancestor at around 125 kya. Martes flavigula likely colonized the Korean Peninsula from Mainland China through the Yellow Sea twice, ca. 60 kya and 20 kya. Korean martens diversified during the Late Pleistocene with at least two dispersal events out of Korea, towards the southwest to Taiwan (ca. 80 kya) and towards the North into Russia and eastern China; most likely after the Last Glacial Maxima (ca. 20 kya). We argue that the lack of population structure and mixed populations is possibly a consequence of the high dispersal capability of the species. The Bayesian skyline plot revealed a population decline within the last 5000 years, suggesting potential negative biotic and anthropogenic effects in the area. We find that local populations are not genetically differentiated, therefore no perceptible population structure within Korea was found. CONCLUSIONS The topography and geography of the Korean Peninsula has played a pivotal role in its colonization. Connections between the Korean Peninsula and the Mainland through sea-level drops of the Yellow Sea at times of glacial maxima and the high dispersal capability of M. flavigula adds to the lack of geographical structure in this species and the paraphyly of Korean lineages.
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Hwang JY, Cho GJ. Identification of novel haplotypes and interpretation of gene flow of mitochondrial DNA control region of Eurasian otter (Lutra lutra) for the effective conservation. J Vet Med Sci 2018; 80:1791-1800. [PMID: 30224573 PMCID: PMC6261830 DOI: 10.1292/jvms.17-0678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The number and distribution of Eurasian otters have declined during twentieth century due to human activity and water pollution. The global conservation status of Eurasian otter is
presently ‘Near Threatened (NT)’ and strictly protected by being listed on the international legislation and conventions. A number of studies using the mitochondrial DNA (mtDNA) control
region (CR) have been conducted in order to effectively apply conservation and reintroduction programs, especially in Europe. However, aside from Europe, there have been few studies
concerning genetic diversity and phylogeny of Eurasian otters. Therefore, in this study, we sequenced partial mtDNA CR sequences (232 bp) from five South Korean Eurasian otters and analyzed
27 otters originating from parts of northeast Asia (South Korea, China, Japan and Russia (Sakhalin)), and Europe. Out of 232 bp partial mtDNA CR sequences, 13 polymorphic sites (5.6%) were
identified and 4 novel mtDNA CR haplotypes (Lut16–19) were discovered from 12 Eurasian otters originating from northeast Asian region. In this study, a comprehensive analysis of genetic
diversity and population structure of Eurasian otter between Europe and northeast Asia continents were conducted. Of these, different past demographic histories in Pleistocene period might
have largely impacted the genetic structure of each population differently. In addition, low degree of gene flow, isolation by distance (IBD) pattern from geographically wide distanced
dataset and analysis of molecular variance (AMOVA) also represented distinct genetic characteristics of Eurasian otter between Europe and northeast Asia.
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Affiliation(s)
- Ji-Yong Hwang
- Institute of Equine Science, College of Veterinary Medicine, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
| | - Gil-Jae Cho
- Institute of Equine Science, College of Veterinary Medicine, Kyungpook National University, 80, Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea
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14
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Sun Z, Wang H, Zhou W, Shi W, Zhu W, Zhang B. How rivers and historical climate oscillations impact on genetic structure in Chinese Muntjac ( Muntiacus reevesi)? DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Zhonglou Sun
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
- Department of Medicine; University of Utah; Salt Lake City Utah USA
| | - Hui Wang
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
| | - Wenliang Zhou
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
| | - Wenbo Shi
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
| | - Weiquan Zhu
- Department of Medicine; University of Utah; Salt Lake City Utah USA
| | - Baowei Zhang
- School of Life Sciences; Anhui Key Laboratory of Eco-engineering and Bio-technique; Anhui University; Hefei Anhui China
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15
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Mysteries of host switching: Diversification and host specificity in rodent-coccidia associations. Mol Phylogenet Evol 2018; 127:179-189. [PMID: 29753710 DOI: 10.1016/j.ympev.2018.05.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 11/21/2022]
Abstract
Recent studies show that host switching is much more frequent than originally believed and constitutes an important driver in evolution of host-parasite associations. However, its frequency and ecological mechanisms at the population level have been rarely investigated. We address this issue by analyzing phylogeny and population genetics of an extensive sample, from a broad geographic area, for commonly occurring parasites of the genus Eimeria within the abundant rodent genera Apodemus, Microtus and Myodes, using two molecular markers. At the most basal level, we demonstrate polyphyletic arrangement, i.e. multiple origin, of the rodent-specific clusters within the Eimeria phylogeny, and strong genetic/phylogenetic structure within these lineages determined at least partially by specificities to different host groups. However, a novel and the most important observation is a repeated occurrence of host switches among closely related genetic lineages which may become rapidly fixed. Within the studied model, this phenomenon applies particularly to the switches between the eimerians from Apodemus flavicollis/Apodemus sylvaticus and Apodemus agrarius groups. We show that genetic differentiation and isolation between A. flavicollis/A. sylvaticus and A. agrarius faunas is a secondary recent event and does not reflect host-parasite coevolutionary history. Rather, it provides an example of rapid ecology-based differentiation in the parasite population.
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Phylogeography of the Japanese ratsnake, Elaphe climacophora (Serpentes: Colubridae): impacts of Pleistocene climatic oscillations and sea-level fluctuations on geographical range. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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17
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Lee SJ, Lee MY, Lin LK, Lin YK, Li Y, Shin EH, Han SH, Min MS, Lee H, Kim KS. Phylogeography of the Asian lesser white-toothed shrew, Crocidura shantungensis, in East Asia: role of the Korean Peninsula as refugium for small mammals. Genetica 2018; 146:211-226. [DOI: 10.1007/s10709-018-0014-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 02/06/2018] [Indexed: 10/18/2022]
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18
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Ultrastructure of Acinar Secretory Granules of Submandibular and Parotid Salivary Gland in the Korean Striped Field Mouse, Apodemus agrarius(Rodentia, Murinae). Appl Microsc 2017. [DOI: 10.9729/am.2017.47.1.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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19
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Sheremetyeva IN, Kartavtseva IV, Pavlenko MV, Kostenko VA, Sheremetyev IS, Katin IO, Kosoy ME. Morphological and genetic variability in small island populations of the striped field mouse Apodemus agrarius Pallas, 1771. BIOL BULL+ 2017. [DOI: 10.1134/s1062359016050113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Pereverzeva VV, Primak AA, Pavlenko MV, Dokuchaev NE, Evdokimova AA. Genetic features and the putative sources of formation of isolated populations of the striped field mouse Apodemus agrarius Pallas, 1771 in Magadan oblast. RUSSIAN JOURNAL OF BIOLOGICAL INVASIONS 2017. [DOI: 10.1134/s2075111717010106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Phylogenetic relationships and genetic diversity of badgers from the Korean Peninsula: Implications for the taxonomic status of the Korean badger. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Genetic diversity of Bartonella genotypes found in the striped field mouse (Apodemus agrarius) in Central Europe. Parasitology 2016; 143:1437-42. [PMID: 27279125 DOI: 10.1017/s0031182016000962] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We investigated the diversity of Bartonella in Apodemus agrarius, an important rodent of peri-domestic habitats, which has spread into Europe in the past 1000 years. Spleen samples of 344 A. agrarius from Eastern Slovakia were screened for the presence of Bartonella spp. using 16S-23S rRNA internal transcribed spacer region and bacteria were detected in 9% of rodents. Based on sequencing of three housekeeping genes (gltA, rpoB and groEL) Bartonella genotypes were ascribed to the species typical for mice and voles: B. grahamii, B. taylorii and B. birtlesii. However, the study also confirmed presence of genotypes belonging to the B. clarridgeiae/B. rochalimae clade, and the B. elizabethae/B. tribocorum clade, which are not commonly found in woodland rodents. In addition, a potential recombination event between these two genotypes was noted, which highlights an important role of A. agrarius in shaping Bartonella diversity and evolution.
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Nkouawa A, Haukisalmi V, Li T, Nakao M, Lavikainen A, Chen X, Henttonen H, Ito A. Cryptic diversity in hymenolepidid tapeworms infecting humans. Parasitol Int 2016; 65:83-6. [DOI: 10.1016/j.parint.2015.10.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/25/2015] [Accepted: 10/28/2015] [Indexed: 11/24/2022]
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24
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Lv X, Xia L, Ge D, Wen Z, Qu Y, Lu L, Yang Q. Continental Refugium in the Mongolian Plateau during Quaternary Glacial Oscillations: Phylogeography and Niche Modelling of the Endemic Desert Hamster, Phodopus roborovskii. PLoS One 2016; 11:e0148182. [PMID: 26839955 PMCID: PMC4740458 DOI: 10.1371/journal.pone.0148182] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/14/2016] [Indexed: 11/25/2022] Open
Abstract
The Mongolian Plateau (MP), which is situated in the interior of Asia and possesses a typical continental climate, experienced harsh climatic conditions during the Quaternary glacial fluctuations. Although these events likely had huge impacts on the local animal populations, the current effects have hardly been explored. To investigate whether the MP supported a refugium along an oceanic-continental gradient (ROCG), and whether this refugium was glacial or interglacial, we investigated the demographic and phylogeographic history of an endemic mammal species, the desert hamster Phodopus roborovskii. We reconstructed the demographic variation, the phylogeographic diffusion, and modelled the potential habitat during historical periods. The genetic diversity in the MP was the highest among all the localities, and the MP was a suitable habitat throughout the modelled historical periods. A phylogeographic diffusion analysis emphasized the importance of the MP as the centre of origin, preservation and spread for P. roborovskii. The homogeneous landscape provided the opportunity for a wide gene flow, which resulted in low resolution of the phylogenetic relationships. Moreover, P. roborovskii was favoured by the interglacial condition, with both its demographical and geographical ranges expanded within the interglacial periods. The range variation from the Last Glacial Maximum to the current condition reflects a distinct longitudinal shift, while both ranges largely contracted from that of the Last Interglacial. Our results support that the MP served as a refugium and spread centre for P. roborovskii during the Quaternary climate fluctuations. The interglacial expansion and the longitudinal shifts highlighted the important effects of precipitations on the distribution range of species adapted to arid and semi-arid during glacial oscillations.
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Affiliation(s)
- Xue Lv
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Science, Beijing 100049, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Lu
- National Institute for Communicable Disease Control and Prevention, Chinese Centre of Disease Control and Prevention, Beijing 102206, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Comparative phylogeography of Meriones meridianus, Dipus sagitta, and Allactaga sibirica: Potential indicators of the impact of the Qinghai-Tibetan Plateau uplift. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2015.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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26
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Genetic isolation of Korean populations of Apodemus peninsulae (Rodentia: Muridae) from their neighboring populations. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0331-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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27
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Song G, Zhang R, DuBay SG, Qu Y, Dong L, Wang W, Zhang Y, Lambert DM, Lei F. East Asian allopatry and north Eurasian sympatry in Long-tailed Tit lineages despite similar population dynamics during the late Pleistocene. ZOOL SCR 2015. [DOI: 10.1111/zsc.12148] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Gang Song
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- Environmental Futures Research Institute; Griffith University; Nathan Qld 4111 Australia
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
- Center for Developmental Biology; Institute of Genetics and Developmental Biology; Chinese Academy of Sciences; Beijing 100101 China
| | - Shane G. DuBay
- Committee on Evolutionary Biology; University of Chicago; Chicago IL 60637 USA
- Life Sciences Section; Integrative Research Center; Field Museum of Natural History; Chicago IL 60605 USA
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - Wenjuan Wang
- Center for Watershed Ecology; Institute of Life Science; Nanchang University; Nanchang 330031 China
| | - Yanyun Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering; College of Life Sciences; Beijing Normal University; Beijing 100875 China
| | - David M. Lambert
- Environmental Futures Research Institute; Griffith University; Nathan Qld 4111 Australia
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beijing 100101 China
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Kim HR, Park YC. Genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae (Muridae, Rodentia) in Korea. Gene 2015; 572:292-7. [PMID: 26263836 DOI: 10.1016/j.gene.2015.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 07/15/2015] [Accepted: 08/07/2015] [Indexed: 11/25/2022]
Abstract
The aim of this study was to investigate the genetic diversity and genetic structure of the striped field mouse Apodemus agrarius coreae in Korea. The Korean A. a. coreae is characterized by high levels of haplotype diversity (Hd=0.967) and low levels of nucleotide diversity (π=0.00683). Haplogroup 1 is well separated from the haplotypes of the neighboring regions of the Korean Peninsula, while the other haplogroups are closely related to those from the Russian Far East. Thus, further investigations are required to confirm the validity of the subspecies status of A. a. coreae by implementing additional morphological characters as well as genetic data from the populations present in the Korean Peninsula and its neighboring countries. Haplogroup 1 includes most Korean haplotypes and forms a star-like haplotype network structure, which reveals relatively low levels of sequence divergence and high frequency of unique mutations (only few mutations are shared in most of the haplotype nodes). The results indicate that the haplotypes of Haplogroup 1 might have experienced population expansion since their migration into Korea, which was further corroborated with negative results of neutrality tests for Korean population of A. a. coreae.
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Affiliation(s)
- Hye Ri Kim
- College of Forest and Environmental Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Yung Chul Park
- College of Forest and Environmental Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
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29
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YE J, XIAO Z, LI C, WANG F, LIAO J, FU J, ZHANG Z. Past climate change and recent anthropogenic activities affect genetic structure and population demography of the greater long-tailed hamster in northern China. Integr Zool 2015. [DOI: 10.1111/1749-4877.12150] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Junbin YE
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
| | - Zhenlong XIAO
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
| | - Chuanhai LI
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
| | - Fusheng WANG
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
| | - Jicheng LIAO
- School of Life Sciences; Lanzhou University; Lanzhou China
| | - Jinzhong FU
- Department of Integrative Biology; University of Guelph; Guelph Ontario Canada
| | - Zhibin ZHANG
- State Key Laboratory of Integrated Pest Management; Institute of Zoology, Chinese Academy of Sciences; Beijing China
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30
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Kaneko Y. Latitudinal Geographical Variation of External and Cranial Measurements inApodemus peninsulae,A. draco, andA. latronum. MAMMAL STUDY 2015. [DOI: 10.3106/041.040.0303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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31
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Kim SI, Oshida T, Lee H, Min MS, Kimura J. Evolutionary and biogeographical implications of variation in skull morphology of raccoon dogs (Nyctereutes procyonoides, Mammalia: Carnivora). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12629] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sang-In Kim
- Conservation Genome Resource Bank for Korean Wildlife (CGRB) and Research Institute for Veterinary Science; College of Veterinary Medicine; Seoul National University; Seoul 151-742 Korea
- Department of Anatomy and Cell Biology; College of Veterinary Medicine; Seoul National University; Seoul 151-742 Korea
| | - Tatsuo Oshida
- Laboratory of Wildlife Biology; Obihiro University of Agriculture and Veterinary Medicine; Obihiro 080-8555 Japan
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife (CGRB) and Research Institute for Veterinary Science; College of Veterinary Medicine; Seoul National University; Seoul 151-742 Korea
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife (CGRB) and Research Institute for Veterinary Science; College of Veterinary Medicine; Seoul National University; Seoul 151-742 Korea
| | - Junpei Kimura
- Department of Anatomy and Cell Biology; College of Veterinary Medicine; Seoul National University; Seoul 151-742 Korea
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32
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Kinoshita G, Sato JJ, Meschersky IG, Pishchulina SL, Simakin LV, Rozhnov VV, Malyarchuk BA, Derenko MV, Denisova GA, Frisman LV, Kryukov AP, Hosoda T, Suzuki H. Colonization history of the sableMartes zibellina(Mammalia, Carnivora) on the marginal peninsula and islands of northeastern Eurasia. J Mammal 2015. [DOI: 10.1093/jmammal/gyu021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Rubtsov NB, Kartavtseva IV, Roslik GV, Karamysheva TV, Pavlenko MV, Iwasa MA, Koh HS. Features of the B chromosome in Korean field mouse Apodemus peninsulae (Thomas, 1906) from Transbaikalia and the Far East identified by the FISH method. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415030114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Bazhenov YA, Pavlenko MV, Korablev VP, Kardash AI. Current distribution of the striped field mouse (Apodemus agrarius Pallas, 1771) in Eastern Transbaikalia: New findings in the disjunction area. RUSSIAN JOURNAL OF BIOLOGICAL INVASIONS 2015. [DOI: 10.1134/s2075111715010026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Chelomina GN, Tatonova YV, Hung NM, Ngo HD. Genetic diversity of the Chinese liver fluke Clonorchis sinensis from Russia and Vietnam. Int J Parasitol 2014; 44:795-810. [DOI: 10.1016/j.ijpara.2014.06.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/01/2014] [Accepted: 06/02/2014] [Indexed: 11/24/2022]
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36
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Li S, Liu SY. Geographic variation of the large-eared field mouse (Apodemus latronum Thomas, 1911) (Rodentia: Muridae) with one new subspecies description verified via cranial morphometric variables and pelage characteristics. Zool Stud 2014. [DOI: 10.1186/s40555-014-0023-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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37
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Pereverzeva VV, Pavlenko MV. Diversity of the mitochondrial DNA cytochrome b gene of the field mouse Apodemus agrarius Pallas, 1771 in the south of the Russian Far East. BIOL BULL+ 2014. [DOI: 10.1134/s1062359013060101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Kim SI, Park SK, Lee H, Oshida T, Kimura J, Kim YJ, Nguyen ST, Sashika M, Min MS. Phylogeography of Korean raccoon dogs: implications of peripheral isolation of a forest mammal in East Asia. J Zool (1987) 2013. [DOI: 10.1111/jzo.12031] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S.-I. Kim
- Conservation Genome Resource Bank for Korean Wildlife (CGRB); Research Institute for Veterinary Science; College of Veterinary Medicine; Seoul National University; Seoul Korea
- Laboratory of Veterinary Anatomy and Cell Biology; Research Institute for Veterinary Science; College of Veterinary Medicine; Seoul National University; Seoul Korea
| | - S.-K. Park
- Conservation Genome Resource Bank for Korean Wildlife (CGRB); Research Institute for Veterinary Science; College of Veterinary Medicine; Seoul National University; Seoul Korea
| | - H. Lee
- Conservation Genome Resource Bank for Korean Wildlife (CGRB); Research Institute for Veterinary Science; College of Veterinary Medicine; Seoul National University; Seoul Korea
| | - T. Oshida
- Laboratory of Wildlife Biology; Obihiro University of Agriculture and Veterinary Medicine; Obihiro Japan
| | - J. Kimura
- Laboratory of Veterinary Anatomy and Cell Biology; Research Institute for Veterinary Science; College of Veterinary Medicine; Seoul National University; Seoul Korea
| | - Y.-J. Kim
- Chungnam Wild Animal Rescue Center; Yesan Chungnam Korea
| | - S. T. Nguyen
- Department of Vertebrate Zoology; Institute of Ecology and Biological Resources; Vietnam Academy of Sciences and Technology; Hanoi Vietnam
| | - M. Sashika
- Laboratory of Wildlife Biology and Medicine; Graduate School of Veterinary Medicine; Hokkaido University; Sapporo Japan
| | - M.-S. Min
- Conservation Genome Resource Bank for Korean Wildlife (CGRB); Research Institute for Veterinary Science; College of Veterinary Medicine; Seoul National University; Seoul Korea
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Kinoshita G, Nunome M, Han SH, Hirakawa H, Suzuki H. Ancient colonization and within-island vicariance revealed by mitochondrial DNA phylogeography of the mountain hare (Lepus timidus) in Hokkaido, Japan. Zoolog Sci 2013; 29:776-85. [PMID: 23106564 DOI: 10.2108/zsj.29.776] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We examined the phylogenetic status and history of the mountain hare Lepus timidus in and around Hokkaido using mitochondrial cytochrome b (cyt b) sequences from 158 samples from Hokkaido and 14 from Sakhalin, as well as four samples from the Korean hare, L. coreanus. The phylogenetic analysis of the cyt b sequences generated in this study and obtained from DNA databases showed the clear genetic specificity of the Hokkaido lineage as a clade. The Hokkaido lineage was estimated to have diverged from the other conspecific and L. coreanus lineages 0.46 and 0.30 million years ago (Mya), respectively. These results suggest that the common ancestor of the mitochondrial lineage in Hokkaido and Korea inhabited Far East Asia before colonization by the present continental lineages of L. timidus, including the Sakhalin population. We estimated the time of the most recent common ancestor of the Hokkaido population to be 0.17 Mya, and found two distinct haplogroups within the island. One group had greater genetic diversity (mean number of pairwise differences: π = 0.0188 ± 0.0108) and appears to have expanded from the west to the entire island of Hokkaido. The other had lower genetic diversity (π = 0.0038 ± 0.0037) and its distribution was concentrated in the east. These contrasting west/east trends indicate that the Hokkaido population was fragmented in the past, and then subsequently expanded. Our study suggests that Hokkaido was an important refugium for boreal species in the far eastern region, and allowed the formation of various population genetic structures within the island.
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Affiliation(s)
- Gohta Kinoshita
- Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo, Japan.
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40
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Zhang R, Song G, Qu Y, Alström P, Ramos R, Xing X, Ericson PG, Fjeldså J, Wang H, Yang X, Kristin A, Shestopalov AM, Choe JC, Lei F. Comparative phylogeography of two widespread magpies: Importance of habitat preference and breeding behavior on genetic structure in China. Mol Phylogenet Evol 2012; 65:562-72. [DOI: 10.1016/j.ympev.2012.07.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 07/11/2012] [Accepted: 07/14/2012] [Indexed: 01/11/2023]
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41
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Kaneko Y. Horizontal and Elevational Distributions ofApodemus peninsulae,A. dracoandA. latronum. MAMMAL STUDY 2012. [DOI: 10.3106/041.037.0303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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42
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Ledevin R, Quéré JP, Michaux JR, Renaud S. Can tooth differentiation help to understand species coexistence? The case of wood mice in China. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2012.00666.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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43
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Fan Z, Liu S, Liu Y, Liao L, Zhang X, Yue B. Phylogeography of the South China field mouse (Apodemus draco) on the southeastern Tibetan Plateau reveals high genetic diversity and glacial refugia. PLoS One 2012; 7:e38184. [PMID: 22666478 PMCID: PMC3364228 DOI: 10.1371/journal.pone.0038184] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 05/01/2012] [Indexed: 11/30/2022] Open
Abstract
The southeastern margin of the Tibetan Plateau (SEMTP) is a particularly interesting region due to its topographic complexity and unique geologic history, but phylogeographic studies that focus on this region are rare. In this study, we investigated the phylogeography of the South China field mouse, Apodemus draco, in order to assess the role of geologic and climatic events on the Tibetan Plateau in shaping its genetic structure. We sequenced mitochondrial cytochrome b (cyt b) sequences in 103 individuals from 47 sampling sites. In addition, 23 cyt b sequences were collected from GenBank for analyses. Phylogenetic, demographic and landscape genetic methods were conducted. Seventy-six cyt b haplotypes were found and the genetic diversity was extremely high (π = 0.0368; h = 0.989). Five major evolutionary clades, based on geographic locations, were identified. Demographic analyses implied subclade 1A and subclade 1B experienced population expansions at about 0.052-0.013 Mya and 0.014-0.004 Mya, respectively. The divergence time analysis showed that the split between clade 1 and clade 2 occurred 0.26 Mya, which fell into the extensive glacial period (EGP, 0.5-0.17 Mya). The divergence times of other main clades (2.20-0.55 Mya) were congruent with the periods of the Qingzang Movement (3.6-1.7 Mya) and the Kun-Huang Movement (1.2-0.6 Mya), which were known as the most intense uplift events in the Tibetan Plateau. Our study supported the hypothesis that the SEMTP was a large late Pleistocene refugium, and further inferred that the Gongga Mountain Region and Hongya County were glacial refugia for A. draco in clade 1. We hypothesize that the evolutionary history of A. draco in the SEMTP primarily occurred in two stages. First, an initial divergence would have been shaped by uplift events of the Tibetan Plateau. Then, major glaciations in the Pleistocene added complexity to its demographic history and genetic structure.
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Affiliation(s)
- Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, People’s Republic of China
| | - Shaoying Liu
- Sichuan Academy of Forestry, Chengdu, People’s Republic of China
| | - Yang Liu
- Sichuan Academy of Forestry, Chengdu, People’s Republic of China
| | - Lihuan Liao
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), Sichuan University, Chengdu, People’s Republic of China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, People’s Republic of China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), Sichuan University, Chengdu, People’s Republic of China
- * E-mail:
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Kim HR, Park YC. The complete mitochondrial genome of the striped field mouse, Apodemus agrarius (Rodentia, Murinae) from Korea. MITOCHONDRIAL DNA 2012; 23:145-7. [PMID: 22409759 DOI: 10.3109/19401736.2012.660931] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The striped field mouse, Apodemus agrarius, is the most common rodents in temperate forests of the Korean peninsula. We have determined the complete mitochondrial genome (JN629047) of A. agrarius from Korea. Apodemus agrarius mitogenome is 16,263 bp in length and has a base composition of 33.9% A, 29.9% T, 23.6% C, and 12.5% G. The total length of the 13 protein-coding genes is 11,398 bp long.
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Affiliation(s)
- Hye Ri Kim
- Department of Forest Environment Protection, College of Forest and Environmental Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
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Liu Q, Chen P, He K, Kilpatrick CW, Liu SY, Yu FH, Jiang XL. Phylogeographic study of Apodemus ilex (Rodentia: Muridae) in Southwest China. PLoS One 2012; 7:e31453. [PMID: 22347481 PMCID: PMC3274519 DOI: 10.1371/journal.pone.0031453] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 01/10/2012] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The Mountains of southwest China have complex river systems and a profoundly complex topography and are among the most important biodiversity hotspots in the world. However, only a few studies have shed light on how the mountains and river valleys promote genetic diversity. Apodemus ilex is a fine model for investigating this subject. METHODOLOGY/PRINCIPAL FINDINGS To assess the genetic diversity and biogeographic patterns of Apodemus ilex, the complete cytochrome b gene sequences (1,140 bp) were determined from 203 samples of A. draco/ilex that were collected from southwest China. The results obtained suggested that A. ilex and A. draco are sistergroups and diverged from each other approximately 2.25 million years ago. A. ilex could be divided into Eastern and Western phylogroups, each containing two sub-groups and being widespread in different geographical regions of the southern Hengduan Mountains and the western Yunnan - Guizhou Plateau. The population expansions of A. ilex were roughly from 0.089 Mya to 0.023 Mya. CONCLUSIONS Our result suggested that A. ilex is a valid species rather than synonym of A. draco. As a middle-high elevation inhabitant, the phylogenetic pattern of A. ilex was strongly related to the complex geographical structures in southwest China, particularly the existence of deep river valley systems, such as the Mekong and Salween rivers. Also, it appears that the evolutionary history of A. ilex, such as lineage divergences and population expansions were strongly affected by climate fluctuation in the Late Pleistocene.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Peng Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - C. William Kilpatrick
- Department of Biology, University of Vermont, Burlington, Vermont, United States of America
| | | | - Fa-Hong Yu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America
| | - Xue-Long Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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WANG Z, WANG B, LU J. Behavioral and physiological responses of striped field mice (Apodemus agrarius) to predator odor. Integr Zool 2011; 6:334-40. [DOI: 10.1111/j.1749-4877.2011.00262.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sato JJ, Hosoda T, Kryukov AP, Kartavtseva IV, Suzuki H. Genetic Diversity of the Sable (Martes zibellina, Mustelidae) in Russian Far East and Hokkaido Inferred from Mitochondrial NADH Dehydrogenase Subunit 2 Gene Sequences. MAMMAL STUDY 2011. [DOI: 10.3106/041.036.0404] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Yue H, Fan Z, Liu S, Liu Y, Song Z, Zhang X. A mitogenome of the Chevrier's field mouse (Apodemus chevrieri) and genetic variations inferred from the cytochrome b gene. DNA Cell Biol 2011; 31:460-9. [PMID: 21870961 DOI: 10.1089/dna.2011.1301] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Chevrier's field mouse (Apodemus chevrieri) is an endemic species to China and is an important pest in agriculture and human diseases. In this study, the complete mitochondrial genome of this species was sequenced and its size was 16,298 bases (accession no.: HQ896683). The mitogenome structure was similar compared with other reported rodent mitochondrial genomes and includes 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and 1 control region. This was the first complete mitogenome sequenced in genus Apodemus. The phylogenetic analyses based on the sequences of 12 heavy-strand protein-coding genes demonstrated that A. chevrieri clustered together with genus Mus. Additionally, extremely high haplotype and nucleotide diversities (h=0.978, π=2.6%) were observed based on 44 mitochondrial cytochrome b (cyt b) gene sequences. This suggests adaptive divergence of this species to a variety of living habitats and potential refuges in the eastern margin of the Hengduan Mountains during the Quaternary ice ages. No population expansions or genetic bottlenecks were observed in demographic analyses. The phylogenetic analysis of cyt b sequences and haplotypes revealed a genetic differentiation between north and south populations. The divergence between north clade and south clade occurred probably in the middle Pleistocene 1.1815 million years ago (Mya) (95% highest posterior density 2.3189-0.2737 Mya), which was congruent with the periods of the most tense uplift events in the Tibetan Plateau.
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Affiliation(s)
- Hao Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
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HU YIBO, GUO YU, QI DUNWU, ZHAN XIANGJIANG, WU HUA, BRUFORD MICHAELW, WEI FUWEN. Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA. Mol Ecol 2011; 20:2662-75. [DOI: 10.1111/j.1365-294x.2011.05126.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Groenenberg D, Dekker R. A mouse's tail: How to settle an insurance dispute. Forensic Sci Int 2011; 207:e24-7. [DOI: 10.1016/j.forsciint.2010.11.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 10/11/2010] [Accepted: 11/23/2010] [Indexed: 10/18/2022]
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