1
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Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557637. [PMID: 37745602 PMCID: PMC10515900 DOI: 10.1101/2023.09.13.557637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.
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Affiliation(s)
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan E. Pekar
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA
| | - Stephen A. Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Reema Singh
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, Lisbon, Av. da Republica, 2780-157, Oeiras, Portugal
| | - Karthik Gangavarapu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Matthew B. Rogers
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Niema Moshiri
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Robert F. Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA; Zalgen Labs, Frederick, MD 21703, USA; Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marion P. G. Koopmans
- Department of Viroscience, and Pandemic and Disaster Preparedness Centre., Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Saskia Popescu
- University of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L. Robertson
- MRC-University of Glasgow Center for Virus Research, Glasgow, G61 1QH, UK
| | - Marc A. Suchard
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Florence Débarre
- Institut d’Écologie et des Sciences de l’Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France
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2
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Fu J, Wen L. Impacts of Quaternary glaciation, geological history and geography on animal species history in continental East Asia: A phylogeographic review. Mol Ecol 2023; 32:4497-4514. [PMID: 37332105 DOI: 10.1111/mec.17053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/20/2023]
Abstract
Continental East Asia has a mild Pleistocene climate and a complex recent geological history. Phylogeographic studies of animals over the last 30 years have produced several distinctive patterns. Glaciation refugia are numerous and are not restricted to any particular regions. Most of them are localized and species-specific, although several large refugia, for example the mountains of SW China, are shared by multiple species and have refugia-within-refugia. Furthermore, postglaciation range expansion events vary greatly in time, scale and direction. Large-scale south-to-north post-LGM expansions are few and mostly occurred in the northern regions. Additionally, several unique geographic features, including the three-step terrain of China and the northern arid belt, have significant impacts on many species histories. Overall, the impacts of Pleistocene glaciations, particularly the LGM, on species history vary drastically from nondetectable to significant. The impacts are the least for species from the southwestern region and are most dominant for species from the north. Geological events play a more significant role in shaping species history than Pleistocene climatic changes. Phylogeographic patterns among animals species are highly consistent with those of plants. Future phylogeographic endeavour in East Asia should be hypothesis-driven and seek processes that underlie common patterns. The wide use of genomic data allow accurate estimates of historical population processes and exploration of older history beyond the Pleistocene.
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Affiliation(s)
- Jinzhong Fu
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Longying Wen
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Key Laboratory of Sichuan Institute for Protecting Endangered Birds in the Southwest Mountains, College of Life Sciences, Leshan Normal University, Leshan, China
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3
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Van Pham T, Trinh MT, Gray RJ, Cao LN, Van Nguyen T, Van Nguyen M, Vo TCA, Nguyen NT, Nguyen LT, Tran CX, Willcox D, Van TN. Southern extension of raccoon dog Nyctereutes procyonoides (Mammalia: Carnivora: Canidae) range in Vietnam with comments on its conservation status in the country. EUR J WILDLIFE RES 2023. [DOI: 10.1007/s10344-023-01653-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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4
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Ko BJ, An J, Eo SH. Korean Leopard Cat (Prionailurus bengalensis) population with low genetic diversity is distinct from Southeast Asian populations. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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5
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Cui M, Wu Y, Javal M, Giguère I, Roux G, Andres JA, Keena M, Shi J, Wang B, Braswell E, Pfister SE, Hamelin R, Roe A, Porth I. Genome-scale phylogeography resolves the native population structure of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky). Evol Appl 2022; 15:934-953. [PMID: 35782014 PMCID: PMC9234632 DOI: 10.1111/eva.13381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/12/2022] [Accepted: 03/21/2022] [Indexed: 11/26/2022] Open
Abstract
Human-assisted movement has allowed the Asian longhorned beetle (ALB, Anoplophora glabripennis (Motschulsky)) to spread beyond its native range and become a globally regulated invasive pest. Within its native range of China and the Korean peninsula, human-mediated dispersal has also caused cryptic translocation of insects, resulting in population structure complexity. Previous studies used genetic methods to detangle this complexity but were unable to clearly delimit native populations which is needed to develop downstream biosurveillance tools. We used genome-wide markers to define historical population structure in native ALB populations and contemporary movement between regions. We used genotyping-by-sequencing to generate 6102 single-nucleotide polymorphisms (SNPs) and amplicon sequencing to genotype 53 microsatellites. In total, we genotyped 712 individuals from ALB's native distribution. We observed six distinct population clusters among native ALB populations, with a clear delineation between northern and southern groups. Most of the individuals from South Korea were distinct from populations in China. Our results also indicate historical divergence among populations and suggest limited large-scale admixture, but we did identify a restricted number of cases of contemporary movement between regions. We identified SNPs under selection and describe a clinal allele frequency pattern in a missense variant associated with glycerol kinase, an important enzyme in the utilization of an insect cryoprotectant. We further demonstrate that small numbers of SNPs can assign individuals to geographic regions with high probability, paving the way for novel ALB biosurveillance tools.
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Affiliation(s)
- Mingming Cui
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQuébecCanada
- Département des sciences du bois et de la forêtUniversité LavalQuébecQuébecCanada
| | - Yunke Wu
- Forest Pest Methods LaboratoryPlant Protection and Quarantine Science and TechnologyAnimal and Plant Health Inspection ServiceUnited States Department of AgricultureBuzzards BayMassachusettsUSA
| | - Marion Javal
- Centre d'Écologie Fonctionnelle et ÉvolutiveUniversité MontpellierMontpellierFrance
| | - Isabelle Giguère
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQuébecCanada
- Département des sciences du bois et de la forêtUniversité LavalQuébecQuébecCanada
| | - Géraldine Roux
- Institut National de la Recherche AgronomiqueUR633 Zoologie ForestièreOrléansFrance
- COSTUniversité d’OrléansOrléansFrance
| | - Jose A. Andres
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
| | - Melody Keena
- United States Department of AgricultureForest ServiceNorthern Research StationHamdenConnecticutUSA
| | - Juan Shi
- Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
| | - Baode Wang
- Forest Pest Methods LaboratoryPlant Protection and Quarantine Science and TechnologyAnimal and Plant Health Inspection ServiceUnited States Department of AgricultureBuzzards BayMassachusettsUSA
| | - Evan Braswell
- Insect Management and Molecular Diagnostics LaboratoryPlant Protection and Quarantine Science and Technology, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureEdinburgTexasUSA
| | - Scott E. Pfister
- Forest Pest Methods LaboratoryPlant Protection and Quarantine Science and TechnologyAnimal and Plant Health Inspection ServiceUnited States Department of AgricultureBuzzards BayMassachusettsUSA
| | - Richard Hamelin
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQuébecCanada
- Département des sciences du bois et de la forêtUniversité LavalQuébecQuébecCanada
- Department of Forest and Conservation SciencesThe University of British ColumbiaVancouverBritish ColumbiaCanada
| | - Amanda Roe
- Canadian Forest ServiceGreat Lakes Forestry CentreNatural Resources CanadaSault Ste. MarieOntarioCanada
| | - Ilga Porth
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQuébecCanada
- Département des sciences du bois et de la forêtUniversité LavalQuébecQuébecCanada
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6
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Horecka B, Jakubczak A, Ślaska B, Jeżewska-Witkowska G. Raccoon dog ( Nyctereutes procyonoides) phylogeography including the Polish population: local and global aspects. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2070289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- B. Horecka
- Institute of Biological Basis of Animal Production, Faculty of Animal Science and Bioeconomy, University of Life Sciences in Lublin, Lublin
| | - A. Jakubczak
- Institute of Biological Basis of Animal Production, Faculty of Animal Science and Bioeconomy, University of Life Sciences in Lublin, Lublin
| | - B. Ślaska
- Institute of Biological Basis of Animal Production, Faculty of Animal Science and Bioeconomy, University of Life Sciences in Lublin, Lublin
| | - G. Jeżewska-Witkowska
- Institute of Biological Basis of Animal Production, Faculty of Animal Science and Bioeconomy, University of Life Sciences in Lublin, Lublin
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7
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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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8
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Borzée A, Litvinchuk SN, Ri K, Andersen D, Nam TY, Jon GH, Man HS, Choe JS, Kwon S, Othman SN, Messenger K, Bae Y, Shin Y, Kim A, Maslova I, Luedtke J, Hobin L, Moores N, Seliger B, Glenk F, Jang Y. Update on Distribution and Conservation Status of Amphibians in the Democratic People's Republic of Korea: Conclusions Based on Field Surveys, Environmental Modelling, Molecular Analyses and Call Properties. Animals (Basel) 2021; 11:2057. [PMID: 34359183 PMCID: PMC8300379 DOI: 10.3390/ani11072057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/25/2021] [Accepted: 07/01/2021] [Indexed: 11/17/2022] Open
Abstract
Determining the range, status, ecology and behaviour of species from areas where surveys and samplings are uncommon or difficult to conduct is a challenge, such as in the Democratic People's Republic of Korea (DPR Korea). Here, we used genetic samples, field surveys, call recordings, photographic identification and a literature review to estimate the presence, range and status of amphibians in the DPR Korea. From our combined results and based on the IUCN Red List categories and criteria, we were able to estimate the national threat levels for most species. Our results demonstrated the presence of 18 native species and the suspected presence of Karsenia koreana and two Onychodactylus species. We reported the first record for Rana uenoi in the vicinity of Pyongyang using molecular tools and similarly confirmed the presence of Dryophytes japonicus at the same location. Based on distribution and modelling, we can expect the contact zone between species within the Rana and Onychodactylus genera to be located along the Changbai Massif, a mountain range that marks a shift in ecoregions and acts as a barrier to dispersion. The species richness was higher in the lowlands and at lower latitudes, with such areas populated by up to 11 species, while more northern regions were characterised by species richness of about half of that value. The combination of ecological models and known threats resulted in the recommendation of ten species as threatened at the national level following the IUCN Red List categories and criteria. This high number of threatened species was anticipated based on the high threat level to amphibians in bordering nations and globally. While the ecology of species in the DPR Korea is still understudied, we argue that species relying on agricultural wetlands such as rice paddies are not under imminent threat due to the enduring presence of extensive agricultural landscapes with low rates of chemical use and mechanisation. The maintenance of such landscapes is a clear benefit to amphibian species, in contrast to more industrialised agricultural landscapes in neighbouring nations. In comparison, the status of species dependent on forested habitats is unclear and threat levels are likely to be higher because of deforestation, as in neighbouring nations.
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Affiliation(s)
- Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing 210037, China; (Y.B.); (Y.S.)
- Amphibian Specialist Group, IUCN Species Survival Commission, Toronto, ON L5A, Canada; (J.L.); (L.H.)
| | - Spartak N. Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky pr. 4, 194064 St. Petersburg, Russia;
- Department of Zoology and Physiology, Dagestan State University, Gadzhiyev str. 43-a, Makhachkala, 3367000 Dagestan, Russia
| | - Kyongsim Ri
- Department of International Economic Cooperation, Ministry of Land and Environment Protection, Pyongyang, Democratic People’s Republic of Korea
| | - Desiree Andersen
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Tu Yong Nam
- Institute of Zoology, State Academy of Science, Daesong-dong, Daesong District, Pyongyang, Democratic People’s Republic of Korea
| | - Gwang Hyok Jon
- Department of Ecology, State Academy of Science, Daesong-dong, Daesong District, Pyongyang, Democratic People’s Republic of Korea
| | - Ho Song Man
- Department of Ecology, Life Science College, Kim Il Sung University, Ryongnam-dong, Daesong-dong, Daesong District, Pyongyang, Democratic People’s Republic of Korea
| | - Jong Sik Choe
- Department of Ecology, Life Science College, Kim Il Sung University, Ryongnam-dong, Daesong-dong, Daesong District, Pyongyang, Democratic People’s Republic of Korea
| | - Sera Kwon
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Siti N. Othman
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Kevin Messenger
- Herpetology and Applied Conservation Lab, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing 210037, China;
| | - Yoonhyuk Bae
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing 210037, China; (Y.B.); (Y.S.)
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Yucheol Shin
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, 159 Longpan Rd, Nanjing 210037, China; (Y.B.); (Y.S.)
| | - Ajoung Kim
- Interdisciplinary Program of Eco Creative, Ewha Womans University, Seoul 03760, Korea; (D.A.); (S.K.); (S.N.O.); (A.K.)
| | - Irina Maslova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, 690022 Vladivostok, Russia;
| | - Jennifer Luedtke
- Amphibian Specialist Group, IUCN Species Survival Commission, Toronto, ON L5A, Canada; (J.L.); (L.H.)
- Re:wild, Austin, TX 78746, USA
| | - Louise Hobin
- Amphibian Specialist Group, IUCN Species Survival Commission, Toronto, ON L5A, Canada; (J.L.); (L.H.)
| | - Nial Moores
- Birds Korea, 101-1902, Hyundai I Park, Busan 48559, Korea;
| | | | - Felix Glenk
- Hanns Seidel Foundation, Seoul 04419, Korea; (B.S.); (F.G.)
| | - Yikweon Jang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea;
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9
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Chueca LJ, Kochmann J, Schell T, Greve C, Janke A, Pfenninger M, Klimpel S. De novo Genome Assembly of the Raccoon Dog ( Nyctereutes procyonoides). Front Genet 2021; 12:658256. [PMID: 33995489 PMCID: PMC8117329 DOI: 10.3389/fgene.2021.658256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022] Open
Affiliation(s)
- Luis J Chueca
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV-EHU), Vitoria-Gasteiz, Spain
| | - Judith Kochmann
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Tilman Schell
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany
| | - Carola Greve
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany
| | - Axel Janke
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Markus Pfenninger
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Mainz, Germany
| | - Sven Klimpel
- LOEWE-Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Nature Research Society, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
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10
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Evolution of MHC class I genes in Japanese and Russian raccoon dogs, Nyctereutes procyonoides (Carnivora: Canidae). MAMMAL RES 2021; 66:371-383. [PMID: 33747753 PMCID: PMC7957040 DOI: 10.1007/s13364-021-00561-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/03/2021] [Indexed: 10/27/2022]
Abstract
Major histocompatibility complex (MHC) genes have been widely studied to assess the immunological fitness and evolutionary adaptation of animal populations. Among the Canidae, the raccoon dog's adventurous nature, omnivorous behavior, and high variability of intracellular pathogens make it ideal to study selection on MHC class I in a non-model canid species. Here, we examined allelic diversity and evolutionary patterns of MHC class I genes in the raccoon dog (Nyctereutes procyonoides). We identified 48 novel MHC class I alleles from 31 raccoon dogs from Japan and Russia. Some alleles were geographically restricted, whereas others were widely distributed across the species' range. The rate of non-synonymous substitutions was greater than that of synonymous substitutions for both exon 2 and exon 3 encoding α1 and α2 domains, respectively, in the α chain of the MHC class I protein. Positively selected sites at the amino acid level were evident in both the α1 and α2 domains, and a recombination breakpoint was found in exon 3. Bayesian phylogenetic trees showed no evidence of trans-species polymorphism (TSP) with alleles from carnivoran species in other families but did detect TSP between raccoon dogs and the domestic dog, Canis familiaris, indicative of long-term balancing selection in canids. Our results indicate that the extensive allelic diversity of MHC class I in Japanese and Russian raccoon dogs has been influenced and maintained by pathogen-driven positive selection, recombination, and long-term balancing selection. Supplementary Information The online version contains supplementary material available at 10.1007/s13364-021-00561-y.
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11
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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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12
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Hong Y, Lee H, Kim KS, Min MS. Phylogenetic relationships between different raccoon dog (Nyctereutes procyonoides) populations based on four nuclear and Y genes. Genes Genomics 2020; 42:1075-1085. [PMID: 32725576 DOI: 10.1007/s13258-020-00972-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/14/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND The raccoon dog (Nyctereutes procyonoides), endemic to East Asia, is classified as six subspecies according to their geographical distribution including a population introduced to Europe. Studies on phylogenetic relationship or population genetics in both native and introduced areas have been carried out recently. Lately, opinions that Japanese raccoon dogs should be classified as a different species were asserted based on several studies using karyotypes, morphometric characters, mtDNA, and microsatellites analysis. However, no data pertaining to the nuclear DNA (nDNA) or Y chromosome are available. OBJECTIVE To estimate the relationship among the species using different genes is necessary in understanding of the history of this species. METHOD Therefore, we investigated nDNA and Y chromosomes in our study to define relationships: (1) between continental raccoon dog populations, (2) between original and introduced groups, and (3) between continental and Japanese groups. RESULTS The analysis of four nuclear (CHRNA1, VTN, TRSP, WT1) and ZFY genes indicated that there had been no genetic differentiation among the continental populations. However, significant differences were observed between continental and Japanese raccoon dogs in VTN and ZFY genes implying genetic differentiation has been going between them. CONCLUSION To better understand the phylogenetic relationship among raccoon dog populations, further study will be necessary.
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Affiliation(s)
- YoonJee Hong
- Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea.,Environmental Health Research Department, National Institute of Environmental Research, Incheon, 22689, Republic of Korea
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, 50011, USA
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea.
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Bartocillo AMF, Nishita Y, Abramov AV, Masuda R. Molecular evolution of MHC class II DRB exon 2 in Japanese and Russian raccoon dogs, Nyctereutes procyonoides (Carnivora: Canidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractRaccoon dogs, Nyctereutes procyonoides, are native to East Asia, but have been introduced into western Russia and eastern Europe. To determine allelic diversity and elucidate the evolution of major histocompatibility complex (MHC) class II genes in the raccoon dog, we analysed a 237-bp region of DRB exon 2 from 36 individuals of native and introduced populations from Japan and Russia. We detected 23 DRB alleles (Nypr-DRBs), 22 of which were novel. Some alleles were found across the species’ range, while others were geographically restricted. For both native and introduced populations, the ratio of non-synonymous to synonymous substitution rates for codons at predicted antigen-binding sites was significantly greater than 2, indicating that Nypr-DRBs have evolved under positive selection. Mixed effect model evolution analysis and an algorithm to detect recombination showed five positively selected codons and one recombination breakpoint, respectively. Overall, our results suggest that the diversity of MHC class II DRB in N. procyonoides was influenced and maintained by recombination, pathogen-driven positive selection, geographical barriers and the founder effect. A Bayesian phylogenetic tree revealed no evidence of trans-species polymorphism (TSP), but instead showed monophyly for the Nypr-DRB alleles within a larger clade of canid sequences. The lack of TSP may have been due to long-term divergence of raccoon dogs from other canids, or to their having encountered different sets of pathogens due to occupying a different ecological niche.
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Affiliation(s)
- Aye Mee F Bartocillo
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Kita-Ku, Sapporo, Japan
| | - Yoshinori Nishita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo, Japan
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. Saint Petersburg, Russia
| | - Ryuichi Masuda
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo, Japan
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Osaki A, Sashika M, Abe G, Shinjo K, Fujimoto A, Nakai M, Shimozuru M, Tsubota T. Comparison of feeding habits and habitat use between invasive raccoons and native raccoon dogs in Hokkaido, Japan. BMC Ecol 2019; 19:35. [PMID: 31510977 PMCID: PMC6737712 DOI: 10.1186/s12898-019-0249-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 08/29/2019] [Indexed: 11/30/2022] Open
Abstract
Background In Japan, invasive raccoons cause severe ecological and social problems by transmitting pathogens to humans, livestock, and native species, causing substantial crop damage, and competing with native species. Possible competition between invasive raccoons and native raccoon dogs is of concern in Japan because Japanese raccoon dogs have a limited distribution and are native only to Japan and the two species have similar characteristics. We assessed potential competition between raccoons and raccoon dogs by comparing feeding habits and habitat use. Results Both species were captured in Hokkaido, Japan from 2004 to 2017. More raccoons were captured close to agricultural land at the forest periphery (70.1%, 358/511); conversely, more raccoon dogs were captured in the forest core (74.9%, 253/338). Feeding habits were then examined by fecal analysis and stable isotope analyses. Fecal analysis revealed both species to be opportunistic omnivores that consumed easily found food items. However, raccoon feces contained more crops, whereas raccoon dog feces contained more insects, reflecting the different locations in which the species were trapped. Moreover, stable isotope ratios were significantly higher in raccoons than raccoon dogs (Corn has the highest carbon stable isotope (δ13C) value, and amphibians and reptiles are high in nitrogen stable isotope (δ15N); forest resources such as insects and wild fruits are low in δ13C and δ15N). Conclusions We conclude that both species ate similar food types, but their food preferences appeared to differ. Raccoon and raccoon dog habitat use also differed, possibly because the two species inhabited areas where they could easily obtain their preferred foods. Therefore, the current feeding habits and habitat use of raccoons do not appear to overlap sufficiently with those of raccoon dogs to impact the latter. The results of this study, particularly the stable isotope data, may provide a useful precedent for future studies of competition in medium-sized mammals, particularly canids.
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Affiliation(s)
- Aya Osaki
- Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
| | - Mariko Sashika
- Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan.
| | - Go Abe
- Wildlife Research & Consulting Services Ltd, 94-2 Saji, Aogaki, Tamba, Hyogo, 669-3811, Japan
| | - Kohei Shinjo
- Shiretoko Nature Foundation, 531 Iwaubetsu, Shari, Hokkaido, 099-4356, Japan
| | - Ayako Fujimoto
- Raccoon Researchers Group, Kita 21 Nishi 3, Kita-ku, Sapporo, Hokkaido, 001-0021, Japan
| | - Mariko Nakai
- Raccoon Researchers Group, Kita 21 Nishi 3, Kita-ku, Sapporo, Hokkaido, 001-0021, Japan
| | - Michito Shimozuru
- Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
| | - Toshio Tsubota
- Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Kita 18 Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-0818, Japan
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Park HC, Kurihara N, Kim KS, Min MS, Han S, Lee H, Kimura J. What is the taxonomic status of East Asian otter species based on molecular evidence?: focus on the position of the Japanese otter holotype specimen from museum. Anim Cells Syst (Seoul) 2019; 23:228-234. [PMID: 31231587 PMCID: PMC6567078 DOI: 10.1080/19768354.2019.1601133] [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: 08/29/2018] [Revised: 02/17/2019] [Accepted: 03/24/2019] [Indexed: 11/06/2022] Open
Abstract
The Japanese otter (Lutra nippon), once inhabited in most islands of Japan, is now considered as an extinct species. Although the Japanese otter is regarded as a distinct species from the Eurasian otter (L. lutra), its phylogeny and taxonomic status are based on limited information on morphological and genetic data, and thus further clarification is required. Here, we assessed the phylogenetic relationship among the genus Lutra and taxonomic status of L. nippon by using the complete sequences of cytochrome b gene of its holotype. The present phylogenic trees supported that the genus Lutra specimens largely formed monophyletic group, with L. sumatrana as a basal to other Lutra species. Within Lutra species, L. nippon was distantly related with L. lutra. The European otter population of L. l. lutra were clustered together with its subspecies, L. l. chinensis rather than the same subspecies, Korean otter population. The discrepancy between the genetic data and traditional taxonomy justifies the necessity of reexamination of the current subspecific classification system of Eurasian otters. Level of genetic divergence between the holotype of L. nippon and L. lutra was two to three-fold lower than those among the other sister species of the Lutrinae. Based on the level of divergence between the L. nippon and L. lutra, and insufficient evidence of morphological difference between them, it is suggested that designation of Japanese otter as a separate species from L. lutra will be reconsidered.
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Affiliation(s)
- Han-Chan Park
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Nozomi Kurihara
- The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, USA
| | - Mi-Sook Min
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Sungyong Han
- Korean Otter Research Center, Hwacheon, Republic of Korea
| | - Hang Lee
- Conservation Genome Resource Bank for Korean Wildlife, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Junpei Kimura
- Department of Anatomy and Cell Biology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
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16
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Hong Y, Kim KS, Kimura J, Kauhala K, Voloshina I, Goncharuk MS, Yu L, Zhang YP, Sashika M, Lee H, Min MS. Genetic Diversity and Population Structure of East Asian Raccoon Dog (Nyctereutes procyonoides): Genetic Features in Central and Marginal Populations. Zoolog Sci 2019; 35:249-259. [PMID: 29882500 DOI: 10.2108/zs170140] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The raccoon dog (Nyctereutes procyonoides) is endemic to East Asia but has been introduced in Europe. Its high adaptability enabled its rapid colonization of European countries, where population growth has been raising concerns regarding ecosystem disturbance and the spread of zoonotic diseases. The genetic diversity and structure of endemic, source, and introduced populations from seven locations across South Korea, China, Russian Far East, Finland (spread to Finland after introduction to European part of Russia from Russian Far East), Vietnam, and Japan (Honshu and Hokkaido) were examined based on 16 microsatellite loci. Two major and significantly different (FST = 0.236) genetic clusters were found: continental (South Korean, Chinese, Russian, Finnish, and Vietnamese) and island (Japanese) populations. The continental raccoon dog population comprises three subpopulations (Chinese_Russian_Finnish, South Korean, and Vietnamese) and the Japanese population consists of Honshu and Hokkaido subpopulations. The genetic diversity and geographic structure of raccoon dogs in East Asia has been influenced by natural barriers to gene flow and reveals a typical central-marginal trend in genetic diversity (continental vs. island, and central vs. marginal or source vs. introduced within continental populations). The detected differences between continental and island populations agree with those reported in previous studies that considered these populations as different species.
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Affiliation(s)
- YoonJee Hong
- 1 Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Kyung Seok Kim
- 2 Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA 50011, USA
| | - Junpei Kimura
- 3 Laboratory of Anatomy and Cell Biology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Kaarina Kauhala
- 4 Luonnonvarakeskus (Luke)/Natural Resources Institute Finland, Itäinen Pitkäkatu 3 A, FI-20520 Turku, Finland
| | - Inna Voloshina
- 5 Lazovsky State Nature Reserve, Lazo, Primorsky Krai 692980, Russia
| | - Mikhail S Goncharuk
- 6 Zoological Society of London, Regent's Park, London NW1 4RY, United Kingdom
| | - Li Yu
- 7 State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Ya-Ping Zhang
- 8 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
| | - Mariko Sashika
- 9 Laboratory of Wildlife Biology and Medicine, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Hang Lee
- 1 Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
| | - Mi-Sook Min
- 1 Conservation Genome Resource Bank for Korean Wildlife (CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea
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17
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Kryukov AP, Spiridonova LN, Mori S, Arkhipov VY, Red'kin YA, Goroshko OA, Lobkov EG, Haring E. Deep Phylogeographic Breaks in Magpie Pica pica Across the Holarctic: Concordance with Bioacoustics and Phenotypes. Zoolog Sci 2019; 34:185-200. [PMID: 28589845 DOI: 10.2108/zs160119] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We examined sequences of the mitochondrial control region in magpies (Pica pica) from the entire distribution range and found deep genetic splits into four major lineages: (1) group West (Europe-Siberia), (2) group East (southern Far East), (3) P. p. mauritanica (North Africa), and (4) P. p. hudsonia (North America). These lineages show a geographic pattern corresponding to known subspecies or subspecies groups. Genetic variation within the widely-distributed group West is low and neutrality tests supported a recent expansion scenario. The haplotypes from Kamchatka, representing a separated sublineage with clear affinity to the European-Siberian group, are almost identical, implying a recent bottleneck. Group East contained two subclades without clear geographic pattern, presumably due to admixing of populations that had diverged in Pleistocene refuges. The homogeneity of the Kyushu population supports historical reports of introduction of the species from Korea. In contrast, the high variation in the recently established Hokkaido population may reflect an ongoing invasion from several populations of the Far Eastern mainland. Bioacoustic data based on chatter call differentiate groups of subspecies and reflect phylogeographic patterns, i.e., mitochondrial lineages. Furthermore, we report the fast spreading of P. p. jankowskii towards the west along the upper Amur River, and a slower shifting of P. p. leucoptera in the opposite direction thus yielding a new contact zone. Overall, our data support a scenario of divergence in geographic isolation, but the ongoing expansion of distribution ranges may lead to major changes in phylogeographic patterns.
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Affiliation(s)
- Alexey P Kryukov
- 1 Institute of Biology and Soil Science, Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Liudmila N Spiridonova
- 1 Institute of Biology and Soil Science, Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Sayaka Mori
- 2 Rakuno Gakuen University, 582 Midori-machi, Bunkyo-dai, Ebetsu-shi, Hokkaido 069-0836, Japan
| | - Vladimir Yu Arkhipov
- 3 Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Moscow Region 142290, Russia.,4 State Nature Reserve Rdeysky, Kholm, Novgorod 175270, Russia
| | - Yaroslav A Red'kin
- 5 Zoological Museum, Moscow State University, B. Nikitskaya 6, Moscow 125009, Russia
| | - Oleg A Goroshko
- 6 Daursky State Nature Biosphere Reserve, Nizhny Tsasuchey 674480, Russia.,7 Institute of Nature Resources, Ecology and Cryology, Russian Academy of Sciences, Chita 672014, Russia
| | - Evgeny G Lobkov
- 8 Kamchatka State Technical University, Petropavlovsk-Kamchatsky 684010, Russia
| | - Elisabeth Haring
- 9 Museum of Natural History Vienna, Burgring 7, Vienna A-1010, Austria.,10 Department of Integrative Zoology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
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18
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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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19
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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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20
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HONG YJ, KIM KS, MIN MS, LEE H. Population structure of the raccoon dog (Nyctereutes procyonoides) using microsatellite loci analysis in South Korea: Implications for disease management. J Vet Med Sci 2018; 80:1631-1638. [PMID: 30185723 PMCID: PMC6207519 DOI: 10.1292/jvms.17-0456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 04/12/2018] [Indexed: 11/25/2022] Open
Abstract
The prevention and control of infectious diseases transmitted by wildlife are gaining importance. To establish effective management strategies, it is essential to understand the population structure of animals. Raccoon dogs (Nyctereutes procyonoides) in South Korea play a key role in the maintenance of food web stability and possess genetic compositions that are unique compared to those in other areas. However, wild raccoon dogs play another role as the main host of various infectious diseases. To establish long-term strategies for disease management, we investigated the genetic structure and possible geographic barriers that influence the raccoon dog population in South Korea by analyzing 16 microsatellite loci. The present study showed that mountains were the major factors responsible for genetic structuring, along with distance. We proposed potential management units (MUs) for raccoon dogs based on the genetic structuring and gene-flow barrier data obtained in this study. Four MUs were suggested for the Korean raccoon dog population (Northern, Central, Southwestern, and Southeastern). The Korean raccoon dog population structure determined in this study and the proposed MUs will be helpful to establish pragmatic strategies for managing Korean raccoon dog population and for preventing the transmission of infectious diseases.
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Affiliation(s)
- Yoon Jee HONG
- Conservation Genome Resource Bank for Korean Wildlife
(CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine,
Seoul National University, Seoul 08826, Korea
| | - Kyung Seok KIM
- Department of Natural Resource Ecology and Management, Iowa
State University, Ames, IA 50011, U.S.A
| | - Mi-Sook MIN
- Conservation Genome Resource Bank for Korean Wildlife
(CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine,
Seoul National University, Seoul 08826, Korea
| | - Hang LEE
- Conservation Genome Resource Bank for Korean Wildlife
(CGRB), Research Institute for Veterinary Science and College of Veterinary Medicine,
Seoul National University, Seoul 08826, Korea
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21
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Chung MY, Son S, Suh GU, Herrando-Moraira S, Lee CH, López-Pujol J, Chung MG. The Korean Baekdudaegan Mountains: A Glacial Refugium and a Biodiversity Hotspot That Needs to Be Conserved. Front Genet 2018; 9:489. [PMID: 30405696 PMCID: PMC6206444 DOI: 10.3389/fgene.2018.00489] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/01/2018] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mi Yoon Chung
- Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
| | - Sungwon Son
- Plant Conservation Division, Korea National Arboretum, Pocheon, South Korea
| | - Gang Uk Suh
- Plant Conservation Division, Korea National Arboretum, Pocheon, South Korea
| | | | - Cheul Ho Lee
- Plant Conservation Division, Korea National Arboretum, Pocheon, South Korea
| | | | - Myong Gi Chung
- Division of Life Science and the Research Institute of Natural Science, Gyeongsang National University, Jinju, South Korea
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22
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Mitsuhashi I, Sako T, Teduka M, Koizumi R, Saito MU, Kaneko Y. Home range of raccoon dogs in an urban green area of Tokyo, Japan. J Mammal 2018. [DOI: 10.1093/jmammal/gyy033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ibuki Mitsuhashi
- Carnivore Ecology and Conservation Research Group, Tokyo University of Agriculture and Technology, Saiwaicho, Fuchu City, Tokyo, Japan
| | - Takako Sako
- Imperial Household Agency, Chiyoda, Chiyoda-ku, Tokyo, Japan
| | - Makito Teduka
- Fieldwork Office, Asahicho, Akishima City, Tokyo, Japan
| | - Ririko Koizumi
- Carnivore Ecology and Conservation Research Group, Tokyo University of Agriculture and Technology, Saiwaicho, Fuchu City, Tokyo, Japan
| | - Masayuki U Saito
- Carnivore Ecology and Conservation Research Group, Tokyo University of Agriculture and Technology, Saiwaicho, Fuchu City, Tokyo, Japan
| | - Yayoi Kaneko
- Carnivore Ecology and Conservation Research Group, Tokyo University of Agriculture and Technology, Saiwaicho, Fuchu City, Tokyo, Japan
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23
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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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24
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Borzée A, Santos JL, Sánchez-RamÍrez S, Bae Y, Heo K, Jang Y, Jowers MJ. Phylogeographic and population insights of the Asian common toad ( Bufo gargarizans) in Korea and China: population isolation and expansions as response to the ice ages. PeerJ 2017; 5:e4044. [PMID: 29201561 PMCID: PMC5710166 DOI: 10.7717/peerj.4044] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 10/25/2017] [Indexed: 11/20/2022] Open
Abstract
The effects of ice ages on speciation have been well documented for many European and North American taxa. In contrast, very few studies have addressed the consequences of such environmental and topographical changes in North East Asian species. More precisely, the Korean Peninsula offers a unique model to assess patterns and processes of speciation as it hosts the northern- and eastern-most distribution limit of some widespread Asian taxa. Despite this, studies addressing phylogeographic patterns and population genetics in the peninsula and surrounding countries are few and studies for most families are lacking. Here we inferred the phylogenetic relationships of the common toad (Bufo gargarizans) from South Korea and their North East Asian counterpart populations, based on mitochondrial data. Korean B. gargarizans GenBank BLASTs matched few individuals from nearby China, but the presence of a Korean clade suggests isolation on the Korean Peninsula, previous to the last glacial maximum, linked to sea level resurgence. Molecular clock calibrations within this group were used to date the divergence between clades and their relationship to paleo-climatic events in the area. Lack of genetic structure among South Korean populations and strong homogeneity between the Korean and some Chinese localities suggest weak isolation and recent expansion. Geographical projection of continuous coalescent maximum-clade-credibility trees shows an original Chinese expansion towards the Korean Peninsula through the Yellow Sea circa two million years ago with colonisation events dating circa 800 thousand years ago (K. y. a.). Following this colonisation, the data point to outgoing Korean Peninsula dispersal events throughout different periods, towards the North through land, and West through land bridge formations over the Yellow Sea during sea level falls. In accordance, demographic analyses revealed a population expansion in the Koran Peninsula circa 300 K. y. a., likely attributed to glacial cycle fluctuations.
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Affiliation(s)
- Amaël Borzée
- Laboratory of Behavioural Ecology and Evolution, School of Biological Sciences, Seoul National University, Seoul, South Korea.,Department of Life Sciences, Division of EcoScience, Ewha Womans University, Seoul, South Korea
| | - Joana L Santos
- CIBIO/InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Campus Agrario De Vairão, Portugal
| | - Santiago Sánchez-RamÍrez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Yoonhyuk Bae
- Academy of Life Science and Biotechnology, Hallym University, Chuncheon, South Korea
| | - Kyongman Heo
- College of Natural Science, Sangmyung University, Seoul, South Korea
| | - Yikweon Jang
- Department of Life Sciences, Division of EcoScience, Ewha Womans University, Seoul, South Korea
| | - Michael Joseph Jowers
- CIBIO/InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Campus Agrario De Vairão, Portugal.,National Institute of Ecology, Geumgang-ro, Maseo-myeon, Seocheon-gun, South Chungcheong Province, South Korea
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Saito W, Amaike Y, Sako T, Kaneko Y, Masuda R. Population Structure of the Raccoon Dog on the Grounds of the Imperial Palace, Tokyo, Revealed by Microsatellite Analysis of Fecal DNA. Zoolog Sci 2017; 33:485-490. [PMID: 27715424 DOI: 10.2108/zs160066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
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.
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Affiliation(s)
- Wataru Saito
- 1 Department of Natural History Sciences, Graduate School of Science, Hokkaido University,Sapporo 060-0810, Japan
| | - Yosuke Amaike
- 1 Department of Natural History Sciences, Graduate School of Science, Hokkaido University,Sapporo 060-0810, Japan
| | - Takako Sako
- 2 Imperial Household Agency, Tokyo 100-8111, Japan
| | - Yayoi Kaneko
- 3 Institute of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-0057, Japan
| | - Ryuichi Masuda
- 1 Department of Natural History Sciences, Graduate School of Science, Hokkaido University,Sapporo 060-0810, Japan.,4 Department of Biological Sciences, Faculty of Science, Hokkaido University,Sapporo 060-0810, Japan
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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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Asahara M, Takai M. Estimation of diet in extinct raccoon dog species by the molar ratio method. ACTA ZOOL-STOCKHOLM 2016. [DOI: 10.1111/azo.12179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masakazu Asahara
- College of Liberal Arts and Sciences; Mie University; Kurima-Machiya-Cho Tsu Mie 514-8507 Japan
| | - Masanaru Takai
- Primate Research Institute; Kyoto University; Inuyama Aichi 484-8506 Japan
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28
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Kaya S, Çiplak B. Budding speciation via peripheral isolation: thePsorodonotus venosus(Orthoptera, Tettigoniidae) species group example. ZOOL SCR 2016. [DOI: 10.1111/zsc.12174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sarp Kaya
- Department of Biology; Faculty of Science; Akdeniz University Antalya; Antalya Turkey
| | - Battal Çiplak
- Department of Biology; Faculty of Science; Akdeniz University Antalya; Antalya Turkey
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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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ASAHARA MASAKAZU, CHANG CHUNHSIANG, KIMURA JUNPEI, SON NGUYENTRUONG, TAKAI MASANARU. Re-examination of the fossil raccoon dog ( Nyctereutes procyonoides) from the Penghu channel, Taiwan, and an age estimation of the Penghu fauna. ANTHROPOL SCI 2015. [DOI: 10.1537/ase.150710] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- MASAKAZU ASAHARA
- Primate Research Institute, Kyoto University, Inuyama
- College of Liberal Arts and Sciences, Mie University, Tsu
| | | | - JUNPEI KIMURA
- Laboratory of Veterinary Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul
| | - NGUYEN TRUONG SON
- Department of Vertebrate Zoology, Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, Hanoi
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Asahara M. Evolution of Relative Lower Molar Sizes Among Local Populations of the Raccoon Dog (Nyctereutes procyonoides) in Japan. MAMMAL STUDY 2014. [DOI: 10.3106/041.039.0308] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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32
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Shape variation in the Skull Within and Between Wild Populations of the Raccoon Dog (Nyctereutes procyonoides) in Japan. MAMMAL STUDY 2014. [DOI: 10.3106/041.039.0206] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Kim HR, Cho JY, Park YC. Intraspecific comparison of complete mitogenome sequences from two Asian raccoon dogs (Canidae: Nyctereutes procyonoides). MITOCHONDRIAL DNA 2014; 26:827-828. [PMID: 24409844 DOI: 10.3109/19401736.2013.855913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We determined the complete mitochondrial genome (GenBank accession number: KF709435) of the Korean raccoon dog Nyctereutes procyonoides koreensis and compared it with a previously published mitogenome (GenBank accession number: GU256221) of a Chinese raccoon dog. The total length of N. p. koreensis mitogenome is 16,802 bp, with a base composition of 32.1% A, 26.9% T, 26.8% C and 14.2% G. High similarity of 98.7% was found between the complete mitogenome sequences of Korean and Chinese raccoon dogs. Sequence similarity of the two mitogenomes was 99.3% in the other gene regions except for D-loop. The sequence similarity of 99.1% was found in the 13 protein-coding gene regions, whereas 99.6% was identical in mtDNA regions covering all the 22 tRNA genes. There was no variation between 12S rRNAs, whereas 0.5% difference was found between 16S rRNAs.
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Affiliation(s)
- Hye Ri Kim
- a Department of Forest Environment Protection , Kangwon National University , Chuncheon , Republic of Korea and
| | - Jae Youl Cho
- b Department of Genetic Engineering , Sungkyunkwan University , Suwon , Republic of Korea
| | - Yung Chul Park
- a Department of Forest Environment Protection , Kangwon National University , Chuncheon , Republic of Korea and
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