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Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region

Yi ZhangNational Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 ChinaYongfang LuNational Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 ChinaMarnoch YindeeDepartment of Clinical Science and Public Health Faculty of Veterinary Science Mahidol University Kanchanaburi Campus Kanchanaburi 71150 ThailandKuanyi LiDepartment of Animal Science and Technology National Taiwan University Taipei 10673 TaiwanHsiao‐Yun KuoLivestock Research Institute Council of Agriculture Tainan 71246 TaiwanYu‐Ten JuDepartment of Animal Science and Technology National Taiwan University Taipei 10673 TaiwanShaohui YeCollege of Animal Science and Technology Yunnan Agricultural University Kunming 650201 ChinaMd. Omar FaruqueDepartment of Animal Breeding and Genetics Bangladesh Agricultural University Mymensingh 2202 BangladeshQiang LiNational Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 ChinaYachun WangNational Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 ChinaVũ Chí CươngKey Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 VietnamLan Doan PhamKey Laboratory of Animal Cell Technology National Institute of Animal Sciences Tu Liem Hanoi 100000 VietnamBounthong BouahomNational Agriculture and Forestry Research Institute P.O. Box 811 Vientiane Capital Lao P.D.RBingzhuang YangGuangxi Buffalo Research Institute Chinese Academy of Agriculture Sciences Nanning 530001 ChinaXianwei LiangGuangxi Buffalo Research Institute Chinese Academy of Agriculture Sciences Nanning 530001 ChinaZhihua CaiCollege of Animal Science Anhui Science and Technology University Fengyang 233100 ChinaD. VankanThe School of Veterinary Science University of Queensland, Gatton Campus Gatton Qld 4343 AustraliaWallaya ManatchaiworakulDepartment of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 ThailandNonglid KowlimDepartment of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 ThailandSomphot DuangchantrasiriKhao‐Nang‐Ram Wildlife Research Station Department of National Parks Wildlife and Plant Conservation Bangkok 10900 ThailandWorawidh WajjwalkuDepartment of Pathology Faculty of Veterinary Medicine Kasetsart University Kamphaengsaen Nakhon Pathom 73140 ThailandB. ColenbranderFaculty of Veterinary Medicine Utrecht University Yalelaan 104 3584 CM Utrecht The NetherlandsYuan ZhangNational Engineering Laboratory for Animal Breeding Key Laboratory of Animal Genetics and Breeding and Reproduction of MOA College of Animal Science and Technology China Agricultural University Beijing 100193 ChinaPeter BeerliDepartment of Scientific Computing Florida State University Tallahassee FL 32306‐4120 USAJohannes A. LenstraFaculty of Veterinary Medicine Utrecht University Yalelaan 104 3584 CM Utrecht The NetherlandsJ. S. F. BarkerSchool of Environmental and Rural Science University of New England Armidale NSW 2351 Australia

Molecular Ecologyjournal2015en

ABI

Аннотация

The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y-chromosomal ZFY, SRY and DBY sequences. Swamp buffalo has a higher diversity of both maternal and paternal lineages than river buffalo, with also a remarkable contrast between a weak phylogeographic structure of river buffalo and a strong geographic differentiation of swamp buffalo. The highest diversity of the swamp buffalo maternal lineages was found in south China and north Indochina on both banks of the Mekong River, while the highest diversity in paternal lineages was in the China/Indochina border region. We propose that domestication in this region was later followed by introgressive capture of wild cows west of the Mekong. Migration to the north followed the Yangtze valley as well as a more eastern route, but also involved translocations of both cows and bulls over large distances with a minor influence of river buffaloes in recent decades. Bayesian analyses of various migration models also supported domestication in the China/Indochina border region. Coalescence analysis yielded consistent estimates for the expansion of the major swamp buffalo haplogroups with a credibility interval of 900 to 3900 years BP. The spatial differentiation of mtDNA and Y-chromosomal haplotype distributions indicates a lack of gene flow between established populations that is unprecedented in livestock.

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Genetic and phenotypic traits in livestock Livestock Farming and Management Genetic Mapping and Diversity in Plants and Animals

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DOI: 10.1111/mec.13518

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