title: Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region.
abstract: 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.
authors.affiliation: National 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, China.
authors.forename: Yi
authors.identifier: 0000-0003-1642-5890
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: National 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, China.
authors.forename: Yongfang
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Department of Clinical Science and Public Health, Faculty of Veterinary Science, Mahidol University, Kanchanaburi Campus, Kanchanaburi, 71150, Thailand.
authors.forename: Marnoch
authors.initials: M
authors.lastname: Yindee
authors.affiliation: Department of Animal Science and Technology, National Taiwan University, Taipei, 10673, Taiwan.
authors.forename: Kuan-Yi
authors.initials: KY
authors.lastname: Li
authors.affiliation: Livestock Research Institute, Council of Agriculture, Tainan, 71246, Taiwan.
authors.forename: Hsiao-Yun
authors.initials: HY
authors.lastname: Kuo
authors.affiliation: Department of Animal Science and Technology, National Taiwan University, Taipei, 10673, Taiwan.
authors.forename: Yu-Ten
authors.initials: YT
authors.lastname: Ju
authors.affiliation: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
authors.forename: Shaohui
authors.initials: S
authors.lastname: Ye
authors.affiliation: Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
authors.forename: Md Omar
authors.initials: MO
authors.lastname: Faruque
authors.affiliation: National 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, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Li
authors.affiliation: National 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, China.
authors.forename: Yachun
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Tu Liem, Hanoi 100000, Vietnam.
authors.forename: Vu Chi
authors.initials: VC
authors.lastname: Cuong
authors.affiliation: Key Laboratory of Animal Cell Technology, National Institute of Animal Sciences, Tu Liem, Hanoi 100000, Vietnam.
authors.forename: Lan Doan
authors.initials: LD
authors.lastname: Pham
authors.affiliation: National Agriculture and Forestry Research Institute, P.O. Box 811, Vientiane Capital, Lao P.D.R.
authors.forename: Bounthong
authors.initials: B
authors.lastname: Bouahom
authors.affiliation: Guangxi Buffalo Research Institute, Chinese Academy of Agriculture Sciences, Nanning, 530001, China.
authors.forename: Bingzhuang
authors.initials: B
authors.lastname: Yang
authors.affiliation: Guangxi Buffalo Research Institute, Chinese Academy of Agriculture Sciences, Nanning, 530001, China.
authors.forename: Xianwei
authors.initials: X
authors.lastname: Liang
authors.affiliation: College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, China.
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Cai
authors.affiliation: The School of Veterinary Science, University of Queensland, Gatton Campus, Gatton, Qld, 4343, Australia.
authors.forename: Dianne
authors.initials: D
authors.lastname: Vankan
authors.affiliation: Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Kamphaengsaen, Nakhon Pathom, 73140, Thailand.
authors.forename: Wallaya
authors.initials: W
authors.lastname: Manatchaiworakul
authors.affiliation: Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Kamphaengsaen, Nakhon Pathom, 73140, Thailand.
authors.forename: Nonglid
authors.initials: N
authors.lastname: Kowlim
authors.affiliation: Khao-Nang-Ram Wildlife Research Station, Department of National Parks, Wildlife and Plant Conservation, Bangkok, 10900, Thailand.
authors.forename: Somphot
authors.initials: S
authors.lastname: Duangchantrasiri
authors.affiliation: Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Kamphaengsaen, Nakhon Pathom, 73140, Thailand.
authors.forename: Worawidh
authors.initials: W
authors.lastname: Wajjwalku
authors.affiliation: Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584 CM, Utrecht, The Netherlands.
authors.forename: Ben
authors.initials: B
authors.lastname: Colenbrander
authors.affiliation: National 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, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Scientific Computing, Florida State University, Tallahassee, FL, 32306-4120, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Beerli
authors.affiliation: Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584 CM, Utrecht, The Netherlands.
authors.forename: Johannes A
authors.initials: JA
authors.lastname: Lenstra
authors.affiliation: School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
authors.forename: J Stuart F
authors.initials: JS
authors.lastname: Barker
mesh_terms: D000818:Animals; D000829:Animals, Domestic / Q000235:genetics; D001208:Asia; D001499:Bayes Theorem; D002020:Buffaloes / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics*; D005260:Female; D051456:Gene Flow; D005828:Genetics, Population; D006239:Haplotypes; D008297:Male; D008957:Models, Genetic; D058974:Phylogeography; D017422:Sequence Analysis, DNA; D014998:Y Chromosome / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial
keywords: Bubalus bubalis; Y-chromosomal sequences; migration models; mitochondrial DNA