title: Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia.
abstract: BACKGROUND
  Previously reported evidence indicates that pigs were independently domesticated in multiple places throughout the world. However, a detailed picture of the origin and dispersal of domestic pigs in East Asia has not yet been reported.
  
  
  RESULTS
  Population phylogenomic analysis was conducted in domestic pigs and wild boars by screening the haplogroup-specific mutation motifs inferred from a phylogenetic tree of pig complete mitochondrial DNA (mtDNA) sequences. All domestic pigs are clustered into single clade D (which contains subclades D1, D2, D3, and D4), with wild boars from East Asia being interspersed. Three haplogroups within D1 are dominant in the Mekong region (D1a2 and D1b) and the middle and downstream regions of the Yangtze River (D1a1a), and may represent independent founders of domestic pigs. None of the domestic pig samples from North East Asia, the Yellow River region, and the upstream region of the Yangtze River share the same haplogroup status with the local wild boars. The limited regional distributions of haplogroups D1 (including its subhaplogroups), D2, D3, and D4 in domestic pigs suggest at least two different in situ domestication events.
  
  
  CONCLUSIONS
  The use of fine-grained mtDNA phylogenomic analysis of wild boars and domestic pigs is a powerful tool with which to discern the origin of domestic pigs. Our findings show that pig domestication in East Asia mainly occurred in the Mekong region and the middle and downstream regions of the Yangtze River.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China. guishengwu@yahoo.com
authors.forename: Gui-Sheng
authors.initials: GS
authors.lastname: Wu
authors.forename: Yong-Gang
authors.initials: YG
authors.lastname: Yao
authors.forename: Kai-Xing
authors.initials: KX
authors.lastname: Qu
authors.forename: Zhao-Li
authors.initials: ZL
authors.lastname: Ding
authors.forename: Hui
authors.initials: H
authors.lastname: Li
authors.forename: Malliya G
authors.initials: MG
authors.lastname: Palanichamy
authors.forename: Zi-Yuan
authors.initials: ZY
authors.lastname: Duan
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.forename: Yao-Sheng
authors.initials: YS
authors.lastname: Chen
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Zhang
mesh_terms: D000818:Animals; D000829:Animals, Domestic; D000835:Animals, Wild; D001483:Base Sequence; D017931:DNA Primers; D004272:DNA, Mitochondrial / Q000235:genetics*; D005202:Asia, Eastern; D023281:Genomics; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D013552:Swine / Q000235:genetics*
chemical_list: D017931:DNA Primers; D004272:DNA, Mitochondrial