title: The local origin of the Tibetan pig and additional insights into the origin of Asian pigs.
abstract: BACKGROUND
  The domestic pig currently indigenous to the Tibetan highlands is supposed to have been introduced during a continuous period of colonization by the ancestors of modern Tibetans. However, there is no direct genetic evidence of either the local origin or exotic migration of the Tibetan pig.
  
  
  RESULTS
  We analyzed mtDNA hypervariable segment I (HVI) variation of 218 individuals from seven Tibetan pig populations and 1,737 reported mtDNA sequences from domestic pigs and wild boars across Asia. The Bayesian consensus tree revealed a main haplogroup M and twelve minor haplogroups, which suggested a large number of small scale in situ domestication episodes. In particular, haplogroups D1 and D6 represented two highly divergent lineages in the Tibetan highlands and Island Southeastern Asia, respectively. Network analysis of haplogroup M further revealed one main subhaplogroup M1 and two minor subhaplogroups M2 and M3. Intriguingly, M2 was mainly distributed in Southeastern Asia, suggesting for a local origin. Similar with haplogroup D6, M3 was mainly restricted in Island Southeastern Asia. This pattern suggested that Island Southeastern Asia, but not Southeastern Asia, might be the center of domestication of the so-called Pacific clade (M3 and D6 here) described in previous studies. Diversity gradient analysis of major subhaplogroup M1 suggested three local origins in Southeastern Asia, the middle and downstream regions of the Yangtze River, and the Tibetan highlands, respectively.
  
  
  CONCLUSIONS
  We identified two new origin centers for domestic pigs in the Tibetan highlands and in the Island Southeastern Asian region.
authors.affiliation: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.
authors.forename: Shuli
authors.initials: S
authors.lastname: Yang
authors.forename: Hao
authors.initials: H
authors.lastname: Zhang
authors.forename: Huaming
authors.initials: H
authors.lastname: Mao
authors.forename: Dawei
authors.initials: D
authors.lastname: Yan
authors.forename: Shaoxiong
authors.initials: S
authors.lastname: Lu
authors.forename: Linsheng
authors.initials: L
authors.lastname: Lian
authors.forename: Guiying
authors.initials: G
authors.lastname: Zhao
authors.forename: Yulin
authors.initials: Y
authors.lastname: Yan
authors.forename: Weidong
authors.initials: W
authors.lastname: Deng
authors.forename: Xianwei
authors.initials: X
authors.lastname: Shi
authors.forename: Shuxin
authors.initials: S
authors.lastname: Han
authors.forename: Shuai
authors.initials: S
authors.lastname: Li
authors.forename: Xiujuan
authors.initials: X
authors.lastname: Wang
authors.forename: Xiao
authors.initials: X
authors.lastname: Gou
mesh_terms: D025041:Animal Migration; D000818:Animals; D001208:Asia; D001210:Asia, Southeastern; D001499:Bayes Theorem; D004272:DNA, Mitochondrial / Q000235:genetics*; D014644:Genetic Variation; D005843:Geography; D006239:Haplotypes; D034421:Sus scrofa / Q000235:genetics; D013552:Swine / Q000235:genetics; D018609:Tibet
chemical_list: D004272:DNA, Mitochondrial