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Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia

Gui-Sheng Wu1234, Yong-Gang Yao15, Kai-Xing Qu1, Zhao-Li Ding2, Hui Li1, Malliya G Palanichamy2, Zi-Yuan Duan1, Ning Li6, Yao-Sheng Chen7 and Ya-Ping Zhang12*

Author affiliations

1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China

2 Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, 2 North Greenlake Street, Kunming 650091, China

3 The Graduate School of the Chinese Academy of Sciences, 19 Yuquan Street, Beijing, 100039, China

4 Center for Pharmacogenomics, Department of Psychiatry and Behavioral Science, University of Miami Miller School of Medicine, 1580 NW 10th Ave., Miami, Florida 33136, USA

5 Key Laboratory of Animal Models and Human Disease Mechanisms, 32 East Jiaochang Road, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China

6 China Agriculture University, 2 West Yuanmingyuan Street, Beijing 10094, China

7 College of Life Sciences, Sun Yat-sen University, 135 West Xin'gang Street, Guangzhou 510275, China

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Citation and License

Genome Biology 2007, 8:R245  doi:10.1186/gb-2007-8-11-r245

Published: 19 November 2007



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.


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.


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.