Research

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

Gui-Sheng Wu^1,2,3,4 , Yong-Gang Yao^1,5 , Kai-Xing Qu¹ , Zhao-Li Ding² , Hui Li¹ , Malliya G Palanichamy² , Zi-Yuan Duan¹ , Ning Li⁶ , Yao-Sheng Chen⁷ and Ya-Ping Zhang^1,2

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

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

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

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

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

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

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

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Genome Biology 2007, 8:R245doi:10.1186/gb-2007-8-11-r245

Published:	19 November 2007

Subject areas: Evolution, Genome studies

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.

Conclusion

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.