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

Published: 19 November 2007

Additional files

Additional data file 1:

Unrooted NJ tree. Shown is an unrooted NJ tree of 119 mtDNA D-loop sequence haplotypes identified in 722 wild boar and domestic pig samples.

Format: DOC Size: 33KB Download file

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Open Data

Additional data file 2:

Sample information for the complete mtDNAs. Presented is sample information for the complete mtDNAs analyzed in this study.

Format: XLS Size: 34KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 3:

Classification tree of 42 (near) complete mtDNA sequences in clade A. Shown is the classification tree of 42 (near) complete mtDNA sequences in clade A in Figure 1.

Format: PPT Size: 151KB Download file

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Open Data

Additional data file 4:

Phylogenetic trees: maximum parsimony and the Bayesian methods. Presented are phylogenetic trees calculated using the maximum parsimony and the Bayesian methods.

Format: DOC Size: 127KB Download file

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Open Data

Additional data file 5:

mtDNA sequence information and haplogroup classification. Presented are six tables (Tables S1 to S6) listing mtDNA sequence information and haplogroup classification of wild boars and domestic pigs analyzed in this study.

Format: XLS Size: 426KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional data file 6:

Phylogeographic distribution of haplogroups and hypothetical dispersal routes. Presened are phylogeographic distribution of haplogroups and hypothetical dispersal routes of East Asian wild boars and domestic pigs.

Format: DOC Size: 151KB Download file

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Open Data

Additional data file 7:

Genetic diversity of samples. Presented is a table showing genetic diversity of samples in each geographic region.

Format: XLS Size: 19KB Download file

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Open Data

Additional data file 8:

Primers. Presented is a table listing all the primers used for pig complete mtDNA sequencing and haplogroup motif detection.

Format: DOC Size: 92KB Download file

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Open Data