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.

Methods and findings: 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.

Figure 1. Sampling locations used in the study.

Codes 1–7 represent the Tibetan pig populations of Shannan, Linzhi, Changdu, Diqing, Ganzi, Aba and Hezuo, respectively. Codes 8–12 represent the Yunnan pig populations of Baoshan, Diannanxiaoer, Gaoligongshan, Saba and Wujin, respectively.

Figure 2. Median joining networks of haplogroup M in the Pacific Islands (A), ISEA (B), Yunnan (C) and SEA (D) regions.

The haplotypes are symbolized by circles and separated by one substitutional step. The length of each branch is proportional to the number of associated mutations. The size of the circle is proportional to the frequency of the haplotype and the white and black areas of the circle represent the proportion of this frequency made up by domestic pigs and wild boars respectively. Subgroup M2 is identified in B, C and D, and subgroup M3 in A, B, C and D.

Figure 3. Median joining networks of the M1 subgroup.

The haplotypes are symbolized by circles and are separated by one substitutional step. The length of each branch is proportional to the number of associated mutations. The four core haplotypes are indicated with bold lines. The size of the circle is proportional to the frequency of the haplotype and the white and black areas of the circle represent the proportion of this frequency made up by domestic pigs and wild boars. Three large red dots represent the three diversity centers of the Tibetan highlands, Southeastern Asia (SEA) and the middle and down stream region of the Yangtze River (MDYZ). The other 12 regions exhibited diversities that decreased along a gradient (see Table 2 for regional diversity). The abbreviations for the regions are explained in the main text.