Population phylogenomic analysis and origin of mitochondrial DNA in Chinese domestic pig

Huo, Jun-Hong; Wei, Qipeng; Wan, MingChun; Liu, L X; Hu, Li-Li; Zhou, Qianxiong; Xiong, Li-Gen; Yang, Qun; Wu, Yanping

doi:10.3109/19401736.2014.919492

Cited by 8 publications

(5 citation statements)

References 27 publications

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“…The distribution of the swamp buffalo mtDNA haplogroups reveals a clear phylogeographic differentiation (Figure 3), which is consistent with previous studies (Yue et al, 2013;Zhang et al, 2016). And such phylogeographic differentiation pattern also was observed in sheep (Zhao, Yu, Zhang, Kong, & Zhao, 2013), horse (Yue et al, 2012) and pig (Huo et al, 2016). It had been known that several species (cattle, goats, sheep and pig) showed a multiple domestication pattern in different regions (Beja-Pereira et al, 2006;Chen et al, 2018;Larson et al, 2005;Luikart et al, 2001;Pedrosa et al, 2005).…”

Section: Discussionsupporting

confidence: 89%

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Multiple domestication of swamp buffalo in China and South East Asia

Sun

Wang

Chanthakhoun

et al. 2019

J Animal Breeding Genetics

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Section: Discussionsupporting

confidence: 89%

“…The distribution of the swamp buffalo mtDNA haplogroups reveals a clear phylogeographic differentiation (Figure ), which is consistent with previous studies (Yue et al, ; Zhang et al, ). And such phylogeographic differentiation pattern also was observed in sheep (Zhao, Yu, Zhang, Kong, & Zhao, ), horse (Yue et al, ) and pig (Huo et al, ).…”

Section: Discussionmentioning

confidence: 69%

Multiple domestication of swamp buffalo in China and South East Asia

Sun

Wang

Chanthakhoun

et al. 2019

J Animal Breeding Genetics

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“…The geographic differentiation of mtDNA in the Chinese swamp buffalo is strong also in comparison with other livestock species in China, such as sheep (Zhao et al 2013), pigs (Huo et al 2016) and horses (Yue et al 2012), but is comparable to the situation in goats (Zhao et al 2014). For Chinese cattle, the strong phylogeographic structure (Lenstra et al 2014) reflects the presence of both taurine and zebu, cross-fertile species that are as divergent as swamp and river buffalo .…”

Section: Diversity Of Maternal Lineagesmentioning

confidence: 82%

“…), pigs (Huo et al . ) and horses (Yue et al . ), but is comparable to the situation in goats (Zhao et al .…”

Section: Discussionmentioning

confidence: 99%

Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region

Yindee

et al. 2016

Molecular Ecology

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The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y-chromosomal ZFY, SRY and DBY sequences. Swamp buffalo has a higher diversity of both maternal and paternal lineages than river buffalo, with also a remarkable contrast between a weak phylogeographic structure of river buffalo and a strong geographic differentiation of swamp buffalo. The highest diversity of the swamp buffalo maternal lineages was found in south China and north Indochina on both banks of the Mekong River, while the highest diversity in paternal lineages was in the China/Indochina border region. We propose that domestication in this region was later followed by introgressive capture of wild cows west of the Mekong. Migration to the north followed the Yangtze valley as well as a more eastern route, but also involved translocations of both cows and bulls over large distances with a minor influence of river buffaloes in recent decades. Bayesian analyses of various migration models also supported domestication in the China/Indochina border region. Coalescence analysis yielded consistent estimates for the expansion of the major swamp buffalo haplogroups with a credibility interval of 900 to 3900 years BP. The spatial differentiation of mtDNA and Y-chromosomal haplotype distributions indicates a lack of gene flow between established populations that is unprecedented in livestock.

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“…The D-loop region is more variable than other regions, and D-loop variation may indicate a history of past isolation, even in the event of the contemporary admixture of groups that evolved in allopatry (Huo et al, 2016). The mtDNA D-loop region has been used extensively in studying relationships between populations (Giuffra et al, 2000;Wu et al, 2014), because variation in this region is higher than in other mtDNA regions or nuclear genes.…”

Section: Discussionmentioning

confidence: 99%

Complete mitochondrial genome of the Liuyang black goat and its phylogenetic relationship with other Caprinae

Chen

et al. 2016

Genet. Mol. Res.

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ABSTRACT. In this study, the complete mitochondrial genome sequence of the Liuyang black goat was investigated, and phylogenetic relationships between the Liuyang black goat and other species of Caprinae were analyzed. The total length of the mitochondrial genome was 16,715 bp, which consisted of 33.50% A, 27.27% T, 25.98% C, and 13.25% G. The mitochondrial genome contained a major noncoding control region (D-loop region), two ribosomal RNA genes, 13 protein-coding genes, and 22 transfer RNA genes. Neighbor-joining and maximum-parsimony trees of Caprinae constructed using 13 mitochondrial protein-coding genes showed that the Liuyang black goat is phylogenetically closest to Hemitragus jemlahicus (the Himalayan tahr) and Blue sheep to form clade A. Tibetan antelopes clustered separately in clade B and so did sheep in clade C.

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Population phylogenomic analysis and origin of mitochondrial DNA in Chinese domestic pig

Cited by 8 publications

References 27 publications

Multiple domestication of swamp buffalo in China and South East Asia

Multiple domestication of swamp buffalo in China and South East Asia

Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region

Complete mitochondrial genome of the Liuyang black goat and its phylogenetic relationship with other Caprinae

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