2016, Zhang, Yi, Lu, Yongfang, Cuong, Vu Chi, Pham, Lan Doan, Bouahom, Bounthong, Yang, Bingzhuang, Liang, Xianwei, Cai, Zhihua, Vankan, Dianne, Manatchaiworakul, Wallaya, Kowlim, Nonglid, Duangchantrasiri, Somphot, Yindee, Marnoch, Wajjwalku, Worawidh, Colenbrander, Ben, Zhang, Yuan, Beerli, Peter, Lenstra, Johannes A, Barker, J Stuart F, Li, Kuan-Yi, Kuo, Hsiao-Yun, Ju, Yu-Ten, Ye, Shaohui, Faruque, Md Omar, Li, Qiang, Wang, Yachun

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.

2007, Piccinali, R V, Mascord, Lisa, Barker, J Stuart F, Oakeshott, J G, Hasson, E

Several studies have suggested that esterase-2 (EST-2) may be the target of natural selection in the cactophilic fly 'Drosophila buzzatii'. In this work, we analyzed nucleotide variation in a fragment of α-esterase5 (αE5), the gene encoding EST-2, in original (Argentinian) and colonized (Australian) populations of 'D. buzzatii' and in its sibling 'D. koepferae'. Estimates of nucleotide heterozygosity in 'D. buzzatii' were similar in Australia and Argentina, although we detected a loss of singletons in colonized populations, suggesting a moderate founder effect. Interspecific comparisons revealed that 'D. buzzatii' was more polymorphic for nonsynonymous variation, whereas 'D. koepferae' was more variable for synonymous and noncoding sites. The two major chromosomal arrangements (2st and 2j) in 'D. buzzatii' displayed similar levels of nucleotide variation, whereas 2jz3 was monomorphic. The sequenced region allowed the discrimination of a greater number of EST-2 protein variants in the Australian sample than in the Argentinean sample. In 'D. koepferae', nucleotide variation in αE5 does not depart from neutral expectations, although tests of population structure were significant for silent variation. In contrast, 'D. buzzatii' has probably undergone a recent population expansion in its South American range. In addition, the McDonald and Kreitman test revealed an excess of nonsynonymous polymorphism in both original and colonized populations of this species.

2011, Zhang, Y, Vankan, D, Zhang, Yuandan, Barker, James S F

Data from three published studies of genetic variation at 18 microsatellite loci in water buffalo populations in China (18 swamp type, two river type), Nepal (one wild, one domestic river, one hybrid) and south-east Asia (eight swamp, three river) were combined so as to gain a broader understanding of genetic relationships among the populations and their demographic history. Mean numbers of alleles and expected heterozygosities were significantly different among populations. Estimates of θ (a measure of population differentiation) were significant among the swamp populations for all loci and among the river populations for most loci. Differentiation among the Chinese swamp populations (which was due primarily to just one population) was much less than among the south-east Asian. The Nepal wild animals, phenotypically swamp type but genetically like river type, are significantly different from all the domestic river populations and presumably represent the ancestral 'Bubalus arnee' (possibly with some river-type introgression). Relationships among the swamp populations (DA genetic distances, principal component analysis and structure analyses) show the south-east Asian populations separated into two groups by the Chinese populations. Given these relationships and the patterns of genetic variability, we postulate that the swamp buffalo was domesticated in the region of the far south of China, northern Thailand and Indochina. Following domestication, it spread south through peninsular Malaysia to Sumatra, Java and Sulawesi, and north through China, and then to Taiwan, the Philippines and Borneo.

2013, Zhang, Yi, Barker, J Stuart F, Vankan, Dianne, Zhang, Yuandan

Water buffalo is an important livestock species in Asia as well as in the world. The swamp type buffalo, found throughout southeast Asia, from Assam and Nepal in the west to the Yangtse valley of China, is traditionally reared to produce draft power and meat. In this study, microsatellite markers were analyzed to determine genetic origin and population relationships of swamp buffalo in China and south-east Asia. Results showed that populations in south-east Asia and southwest of China had highest level of genetic variability. Differentiation among the Chinese swamp populations was much less than among the southeast Asian. Relationships among the swamp populations (DA genetic distances and STRUCTURE analyses) show the southeast Asian populations separated into two groups by the Chinese populations. Given these relationships and the patterns of genetic variability, we postulate that the swamp buffalo was domesticated in the region of the far south of China, northern Thailand and Indochina. Following domestication, it spread south through peninsular Malaysia to Sumatra, Java and Sulawesi, and north through China, and then to Taiwan, the Philippines and Borneo.