Genomic Evidence For Yak Domestication

Domestication of animals, which provides a stable and reliable food resources for human, is a key factor in triggering the socioeconomic transition in human from a hunter-gatherer lifestyle to nomadic pastoralism or agricultural settlement. The bovine yak(Bos grunniens) species is endemic to the Qinghai-Tibet Plateau(QTP) and regarded as one of the world’s most remarkable domestic animals as it thrives in conditions of extreme hashness and deprivation. Yak is the only Bovidae species that can successfully live at high altitude and provide the basic resources(food, shelter, fuel and transport) that are necessary for Tibetans and other nomadic pastoralists in the high-altitude environments. The ancestral wild yak population, distinct from the domestic yak, is now threatened(numbers of wild yak are likely to be fewer than 15000) and very restricted in their distributions. However, gene flow occurs frequently between wild and domestic yaks. Based on the draft genome sequence of one domestic yak, we resequenced a large number of wild and domestic yaks and constructed a genome-wide variation map between and among these wild and domestic populations. We then further examined the domestication of yak in details. We used coalescent modelling to date yak domestication and population expansions more precisely than can be inferred from available archaeological and paleontological evidence, and relate our findings to information on the prehistoric development of human society on the QTPUsing next-generation sequencing(NGS) technology, we analysed genome sequences from 84 wild and domestic yaks, with wild yaks representing three highly diverged mitochondrial lineages and domestic yaks from different locations on the QTP representing animals from unselected landraces as well as Tianzhu white yaks, which has been bred by strict selection of coat color since 130 years ago. Genome resequencing generated 2.16 Tb raw sequencing data, with total depth of 814.7× and average depth of 9.7×. We mapped paired-end reads to the reference genome with average genome coverage of 98%. We detected a total of 14.56 million high-quality SNPs, most of which(76.4%) are located in intergenic regions. We examined the genome-wide relationships and divergence between wild and domestic yak populations. We obtained similar sequence diversity(π) values of 0.0013 and 0.0014 for wild and domestic yaks respectively and further found that the estimated population-differentiation statistic(FST) between wild and domestic yaks is only 0.058, smaller than between taurine and zebu cattle or between diverged taurine cattle breeds. We detected genomic regions that have been subject to selection as inferred from high wild/domestic π log-ratios and an extreme divergence of allele frequencies of wild and domestic yaks. We identified 182 potential selective sweep regions with 209 annotated protein-coding genes mainly involved in behavior and tameness. We further detected genetic divergence between improved breeds after domestication(Tianzhu White yak) and other domestic yaks.Based on genomic heterozygotes of yak, as well as joint site frequency spectrum of wild and domestic yak populations, we inferred the demographic history and domestication event of yak. Inference of yak population history suggests that domestication of yaks occurred around 7300 years ago. Domestic yak population size expanded 6-fold in population size around 3600 years ago. Analyses of mitochondrial, Y-chromosomal and autosomal DNA data suggested that modern humans began colonizing the QTP approximately 30000 years before present(yr B.P.) and that their population size expanded rapidly firstly between 10000 and 7000 yr B.P. and later between 4000 and 3000 yr B.P.. We suggest that yak domestication and later expansion were closely associated with the expansion of the human population on the QTP during the early Neolithic period age and the late Holocene, respectively. The domestication of yak may have been triggered by and facilitated the first expansion of human population size on the QTP during the early Neolithic age. Following the introduction of agriculture, a further increase in the effective population size of domestic yaks later in the Holocene may have resulted from or contributed to causing a second human population expansion and the subsequent development of human society on the QTP during this period. Our findings add to an understanding of yak domestication and its importance in the early human occupation of the QTP.