Data from: Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.普通牛（taurine cattle）的驯化始于约1万年前的近东地区，其祖先为野生原牛（aurochs，*Bos primigenius*）种群，随后随农耕人群的迁徙扩散至欧洲。尽管在该早期扩散阶段仍存活的野生原牛所介导的基因流（gene flow）仍存在学术争议，但部分现存原始牛种群被认为具有类原牛的原始性状。本研究利用全基因组单核苷酸多态性（genome-wide single nucleotide polymorphisms）标记，对古代原牛样本与欧洲牛种群的亲缘关系、群体混合模式及种群历史动态展开分析；其中多个欧洲牛种群兼具原始性状与粗放型养殖适配性。主成分分析（principal component analysis）、基于模型的聚类分析以及基于距离的网络分析结果，均支持此前研究提出的“西北欧牛与南欧牛具有迥异演化历史”的结论。群体混合分析显示，巴尔干半岛与意大利波洛德牛（Podolic cattle）种群中存在瘤牛（zebu）的基因流。本研究结果佐证了此前关于英、爱尔兰原始牛种群与当地原牛之间存在基因流的报道。此外，本研究在伊比利亚半岛牛种群中发现了原牛基因流的证据，表明原牛曾拥有广泛的地理分布范围。连续纯合子片段（Runs of homozygosity, ROH）分析表明，遗传隔离、品种培育等种群历史动态过程，对欧洲牛种群的基因组变异产生了显著影响；同时ROH分析还揭示了南欧牛种群近期存在近交现象。本研究最终得出结论：除古代人类迁徙、距离隔离以及品种杂交等因素外，家牛与野生原牛之间的基因流同样塑造了欧洲牛种群的基因组构成。