Data from: Reconstructing the origin and spread of horse domestication in the Eurasian steppe

History of horse domestication remains poorly understood. On the basis of current evidence from archaeology, mitochondrial DNA, and Y-chromosomal sequencing, a number of different domestication scenarios have been proposed, ranging from the spread of domestic horses out of a restricted primary area of domestication to the domestication of numerous distinct wild horse populations. In this paper, we reconstruct both the population genetic structure of the extinct wild progenitor of domestic horses, Equus ferus, and the origin and spread of horse domestication in the Eurasian steppes by fitting a spatially explicit stepping-stone model to genotype data from >300 horses sampled across northern Eurasia. We find strong evidence for an expansion of E. ferus out of eastern Eurasia about 160 kya, likely reflecting the colonization of Eurasia by this species. Our best-fitting scenario further suggests that horse domestication originated in the western part of the Eurasian steppe and that domestic herds were repeatedly restocked with local wild horses as they spread out of this area. By showing that horse domestication was initiated in the western Eurasian steppe and that the spread of domestic herds across Eurasia involved extensive introgression from the wild, the Q:7 scenario of horse domestication proposed here unites evidence from archaeology, mitochondrial DNA, and Y-chromosomal DNA.马的驯化历史迄今仍不甚明晰。基于当前考古学、线粒体DNA（mitochondrial DNA）以及Y染色体测序的相关证据，学界已提出多种不同的驯化假说，其范畴涵盖从有限的核心驯化区域向外扩散家养马匹，到对多个独立野生马种群的驯化。本文中，我们通过对欧亚大陆北部采集的300余匹马匹的基因型数据拟合空间显式踏脚石模型，重构了家养马的已灭绝野生祖先——野马（Equus ferus）的种群遗传结构，以及马驯化在欧亚草原的起源与传播路径。我们发现了强有力的证据，表明约16万年前野马从欧亚大陆东部向外扩张，该事件大概率对应该物种对欧亚大陆的殖民过程。最优拟合的驯化假说进一步显示，马的驯化起源于欧亚草原的西部区域，且家养马群在向外扩散的过程中，会反复通过与当地野生马群杂交实现种群更新。鉴于本研究证实马驯化起源于欧亚草原西部，且家养马群在跨欧亚大陆传播的过程中伴随了大量野生种群的基因渐渗，本文提出的Q:7号马驯化假说整合了考古学、线粒体DNA与Y染色体DNA的相关证据。