Data from: Porcine colonization of the Americas: a 60k SNP story

The pig, Sus scrofa, is a foreign species to the American continent. Although pigs originally introduced in the Americas should be related to those from the Iberian Peninsula and Canary islands, the phylogeny of current creole pigs that now populate the continent is likely to be very complex. Because of the extreme climates that America harbours, these populations also provide a unique example of a fast evolutionary phenomenon of adaptation. Here, we provide a genome wide study of these issues by genotyping, with a 60k SNP chip, 206 village pigs sampled across 14 countries and 183 pigs from outgroup breeds that are potential founders of the American populations, including wild boar, Iberian, international and Chinese breeds. Results show that American village pigs are primarily of European ancestry, although the observed genetic landscape is that of a complex conglomerate. There was no correlation between genetic and geographical distances, neither continent wide nor when analysing specific areas. Most populations showed a clear admixed structure where the Iberian pig was not necessarily the main component, illustrating how international breeds, but also Chinese pigs, have contributed to extant genetic composition of American village pigs. We also observe that many genes related to the cardiovascular system show an increased differentiation between altiplano and genetically related pigs living near sea level.

家猪（Sus scrofa）是美洲大陆的外来物种。尽管最初引入美洲的猪群本应与伊比利亚半岛及加那利群岛的猪群存在亲缘关联，但当前栖息于美洲大陆的克里奥尔猪的系统发育关系极可能极为复杂。受美洲境内分布的极端气候环境影响，这些猪群种群为研究快速适应性演化现象提供了独特范例。本研究依托60K单核苷酸多态性（SNP）芯片完成基因分型，对覆盖14个国家的206份村落猪样本，以及183份作为美洲猪群潜在奠基者类群的外群品种猪样本开展全基因组研究；外群品种涵盖野猪、伊比利亚猪、国际培育品种及中国地方品种。研究结果显示，美洲村落猪的遗传起源主要为欧洲血统，但观测到的遗传格局实则呈现为复杂的混合集群结构。无论是在全大陆尺度还是特定区域内分析，遗传距离与地理距离均未呈现显著相关性。多数猪群种群均表现出清晰的遗传混合特征，且伊比利亚猪未必是其主要遗传组分，这表明国际培育品种乃至中国地方猪种均对美洲村落猪的现存遗传组成做出了贡献。本研究同时观测到，诸多与心血管系统相关的基因，在阿尔蒂普拉诺高原（altiplano）猪群与近海平面栖息的遗传同源猪群之间，分化程度显著升高。