Data from: Genome data from a 16th century pig illuminate modern breed relationships

Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds.

古DNA（ancient DNA, aDNA）为塑造现代个体基因组的历史事件提供了直接证据。在家畜研究中，若缺乏古DNA数据，厘清初始驯化与后续现代育种所产生的效应差异并非易事。本研究从西班牙东北部蒙特索里乌城堡（Montsoriu castle）的一处保存状态极佳且物种多样的遗存组合中，获取了一头16世纪猪的鸟枪法全基因组序列数据（shotgun genome sequence data）。此外，我们还新测定了3个现代个体的基因组序列：伊比利亚猪（Iberian pig）、西班牙野猪（Spanish wild boar）以及危地马拉克里奥尔猪（Guatemalan Creole pig）。通过与线粒体基因组（mitochondrial genome）及常染色体基因组（autosomal genome）数据的比对分析，可知该古猪与现存伊比利亚猪以及欧洲野猪（European wild boar）亲缘关系密切。结合D统计量（D-statistics）的分析结果，尽管该古样本明确属于家猪，但也曾与野猪发生过基因渐渗（introgression）。伊比利亚猪、欧洲野猪与该古猪之间的紧密亲缘关系，证实了现代伊比利亚猪中不存在亚洲血统的基因渐渗，或该类渐渗程度可忽略不计。与之形成对比的是，危地马拉克里奥尔猪与伊比利亚猪基因组的聚类结果相距甚远，这大概率是由于其受到了来自国际培育品种的基因渐渗所致。