Data from: Genomic diversity and differentiation of a managed island wild boar population

The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (FST=0.126–0.138), and from DP (FST=0.169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, FST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support the heterogeneity and distinctiveness of the Sardinian population and prompt further investigations on its origins and conservation status.

自然系统中岛屿种群的演化由局部适应与遗传漂变共同驱动。然而，人类活动可通过多种途径改变演化路径。野猪（Wild Boar, WB；学名*Sus scrofa*）是一类标志性猎用物种，广泛分布于诸多岛屿，自史前时代起便已被高强度管理。本研究对99头撒丁岛野猪的49803个单核苷酸多态性位点（single-nucleotide polymorphisms, SNPs）开展基因组多样性分析，并将其与196份欧洲大陆野生野猪样本以及105头家猪（Domestic Pig, DP，隶属于11个品种）进行比对。撒丁岛野猪群体检测到高水平的遗传变异（占总多态位点的80.9%），其中仅部分可与近期的遗传渐渗事件相关联。主成分分析（Principal Component Analysis, PCA）与贝叶斯聚类分析均显示，撒丁岛野猪群体与其他欧洲野猪群体（固定化指数FST=0.126–0.138）以及家猪群体（FST=0.169）均存在显著遗传分化。样本量不均对上述多数结果影响微弱，但在对个体数进行标准化处理后，参考群体的聚类结果发生了改变。撒丁岛野猪的纯合子连续片段（Runs of homozygosity, ROHs）的模式与分布特征，既契合瓶颈效应后曾经历种群扩张的特征（以小片段ROH为主），也反映出近期种群亚结构的影响（存在高度纯合的个体）。本研究观察到非随机选取撒丁岛个体对多样性、FST值及ROH估计结果产生的影响，凸显了采样设计在结构化或存在遗传渐渗的群体研究中的重要性。本研究结果证实了撒丁岛野猪群体的遗传异质性与独特性，并为进一步探究其起源与保护现状提供了科学依据。