Data from: Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations

Restoration of lost species ranges to their native distribution is key for the survival of endangered species. However, reintroductions often fail and long-term genetic consequences are poorly understood. Alpine ibex (Capra ibex) are wild goats that recovered from <100 individuals to ~50,000 within a century by population reintroductions. We analyzed the population genomic consequences of the Alpine ibex reintroduction strategy. We genotyped 101'822 genome-wide single nucleotide polymorphism loci in 173 Alpine ibex, the closely related Iberian ibex (Capra pyrenaica) and domestic goat (Capra hircus). The source population of all Alpine ibex maintained genetic diversity comparable to Iberian ibex, which experienced less severe bottlenecks. All reintroduced Alpine ibex populations had individually and combined lower levels of genetic diversity than the source population. The reintroduction strategy consisted of primary reintroductions from captive-breeding and secondary reintroductions from established populations. This step-wise reintroduction strategy left a strong genomic footprint of population differentiation, which increased with subsequent rounds of reintroductions. Furthermore, analyses of genome-wide runs of homozygosity showed recent inbreeding primarily in individuals of reintroduced populations. We showed that despite the rapid census recovery, Alpine ibex carry a persistent genomic signature of their reintroduction history. We discuss how genomic monitoring can serve as an early indicator of inbreeding.将物种丧失的分布范围恢复至原生分布区域，是濒危物种存续的关键所在。然而，种群重新引入项目往往成功率低下，其长期遗传后果迄今仍未得到充分阐释。阿尔卑斯羱羊（Alpine ibex, Capra ibex）是一种野生山羊，通过种群重新引入策略，其种群数量在一个世纪内从不足100只恢复至约50000只。本研究针对阿尔卑斯羱羊重新引入策略所带来的种群基因组学后果展开了系统分析：研究团队对173只阿尔卑斯羱羊、亲缘关系密切的伊比利亚羱羊（Iberian ibex, Capra pyrenaica）以及家山羊（Capra hircus）的101822个全基因组单核苷酸多态性位点进行了基因分型。所有阿尔卑斯羱羊的源种群所保留的遗传多样性水平，与经历过更为温和种群瓶颈的伊比利亚羱羊相当。所有重新引入的阿尔卑斯羱羊种群，其单独及整体的遗传多样性水平均低于源种群。本次重新引入策略分为两步：首先从人工繁育种群开展首次引入，随后从已建立的稳定种群进行二次引入。这种分阶段的重新引入策略留下了清晰的种群分化基因组印记，且该印记随着后续引入轮次的增加而不断强化。此外，针对全基因组纯合子连续片段（runs of homozygosity, ROH）的分析显示，近期近交现象主要集中于重新引入种群的个体之中。本研究证实，尽管阿尔卑斯羱羊的种群数量在普查层面实现了快速恢复，但其仍携带反映其重新引入历史的持久基因组特征。本研究还探讨了基因组监测可作为近交现象早期预警指标的潜在路径。