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，是濒危物种存续的关键所在。然而，物种再引入项目往往成功率低下，且其长期遗传后果仍鲜为人知。阿尔卑斯羱羊（Capra ibex）是一种野生山羊，通过种群再引入项目，在一个世纪内从不足100只个体恢复至约50000只。本研究针对阿尔卑斯羱羊的再引入策略所带来的种群基因组学后果展开了分析。我们对173只阿尔卑斯羱羊、近缘的伊比利亚羱羊（Capra pyrenaica）以及家山羊（Capra hircus）的全基因组范围内的101822个单核苷酸多态性（single nucleotide polymorphism, SNP）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温和瓶颈事件的伊比利亚羱羊相当。所有经再引入形成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。本次研究的再引入策略包含两个阶段：一是从圈养种群中进行的初次再引入，二是从已建立种群中开展的二次再引入。这种分阶段的再引入策略留下了显著的种群分化基因组印记，且该印记的强度随后续再引入轮次的增加而增强。此外，对全基因组连续纯合片段（runs of homozygosity, ROH）的分析显示，近期近交现象主要出现在再引入种群的个体中。本研究证实，尽管阿尔卑斯羱羊的种群数量在普查数据中快速恢复，但其基因组中仍留存有其再引入历史的持久特征信号。我们还讨论了基因组监测可如何作为近交现象的早期预警指标。