Data from: Genetics at the verge of extinction: insights from the Iberian lynx

Population viability might become compromised by the loss of genetic diversity and the accumulation of inbreeding resulting from population decline and fragmentation. The Iberian lynx (Lynx pardinus) provides a paradigmatic example of a species at the verge of extinction and, because of the well-documented and different demographic histories of the two remaining populations (Doñana and Andújar), it provides the opportunity to evaluate the performance of analytical methods that are commonly applied to detect genetic signatures of demographic decline. We used mitochondrial sequences and a set of 36 microsatellite markers to evaluate the current genetic status of the species and to assess the genetic signatures of its past history. Mitochondrial diversity was extremely low with only two haplotypes, alternatively fixed in each population. Both remnant populations have low levels of genetic diversity at microsatellite markers, particularly the population from Doñana, which has been isolated and at small census sizes at least since the 1950s, and genetic differentiation between the two populations is high. Bayesian coalescent-based methods suggest an earlier decline starting hundreds of years ago, while heterozygosity-excess and M-ratio tests did not provide conclusive and consistent evidence for recent population size changes. Also, a model of gene-flow received overwhelming support over a model of pure drift. The discrepancies observed between some of our results and the known recent history of the species call for caution in the interpretation of the outcomes of some of these methods, especially when no information on previous demographic history is available. Overall, our results suggest that current genetic patterns in the Iberian lynx are mainly the result of its recent decline and fragmentation and alerts on possible genetic risks for its persistence. Conservation strategies should explicitly consider this threat and incorporate an integrated genetic management of captive, wild and reintroduced populations, including the genetic restoration of wild populations through translocations.种群生存力可能因种群衰退与片段化引发的遗传多样性丧失以及近交累积而受损。伊比利亚猞猁（Iberian lynx, *Lynx pardinus*）是濒临灭绝物种的典型范例；其现存的两个种群（多尼亚纳与安杜哈尔）均有详实记录且种群历史动态存在差异，这为评估常用于检测种群衰退遗传信号的分析方法的性能提供了绝佳契机。本研究采用线粒体序列与36个微卫星标记组合，对该物种当前的遗传现状进行评估，并解析其过往历史的遗传信号。研究显示，线粒体多样性水平极低，仅存有两种单倍型，且二者分别在两个种群中固定存在。两个残存种群的微卫星标记遗传多样性水平均较低，其中多尼亚纳种群尤为突出——该种群至少自20世纪50年代起便处于隔离状态，种群普查规模始终偏小；且两个种群间的遗传分化程度较高。基于贝叶斯溯祖理论的分析方法表明，该物种早在数百年前便已出现种群衰退；但杂合子过剩检测与M值检验均未为近期种群规模变化提供确凿且一致的证据。此外，相较于纯粹遗传漂变模型，基因流模型得到了压倒性的支持证据。本研究部分结果与该物种已知的近期种群历史存在矛盾，这提示我们在解读这些分析方法的结果时需保持谨慎，尤其是在缺乏既往种群动态历史信息的情况下。总体而言，本研究结果表明，伊比利亚猞猁当前的遗传格局主要源于其近期的种群衰退与片段化，同时也警示了其物种存续可能面临的遗传风险。保护策略应明确考量这一威胁，并纳入圈养种群、野生种群与再引入种群的整合遗传管理方案，其中包括通过个体易位实现野生种群的遗传修复。