Data from: Towards a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

Endemic gene pools have been severely endangered by human mediated hybridization, which is posing new challenges in the conservation of several vertebrate species. The endangered European wildcat is an example of this problem since several natural populations are suffering introgression of genes from the domestic cat. The implementation of molecular methods for detecting hybridization is crucial for supporting appropriate conservation programs on the wildcat. In this study, genetic variation at 158 single nucleotide polymorphisms (SNPs) was analyzed in 139 domestic cats, 130 putative European wildcats and 5 captive-bred hybrids (N = 274). These SNPs were variable both in wild (HE = 0.107) and domestic cats (HE = 0.340). Although we did not find any SNP that was private in any population, 22 SNPs were monomorphic in wildcats and pairwise FCT values revealed marked differences between domestic and wildcats, with the most divergent 35 loci providing an average FCT > 0.74. The power of all the loci to accurately identify admixture events and discriminate the different hybrid categories was evaluated. Results from simulated and real genotypes show that the 158 SNPs provide successful estimates of admixture, with 100% hybrid individuals (up to 2 - 3 generations in the past) being correctly identified in STRUCTURE and over 92% using the NEWHYBRIDS’ algorithm. None of the unclassified cats were wrongly allocated to another hybrid class. Thirty-five SNPs, showing the highest FCT values, provided the most parsimonious panel for robust inferences of parental and first generations of admixed ancestries. This approach may be used to further reconstruct the evolution of wildcat populations and, hopefully, to develop sound conservation guidelines for its legal protection in Europe.

人为介导的杂交已严重威胁特有基因库的存续，为多种脊椎动物的保护工作带来了全新挑战。濒危欧洲野猫便是这一问题的典型案例：其多个自然种群正遭受家猫的基因渐渗。开发用于检测杂交事件的分子手段，对制定合理的野猫保护方案至关重要。本研究对139只家猫、130只疑似欧洲野猫以及5只人工繁育杂交个体（总样本量N=274）的158个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）位点的遗传变异进行了分析。这些SNPs在野猫（期望杂合度HE=0.107）与家猫（期望杂合度HE=0.340）中均具有多态性。尽管未发现任何群体特有的SNP，但有22个SNPs在野猫中呈单态性；成对FCT值分析显示家猫与野猫之间存在显著遗传分化，其中分化程度最高的35个位点的平均FCT值大于0.74。本研究评估了全部位点精准识别基因混杂事件、区分各类杂交类群的效能。模拟基因型与真实基因型的分析结果显示，这158个SNPs可有效估算基因混杂程度：在STRUCTURE软件中，可100%正确识别（最多追溯2-3个世代的）杂交个体；在NEWHYBRIDS算法中，识别准确率亦可达92%以上。未出现未分类个体被错误归类至其他杂交类群的情况。选取FCT值最高的35个SNPs，可构建最为精简的检测组合，能够可靠推断亲本群体以及混杂谱系的首代杂交个体。该方法可用于进一步解析野猫种群的演化历程，有望为制定欧洲地区针对该物种的法定保护相关合理保护准则提供支撑。