Data from: Quantifying realized inbreeding in wild and captive animal populations

Most molecular measures of inbreeding do not measure inbreeding at the scale that is most relevant for understanding inbreeding depression—namely the proportion of the genome that is identical-by-descent (IBD). The inbreeding coefficient FPed obtained from pedigrees is a valuable estimator of IBD, but pedigrees are not always available, and cannot capture inbreeding loops that reach back in time further than the pedigree. We here propose a molecular approach to quantify the realized proportion of the genome that is IBD (propIBD), and we apply this method to a wild and a captive population of zebra finches (Taeniopygia guttata). In each of 948 wild and 1057 captive individuals we analyzed available single-nucleotide polymorphism (SNP) data (260 SNPs) spread over four different genomic regions in each population. This allowed us to determine whether any of these four regions was completely homozygous within an individual, which indicates IBD with high confidence. In the highly nomadic wild population, we did not find a single case of IBD, implying that inbreeding must be extremely rare (propIBD=0–0.00094, 95% CI). In the captive population, a five-generation pedigree strongly underestimated the average amount of realized inbreeding (FPed=0.013<propIBD=0.064), as expected given that pedigree founders were already related. We suggest that this SNP-based technique is generally useful for quantifying inbreeding at the individual or population level, and we show analytically that it can capture inbreeding loops that reach back up to a few hundred generations.绝大多数分子水平的近交度量方法，均未在与解析近交衰退最相关的尺度上对近交进行量化——即对基因组中同源同基因型（identical-by-descent，IBD）片段占比的测量。基于系谱计算得到的系谱近交系数FPed是一种可靠的IBD估计量，但系谱数据并非总能获取，且无法追溯超出系谱覆盖范围的近交循环。本研究提出一种分子方法，用于量化基因组中实际发生的IBD片段占比（propIBD），并将该方法应用于斑胸草雀（Taeniopygia guttata）的野生种群与圈养种群。本研究对948只野生个体与1057只圈养个体的现有单核苷酸多态性（single-nucleotide polymorphism，SNP）数据进行了分析，这些数据涵盖两个种群各4个不同基因组区域上的260个SNP位点。借此我们得以判断个体的这4个基因组区域中是否存在完全纯合的片段，此类片段可高置信度地判定为IBD片段。在高度游荡性的野生种群中，未发现任何IBD片段案例，这表明近交发生概率极低（propIBD=0–0.00094，95%置信区间）。在圈养种群中，五代系谱对实际平均近交水平的估计严重偏低（FPed=0.013<propIBD=0.064），这与预期相符——系谱的奠基者个体之间本身就存在亲缘关系。本研究表明，这种基于SNP的技术可普遍用于个体或种群水平的近交量化，且通过解析推导证实，该方法可追溯多达数百代的近交循环。