Data from: Estimating genome-wide heterozygosity: effects of demographic history and marker type

Heterozygosity–fitness correlations (HFCs) are often used to link individual genetic variation to differences in fitness. However, most studies examining HFCs find weak or no correlations. Here, we derive broad theoretical predictions about how many loci are needed to adequately measure genomic heterozygosity assuming different levels of identity disequilibrium (ID), a proxy for inbreeding. We then evaluate the expected ability to detect HFCs using an empirical data set of 200 microsatellites and 412 single nucleotide polymorphisms (SNPs) genotyped in two populations of bighorn sheep (Ovis canadensis), with different demographic histories. In both populations, heterozygosity was significantly correlated across marker types, although the strength of the correlation was weaker in a native population compared with one founded via translocation and later supplemented with additional individuals. Despite being bi-allelic, SNPs had similar correlations to genome-wide heterozygosity as microsatellites in both populations. For both marker types, this association became stronger and less variable as more markers were considered. Both populations had significant levels of ID; however, estimates were an order of magnitude lower in the native population. As with heterozygosity, SNPs performed similarly to microsatellites, and precision and accuracy of the estimates of ID increased as more loci were considered. Although dependent on the demographic history of the population considered, these results illustrate that genome-wide heterozygosity, and therefore HFCs, are best measured by a large number of markers, a feat now more realistically accomplished with SNPs than microsatellites.杂合度-适合度相关性（Heterozygosity–fitness correlations, HFCs）常被用于将个体遗传变异与适合度差异关联起来。然而，绝大多数针对HFCs的研究仅能观测到微弱相关性，甚至未发现相关性。本研究首先推导了普适性理论预测：在假定不同水平的同一性不平衡（identity disequilibrium, ID，一种近交替代指标）的前提下，需要多少基因座才能充分衡量基因组杂合度。随后，我们利用一组包含200个微卫星标记与412个单核苷酸多态性（single nucleotide polymorphisms, SNPs）基因分型数据的经验数据集，对检测HFCs的预期能力进行了评估；该数据集来自两个具有不同种群历史的大角羊（Ovis canadensis）种群。两个种群中，不同标记类型的杂合度均呈显著相关，但本土种群的相关强度弱于一个经引种建立、后续又补充了个体的种群。尽管单核苷酸多态性为双等位基因标记，但其与两个种群全基因组杂合度的相关性均与微卫星标记相当。对于两类标记而言，随着标记数量增加，这种相关性会变强且变异程度降低。两个种群均表现出显著的同一性不平衡水平，但本土种群的估计值比另一种群低一个数量级。与杂合度的结果一致，单核苷酸多态性的表现与微卫星标记相近，且同一性不平衡估计值的精度与准确度均随基因座数量增加而提升。尽管研究结果依赖于所关注种群的种群历史，但本研究结果表明，全基因组杂合度（进而杂合度-适合度相关性）的最优衡量方式是使用大量标记，而如今通过单核苷酸多态性标记实现这一目标比微卫星标记更为现实可行。