Data from: Evaluating the role of inbreeding depression in heterozygosity-fitness correlations: how useful are tests for identity disequilibrium?

Heterozygosity-fitness correlations (HFCs) have been observed for several decades, but their causes are often elusive. Tests for identity disequilibrium (ID, correlated heterozygosity between loci) are commonly used to determine if inbreeding depression is a possible cause of HFCs. We used computer simulations to determine how often ID is detected when HFCs are caused by inbreeding depression. We also used ID in conjunction with HFCs to estimate the proportion of variation (r2) in fitness explained by the individual inbreeding coefficient (F). ID was not detected in a large proportion of populations with statistically significant HFCs (sample size = 120 individuals) unless the variance of F was high (σ2(F) ≥ 0.005) or many loci were used (100 microsatellites or 1000 SNPs). For example, with 25 microsatellites, ID was not detected in 49% of populations when HFCs were caused by six lethal equivalents and σ2(F) was typical of vertebrate populations (σ2(F) ≈ 0.002). Estimates of r2 between survival and F based on ID and HFCs were imprecise unless ID was strong and highly statistically significant (P ≈ 0.01). These results suggest that failing to detect ID in HFC studies should not be taken as evidence that inbreeding depression is absent. The number of markers necessary to simultaneously detect HFC and ID depends strongly on σ2(F). Thus the mating system and demography of populations, which influence σ2(F), should be considered when designing HFC studies. ID should be used in conjunction with HFCs to estimate the correlation between fitness and F, because HFCs alone reveal little about the strength of inbreeding depression.

杂合度-适合度相关性（Heterozygosity-fitness correlations, HFCs）已被观测数十年，但其成因往往难以捉摸。同一性不平衡（identity disequilibrium, ID，即位点间杂合度相关）检验通常被用于判断近交衰退是否为HFCs的潜在成因。本研究通过计算机模拟，探究了当HFCs由近交衰退引发时，同一性不平衡被检出的概率。同时，本研究结合同一性不平衡与HFCs，估算了由个体近交系数（F）所解释的适合度变异占比（r²）。在样本量为120个个体、且具有统计学显著性HFCs的种群中，有相当大比例未检测到同一性不平衡，除非个体近交系数的方差较高（σ²(F) ≥ 0.005），或使用了大量遗传位点（如100个微卫星标记或1000个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs））。例如，当HFCs由6个致死当量引发，且个体近交系数方差符合脊椎动物种群的典型水平（σ²(F) ≈ 0.002）时，使用25个微卫星标记的研究中有49%的种群未检测到同一性不平衡。基于同一性不平衡与HFCs估算的存活与个体近交系数间的r²值精度较低，除非同一性不平衡效应较强且具有极高的统计学显著性（P ≈ 0.01）。上述结果表明，在HFC研究中未检测到同一性不平衡，不应被视作近交衰退不存在的证据。能够同时检出HFC与同一性不平衡所需的标记数量，高度依赖于个体近交系数的方差。因此，在设计HFC研究时，应考虑影响该方差的种群交配系统与种群动态特征。由于仅通过HFCs几乎无法反映近交衰退的强度，因此应结合同一性不平衡与HFCs来估算适合度与个体近交系数间的相关性。