Data from: Measuring individual inbreeding in the age of genomics: marker-based measures are better than pedigrees

Inbreeding (mating between relatives) can dramatically reduce the fitness of offspring by causing parts of the genome to be identical by descent. Thus, measuring individual inbreeding is crucial for ecology, evolution, and conservation biology. We used computer simulations to test if the realized proportion of the genome that is identical by descent (IBDG) is predicted better by the pedigree inbreeding coefficient (FP) or by genomic (marker-based) measures of inbreeding. Genomic estimators of IBDG included the reduction in individual heterozygosity relative to Hardy-Weinberg mean expected heterozygosity (FH), and two measures (FROH, and FE) that use mapped genetic markers to estimate IBDG. IBDG was more strongly correlated with FH, FE, and FROH than with FP across a broad range of simulated scenarios when thousands of SNPs were used. For example, IBDG was more strongly correlated with FROH, FH, and FE (estimated with {greater than or equal to}10,000 SNPs) than with FP
(estimated with 20 generations of complete pedigree) in populations with a recent reduction in the effective populations size (from Ne=500 to Ne=75). FROH, FH, and FE generally explained >90% of the variance in IBDG (among individuals) when 35K or more SNPs were used. FP explained <80% of the variation in IBDG on average in all simulated scenarios, even when pedigrees included 20 generations. Our results demonstrate that IBDG can be more precisely estimated with large numbers of genetic markers than with pedigrees. We encourage researchers to adopt genomic marker-based measures of IBDG as thousands of loci can now be genotyped in any species.

近交（亲缘个体间的交配）可通过使基因组部分区域发生同源同缘（identical by descent, IBD）现象，显著降低后代适合度。因此，个体近交程度的测定在生态学、进化生物学与保护生物学领域均具有关键意义。本研究通过计算机模拟，对比了谱系近交系数（pedigree inbreeding coefficient, FP）与基于基因组（标记辅助）的近交度量，何者能更准确地预测实际同源同缘基因组比例（identity by descent genome, IBDG）。IBDG的基因组估计量包括：相对于哈迪-温伯格（Hardy-Weinberg）平均期望杂合度的个体杂合度降低量（FH），以及两种利用已定位遗传标记估算IBDG的度量指标——FROH与FE。在使用数千个单核苷酸多态性（single nucleotide polymorphism, SNPs）的广泛模拟场景中，IBDG与FH、FE及FROH的相关性显著强于其与FP的相关性。例如，在有效种群规模近期从Ne=500降至Ne=75的种群中，当使用≥10000个SNPs估算时，IBDG与FROH、FH及FE的相关性显著高于其与FP（基于20代完整谱系估算）的相关性。当使用3.5万个及以上的SNPs时，FROH、FH与FE平均可解释个体间IBDG变异的90%以上；而在所有模拟场景中，FP平均仅能解释IBDG变异的80%以下，即便谱系涵盖20代亦然。本研究结果表明，相较于基于谱系的估算方法，利用大量遗传标记可更为精准地估算IBDG。鉴于当前已可在任意物种中对数千个基因座进行基因分型，我们呼吁研究者采用基于基因组标记的IBDG度量方法。