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 whether 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 increase in individual homozygosity relative to mean Hardy–Weinberg expected homozygosity (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 to10 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 35 K 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.

近亲交配（亲缘个体间的交配）可通过使基因组部分区域呈现同源同一（identity by descent, IBD）状态，显著降低子代适合度。因此，个体近交水平的定量测定对于生态学、进化生物学与保护生物学研究至关重要。本研究通过计算机模拟实验，对比了系谱近交系数（FP）与基因组（基于遗传标记）近交度量对基因组同源同一片段比例（IBDG）的预测精度。其中，基因组水平的IBDG估算方法包括：个体纯合度相较于哈迪-温伯格预期平均纯合度的增量（FH），以及两种利用已定位遗传标记估算IBDG的指标——FROH与FE。当使用数千个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）标记时，在广泛的模拟场景中，IBDG与FH、FE及FROH的相关性显著高于其与FP的相关性。例如，在有效种群大小（Ne）近期缩减（从Ne=500降至Ne=75）的种群中，当使用不少于10000个SNPs进行估算时，IBDG与FROH、FH及FE的相关性均高于其与基于20代完整系谱估算的FP的相关性。当使用35000个及以上SNPs时，FROH、FH与FE通常可解释个体间IBDG变异的90%以上；而在所有模拟场景中，即便系谱包含20代完整信息，FP平均仅能解释不足80%的IBDG变异。本研究结果表明，相较于传统系谱方法，利用大量遗传标记可更精准地估算IBDG。鉴于当前已可在任意物种中完成数千个基因位点的基因分型，我们呼吁研究者采用基于基因组标记的IBDG度量方法。