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 ⩾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 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.
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机译:近亲繁殖(亲戚之间的交配)可以通过使后代的基因组部分相同来显着降低后代的适应性。因此,测量个体近交对生态,进化和保护生物学至关重要。我们使用计算机模拟来测试通过血统近亲繁殖系数(FP)或通过基因组(基于标记的近亲繁殖)措施,可以更好地预测由血统(IBDG)相同的基因组的实现比例。 IBDG的基因组估计包括相对于平均Hardy-Weinberg期望纯合度(FH)的个体纯合度的增加,以及使用映射的遗传标记来估计IBDG的两项测量(FROH和FE)。在使用数千个SNP的广泛模拟场景中,IBDG与FH,FE和FROH的相关性比与FP的相关性更强。例如,IBDG与FROH,FH和FE(以⩾10000 SNP估计)的相关性比与 F em> P sub>(以20代完整谱系的估计)更强。有效人口规模最近减少的人口(从 N em> e sub> = 500到 N em> e sub> = 75) 。 F em> ROH sub>, F em> H sub>和 F em> E sub>当使用35 K或更多的SNP时,通常可以解释 IBD em> G sub>(在个体中)中> 90%的方差。 F em> P sub>解释了在所有模拟情况下,即使在系谱中,平均 IBD em> G sub>的变化<80%包括20代我们的结果表明,与系谱相比,使用大量遗传标记可以更准确地估算 IBD em> G sub>。我们鼓励研究人员采用基于基因组标记的 IBD em> G sub>措施,因为现在可以在任何物种中对数千个基因座进行基因分型。
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