Wang Jinliang
Institute of Zoology, Zoological Society of London, London NW1 4RY, United Kingdom.
Theor Popul Biol. 2016 Feb;107:4-13. doi: 10.1016/j.tpb.2015.08.006. Epub 2015 Sep 3.
Individual inbreeding coefficient (F) and pairwise relatedness (r) are fundamental parameters in population genetics and have important applications in diverse fields such as human medicine, forensics, plant and animal breeding, conservation and evolutionary biology. Traditionally, both parameters are calculated from pedigrees, but are now increasingly estimated from genetic marker data. Conceptually, a pedigree gives the expected F and r values, FP and rP, with the expectations being taken (hypothetically) over an infinite number of individuals with the same pedigree. In contrast, markers give the realised (actual) F and r values at the particular marker loci of the particular individuals, FM and rM. Both pedigree (FP, rP) and marker (FM, rM) estimates can be used as inferences of genomic inbreeding coefficients FG and genomic relatedness rG, which are the underlying quantities relevant to most applications (such as estimating inbreeding depression and heritability) of F and r. In the pre-genomic era, it was widely accepted that pedigrees are much better than markers in delineating FG and rG, and markers should better be used to validate, amend and construct pedigrees rather than to replace them. Is this still true in the genomic era when genome-wide dense SNPs are available? In this simulation study, I showed that genomic markers can yield much better estimates of FG and rG than pedigrees when they are numerous (say, 10(4) SNPs) under realistic situations (e.g. genome and population sizes). Pedigree estimates are especially poor for species with a small genome, where FG and rG are determined to a large extent by Mendelian segregations and may thus deviate substantially from their expectations (FP and rP). Simulations also confirmed that FM, when estimated from many SNPs, can be much more powerful than FP for detecting inbreeding depression in viability. However, I argue that pedigrees cannot be replaced completely by genomic SNPs, because the former allows for the calculation of more complicated IBD coefficients (involving more than 2 individuals, more than one locus, and more than 2 genes at a locus) for which the latter may have reduced capacity or limited power, and because the former has social and other significance for remote relationships which have little genetic significance and cannot be inferred reliably from markers.
个体近亲繁殖系数（F）和成对亲缘关系（r）是群体遗传学中的基本参数，在人类医学、法医学、动植物育种、保护生物学和进化生物学等不同领域有着重要应用。传统上，这两个参数都是根据系谱计算得出的，但现在越来越多地从遗传标记数据中进行估计。从概念上讲，系谱给出了预期的F和r值，即FP和rP，这些预期是（假设地）对具有相同系谱的无限多个个体进行统计得到的。相比之下，标记给出了特定个体在特定标记位点的实际（真实）F和r值，即FM和rM。系谱（FP，rP）估计值和标记（FM，rM）估计值都可以用作基因组近亲繁殖系数FG和基因组亲缘关系rG的推断值，而FG和rG是与F和r的大多数应用（如估计近亲繁殖衰退和遗传力）相关的基础量。在前基因组时代，人们普遍认为在描绘FG和rG方面，系谱比标记要好得多，标记最好用于验证、修正和构建系谱，而不是取代它们。在有全基因组密集单核苷酸多态性（SNP）的基因组时代，情况仍然如此吗？在这项模拟研究中，我表明，在实际情况（如基因组和种群大小）下，当基因组标记数量众多（例如10⁴个SNP）时，它们能够比系谱更好地估计FG和rG。对于基因组较小的物种，系谱估计尤其不准确，在这些物种中，FG和rG在很大程度上由孟德尔分离决定，因此可能与预期值（FP和rP）有很大偏差。模拟还证实，当从许多SNP估计FM时，在检测生存能力方面的近亲繁殖衰退时，FM比FP更有效。然而，我认为系谱不能完全被基因组SNP取代，因为前者允许计算更复杂的同宗系数（涉及多于2个个体、多于1个位点以及位点上多于2个基因），而对于这些系数，后者的能力可能会降低或功效有限，还因为前者对于几乎没有遗传意义且无法从标记可靠推断的远亲关系具有社会和其他方面的意义。
