Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data
Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data
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DOI：
10.1534/genetics.116.190660
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发表时间：
2017-05-01
期刊：
影响因子：
3.3
通讯作者：
Lynch, Michael
中科院分区：
文献类型：
--
作者：
Ackerman, Matthew S.;Johri, Parul;Lynch, Michael
群体结构可以用群体间的基因型相关系数来描述，其中最基本的是任何两个个体之间的成对相关系数。在最一般的模型中有9个成对相关系数，我们表明，对于双等位基因位点，这些系数可以减少到7个。虽然所有九个系数都可以从谱系中估计出来，但有六个系数已经超出了经验的范围。我们提供了一个数值优化程序，估计所有七个减少人口基因组数据的系数。模拟结果表明，该程序几乎是无偏的，即使在33覆盖率，在七个系数中的五个误差是统计不相关的。其余两个系数具有误差的负相关，但它们的总和提供了两个个体之间杂合性的总体相关性的无偏评估。应用这些新的方法，淡水甲壳动物蚤状水蚤的四个种群揭示了发生在我们的样本中的半兄弟姐妹，以及一些相同的个人，可能是专性无性克隆伴侣。这些成对相关系数（包括通常为负的近亲繁殖系数）的统计显著负估计值强调了将基因型相关性解释为等位基因在血统上相同的概率估计时所出现的困难。
Population structure can be described by genotypic-correlation coefficients between groups of individuals, the most basic of which are the pairwise relatedness coefficients between any two individuals. There are nine pairwise relatedness coefficients in the most general model, and we show that these can be reduced to seven coefficients for biallelic loci. Although all nine coefficients can be estimated from pedigrees, six coefficients have been beyond empirical reach. We provide a numerical optimization procedure that estimates all seven reduced coefficients from population-genomic data. Simulations show that the procedure is nearly unbiased, even at 33 coverage, and errors in five of the seven coefficients are statistically uncorrelated. The remaining two coefficients have a negative correlation of errors, but their sum provides an unbiased assessment of the overall correlation of heterozygosity between two individuals. Application of these new methods to four populations of the freshwater crustacean Daphnia pulex reveal the occurrence of half siblings in our samples, as well as a number of identical individuals that are likely obligately asexual clone mates. Statistically significant negative estimates of these pairwise relatedness coefficients, including inbreeding coefficients that were typically negative, underscore the difficulties that arise when interpreting genotypic correlations as estimations of the probability that alleles are identical by descent.