A Unified Characterization of Population Structure and Relatedness.
A Unified Characterization of Population Structure and Relatedness.
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DOI：
10.1534/genetics.116.198424
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发表时间：
2017-08
期刊：
影响因子：
3.3
通讯作者：
Goudet J
中科院分区：
文献类型：
--
作者：
Weir BS;Goudet J
许多群体遗传活动，从进化研究到关联作图，再到法医鉴定，都依赖于对群体结构或亲缘关系的适当估计。所有应用都需要认识到，具有等位基因依赖性的潜在含义的量不是以绝对意义定义的，而是相对于除靶集合之外的一些等位基因集合进行“相对”的。1984年的Weir和Cockerham估计明确了等位基因的参考集是跨人群的，而标准的亲属关系估计并没有明确参考。Weir和Cockerham表示，他们的估计是针对独立的群体，而标准的亲属关系估计有一个隐含的假设，即研究样本中的个体对，而不是目标对，是无关的或不是近亲繁殖的。然而，当种群之间存在迁移时，种群失去独立性，并且种群中的个体对之间的依赖性存在于多个目标对。因此，我们重新设计了对群体结构、亲缘关系和近亲繁殖的处理方法，以明确目标和参考等位基因组之间等位基因依赖程度的差异，因此可以是负的。我们将参考集作为研究个体抽样的总体。我们提供了简单的时刻估计这些参数，措辞的等位基因匹配内和个体之间的相关性和近亲繁殖，或内和人口之间的人口结构。个体内等位基因、群体内个体间等位基因和群体间等位基因的多层次结构允许对相关性和群体结构进行统一处理。我们希望我们的新措施有广泛的应用，但我们注意到，他们的估计是敏感的罕见或私人的变异：一些人口特征的应用程序建议利用这些敏感性，而相关性的估计可能最好使用所有的遗传标记，而不过滤次要等位基因频率。
Many population genetic activities, ranging from evolutionary studies to association mapping, to forensic identification, rely on appropriate estimates of population structure or relatedness. All applications require recognition that quantities with an underlying meaning of allelic dependence are not defined in an absolute sense, but instead are made “relative to” some set of alleles other than the target set. The 1984 Weir and Cockerham estimate made explicit that the reference set of alleles was across populations, whereas standard kinship estimates do not make the reference explicit. Weir and Cockerham stated that their estimates were for independent populations, and standard kinship estimates have an implicit assumption that pairs of individuals in a study sample, other than the target pair, are unrelated or are not inbred. However, populations lose independence when there is migration between them, and dependencies between pairs of individuals in a population exist for more than one target pair. We have therefore recast our treatments of population structure, relatedness, and inbreeding to make explicit that the parameters of interest involve the differences in degrees of allelic dependence between the target and the reference sets of alleles, and so can be negative. We take the reference set to be the population from which study individuals have been sampled. We provide simple moment estimates of these parameters, phrased in terms of allelic matching within and between individuals for relatedness and inbreeding, or within and between populations for population structure. A multi-level hierarchy of alleles within individuals, alleles between individuals within populations, and alleles between populations, allows a unified treatment of relatedness and population structure. We expect our new measures to have a wide range of applications, but we note that their estimates are sensitive to rare or private variants: some population-characterization applications suggest exploiting those sensitivities, whereas estimation of relatedness may best use all genetic markers without filtering on minor allele frequency.