Identifying consistent allele frequency differences in studies of stratified populations

1. With increasing application of pooled-sequencing approaches to population genomics robust methods are needed to accurately quantify allele frequency differences between populations. Identifying consistent differences across stratified populations can allow us to detect genomic regions under selection and that differ between populations with different histories or attributes. Current popular statistical tests are easily implemented in widely available software tools which make them simple for researchers to apply. However, there are potential problems with the way such tests are used ,which means that underlying assumptions about the data are frequently violated.
2. These problems are highlighted by simulation of simple but realistic population genetic models of neutral evolution and the performance of different tests are assessed. We present alternative tests (including GLMs with quasibinomial error structure) with attractive properties for the analysis of allele frequency differenc...

1. 随着混合测序（pooled sequencing）方法在群体基因组学（population genomics）中的应用日益广泛，亟需开发稳健的方法以精准量化不同群体间的等位基因频率（allele frequency）差异。识别分层群体间的一致性差异，可帮助我们检测处于选择压力下的基因组区域，以及在具有不同演化历史或特征的群体间存在差异的区域。当前主流的统计检验方法可通过广泛可用的软件工具轻松实现，令研究者能够便捷地应用此类方法。然而，此类检验在实际使用场景中存在潜在问题，这意味着关于数据的底层假设常常被违背。
2. 我们通过构建简单但贴合实际的中性演化（neutral evolution）群体遗传模型进行模拟，凸显了上述问题，并评估了不同检验方法的性能表现。本文提出若干具备优良特性的替代检验方法（包含带有准二项误差结构的广义线性模型（GLMs）），用于等位基因频率差异的分析……