Population differentiation as a test for selective sweeps
Population differentiation as a test for selective sweeps
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DOI：
10.1101/gr.100545.109
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发表时间：
2010-03-01
期刊：
影响因子：
7
通讯作者：
Reich, David
中科院分区：
文献类型：
--
作者：
Chen, Hua;Patterson, Nick;Reich, David
选择性扫描会增加种群间的遗传分化，使等位基因频率谱偏离中性预期。我们提出了一种似然方法检测选择性扫描，涉及联合建模两个群体之间的多位点等位基因频率分化。我们使用布朗运动模型的遗传漂变下的中性，和一个确定性模型近似的影响，选择性扫描单核苷酸多态性（SNP）在附近。我们测试的方法与广泛的模拟数据，并表明，在某些情况下，该方法提供了更高的功率比以前报道的方法来检测选择性扫描，并可以提供令人惊讶的良好定位的位置选择的等位基因。我们的技术的优势在于，它使用群体之间的等位基因频率差异，这比基于等位基因频谱的方法对SNP发现中的确定偏差更稳健。我们应用这种方法来比较大陆不同的人群，以及北方和南欧人。我们的分析确定了一系列基因座作为选择的候选靶点，包括众所周知的选择基因座和先前扫描未突出显示的新区域。
Selective sweeps can increase genetic differentiation among populations and cause allele frequency spectra to depart from the expectation under neutrality. We present a likelihood method for detecting selective sweeps that involves jointly modeling the multilocus allele frequency differentiation between two populations. We use Brownian motion to model genetic drift under neutrality, and a deterministic model to approximate the effect of a selective sweep on single nucleotide polymorphisms (SNPs) in the vicinity. We test the method with extensive simulated data, and demonstrate that in some scenarios the method provides higher power than previously reported approaches to detect selective sweeps, and can provide surprisingly good localization of the position of a selected allele. A strength of our technique is that it uses allele frequency differentiation between populations, which is much more robust to ascertainment bias in SNP discovery than methods based on the allele frequency spectrum. We apply this method to compare continentally diverse populations, as well as Northern and Southern Europeans. Our analysis identifies a list of loci as candidate targets of selection, including well-known selected loci and new regions that have not been highlighted by previous scans for selection.