Linkage disequilibrium as a signature of selective sweeps
Linkage disequilibrium as a signature of selective sweeps
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DOI：
10.1534/genetics.103.025387
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发表时间：
2004-07-01
期刊：
影响因子：
3.3
通讯作者：
Nielsen, R
中科院分区：
文献类型：
--
作者：
Kim, Y;Nielsen, R
有益突变的搭便车效应或选择性扫描产生了等位基因频率的独特分布和多态位点的空间分布。一个复合似然检验先前设计检测这些签名的选择性扫描，仅根据多态性的空间分布和边际等位基因频率。由于过量的连锁不平衡（LD）也被称为是一个强有力的签名的选择性扫描，我们调查有多少统计能力增加了列入信息LD。LD的预期模式是通过系谱方法预测的。理论和模拟都表明，强LD产生于有益突变位置两侧的狭窄区域。然而，预计双方都缺乏LD。我们探索各种方法来检测这个签名的选择性扫描的统计检验。提出了一种新的复合似然方法，将有关LD的信息。这种方法使我们能够检测选择性扫描和估计的选择模型的参数比以前的复合似然方法，不考虑LD。然而，通过包括LD所取得的改善是相当小的，这表明关于选择性扫描的大部分相关信息是由多态性的空间分布和边缘等位基因频率捕获的。
The hitchhiking effect of a beneficial mutation, or a selective sweep, generates a unique distribution of allele frequencies and spatial distribution of polymorphic sites. A composite-likelihood test was previously designed to detect these signatures of a selective sweep, solely on the basis of the spatial distribution and marginal allele frequencies of polymorphisms. As an excess of linkage disequilibrium (LD) is also known to be a strong signature of a selective sweep, we investigate how much statistical power is increased by the inclusion of information regarding LD. The expected pattern of LD is predicted by a genealogical approach. Both theory and simulation suggest that strong LD is generated in narrow regions at both sides of the location of beneficial mutation. However, a lack of LD is expected across the two sides. We explore various ways to detect this signature of selective sweeps by statistical tests. A new composite-likelihood method is proposed to incorporate information regarding LD. This method enables us to detect selective sweeps and estimate the parameters of the selection model better than the previous composite-likelihood method that does not take LD into account. However, the improvement made by including LD is rather small, suggesting that most of the relevant information regarding selective sweeps is captured by the spatial distribution and marginal allele frequencies of polymorphisms.