On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations
On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in nonequilibrium populations
复制标题
DOI：
10.1534/genetics.106.069450
复制
发表时间：
2007-08-01
期刊：
影响因子：
3.3
通讯作者：
Aquadro, Charles E.
中科院分区：
文献类型：
--
作者：
Jensen, Jeffrey D.;Thornton, Kevin R.;Aquadro, Charles E.
经验种群遗传学中一个至关重要的挑战是区分中性的非平衡过程和产生类似变异模式的选择性力量。我们在这里研究连锁不平衡(即标记之间的非随机关联)在多大程度上改善了这种区分。我们证明了最近提出的搭便车模型特有的链接不平衡模式在非平衡中性模型下被复制。我们还证明，联合考虑变种之间的空间关联模式以及站点-频谱仍然是有价值的。通过对平衡中性、非平衡中性、平衡搭便车、非平衡搭便车和重复搭便车模型的比较，我们评估了一个连锁不平衡(LD)统计量(omega(Max))，该统计量似乎有能力识别最近被正选择塑造的区域。最值得注意的是，对于与非非洲黑腹果蝇种群相关的人口统计学参数，我们利用这个统计数据证明了选定的基因座与中性基因座是可以区分的。
A critically important challenge in empirical population genetics is distinguishing neutral nonequilibrium processes from selective forces that produce similar patterns of variation. We here examine the extent to which linkage disequilibrium (i.e., nonrandom associations between markers) improves this discrimination. We show that patterns of linkage disequilibrium recently proposed to be unique to hitchhiking models are replicated under nonequilibrium neutral models. We also demonstrate that jointly considering spatial patterns of association among variants alongside the site-frequency spectrum is nonetheless of value. Through a comparison of models of equilibrium neutrality, nonequilibrium neutrality, equilibrium hitchhiking, nonequilibrium hitchhiking, and recurrent hitchhiking, we evaluate a linkage disequilibrium (LD) statistic (omega(max)) that appears to have power to identify regions recently shaped by positive selection. Most notably, for demographic parameters relevant to non-African populations of Drosophila melanogaster, we demonstrate that selected loci are distinguishable from neutral loci using this statistic.