Detecting loci under selection in a hierarchically structured population
Detecting loci under selection in a hierarchically structured population
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DOI：
10.1038/hdy.2009.74
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发表时间：
2009-10-01
期刊：
影响因子：
3.8
通讯作者：
Foll, M.
中科院分区：
文献类型：
--
作者：
Excoffier, L.;Hofer, T.;Foll, M.
在基因组扫描中，种群间的遗传多样性模式经常被用来检测选择下的基因座。事实上，参与局部适应的基因座应显示高FST值，而平衡选择下的基因座应显示低FST值。大多数基于FST的选择检验使用在简单的群体分化岛模型下产生的零分布。虽然这一模型已被证明是强大的，许多物种有一个更复杂的遗传结构，与一些人口共享最近的祖先或由于存在障碍，基因流动之间的不同部分的物种范围。在本文中，我们提出了一个层次岛模型，其中demes交换组内比组间更多的移民，产生的联合分布的遗传多样性内和种群之间的使用。我们发现，测试不占一个层次结构，当它存在时，产生大量的假阳性位点，而分层岛模型是强大的不确定性的确切数目的组和群体中的每组demes系统。我们的方法还明确考虑了突变过程，而不仅仅依赖于等位基因频率，这对短串联重复序列（STR）数据很重要。人类和棘鱼STR数据集的应用程序揭示了一个显着的基因座比以前获得的非层次模型下的数量少得多。从基因组扫描中消除假阳性位点应该使我们能够更好地确定哪一类基因选择正在起作用。Heredity（2009）103，285-298; doi：10.1038/hdy.2009.74;在线发表2009年7月22日
Patterns of genetic diversity between populations are often used to detect loci under selection in genome scans. Indeed, loci involved in local adaptations should show high FST values, whereas loci under balancing selection should rather show low FST values. Most tests of selection based on FST use a null distribution generated under a simple island model of population differentiation. Although this model has been shown to be robust, many species have a more complex genetic structure, with some populations sharing a recent ancestry or due to the presence of barriers to gene flow between different parts of a species range. In this paper, we propose the use of a hierarchical island model, in which demes exchange more migrants within groups than between groups, to generate the joint distribution of genetic diversity within and between populations. We show that tests not accounting for a hierarchical structure, when it exists, do generate a large excess of false positive loci, whereas the hierarchical island model is robust to uncertainties about the exact number of groups and demes per group in the system. Our approach also explicitly takes into account the mutational process, and does not just rely on allele frequencies, which is important for short tandem repeat (STR) data. An application to human and stickleback STR data sets reveals a much lower number of significant loci than previously obtained under a non-hierarchical model. The elimination of false positive loci from genome scans should allow us to better determine on which specific class of genes selection is operating. Heredity (2009) 103, 285-298; doi: 10.1038/hdy.2009.74; published online 22 July 2009