A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective
A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective
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DOI：
10.1534/genetics.108.092221
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发表时间：
2008-10-01
期刊：
影响因子：
3.3
通讯作者：
Gaggiotti, Oscar
中科院分区：
文献类型：
--
作者：
Foll, Matthieu;Gaggiotti, Oscar
从基因组调查中识别自然选择下的基因座在不同的研究领域都有很大的兴趣。分离中性效应和适应性效应的常用方法是基于基因座特异性群体分化系数来识别离群值。在这里，我们扩展这样的方法来直接估计的概率，每个位点是使用贝叶斯方法进行选择。我们还将其扩展到允许使用AFLP等主导市场。结果表明，该模型是稳健的。中性遗传分化的复杂人口统计学情景。在这里，我们表明，包含经历了强大瓶颈的孤立群体可能会导致高误报率。然而，我们证明，通过仔细选择应纳入分析的人群，可以避免这些问题。我们分析了两个以前发表的数据集：人类的数据集的共显性标记和岩藻的显性标记数据集。我们还进行了详细的敏感性研究，以比较该方法的功率上升扩增片段长度多态性（AFLP），SNP和微卫星标记。该方法已在我们的网站（http：//www-leca.ujf-grenoble.fr/logiciels.htm）上提供的新软件中实施。
Identifying loci under natural selection from genomic surveys is of great interest in different research areas. Commonly used methods to separate neutral effects front adaptive effects are based on locus-specific population differentiation coefficients to identify outliers. Here we extend Such an approach to estimate directly the probability that each locus is subject to selection using a Bayesian method. We also extend it to allow the use of dominant markets like AFLPs. It has been shown that this model is robust. to complex demographic scenarios for neutral genetic differentiation. Here we show that the inclusion of isolated Populations that underwent a strong bottleneck can lead to a high rate of false positives. Nevertheless, we demonstrate that it is possible to avoid them by carefully choosing the populations that should be included in the analysis. We analyze two previously published data sets: a human data set of codominant markers and a Littorina saxatilis data set of dominant markers. We also perform a detailed sensitivity study to compare the power of the method rising amplified fragment length polymorphism (AFLP), SNP, and microsatellite markers. The method has been implemented in a new software available at our website (http://www-leca.ujf-grenoble.fr/logiciels.htm).