On the distribution of temporal variations in allele frequency: Consequences for the estimation of effective population size and the detection of loci undergoing selection
On the distribution of temporal variations in allele frequency: Consequences for the estimation of effective population size and the detection of loci undergoing selection
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DOI：
10.1534/genetics.103.025908
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发表时间：
2004-09-01
期刊：
影响因子：
3.3
通讯作者：
Bataillon, T
中科院分区：
文献类型：
--
作者：
Goldringer, I;Bataillon, T
有效群体大小（N-e，）经常使用中性标记的等位基因频率的时间变化来估计。等位基因频率的这种时间变化通常从等位基因频率的标准化方差（F-c）估计。我们模拟Wright-Fisher群体，以生成（F）在bar（c）上的预期分布和F-e（F-c在几个位点上的平均值）。我们探索这些模拟（F）在酒吧（c）分布的卡方分布的调整，并评估各种情况下N-e估计的精度。接下来，我们概述了一个程序，以测试跨基因座的单个F-c的同质性，并确定与基因组的其余部分相比表现出极端F-c值的标记。这样的基因座很可能是在基因组区域进行选择，驱动F-c值大于（或小于）下的漂移单独预期。我们的程序在零假设（漂移在整个基因组中是均匀的）下为每个位点分配一个P值，同时控制被宣布为显著偏离磨坊的位点之间的假阳性率。该程序说明使用两个已公布的数据集：（i）实验小麦人口自然选择和（ii）玉米人口进行轮回选择。
The effective population size (N-e,) is frequently estimated using temporal changes in allele frequencies at neutral markers. Such temporal changes in allele frequencies are usually estimated from the standardized variance in allele frequencies (F-c). We simulate Wright-Fisher populations to generate expected distributions of (F) over bar (c) and of F-e (F-c averaged over several loci). We explore the adjustment of these Simulated (F) over bar (c) distributions to a chi-square distribution and evaluate the resulting precision on the estimation of N-e for various scenarios. Next, we outline a procedure to test for the homogeneity of the individual F-c across loci and identify markers exhibiting extreme F-c-values compared to the rest of the genome. Such loci are likely to be in genomic areas undergoing selection, driving F-c to values greater (or smaller) than expected under drift alone. Our procedure assigns a P-value to each locus under the null hypothesis (drift is homogeneous throughout the genome) and simultaneously controls the rate of false positive among loci declared as departing significantly from the mill. The procedure is illustrated using two published data sets: (i) an experimental wheat population subject to natural selection and (ii) a maize population undergoing recurrent selection.