Estimation of 2Nes from temporal allele frequency data
Estimation of 2Nes from temporal allele frequency data
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DOI：
10.1534/genetics.107.085019
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发表时间：
2008-05-01
期刊：
影响因子：
3.3
通讯作者：
Nielsen, Rasmus
中科院分区：
文献类型：
--
作者：
Bollback, Jonathan P.;York, Thomas L.;Nielsen, Rasmus
我们发展了一种新的方法来估计有效群体规模N-e和选择系数S，从单个双等位基因座位的等位基因频率时间序列数据中估计。该方法的基础是计算转移概率，使用扩散过程的数值解，并假设在每个时间点从该扩散过程中进行独立的二项抽样。我们将该方法应用于两个实例应用中。首先，我们根据已公布的现代和古代人类DNA样本，估计作用于CCR5-Delta 32突变的选择系数。我们表明，这些数据与S=0的假设是兼容的，尽管不能排除作用于这种突变的适度数量的选择。在我们的第二个例子中，我们估计了作用于在实验噬菌体种群中分离的突变的选择系数。结果表明，作用于该突变的选择系数接近于0.43。
We develop a new method for estimating effective population sizes, N-e, and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical Solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-Delta 32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s = 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is similar to 0.43.