Przeworski Molly
Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
Genetics. 2003 Aug;164(4):1667-76. doi: 10.1093/genetics/164.4.1667.
The fixation of a beneficial allele in a population leaves a well-characterized signature in patterns of nucleotide variation at linked sites. This signature can be used to estimate the time since fixation from patterns of polymorphism in extant individuals. I introduce a method to assess the support in polymorphism data for a recent episode of directional positive selection and to estimate the time since fixation. I summarize the polymorphism data by three statistics that carry information about levels of diversity, the allele frequency spectrum, and the extent of allelic associations. Simulations are then used to obtain a sample from the posterior distribution of the time since fixation, conditional on the observed summaries. I test the performance of the approach on simulated data and apply it to the gene tb1 in maize. The data support the recent fixation of a favored allele, consistent with what is known about the importance of tb1 in the domestication process of maize.
有益等位基因在种群中的固定会在连锁位点的核苷酸变异模式中留下特征明显的印记。这一印记可用于根据现存个体的多态性模式来估计自固定以来的时间。我介绍了一种方法，用于评估多态性数据对近期定向正选择事件的支持程度，并估计自固定以来的时间。我通过三个统计量来总结多态性数据，这三个统计量携带了有关多样性水平、等位基因频率谱和等位基因关联程度的信息。然后利用模拟来获得自固定以来时间的后验分布样本，条件是基于观察到的总结。我在模拟数据上测试了该方法的性能，并将其应用于玉米中的tb1基因。数据支持了一个有利等位基因近期的固定，这与已知的tb1在玉米驯化过程中的重要性相符。
