Estimating Allele Age and Selection Coefficient from Time-Serial Data
Estimating Allele Age and Selection Coefficient from Time-Serial Data
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DOI：
10.1534/genetics.112.140939
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发表时间：
2012-10-01
期刊：
影响因子：
3.3
通讯作者：
Slatkin, Montgomery
中科院分区：
文献类型：
--
作者：
Malaspinas, Anna-Sapfo;Malaspinas, Orestis;Slatkin, Montgomery
测序技术的最新进展使得越来越多的古代基因组数据变得可用。特别是，现在可以在不同时间点针对多个样本中的特定单核苷酸多态性。此类时间序列数据也可在实验或病毒进化的背景下获得。时间序列数据应该能够更精确地推断群体遗传参数，并检验有关自然选择近期行为的假设。在这篇手稿中，我们开发了一种似然方法来根据时间序列数据联合估计选择系数和等位基因的年龄。我们的方法可用于从单个双等位基因座采样的等位基因频率。通过一步过程逼近 Wright-Fisher 模型的标准扩散方程来计算转移概率。我们证明我们的方法可以产生无偏估计。通过模拟测试该方法的准确性。最后，通过对马的几个编码毛色的基因座的应用来说明该方法的实用性，这种模式以前与驯化有关。重要的是，考虑到我们估计等位基因年龄的能力，有可能在区分新突变选择和固定变异选择这一重要问题上获得关注。例如，在这个毛色示例中，我们估计了该等位基因的年龄，该等位基因被发现早于驯化。
Recent advances in sequencing technologies have made available an ever-increasing amount of ancient genomic data. In particular, it is now possible to target specific single nucleotide polymorphisms in several samples at different time points. Such time-series data are also available in the context of experimental or viral evolution. Time-series data should allow for a more precise inference of population genetic parameters and to test hypotheses about the recent action of natural selection. In this manuscript, we develop a likelihood method to jointly estimate the selection coefficient and the age of an allele from time-serial data. Our method can be used for allele frequencies sampled from a single diallelic locus. The transition probabilities are calculated by approximating the standard diffusion equation of the Wright-Fisher model with a one-step process. We show that our method produces unbiased estimates. The accuracy of the method is tested via simulations. Finally, the utility of the method is illustrated with an application to several loci encoding coat color in horses, a pattern that has previously been linked with domestication. Importantly, given our ability to estimate the age of the allele, it is possible to gain traction on the important problem of distinguishing selection on new mutations from selection on standing variation. In this coat color example for instance, we estimate the age of this allele, which is found to predate domestication.