Navascués Miguel, Hardy Olivier J, Burgarella Concetta
Equipe Eco-Evolution Mathématique, CNRS UMR 7625 Ecologi et Evolution, Université Pierre et Marie Curie and Ecole Normale Supérieure, Paris, France.
Genetics. 2009 Mar;181(3):1013-9. doi: 10.1534/genetics.108.098194. Epub 2008 Dec 22.
This work extends the methods of demographic inference based on the distribution of pairwise genetic differences between individuals (mismatch distribution) to the case of linked microsatellite data. Population genetics theory describes the distribution of mutations among a sample of genes under different demographic scenarios. However, the actual number of mutations can rarely be deduced from DNA polymorphisms. The inclusion of mutation models in theoretical predictions can improve the performance of statistical methods. We have developed a maximum-pseudolikelihood estimator for the parameters that characterize a demographic expansion for a series of linked loci evolving under a stepwise mutation model. Those loci would correspond to DNA polymorphisms of linked microsatellites (such as those found on the Y chromosome or the chloroplast genome). The proposed method was evaluated with simulated data sets and with a data set of chloroplast microsatellites that showed signal for demographic expansion in a previous study. The results show that inclusion of a mutational model in the analysis improves the estimates of the age of expansion in the case of older expansions.
这项工作将基于个体间成对遗传差异分布（错配分布）的人口统计学推断方法扩展到连锁微卫星数据的情况。群体遗传学理论描述了在不同人口统计学情景下基因样本中突变的分布。然而，实际的突变数量很少能从DNA多态性中推导出来。在理论预测中纳入突变模型可以提高统计方法的性能。我们针对在逐步突变模型下进化的一系列连锁位点，开发了一种用于表征人口扩张的参数的最大伪似然估计器。这些位点将对应于连锁微卫星的DNA多态性（如在Y染色体或叶绿体基因组上发现的那些）。我们用模拟数据集以及一个叶绿体微卫星数据集对所提出的方法进行了评估，该叶绿体微卫星数据集在之前的一项研究中显示出人口扩张的信号。结果表明，在分析中纳入突变模型在扩张时间较久的情况下能改善对扩张时间的估计。
