Microsatellite null alleles and estimation of population differentiation
Microsatellite null alleles and estimation of population differentiation
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DOI：
10.1093/molbev/msl191
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发表时间：
2007-03-01
影响因子：
10.7
通讯作者：
Estoup, Arnaud
中科院分区：
文献类型：
--
作者：
Chapuis, Marie-Pierre;Estoup, Arnaud
微卫星无效等位基因是群体遗传学研究中常见的现象，但其对群体分化的影响尚不清楚。基于合并的计算机模拟被用来研究无效等位基因的进化动力学，它们对F（ST）和遗传距离的影响，以及无效等位基因频率估计的效率。此外，我们探讨了现有的方法来校正基因型数据的无效等位基因进行估计F（ST）和遗传距离，我们比较了这种方法与一种新的方法在这里提出的（仅为F（ST））。等位基因很可能在有效大小较大的群体中遇到，在侧翼区域具有异常高的突变率，并且与克隆等位基因状态和引物设计的群体不同。当群体分化显著时，F（ST）和遗传距离在无效等位基因的存在下被高估。使用Dempster等人（1977）中提出的算法精确估计无效等位基因的频率。校正无效等位基因的基因型数据的传统方法没有提供F（ST）和遗传距离的准确估计。然而，使用Cavalli-Sforza和Edwards（1967）的遗传距离，经传统方法校正后，得到的估计值比未经校正的估计值更好。F（ST）估计校正基因型频率进行时，限制可见的等位基因大小。所提出的方法和传统的校正方法都已经在http://www.montpellier.inra.fr/URLB/上免费提供的程序中实现。我们使用2个已发表的微卫星数据集的基础上，原始和重新设计的引物对，以经验证实我们的模拟结果。
Microsatellite null alleles are commonly encountered in population genetics studies, yet little is known about their impact on the estimation of population differentiation. Computer simulations based on the coalescent were used to investigate the evolutionary dynamics of null alleles, their impact on F(ST) and genetic distances, and the efficiency of estimators of null allele frequency. Further, we explored how the existing method for correcting genotype data for null alleles performed in estimating F(ST) and genetic distances, and we compared this method with a new method proposed here (for F(ST) only). Null alleles were likely to be encountered in populations with a large effective size, with an unusually high mutation rate in the flanking regions, and that have diverged from the population from which the cloned allele state was drawn and the primers designed. When populations were significantly differentiated, F(ST) and genetic distances were overestimated in the presence of null alleles. Frequency of null alleles was estimated precisely with the algorithm presented in Dempster et al. (1977). The conventional method for correcting genotype data for null alleles did not provide an accurate estimate of F(ST) and genetic distances. However, the use of the genetic distance of Cavalli-Sforza and Edwards (1967) corrected by the conventional method gave better estimates than those obtained without correction. F(ST) estimation from corrected genotype frequencies performed well when restricted to visible allele sizes. Both the proposed method and the traditional correction method have been implemented in a program that is available free of charge at http://www.montpellier.inra.fr/URLB/. We used 2 published microsatellite data sets based on original and redesigned pairs of primers to empirically confirm our simulation results.