Data from: The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness

We explore factors affecting patterns of polymorphism and divergence (as captured by the neutrality index) at mammalian mitochondrial loci. To do this, we develop a population genetic model that incorporates a fraction of neutral amino acid sites, mutational bias, and a probability distribution of selection coefficients against new nonsynonymous mutations. We confirm, by reanalyzing publicly available data sets, that the mitochondrial cyt-b gene shows a broad range of neutrality indices across mammalian taxa, and explore the biological factors that can explain this observation. We find that observed patterns of differences in the neutrality index, polymorphism and divergence are not caused by differences in mutational bias. They can, however, be explained by a combination of a small fraction of neutral amino acid sites, weak selection acting on most amino acid mutations, and differences in effective population size among taxa.本研究探讨了影响哺乳动物线粒体基因座多态性与分化模式（以中性指数（neutrality index）表征）的相关因素。为此，我们构建了一款群体遗传模型，该模型纳入了中性氨基酸位点占比、突变偏倚以及针对新发非同义突变的选择系数概率分布。通过重新分析公开可用的数据集，我们证实：哺乳动物类群的线粒体细胞色素b（cyt-b）基因的中性指数存在宽泛的取值范围；并进一步探索了可解释该观测结果的生物学因素。研究发现，观测到的中性指数、多态性与分化模式的差异，并非由突变偏倚的差异所导致。不过，该差异可通过以下因素的组合得到合理解释：中性氨基酸位点占比较低、多数氨基酸突变受到弱选择作用，以及不同类群间有效种群大小（effective population size）存在差异。