Department of Mathematical Sciences, University of Nevada, Las Vegas, Nevada, United States of America.
54 Crescent Ave, Apt G, Dorchester, Massachusetts, United States of America.
PLoS One. 2019 Jan 18;14(1):e0194709. doi: 10.1371/journal.pone.0194709. eCollection 2019.
We have developed a Poisson random field model for estimating the distribution of selective effects of newly arisen nonsynonymous mutations that could be observed as polymorphism or divergence in samples of two related species under the assumption that the two species populations are not at mutation-selection-drift equilibrium. The model is applied to 91Drosophila genes by comparing levels of polymorphism in an African population of D. melanogaster with divergence to a reference strain of D. simulans. Based on the difference of gene expression level between testes and ovaries, the 91 genes were classified as 33 male-biased, 28 female-biased, and 30 sex-unbiased genes. Under a Bayesian framework, Markov chain Monte Carlo simulations are implemented to the model in which the distribution of selective effects is assumed to be Gaussian with a mean that may differ from one gene to the other to sample key parameters. Based on our estimates, the majority of newly-arisen nonsynonymous mutations that could contribute to polymorphism or divergence in Drosophila species are mildly deleterious with a mean scaled selection coefficient of -2.81, while almost 86% of the fixed differences between species are driven by positive selection. There are only 16.6% of the nonsynonymous mutations observed in sex-unbiased genes that are under positive selection in comparison to 30% of male-biased and 46% of female-biased genes that are beneficial. We also estimated that D. melanogaster and D. simulans may have diverged 1.72 million years ago.
我们开发了泊松随机场模型，用于估计新出现的非同义突变的选择效应在两个相关物种的样本中作为多态性或分歧的分布，前提是两个物种群体没有达到突变-选择-漂变平衡。该模型通过比较非洲黑腹果蝇种群中的多态性水平与参考品系黑腹果蝇的分歧，应用于 91 个果蝇基因。根据睾丸和卵巢之间的基因表达水平差异，将 91 个基因分为 33 个雄性偏倚基因、28 个雌性偏倚基因和 30 个性别无偏倚基因。在贝叶斯框架下，通过马尔可夫链蒙特卡罗模拟实现了模型，其中假设选择效应的分布为均值可能因基因而异的高斯分布，以抽样关键参数。根据我们的估计，大多数可能导致果蝇物种多态性或分歧的新出现的非同义突变具有轻度有害性，平均缩放选择系数为-2.81，而物种之间的固定差异几乎 86%是由正选择驱动的。与 30%的雄性偏倚基因和 46%的雌性偏倚基因有利相比，在性别无偏倚基因中观察到的只有 16.6%的非同义突变受到正选择的影响。我们还估计，黑腹果蝇和黑腹果蝇可能在 172 万年前就已经分化。
