Inferring the distribution of selective effects from a time inhomogeneous model

• Published in: PloS one Vol. 14; no. 1; p. e0194709
• Main Authors: Amei, Amei, Zhou, Shilei
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 18.01.2019; Public Library of Science (PLoS)
• Subjects: Animals; Bayes Theorem; Bayesian analysis; Biology and Life Sciences; Computer simulation; Divergence; Drosophila; Drosophila melanogaster; Drosophila simulans; Evolution, Molecular; Gene expression; Gene loci; Gene mutation; Gene polymorphism; Genes; Genetic aspects; Genetic polymorphisms; Markov analysis; Markov chains; Models, Genetic; Mutation; Normal distribution; Ovaries; Parameter estimation; Physical sciences; Polymorphism; Polymorphism, Genetic; Positive selection; Research and Analysis Methods; Sex; Species; Testes; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0194709

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.