ArticleProceedings of the National Academy of Sciences of the United States of America2007
Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed, 163 citations in OpenAlex.
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- Genetic polymorphisms in malaria vaccine candidate Plasmodium falciparum reticulocyte-binding protein homologue-5 among populations in Lagos, Nigeria.Malaria journal · 2020Article
- The stabilization of equilibria in evolutionary game dynamics through mutation: mutation limits in evolutionary games.Proceedings. Mathematical, physical, and engineering sciences · 2019Article
- Developing a High-Quality Linkage Map for the Atlantic KillifishG3 (Bethesda, Md.) · 2019Article
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- Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence.Molecular biology and evolution · 2017Article
- nala: text mining natural language mutation mentions.Bioinformatics (Oxford, England) · 2017Article
- Transcriptional Interference Promotes Rapid Expression Divergence of Drosophila Nested Genes.Genome biology and evolution · 2016Article
- Widespread adaptive evolution during repeated evolutionary radiations in New World lupins.Nature communications · 2016Article
- Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow.Current genomics · 2015Article
- ConPADE: genome assembly ploidy estimation from next-generation sequencing data.PLoS computational biology · 2015Article
- Causes of natural variation in fitness: evidence from studies of Drosophila populations.Proceedings of the National Academy of Sciences of the United States of America · 2015Review
- Genomics of ecological adaptation in cactophilic Drosophila.Genome biology and evolution · 2014Article
5 more citing papers are in PubMed but not listed here.
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4 authors at 3 institutions in 2 countries.
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Abstract
We have estimated the selective effects of amino acid replacements in natural populations by comparing levels of polymorphism in 91 genes in African populations of Drosophila melanogaster with their divergence from Drosophila simulans. The genes include about equal numbers whose level of expression in adults is greater in males, greater in females, or approximately equal in the sexes. Markov chain Monte Carlo methods were used to sample key parameters in the stationary distribution of polymorphism and divergence in a model in which the selective effect of each nonsynonymous mutation is regarded as a random sample from some underlying normal distribution whose mean may differ from one gene to the next. Our analysis suggests that approximately 95% of all nonsynonymous mutations that could contribute to polymorphism or divergence are deleterious, and that the average proportion of deleterious amino acid polymorphisms in samples is approximately 70%. On the other hand, approximately 95% of fixed differences between species are positively selected, although the scaled selection coefficient (N(e)s) is very small. We estimate that approximately 46% of amino acid replacements have N(e)s < 2, approximately 84% have N(e)s < 4, and approximately 99% have N(e)s < 7. Although positive selection among amino acid differences between species seems pervasive, most of the selective effects could be regarded as nearly neutral. There are significant differences in selection between sex-biased and unbiased genes, which relate primarily to the mean of the distributions of mutational effects and the fraction of slightly deleterious and weakly beneficial mutations that are fixed.
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