ArticleMolecular biology and evolution2010
Detecting positive and purifying selection at synonymous sites in yeast and worm.
Article in Molecular biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Synonymous Codons as Potential Contributors to Chromatin Stability and Gene Body Methylation in Plants.Journal of molecular evolution · 2026Article
- Selection profiles in RNA viruses reflect the characteristics of viruses more than individual proteins.PLoS pathogens · 2026Article
- Synonymous edits in theProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Deleterious Variation in Natural Populations and Implications for Conservation Genetics.Annual review of animal biosciences · 2023Review
- Genome Wide Identification and Annotation of NGATHA Transcription Factor Family in Crop Plants.International journal of molecular sciences · 2022Article
- No evidence for widespread positive selection on double substitutions within codons in primates and yeasts.Frontiers in genetics · 2022Article
- Decoding the effects of synonymous variants.Nucleic acids research · 2021Article
- Avoidance of protein unfolding constrains protein stability in long-term evolution.Biophysical journal · 2021Article
- Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril.Molecular biology and evolution · 2020Article
- Identifying the drivers of computationally detected correlated evolution among sites under antibiotic selection.Evolutionary applications · 2020Article
- A comprehensive analysis of the B3 superfamily identifies tissue-specific and stress-responsive genes in chickpea (3 Biotech · 2019Article
- Evolutionary insights ofPeerJ · 2019Article
- The Contribution of Purifying Selection, Linkage, and Mutation Bias to the Negative Correlation between Gene Expression and Polymorphism Density in Yeast Populations.Genome biology and evolution · 2018Article
- Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation.Scientific reports · 2018Article
- Widespread position-specific conservation of synonymous rare codons within coding sequences.PLoS computational biology · 2017Article
- Article
- Are Synonymous Sites in Primates and Rodents Functionally Constrained?Journal of molecular evolution · 2016Article
- Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana.Genome biology and evolution · 2015Article
- Functional and Structural Consequence of Rare Exonic Single Nucleotide Polymorphisms: One Story, Two Tales.Genome biology and evolution · 2015Article
- The relationship between dN/dS and scaled selection coefficients.Molecular biology and evolution · 2015Article
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3 authors.
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Abstract
We present a new computational method to identify positive and purifying selection at synonymous sites in yeast and worm. We define synonymous substitutions that change codons from preferred to unpreferred or vice versa as nonconservative synonymous substitutions and all other substitutions as conservative. Using a maximum-likelihood framework, we then test whether conservative and nonconservative synonymous substitutions occur at equal rates. Our approach replaces the standard rate of synonymous substitutions per synonymous site, dS, with two new rates, the conservative synonymous substitution rate (dS(C)) and the nonconservative synonymous substitution rate (dS(N)). Based on the ratio dS(N)/dS(C), we find that 0.05% of all yeast genes and none of worm genes show evidence of positive selection at synonymous sites (dS(N)/dS(C) > 1). On the other hand, 9.44% of all yeast genes and 5.12% of all worm genes show evidence of significant purifying selection on synonymous sites (dS(N)/dS(C) < 1). We also find that dS(N) correlates strongly with gene expression level, whereas the correlation between expression level and dS(C) is very weak. Thus, dS(N) captures most of the signal of selection for translational accuracy and speed, whereas dS(C) is not strongly influenced by this selection pressure. We suggest that the ratio dN/dS(C) may be more appropriate than the ratio dN/dS to identify positive or purifying selection on amino acids.
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