ArticleGenetics2003
The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias.
Article in Genetics, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
41 citing papers in PubMed.
- Substitution-Mutation Rate Ratio (c/µ) As Molecular Adaptation Test Beyond Ka/Ks: A SARS-COV-2 Case Study.Journal of molecular evolution · 2025Article
- Characterization of Firmiana danxiaensis plastomes and comparative analysis of Firmiana: insight into its phylogeny and evolution.BMC genomics · 2024Article
- Comparative and phylogenetic analyses of nine complete chloroplast genomes of Orchidaceae.Scientific reports · 2023Article
- Base Composition, Codon Usage, and Patterns of Gene Sequence Evolution in Butterflies.Genome biology and evolution · 2023Article
- Hunting for Beneficial Mutations: Conditioning on SIFT Scores When Estimating the Distribution of Fitness Effect of New Mutations.Genome biology and evolution · 2022Article
- Slow evolution of sex-biased genes in the reproductive tissue of the dioecious plant Salix viminalis.Molecular ecology · 2018Article
- Selfing in Haploid Plants and Efficacy of Selection: Codon Usage Bias in the Model Moss Physcomitrella patens.Genome biology and evolution · 2017Article
- Adaptive Evolution Is Substantially Impeded by Hill-Robertson Interference in Drosophila.Molecular biology and evolution · 2016Article
- Faster-X effects in two Drosophila lineages.Genome biology and evolution · 2014Article
- Differential strengths of positive selection revealed by hitchhiking effects at small physical scales in Drosophila melanogaster.Molecular biology and evolution · 2014Article
- Modeling the effect of changing selective pressures on polymorphism and divergence.Theoretical population biology · 2013Article
- Trade-off between selection for dosage compensation and masculinization on the avian Z chromosome.Genetics · 2012Article
- Modeling coding-sequence evolution within the context of residue solvent accessibility.BMC evolutionary biology · 2012Article
- Weak selection and protein evolution.Genetics · 2012Review
- The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes.Genome biology and evolution · 2012Article
- Article
- Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma.Genetics · 2011Article
- Factors affecting synonymous codon usage bias in chloroplast genome of oncidium gower ramsey.Evolutionary bioinformatics online · 2011Article
- Detecting positive and purifying selection at synonymous sites in yeast and worm.Molecular biology and evolution · 2010Article
- Characterising functionally important and ecologically meaningful genetic diversity using a candidate gene approach.Genetica · 2010Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most methods for estimating the rate of synonymous and nonsynonymous substitution per site define a site as a mutational opportunity: the proportion of sites that are synonymous is equal to the proportion of mutations that would be synonymous under the model of evolution being considered. Here we demonstrate that this definition of a site can give misleading results and that a physical definition of site should be used in some circumstances. We illustrate our point by reexamining the relationship between codon usage bias and the synonymous substitution rate. It has recently been shown that the rate of synonymous substitution, calculated using the Goldman-Yang method, which encapsulates the mutational-opportunity definition of a site at a high level of sophistication, is either positively correlated or uncorrelated to synonymous codon bias in Drosophila. Using other methods, which account for synonymous codon bias but define a site physically, we show that there is a negative correlation between the synonymous substitution rate and codon bias and that the lack of a negative correlation using the Goldman-Yang method is due to the way in which the number of synonymous sites is counted. We also show that there is a positive correlation between the synonymous substitution rate and third position GC content in mammals, but that the relationship is considerably weaker than that obtained using the Goldman-Yang method. We argue that the Goldman-Yang method is misleading in this context and conclude that methods that rely on a mutational-opportunity definition of a site should be used with caution.
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