ArticleGenetics2009
Estimating selection intensity on synonymous codon usage in a nonequilibrium population.
Article in Genetics, 2009. 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.
- Isolating selective from non-selective forces using site frequency ratios.PLoS genetics · 2025Article
- Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster.Nature communications · 2024Article
- How does evolution work in superabundant microbes?Trends in microbiology · 2024Review
- Article
- Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2.Genome biology and evolution · 2021Article
- Mutation rates and selection on synonymous mutations in SARS-CoV-2.bioRxiv : the preprint server for biology · 2021Article
- Article
- Population Genomics on the Fly: Recent Advances in Drosophila.Methods in molecular biology (Clifton, N.J.) · 2020Review
- Evolution of Codon Usage Bias in Diatoms.Genes · 2019Article
- Synonymous Codon Usages as an Evolutionary Dynamic forInternational journal of molecular sciences · 2018Article
- Evolutionary forces affecting synonymous variations in plant genomes.PLoS genetics · 2017Article
- Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila.Genome biology and evolution · 2017Article
- Article
- Expression-Linked Patterns of Codon Usage, Amino Acid Frequency, and Protein Length in the Basally Branching Arthropod Parasteatoda tepidariorum.Genome biology and evolution · 2016Article
- Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae.Journal of molecular evolution · 2016Article
- The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations.Heredity · 2015Article
- Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura.G3 (Bethesda, Md.) · 2014Article
- Effective population size does not predict codon usage bias in mammals.Ecology and evolution · 2014Article
- Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models.Molecular biology and evolution · 2013Article
- Stabilizing selection, purifying selection, and mutational bias in finite populations.Genetics · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Codon usage bias is the nonrandom use of synonymous codons for the same amino acid. Most population genetic models of codon usage evolution assume that the population is at mutation-selection-drift equilibrium. Natural populations, however, frequently deviate from equilibrium, often because of recent demographic changes. Here, we construct a matrix model that includes the effects of a recent change in population size on estimates of selection on preferred vs. unpreferred codons. Our results suggest that patterns of synonymous polymorphisms affecting codon usage can be quite erratic after such a change; statistical methods that fail to take demographic effects into account can then give incorrect estimates of important parameters. We propose a new method that can accurately estimate both demographic and codon usage parameters. The method also provides a simple way of testing for the effects of covariates such as gene length and level of gene expression on the intensity of selection, which we apply to a large Drosophila melanogaster polymorphism data set. Our analyses of twofold degenerate codons reveal that (i) selection acts in favor of preferred codons, (ii) there is mutational bias in favor of unpreferred codons, (iii) shorter genes and genes with higher expression levels are under stronger selection, and (iv) there is little evidence for a recent change in population size in the Zimbabwe population of D. melanogaster.
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