ReviewPhilosophical transactions of the Royal Society of London. Series B, Biological sciences2010
Forces that influence the evolution of codon bias.
Review in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 195 papers.
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Who cites it
195 citing papers in PubMed.
- Natural Selection Drives Codon Usage Bias in the Mitochondrial Genome ofAnimals : an open access journal from MDPI · 2026Article
- Article
- GGAR: gradient guided adaptive regularization enhances deep learning classification of brassica species using codon usage bias.BMC bioinformatics · 2026Article
- Integrative chloroplast genomics of Polygonaceae: evolutionary dynamics, codon optimization, and phylogenetic resolution.BMC plant biology · 2026Article
- Refined chloroplast annotations, repeat profiles, and phylogenomic evidence reveal maternal lineage shifts and independent evolution in the Triticum-Aegilops complex.BMC plant biology · 2026Article
- Synonymous but not silent: functional codon bias reveals decoupled mitonuclear evolution in parasitic worms.Bioinformatics advances · 2026Article
- Codon Usage Bias Analysis of Citrus Leaf Blotch Virus.Viruses · 2025Article
- Article
- Molecular identification and phylogenetic analysis of Polygonatum Kingianum with different floral colors on the basis of chloroplast genomes.BMC plant biology · 2025Article
- Mitochondrial Genomes of Three Species of the Family Camaenidae (Gastropoda: Stylommatophora): Structural Features, Codon Usage Patterns, and Phylogenetic Implications.Ecology and evolution · 2025Article
- Comparative mitogenomics reveals evolutionary drivers of Strongyloidea nematodes dwelling in gastrointestinal tract.BMC genomics · 2025Article
- Are Bacterial Processes Dependent on Global Ribosome Pausing Affected by tRNA Modification Defects?Journal of molecular biology · 2025Review
- Dinucleotide preferences underlie apparent codon preference reversals in theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- The effectiveness of selection in a species affects the direction of amino acid frequency evolution.bioRxiv : the preprint server for biology · 2025Article
- A model of Hill-Robertson interference caused by purifying selection in a nonrecombining genome.Genetics · 2025Article
- Article
- Phylogeny and evolutionary dynamics of the Rubia genus based on the chloroplast genome of Rubia tibetica.Scientific reports · 2025Article
- Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera.mBio · 2025Article
- Efficient discovery of frequently co-occurring mutations in a sequence database with matrix factorization.PLoS computational biology · 2025Article
- Interpreting mammalian synonymous site conservation in light of the unwanted transcript hypothesis.Nature communications · 2025Article
135 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
The frequencies of alternative synonymous codons vary both among species and among genes from the same genome. These patterns have been inferred to reflect the action of natural selection. Here we evaluate this in bacteria. While intragenomic variation in many species is consistent with selection favouring translationally optimal codons, much of the variation among species appears to be due to biased patterns of mutation. The strength of selection on codon usage can be estimated by two different approaches. First, the extent of bias in favour of translationally optimal codons in highly expressed genes, compared to that in genes where selection is weak, reveals the long-term effectiveness of selection. Here we show that the strength of selected codon usage bias is highly correlated with bacterial growth rate, suggesting that selection has favoured translational efficiency. Second, the pattern of bias towards optimal codons at polymorphic sites reveals the ongoing action of selection. Using this approach we obtained results that were completely consistent with the first method; importantly, the frequency spectra of optimal codons at polymorphic sites were similar to those predicted under an equilibrium model. Highly expressed genes in Escherichia coli appear to be under continuing strong selection, whereas selection is very weak in genes expressed at low levels.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.