ArticleProceedings of the National Academy of Sciences of the United States of America2011
Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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101 citing papers in PubMed.
- Estimating the evolutionary fitness of specific synonymous codon changes.Molecular biology and evolution · 2026Article
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- The importance of nonsense errors: Estimating the rates and implications of ribosome drop-off during protein synthesis.PLoS genetics · 2026Article
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- Mitochondrial Genome ofAnimals : an open access journal from MDPI · 2026Article
- Evolution and Functional Implications of Codon Usage Bias in Eukaryotes.Journal of molecular evolution · 2026Review
- Natural Selection Drives AT-Biased Codon Usage in Mitochondrial Genomes of Early-DivergingJournal of fungi (Basel, Switzerland) · 2026Article
- Synonymous codon usage defines functional gene families.BMC biology · 2026Article
- Availability of Charged tRNAs Drives Maximal Protein Synthesis at Intermediate Levels of Codon Usage Bias.Bulletin of mathematical biology · 2026Article
- The Complete Mitochondrial Genome ofBiology · 2025Article
- Patterns and drivers of genome-wide codon usage bias in the fungal order Sordariales.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Macroevolutionary changes in natural selection on codon usage reflect evolution of the tRNA pool across a budding yeast subphylum.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera.mBio · 2025Article
- Variation in the fitness impact of translationally optimal codons among animals.Genome research · 2025Article
- Codon usage analysis in selected virulence genes of Staphylococcal species.Current genetics · 2025Article
- Comprehensive analysis of the codon usage patterns in the polyprotein coding sequences of the honeybee viruses.Frontiers in veterinary science · 2025Article
- Comparative chloroplast genomics of Cypripedioideae: structural divergence, adaptive evolution, and phylogenomic insights.Frontiers in plant science · 2025Article
- Compare Analysis of Codon Usage Bias of Nuclear Genome in Eight Sapindaceae Species.International journal of molecular sciences · 2024Article
- Description of mitochondrial genomes and phylogenetic analysis of Megophthalminae (Hemiptera: Cicadellidae).Journal of insect science (Online) · 2024Article
41 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
The genetic code is redundant with most amino acids using multiple codons. In many organisms, codon usage is biased toward particular codons. Understanding the adaptive and nonadaptive forces driving the evolution of codon usage bias (CUB) has been an area of intense focus and debate in the fields of molecular and evolutionary biology. However, their relative importance in shaping genomic patterns of CUB remains unsolved. Using a nested model of protein translation and population genetics, we show that observed gene level variation of CUB in Saccharomyces cerevisiae can be explained almost entirely by selection for efficient ribosomal usage, genetic drift, and biased mutation. The correlation between observed codon counts within individual genes and our model predictions is 0.96. Although a variety of factors shape patterns of CUB at the level of individual sites within genes, our results suggest that selection for efficient ribosome usage is a central force in shaping codon usage at the genomic scale. In addition, our model allows direct estimation of codon-specific mutation rates and elongation times and can be readily applied to any organism with high-throughput expression datasets. More generally, we have developed a natural framework for integrating models of molecular processes to population genetics models to quantitatively estimate parameters underlying fundamental biological processes, such a protein translation.
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