ArticleProceedings of the National Academy of Sciences of the United States of America2021
Weak selection on synonymous codons substantially inflates
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 49 citations in OpenAlex.
- Cancer treatment alters mutant selection in normal esophagus.Nature genetics · 2026Article
- Synonymous Codons as Potential Contributors to Chromatin Stability and Gene Body Methylation in Plants.Journal of molecular evolution · 2026Article
- Estimating the evolutionary fitness of specific synonymous codon changes.Molecular biology and evolution · 2026Article
- Selection profiles in RNA viruses reflect the characteristics of viruses more than individual proteins.PLoS pathogens · 2026Article
- Molecular Evidence for the Parallel Evolution of Anosmia in Multiple Odontoceti (Toothed Whales) Clades.Genes · 2026Article
- A naturally synonymous mutation modulates an ERK-centered regulatory network to mediate thermotolerance divergence in Crassostrea oysters.Communications biology · 2026Article
- Estimating the evolutionary fitness of specific synonymous codon changes.bioRxiv : the preprint server for biology · 2026Article
- Cross-continental transmission and host adaptation ofiMetaOmics · 2025Article
- Leveraging FracMinHash Containment for GenomicbioRxiv : the preprint server for biology · 2025Article
- Functional synonymous mutations and their evolutionary consequences.Nature reviews. Genetics · 2025Review
- Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex.Nature reviews. Microbiology · 2025Review
- Quantifying the Evolution of SNPs That Affect RNA Secondary Structure in Arabidopsis thaliana Genes.Molecular biology and evolution · 2025Article
- A New Comparative Framework for Estimating Selection on Synonymous Substitutions.Molecular biology and evolution · 2025Article
- A new comparative framework for estimating selection on synonymous substitutions.bioRxiv : the preprint server for biology · 2025Article
- Dinucleotide codon substitutions as a signature of diversifying selection inFrontiers in molecular biosciences · 2025Article
- Concepts and Methods for Predicting Viral Evolution.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Concepts and methods for predicting viral evolution.bioRxiv : the preprint server for biology · 2024Article
- Article
- NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data.Nucleic acids research · 2024Article
- Patterns of Change in Nucleotide Diversity Over Gene Length.Genome biology and evolution · 2024Article
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4 authors at 1 institution in 1 country.
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Abstract
Synonymous codon substitutions are not always selectively neutral as revealed by several types of analyses, including studies of codon usage patterns among genes. We analyzed codon usage in 13 bacterial genomes sampled from across a large order of bacteria, Enterobacterales, and identified presumptively neutral and selected classes of synonymous substitutions. To estimate substitution rates, given a neutral/selected classification of synonymous substitutions, we developed a flexible [Formula: see text] substitution model that allows multiple classes of synonymous substitutions. Under this multiclass synonymous substitution (MSS) model, the denominator of [Formula: see text] includes only the strictly neutral class of synonymous substitutions. On average, the value of [Formula: see text] under the MSS model was 80% of that under the standard codon model in which all synonymous substitutions are assumed to be neutral. The indication is that conventional [Formula: see text] analyses overestimate these values and thus overestimate the frequency of positive diversifying selection and underestimate the strength of purifying selection. To quantify the strength of selection necessary to explain this reduction, we developed a model of selected compensatory codon substitutions. The reduction in synonymous substitution rate, and thus the contribution that selection makes to codon bias variation among genes, can be adequately explained by very weak selection, with a mean product of population size and selection coefficient, [Formula: see text].
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