ArticleJournal of molecular evolution2004
Correlated evolution of synonymous and nonsynonymous sites in Drosophila.
Article in Journal of molecular evolution, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- 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
- The Effects of De Novo Mutation on Gene Expression and the Consequences for Fitness in Chlamydomonas reinhardtii.Molecular biology and evolution · 2024Article
- Weak selection on synonymous codons substantially inflatesProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Selfing in Haploid Plants and Efficacy of Selection: Codon Usage Bias in the Model Moss Physcomitrella patens.Genome biology and evolution · 2017Article
- Article
- Effective population size does not predict codon usage bias in mammals.Ecology and evolution · 2014Article
- Background selection as baseline for nucleotide variation across the Drosophila genome.PLoS genetics · 2014Article
- The impact of trans-regulation on the evolutionary rates of metazoan proteins.Nucleic acids research · 2013Article
- Three independent determinants of protein evolutionary rate.Journal of molecular evolution · 2013Review
- Widespread polymorphism in the positions of stop codons in Drosophila melanogaster.Genome biology and evolution · 2012Article
- Molecular evolution in nonrecombining regions of the Drosophila melanogaster genome.Genome biology and evolution · 2012Article
- Factors affecting synonymous codon usage bias in chloroplast genome of oncidium gower ramsey.Evolutionary bioinformatics online · 2011Article
- Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura.Journal of molecular evolution · 2009Article
- Protein rates of evolution are predicted by double-strand break events, independent of crossing-over rates.Genome biology and evolution · 2009Article
- Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila.Molecular biology and evolution · 2009Article
- Elevated levels of expression associated with regions of the Drosophila genome that lack crossing over.Biology letters · 2008Article
- Similar rates of protein adaptation in Drosophila miranda and D. melanogaster, two species with different current effective population sizes.BMC evolutionary biology · 2008Article
- Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.Cell · 2008Article
- No effect of recombination on the efficacy of natural selection in primates.Genome research · 2008Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent work has shown that Drosophila melanogaster genes with fast-evolving nonsynonymous sites have lower codon usage bias. This pattern has been attributed to interference between positive selection at nonsynonymous sites and weak selection on codon usage. Here we have looked for this correlation in a much larger and less biased dataset, comprising 630 gene pairs from D. melanogaster and D. yakuba. We confirmed that there is a negative correlation between the rate of nonsynonymous substitutions (d(N)) and codon bias in D. melanogaster. We then tested the interference hypothesis and other alternative explanations, including one involving gene expression. We found that d(N) indeed correlates with the level of gene expression. Given that gene expression is a strong determinant of codon bias, the relationship between d(N) and codon bias might be a by-product of gene expression. However, our tests show that none of the hypotheses we consider seem to explain the data fully.
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Registered trials
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.