ArticleGenetics1998
The correlation between synonymous and nonsynonymous substitutions in Drosophila: mutation, selection or relaxed constraints?
Article in Genetics, 1998. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Review
- Decoding the effects of synonymous variants.Nucleic acids research · 2021Article
- A Genome-Wide Profiling of Glioma Patients with an IDH1 Mutation Using the Catalogue of Somatic Mutations in Cancer Database.Cancers · 2021Article
- Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation.Nature ecology & evolution · 2019Article
- Comparative Transcriptome Profiling of the LoachesFrontiers in genetics · 2019Article
- Evolutionary patterns of Toll-like receptor signaling pathway genes in the Suidae.BMC evolutionary biology · 2016Article
- Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana.Genome biology and evolution · 2015Article
- Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea.G3 (Bethesda, Md.) · 2015Article
- Effective population size does not predict codon usage bias in mammals.Ecology and evolution · 2014Article
- Mitochondrial-nuclear interactions: compensatory evolution or variable functional constraint among vertebrate oxidative phosphorylation genes?Genome biology and evolution · 2013Article
- Divergent patterns of selection on the DAB and DXB MHC class II loci in Xiphophorus fishes.Genetica · 2009Article
- Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.PLoS biology · 2007Article
- Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Determination of mutation trend in proteins by means of translation probability between RNA codes and mutated amino acids.Biochemical and biophysical research communications · 2005Article
- The soluble epoxide hydrolase gene harbors sequence variation associated with susceptibility to and protection from incident ischemic stroke.Human molecular genetics · 2005Article
- Codon bias and noncoding GC content correlate negatively with recombination rate on the Drosophila X chromosome.Journal of molecular evolution · 2005Article
- Patterns of synonymous codon usage in Drosophila melanogaster genes with sex-biased expression.Genetics · 2005Article
- Ancient divergence in bathypelagic lake tanganyika deepwater cichlids: mitochondrial phylogeny of the tribe bathybatini.Journal of molecular evolution · 2005Article
- Correlated evolution of synonymous and nonsynonymous sites in Drosophila.Journal of molecular evolution · 2004Article
- An evolutionary analysis of orphan genes in Drosophila.Genome research · 2003Article
Corrections and comments
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2 authors.
Funding
Abstract
Codon usage bias, the preferential use of particular codons within each codon family, is characteristic of synonymous base composition in many species, including Drosophila, yeast, and many bacteria. Preferential usage of particular codons in these species is maintained by natural selection acting largely at the level of translation. In Drosophila, as in bacteria, the rate of synonymous substitution per site is negatively correlated with the degree of codon usage bias, indicating stronger selection on codon usage in genes with high codon bias than in genes with low codon bias. Surprisingly, in these organisms, as well as in mammals, the rate of synonymous substitution is also positively correlated with the rate of nonsynonymous substitution. To investigate this correlation, we carried out a phylogenetic analysis of substitutions in 22 genes between two species of Drosophila, Drosophila pseudoobscura and D. subobscura, in codons that differ by one replacement and one synonymous change. We provide evidence for a relative excess of double substitutions in the same species lineage that cannot be explained by the simultaneous mutation of two adjacent bases. The synonymous changes in these codons also cannot be explained by a shift to a more preferred codon following a replacement substitution. We, therefore, interpret the excess of double codon substitutions within a lineage as being the result of relaxed constraints on both kinds of substitutions in particular codons.
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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.