ArticleGenetics2001
Substitution rates in Drosophila nuclear genes: implications for translational selection.
Article in Genetics, 2001. 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.
- Article
- Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias.Molecular biology and evolution · 2021Article
- Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila.Genome biology and evolution · 2017Article
- Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana.Genome biology and evolution · 2015Article
- Elevated levels of adaption in Helicobacter pylori genomes from Japan; a link to higher incidences of gastric cancer?Evolution, medicine, and public health · 2015Article
- The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species.BMC genomics · 2014Article
- The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment.Genome biology · 2014Article
- Mitochondrial-nuclear interactions: compensatory evolution or variable functional constraint among vertebrate oxidative phosphorylation genes?Genome biology and evolution · 2013Article
- Weak selection and protein evolution.Genetics · 2012Review
- Molecular evolution of the ent-kaurenoic acid oxidase gene in Oryzeae.Genetics and molecular biology · 2012Article
- Interspecific and intragenic differences in codon usage bias among vertebrate myosin heavy-chain genes.Journal of molecular evolution · 2011Article
- Recurrent events of positive selection in independent Drosophila lineages at the spermatogenesis gene roughex.Genetics · 2008Article
- Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.PLoS biology · 2007Article
- Article
- Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human.PLoS computational biology · 2006Article
- X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution.Genome research · 2006Article
- Article
- Evolutionary rates and expression level in Chlamydomonas.Genetics · 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
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The relationships between synonymous and nonsynonymous substitution rates and between synonymous rate and codon usage bias are important to our understanding of the roles of mutation and selection in the evolution of Drosophila genes. Previous studies used approximate estimation methods that ignore codon bias. In this study we reexamine those relationships using maximum-likelihood methods to estimate substitution rates, which accommodate the transition/transversion rate bias and codon usage bias. We compiled a sample of homologous DNA sequences at 83 nuclear loci from Drosophila melanogaster and at least one other species of Drosophila. Our analysis was consistent with previous studies in finding that synonymous rates were positively correlated with nonsynonymous rates. Our analysis differed from previous studies, however, in that synonymous rates were unrelated to codon bias. We therefore conducted a simulation study to investigate the differences between approaches. The results suggested that failure to properly account for multiple substitutions at the same site and for biased codon usage by approximate methods can lead to an artifactual correlation between synonymous rate and codon bias. Implications of the results for translational selection are discussed.
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