ArticleGenetics2001
Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila.
Article in Genetics, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
71 citing papers in PubMed, 145 citations in OpenAlex.
- Estimating the evolutionary fitness of specific synonymous codon changes.Molecular biology and evolution · 2026Article
- Estimating the evolutionary fitness of specific synonymous codon changes.bioRxiv : the preprint server for biology · 2026Article
- Comprehensive Codon Usage Analysis Across Diverse Plant Lineages.Biochemical genetics · 2026Article
- Genomic factors shaping codon usage across the Saccharomycotina subphylum.G3 (Bethesda, Md.) · 2024Article
- Decoding the effects of synonymous variants.Nucleic acids research · 2021Article
- Article
- Demographic history and adaptive synonymous and nonsynonymous variants of nuclear genes in Rhododendron oldhamii (Ericaceae).Scientific reports · 2020Article
- Variation and selection on codon usage bias across an entire subphylum.PLoS genetics · 2019Article
- Pleiotropy Modulates the Efficacy of Selection in Drosophila melanogaster.Molecular biology and evolution · 2019Article
- 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
- SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage.Genome biology and evolution · 2016Article
- Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae.Journal of molecular evolution · 2016Article
- Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea.G3 (Bethesda, Md.) · 2015Article
- Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution.Genetics · 2015Article
- Effective population size does not predict codon usage bias in mammals.Ecology and evolution · 2014Article
- Differential strengths of positive selection revealed by hitchhiking effects at small physical scales in Drosophila melanogaster.Molecular biology and evolution · 2014Article
- Strong purifying selection at synonymous sites in D. melanogaster.PLoS genetics · 2013Article
- A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.Genome research · 2013Article
- A universal scaling law determines time reversibility and steady state of substitutions under selection.Theoretical population biology · 2012Article
- The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome.Molecular biology and evolution · 2012Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Selection acting on codon usage can cause patterns of synonymous evolution to deviate considerably from those expected under neutrality. To investigate the quantitative relationship between parameters of mutation, selection, and demography, and patterns of synonymous site divergence, we have developed a novel combination of population genetic models and likelihood methods of phylogenetic sequence analysis. Comparing 50 orthologous gene pairs from Drosophila melanogaster and D. virilis and 27 from D. melanogaster and D. simulans, we show considerable variation between amino acids and genes in the strength of selection acting on codon usage and find evidence for both long-term and short-term changes in the strength of selection between species. Remarkably, D. melanogaster shows no evidence of current selection on codon usage, while its sister species D. simulans experiences only half the selection pressure for codon usage of their common ancestor. We also find evidence for considerable base asymmetries in the rate of mutation, such that the average synonymous mutation rate is 20-30% higher than in noncoding regions. A Bayesian approach is adopted to investigate how accounting for selection on codon usage influences estimates of the parameters of mutation.
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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.