ArticleJournal of molecular evolution2010
Studying patterns of recent evolution at synonymous sites and intronic sites in Drosophila melanogaster.
Article in Journal of molecular evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed, 61 citations in OpenAlex.
- Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster.Nature communications · 2024Article
- Recommendations for improving statistical inference in population genomics.PLoS biology · 2022Article
- Inferring the distribution of fitness effects in patient-sampled and experimental virus populations: two case studies.Heredity · 2022Article
- Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster.G3 (Bethesda, Md.) · 2021Article
- The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects.Molecular biology and evolution · 2021Article
- Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes.BMC genomics · 2021Article
- The impact of purifying and background selection on the inference of population history: problems and prospects.bioRxiv : the preprint server for biology · 2021Article
- Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection.Genetics · 2020Article
- Article
- Transcription-Associated Compositional Skews in Drosophila Genes.Genome biology and evolution · 2018Article
- Population Genomics ofGenetics · 2017Article
- Evolutionary forces affecting synonymous variations in plant genomes.PLoS genetics · 2017Article
- 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
- Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae.Journal of molecular evolution · 2016Article
- Functional marker detection and analysis on a comprehensive transcriptome of large yellow croaker by next generation sequencing.PloS one · 2015Article
- Effective population size does not predict codon usage bias in mammals.Ecology and evolution · 2014Article
- The disparity mutagenesis model predicts rescue of living things from catastrophic errors.Frontiers in genetics · 2014Review
- Whole-genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection.Molecular ecology · 2013Article
- Strong purifying selection at synonymous sites in D. melanogaster.PLoS genetics · 2013Article
- Molecular hyperdiversity and evolution in very large populations.Molecular ecology · 2013Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most previous studies of the evolution of codon usage bias (CUB) and intronic GC content (iGC) in Drosophila melanogaster were based on between-species comparisons, reflecting long-term evolutionary events. However, a complete picture of the evolution of CUB and iGC cannot be drawn without knowledge of their more recent evolutionary history. Here, we used a polymorphism dataset collected from Zimbabwe to study patterns of the recent evolution of CUB and iGC. Analyzing coding and intronic data jointly with a model which can simultaneously estimate selection, mutational, and demographic parameters, we have found that: (1) natural selection is probably acting on synonymous codons; (2) a constant population size model seems to be sufficient to explain most of the observed synonymous polymorphism patterns; (3) GC is favored over AT in introns. In agreement with the long-term evolutionary patterns, ongoing selection acting on X-linked synonymous codons is stronger than that acting on autosomal codons. The selective differences between preferred and unpreferred codons tend to be greater than the differences between GC and AT in introns, suggesting that natural selection, not just biased gene conversion, may have influenced the evolution of CUB. Interestingly, evidence for non-equilibrium evolution comes exclusively from the intronic data. However, three different models, an equilibrium model with two classes of selected sites and two non-equilibrium models with changes in either population size or mutational parameters, fit the intronic data equally well. These results show that using inadequate selection (or demographic) models can result in incorrect estimates of demographic (or selection) parameters.
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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.