ArticleMolecular biology and evolution2013
Codon usage bias and effective population sizes on the X chromosome versus the autosomes in Drosophila melanogaster.
Article in Molecular biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Different mRNAs encoding identical proteins: how and why?Journal of applied genetics · 2026Article
- Estimating the additive genetic variance for relative fitness from changes in allele frequency.Genetics · 2026Article
- Systematic revelation and meditation on the significance of long exons using representative eukaryotic genomes.BMC genomics · 2025Article
- Analysis of synonymous codon usage bias in the chloroplast genome of five Caragana.BMC plant biology · 2025Article
- Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster.Nature communications · 2024Article
- Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species.Genetics · 2024Article
- Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species.bioRxiv : the preprint server for biology · 2023Article
- Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster.G3 (Bethesda, Md.) · 2021Article
- Rapid Evolution of Autosomal Binding Sites of the Dosage Compensation Complex inFrontiers in genetics · 2021Article
- Article
- Population Genomics on the Fly: Recent Advances in Drosophila.Methods in molecular biology (Clifton, N.J.) · 2020Review
- The Effects on Neutral Variability of Recurrent Selective Sweeps and Background Selection.Genetics · 2019Article
- Genomics of parallel adaptation at two timescales in Drosophila.PLoS genetics · 2017Article
- Estimating the parameters of background selection and selective sweeps inProceedings of the National Academy of Sciences of the United States of America · 2017Article
- Population Genomics ofGenetics · 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
- Autosomal and X-Linked Additive Genetic Variation for Lifespan and Aging: Comparisons Within and Between the Sexes in Drosophila melanogaster.G3 (Bethesda, Md.) · 2016Article
- Article
- Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae.Journal of molecular evolution · 2016Article
- Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution.Genetics · 2015Article
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5 authors.
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Abstract
Codon usage bias (CUB) in Drosophila is higher for X-linked genes than for autosomal genes. One possible explanation is that the higher effective recombination rate for genes on the X chromosome compared with the autosomes reduces their susceptibility to Hill-Robertson effects, and thus enhances the efficacy of selection on codon usage. The genome sequence of D. melanogaster was used to test this hypothesis. Contrary to expectation, it was found that, after correcting for the effective recombination rate, CUB remained higher on the X than on the autosomes. In contrast, an analysis of polymorphism data from a Rwandan population showed that mean nucleotide site diversity at 4-fold degenerate sites for genes on the X is approximately three-quarters of the autosomal value after correcting for the effective recombination rate, compared with approximate equality before correction. In addition, these data show that selection for preferred versus unpreferred synonymous variants is stronger on the X than the autosomes, which accounts for the higher CUB of genes on the X chromosome. This difference in the strength of selection does not appear to reflect the effects of dominance of mutations affecting codon usage, differences in gene expression levels between X and autosomes, or differences in mutational bias. Its cause therefore remains unexplained. The stronger selection on CUB on the X chromosome leads to a lower rate of synonymous site divergence compared with the autosomes; this will cause a stronger upward bias for X than A in estimates of the proportion of nonsynonymous mutations fixed by positive selection, for methods based on the McDonald-Kreitman test.
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