ArticleGenetics2006
Molecular evolution in the Drosophila melanogaster species subgroup: frequent parameter fluctuations on the timescale of molecular divergence.
Article in Genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- 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
- Dinucleotide preferences underlie apparent codon preference reversals in theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Long-term evolution of quantitative traits in the Drosophila melanogaster species subgroup.Genetica · 2022Article
- Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster.G3 (Bethesda, Md.) · 2021Article
- Distinguishing Among Evolutionary Forces Acting on Genome-Wide Base Composition: Computer Simulation Analysis of Approximate Methods for Inferring Site Frequency Spectra of Derived Mutations.G3 (Bethesda, Md.) · 2018Article
- 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
- Differential strengths of positive selection revealed by hitchhiking effects at small physical scales in Drosophila melanogaster.Molecular biology and evolution · 2014Article
- Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models.Molecular biology and evolution · 2013Article
- Population genomic analysis of base composition evolution in Drosophila melanogaster.Genome biology and evolution · 2012Article
- Effects of natural selection and gene conversion on the evolution of human glycophorins coding for MNS blood polymorphisms in malaria-endemic African populations.American journal of human genetics · 2011Article
- Studying patterns of recent evolution at synonymous sites and intronic sites in Drosophila melanogaster.Journal of molecular evolution · 2010Article
- Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila.Molecular biology and evolution · 2009Article
- Locus-specific decoupling of base composition evolution at synonymous sites and introns along the Drosophila melanogaster and Drosophila sechellia lineages.Genome biology and evolution · 2009Article
- Molecular evolution of synonymous codon usage in Populus.BMC evolutionary biology · 2008Article
- Article
- Non-neutral processes drive the nucleotide composition of non-coding sequences in Drosophila.Biology letters · 2008Article
- Recurrent events of positive selection in independent Drosophila lineages at the spermatogenesis gene roughex.Genetics · 2008Article
- A new test for selection applied to codon usage in Drosophila simulans and D. mauritiana.Journal of molecular evolution · 2008Article
- Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although mutation, genetic drift, and natural selection are well established as determinants of genome evolution, the importance (frequency and magnitude) of parameter fluctuations in molecular evolution is less understood. DNA sequence comparisons among closely related species allow specific substitutions to be assigned to lineages on a phylogenetic tree. In this study, we compare patterns of codon usage and protein evolution in 22 genes (>11,000 codons) among Drosophila melanogaster and five relatives within the D. melanogaster subgroup. We assign changes to eight lineages using a maximum-likelihood approach to infer ancestral states. Uncertainty in ancestral reconstructions is taken into account, at least to some extent, by weighting reconstructions by their posterior probabilities. Four of the eight lineages show potentially genomewide departures from equilibrium synonymous codon usage; three are decreasing and one is increasing in major codon usage. Several of these departures are consistent with lineage-specific changes in selection intensity (selection coefficients scaled to effective population size) at silent sites. Intron base composition and rates and patterns of protein evolution are also heterogeneous among these lineages. The magnitude of forces governing silent, intron, and protein evolution appears to have varied frequently, and in a lineage-specific manner, within the D. melanogaster subgroup.
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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.