ArticleMolecular biology and evolution2009
Strong evidence for lineage and sequence specificity of substitution rates and patterns in Drosophila.
Article in Molecular biology and evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed, 62 citations in OpenAlex.
- Estimating the evolutionary fitness of specific synonymous codon changes.Molecular biology and evolution · 2026Article
- The birth, death, and evolutionary compensation of uORFs in Drosophila.Nucleic acids research · 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
- PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance.Molecular biology and evolution · 2023Article
- Molecular evolution and the decline of purifying selection with age.Nature communications · 2021Article
- Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated.Bioinformatics (Oxford, England) · 2020Article
- Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses.Molecular biology and evolution · 2020Article
- 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
- Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network.PloS one · 2017Article
- 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
- Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci.RNA (New York, N.Y.) · 2015Article
- De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.BMC genomics · 2014Article
- Background selection as baseline for nucleotide variation across the Drosophila genome.PLoS genetics · 2014Article
- Strong purifying selection at synonymous sites in D. melanogaster.PLoS genetics · 2013Article
- Conserved substitution patterns around nucleosome footprints in eukaryotes and Archaea derive from frequent nucleosome repositioning through evolution.PLoS computational biology · 2013Article
- Inferences of demography and selection in an African population of Drosophila melanogaster.Genetics · 2013Article
- Comparative analysis of context-dependent mutagenesis using human and mouse models.BioMed research international · 2013Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Rates of single nucleotide substitution in Drosophila are highly variable within the genome, and several examples illustrate that evolutionary rates differ among Drosophila species as well. Here, we use a maximum likelihood method to quantify lineage-specific substitutional patterns and apply this method to 4-fold degenerate synonymous sites and introns from more than 8,000 genes aligned in the Drosophila melanogaster group. We find that within species, different classes of sequence evolve at different rates, with long introns evolving most slowly and short introns evolving most rapidly. Relative rates of individual single nucleotide substitutions vary approximately 3-fold among lineages, yielding patterns of substitution that are comparatively less GC-biased in the melanogaster species complex relative to Drosophila yakuba and Drosophila erecta. These results are consistent with a model coupling a mutational shift toward reduced GC content, or a shift in mutation-selection balance, in the D. melanogaster species complex, with variation in selective constraint among different classes of DNA sequence. Finally, base composition of coding and intronic sequences is not at equilibrium with respect to substitutional patterns, which primarily reflects the slow rate of the substitutional process. These results thus support the view that mutational and/or selective processes are labile on an evolutionary timescale and that if the process is indeed selection driven, then the distribution of selective constraint is variable across the genome.
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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.