ArticleMolecular biology and evolution2010
On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila.
Article in Molecular biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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63 citing papers in PubMed.
- Article
- 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
- The impact of non-neutral synonymous mutations when inferring selection on nonsynonymous mutations.Genetics · 2025Article
- Natural Selection in Transcription Factor-DNA Interaction Motifs: A Comparative and Population Genomics Perspective.Genome biology and evolution · 2025Article
- Isolating selective from non-selective forces using site frequency ratios.PLoS genetics · 2025Article
- Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster.Nature communications · 2024Article
- From sub-Saharan Africa to China: Evolutionary history and adaptation ofScience advances · 2024Article
- Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract.Journal of evolutionary biology · 2023Article
- Variation in mutation, recombination, and transposition rates inGenome research · 2023Article
- KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences.Genomics, proteomics & bioinformatics · 2022Article
- Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila.Nature communications · 2022Article
- Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster.G3 (Bethesda, Md.) · 2021Article
- The Genomic Architecture of Adaptation to Larval Malnutrition Points to a Trade-off with Adult Starvation Resistance in Drosophila.Molecular biology and evolution · 2021Article
- Allelic polymorphism at foxo contributes to local adaptation in Drosophila melanogaster.Molecular ecology · 2021Article
- The search for sexually antagonistic genes: Practical insights from studies of local adaptation and statistical genomics.Evolution letters · 2020Article
- Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses.Molecular biology and evolution · 2020Article
- Article
- Demographic History of the Human Commensal Drosophila melanogaster.Genome biology and evolution · 2019Article
3 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
Abstract
The detection of selection, both positive and negative, acting on a DNA sequence or class of nucleotide sites requires comparison with a reference sequence that is unaffected by selection. In Drosophila, recent findings of widespread selective constraint, as well as adaptive evolution, in both coding and noncoding regions highlight the difficulties in choosing such a reference sequence. Here, we investigate the utility of short intron sequences as a reference for the detection of selection. For a set of 119 Drosophila melanogaster genes containing 195 short introns (<or=120 bp), we analyzed polymorphism and divergence at 1) 4-fold synonymous sites, 2) all sites of introns <or=120 bp, 3) all sites of introns <or=65 bp, 4) bases 8-30 of introns <or=120 bp, and 5) bases 8-30 of introns <or=65 bp. The last class of sites shows the highest levels of both interspecific divergence and intraspecific polymorphism, suggesting that these sites are under the least selective constraint. Bases 8-30 of introns <or=65 bp also have the lowest ratio of divergence to polymorphism, which may indicate that a small proportion of substitutions in the other classes of sites are the result of adaptive evolution. Although there is little signal of selection on the primary sequence of short introns, patterns of insertion-deletion polymorphism and divergence suggest that both positive and negative selection act to maintain an optimal intron length.
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