ArticleMolecular biology and evolution2008
Positive and negative selection on noncoding DNA in Drosophila simulans.
Article in Molecular biology and evolution, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 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
68 citing papers in PubMed, 112 citations in OpenAlex.
- Natural Selection in Transcription Factor-DNA Interaction Motifs: A Comparative and Population Genomics Perspective.Genome biology and evolution · 2025Article
- Dynamic Outlier Slicing Allows Broader Exploration of Adaptive Divergence: A Comparison of Individual Genome and Pool-Seq Data Linked to Humic Adaptation in Perch.Molecular ecology · 2025Article
- Assessing Mechanisms of Potential Local Adaptation Through a Seascape Genomic Approach in a Marine Gastropod, Littoraria flava.Genome biology and evolution · 2024Article
- Genomic analyses indicate the North American Ap-ha variant of the tick-vectored bacterium Anaplasma phagocytophilum was introduced from Europe.Parasites & vectors · 2023Article
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- Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster.G3 (Bethesda, Md.) · 2021Article
- Molecular population genetics of Sex-lethal (Sxl) in the Drosophila melanogaster species group: a locus that genetically interacts with Wolbachia pipientis in Drosophila melanogaster.G3 (Bethesda, Md.) · 2021Article
- On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae).Heredity · 2021Article
- Impact of Genetic Variation in Gene Regulatory Sequences: A Population Genomics Perspective.Frontiers in genetics · 2021Review
- Genetic signatures of microbial altruism and cheating in social amoebas in the wild.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- The Rate of Evolution of Postmating-Prezygotic Reproductive Isolation in Drosophila.Molecular biology and evolution · 2018Article
- A Large Panel of Drosophila simulans Reveals an Abundance of Common Variants.Genome biology and evolution · 2018Article
- Bioinformatically predicted deleterious mutations reveal complementation in the interior spruce hybrid complex.BMC genomics · 2017Article
- Natural Selection Drives Rapid Functional Evolution of Young Drosophila Duplicate Genes.Molecular 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
- Weak Polygenic Selection Drives the Rapid Adaptation of the Chemosensory System: Lessons from the Upstream Regions of the Major Gene Families.Genome biology and evolution · 2016Article
- Article
- Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution.Genetics · 2015Article
- Varying influences of selection and demography in host-adapted populations of the tick-transmitted bacterium, Anaplasma phagocytophilum.BMC evolutionary biology · 2015Article
- The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations.Genetics · 2015Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
Abstract
There is now a wealth of evidence that some of the most important regions of the genome are found outside those that encode proteins, and noncoding regions of the genome have been shown to be subject to substantial levels of selective constraint, particularly in Drosophila. Recent work has suggested that these regions may also have been subject to the action of positive selection, with large fractions of noncoding divergence having been driven to fixation by adaptive evolution. However, this work has focused on Drosophila melanogaster, which is thought to have experienced a reduction in effective population size (N(e)), and thus a reduction in the efficacy of selection, compared with its closest relative Drosophila simulans. Here, we examine patterns of evolution at several classes of noncoding DNA in D. simulans and find that all noncoding DNA is subject to the action of negative selection, indicated by reduced levels of polymorphism and divergence and a skew in the frequency spectrum toward rare variants. We find that the signature of negative selection on noncoding DNA and nonsynonymous sites is obscured to some extent by purifying selection acting on preferred to unpreferred synonymous codon mutations. We investigate the extent to which divergence in noncoding DNA is inferred to be the product of positive selection and to what extent these inferences depend on selection on synonymous sites and demography. Based on patterns of polymorphism and divergence for different classes of synonymous substitution, we find the divergence excess inferred in noncoding DNA and nonsynonymous sites in the D. simulans lineage difficult to reconcile with demographic explanations.
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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.