ArticlePLoS genetics2016
A Genomic Map of the Effects of Linked Selection in Drosophila.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.
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96 citing papers in PubMed.
- A Genomic Perspective on Cryptic Species Reveals Complex Evolutionary Dynamics in the Gray Zone of the Speciation Continuum.Systematic biology · 2026Article
- Evolution of quantitative traits with background selection.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Epistasis among clustered lineage-specific amino acid substitutions in the Drosophila Trio protein.PLoS genetics · 2026Article
- Overdominance for fitness: a genomic comparison between empirical and simulated data with Drosophila melanogaster.Genetics · 2026Article
- Ubiquitous impact of natural selection on nucleotide diversity in 178 species of primates.Genome biology · 2026Article
- Background selection in recombining genomes and its consequences for the maintenance of variation in complex traits.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- ThebioRxiv : the preprint server for biology · 2026Article
- The distribution of fitness effects of new mutations in regulatory regions of thebioRxiv : the preprint server for biology · 2026Article
- Article
- Estimating the Reduction in Genetic Diversity from Background Selection under Non-equilibrium Demography and Partial Selfing.Molecular biology and evolution · 2026Article
- The impact of non-neutral synonymous mutations when inferring selection on nonsynonymous mutations.Genetics · 2025Article
- Epistasis among clustered lineage-specific adaptive amino acid substitutions in the Drosophila Trio protein.bioRxiv : the preprint server for biology · 2025Article
- A model for background selection in non-equilibrium populations.bioRxiv : the preprint server for biology · 2025Article
- Testing for the Genomic Footprint of Conflict Between Life Stages in an Angiosperm and Moss Species.Genome biology and evolution · 2025Article
- Drivers of genetic diversity across the marine tree of life.bioRxiv : the preprint server for biology · 2025Article
- When should adaptation arise from a polygenic response versus few large effect changes?bioRxiv : the preprint server for biology · 2025Article
- Mating systems and recombination landscape strongly shape genetic diversity and selection in wheat relatives.Evolution letters · 2024Article
- Population Genomic Scans for Natural Selection and Demography.Annual review of genetics · 2024Review
- Evolution of the Correlated Genomic Variation Landscape Across a Divergence Continuum in the Genus Castanopsis.Molecular biology and evolution · 2024Article
- Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection.Molecular biology and evolution · 2024Article
36 more citing papers are in PubMed but not listed here.
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8 authors.
Funding
Abstract
Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of "linked selection" on levels of genetic diversity is key to making reliable inference about demography, building a null model in scans for targets of adaptation, and learning about the dynamics of natural selection. Here, we introduce the first method that jointly infers parameters of distinct modes of linked selection, notably background selection and selective sweeps, from genome-wide diversity data, functional annotations and genetic maps. The central idea is to calculate the probability that a neutral site is polymorphic given local annotations, substitution patterns, and recombination rates. Information is then combined across sites and samples using composite likelihood in order to estimate genome-wide parameters of distinct modes of selection. In addition to parameter estimation, this approach yields a map of the expected neutral diversity levels along the genome. To illustrate the utility of our approach, we apply it to genome-wide resequencing data from 125 lines in Drosophila melanogaster and reliably predict diversity levels at the 1Mb scale. Our results corroborate estimates of a high fraction of beneficial substitutions in proteins and untranslated regions (UTR). They allow us to distinguish between the contribution of sweeps and other modes of selection around amino acid substitutions and to uncover evidence for pervasive sweeps in untranslated regions (UTRs). Our inference further suggests a substantial effect of other modes of linked selection and of adaptation in particular. More generally, we demonstrate that linked selection has had a larger effect in reducing diversity levels and increasing their variance in D. melanogaster than previously appreciated.
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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.