ArticleGenetics2004
Linkage disequilibrium as a signature of selective sweeps.
Article in Genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 235 papers.
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Who cites it
235 citing papers in PubMed.
- Allelic gene conversion softens selective sweeps.Genetics · 2026Article
- Progeny-based genomic selection reveals untapped genetic potential in an underutilized medicinal plant,Molecular breeding : new strategies in plant improvement · 2026Article
- Article
- Haplotype-Based Models Improve Sweep Detection in Ancient Populations with Complex Demography.bioRxiv : the preprint server for biology · 2026Article
- Insights into human adaptation from ancient DNA.Nature genetics · 2026Review
- Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Across Urban, Rural, and Forested Environments in Gabon.Molecular ecology · 2026Article
- Soft Selective Sweeps Predominate in the Yellow Fever Mosquito Aedes aegypti.Molecular biology and evolution · 2026Article
- Genome-wide detection of selection signatures in roses.BMC plant biology · 2026Article
- Recent advances in methods to characterize archaic introgression in modern humans.Genome research · 2026Review
- GENERAL MOMENT CLOSURE FOR THE NEUTRAL TWO-LOCUS WRIGHT-FISHER DYNAMICS.bioRxiv : the preprint server for biology · 2026Article
- Bovine Genome Database: new curated collection of selective sweeps in bovine populations across the world.Nucleic acids research · 2026Article
- Composite selection signal analysis: Uncovering candidate genes and quantitative trait loci in Indian sheep breeds.PloS one · 2026Article
- Towards an evolutionary baseline model ofbioRxiv : the preprint server for biology · 2025Article
- Article
- Pervasive and recurrent hybridization prevents inbreeding in Europe's most threatened seabird.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Latitudinal-environmental variations driving the local adaptation ofMarine life science & technology · 2025Article
- Signatures of soft selective sweeps predominate in the yellow fever mosquitobioRxiv : the preprint server for biology · 2025Article
- A whole-genome scan for evidence of positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model.G3 (Bethesda, Md.) · 2025Article
- Article
- Efficient Detection and Characterization of Targets of Natural Selection Using Transfer Learning.Molecular biology and evolution · 2025Article
175 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The hitchhiking effect of a beneficial mutation, or a selective sweep, generates a unique distribution of allele frequencies and spatial distribution of polymorphic sites. A composite-likelihood test was previously designed to detect these signatures of a selective sweep, solely on the basis of the spatial distribution and marginal allele frequencies of polymorphisms. As an excess of linkage disequilibrium (LD) is also known to be a strong signature of a selective sweep, we investigate how much statistical power is increased by the inclusion of information regarding LD. The expected pattern of LD is predicted by a genealogical approach. Both theory and simulation suggest that strong LD is generated in narrow regions at both sides of the location of beneficial mutation. However, a lack of LD is expected across the two sides. We explore various ways to detect this signature of selective sweeps by statistical tests. A new composite-likelihood method is proposed to incorporate information regarding LD. This method enables us to detect selective sweeps and estimate the parameters of the selection model better than the previous composite-likelihood method that does not take LD into account. However, the improvement made by including LD is rather small, suggesting that most of the relevant information regarding selective sweeps is captured by the spatial distribution and marginal allele frequencies of polymorphisms.
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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.