ArticleGenome research2006
How reliable are empirical genomic scans for selective sweeps?
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 217 papers, 3 of them syntheses that pooled it.
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Who cites it
217 citing papers in PubMed, 3 syntheses or guidelines pooled it, 413 citations in OpenAlex.
- Genomic investigations of successful invasions: the picture emerging from recent studies.Biological reviews of the Cambridge Philosophical Society · 2025Pooled it
- Discovery of new risk loci for IgA nephropathy implicates genes involved in immunity against intestinal pathogens.Nature genetics · 2014Pooled it
- Recent adaptive events in human brain revealed by meta-analysis of positively selected genes.PloS one · 2013Pooled it
- Inferring the Relative Contributions of Evolutionary Processes Shaping X Chromosome Dynamics in the Common Marmoset (Callithrix jacchus) in the Presence of Twinning and Hematopoietic Chimerism.Genome biology and evolution · 2026Article
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- Inferring Patterns of Purifying, Positive, and Balancing Selection in the Coppery Titi Monkey (Plecturocebus cupreus) Utilizing a Well-Fit Evolutionary Baseline Model.Genome biology and evolution · 2026Article
- Soft Selective Sweeps Predominate in the Yellow Fever Mosquito Aedes aegypti.Molecular biology and evolution · 2026Article
- Genetic Variation in the Main Cultivar Collection ofCurrent issues in molecular biology · 2026Article
- Towards an evolutionary baseline model ofbioRxiv : the preprint server for biology · 2025Article
- Recent Insights Into the Evolutionary Genomics of the Critically Endangered Aye-Aye (Daubentonia madagascariensis).American journal of primatology · 2025Review
- Article
- Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource.Molecular biology and evolution · 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
- Sweeps in Space: Leveraging Geographic Data to Identify Beneficial Alleles in Anopheles gambiae.Molecular biology and evolution · 2025Article
- Parallel and convergent evolution in genes underlying seasonal migration.Evolution letters · 2025Article
- Deep learning insights into distinct patterns of polygenic adaptation across human populations.Nucleic acids research · 2024Article
- A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (bioRxiv : the preprint server for biology · 2024Article
- Genomes of Microtus Rodents Highlight the Importance of Olfactory and Immune Systems in Their Fast Radiation.Genome biology and evolution · 2024Article
- Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection.Molecular biology and evolution · 2024Article
157 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The beneficial substitution of an allele shapes patterns of genetic variation at linked sites. Thus, in principle, adaptations can be mapped by looking for the signature of directional selection in polymorphism data. In practice, such efforts are hampered by the need for an accurate characterization of the demographic history of the species and of the effects of positive selection. In an attempt to circumvent these difficulties, researchers are increasingly taking a purely empirical approach, in which a large number of genomic regions are ordered by summaries of the polymorphism data, and loci with extreme values are considered to be likely targets of positive selection. We evaluated the reliability of the "empirical" approach, focusing on applications to human data and to maize. To do so, we considered a coalescent model of directional selection in a sensible demographic setting, allowing for selection on standing variation as well as on a new mutation. Our simulations suggest that while empirical approaches will identify several interesting candidates, they will also miss many--in some cases, most--loci of interest. The extent of the trade-off depends on the mode of positive selection and the demographic history of the population. Specifically, the false-discovery rate is higher when directional selection involves a recessive rather than a co-dominant allele, when it acts on a previously neutral rather than a new allele, and when the population has experienced a population bottleneck rather than maintained a constant size. One implication of these results is that, insofar as attributes of the beneficial mutation (e.g., the dominance coefficient) affect the power to detect targets of selection, genomic scans will yield an unrepresentative subset of loci that contribute to adaptations.
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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.