ArticleMolecular biology and evolution2023
Versatile Detection of Diverse Selective Sweeps with Flex-Sweep.
Article in Molecular biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
- Allelic gene conversion softens selective sweeps.Genetics · 2026Article
- Fast pairwise coalescence enables gene-resolution scans for recent selection in diverse human populations.bioRxiv : the preprint server for biology · 2026Article
- Identifying Adaptive Footprints in the Presence of Demographic Uncertainty.Genome biology and evolution · 2026Article
- AI solutions for evolutionary genomics of nonmodel species.Evolution letters · 2026Review
- Detecting Positive Selection by Modeling Structure Within Images of Genetic Variation.Genome biology and evolution · 2026Article
- Summary statistics and approximate bayesian computation are comparable to convolutional neural networks for inferring times to fixation.bioRxiv : the preprint server for biology · 2026Article
- Fast and Memory-Efficient Dynamic Programming Approach for Large-Scale EHH-Based Selection Scans.Molecular biology and evolution · 2025Article
- Fast and Memory-Efficient Dynamic Programming Approach for Large-Scale EHH-Based Selection Scans.bioRxiv : the preprint server for biology · 2025Article
- Article
- Sweeps in Space: Leveraging Geographic Data to Identify Beneficial Alleles in Anopheles gambiae.Molecular biology and evolution · 2025Article
- Efficient Detection and Characterization of Targets of Natural Selection Using Transfer Learning.Molecular biology and evolution · 2025Article
- Efficient detection and characterization of targets of natural selection using transfer learning.bioRxiv : the preprint server for biology · 2025Article
- Digital Image Processing to Detect Adaptive Evolution.Molecular biology and evolution · 2024Article
- Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies.Molecular ecology · 2024Article
- Tree Sequences as a General-Purpose Tool for Population Genetic Inference.Molecular biology and evolution · 2024Article
- Tree sequences as a general-purpose tool for population genetic inference.bioRxiv : the preprint server for biology · 2024Article
- Detecting adaptive changes in gene copy number distribution accompanying the human out-of-Africa expansion.Human genome variation · 2024Article
- A Novel Approach Utilizing Domain Adversarial Neural Networks for the Detection and Classification of Selective Sweeps.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Forty Years of Inferential Methods in the Journals of the Society for Molecular Biology and Evolution.Molecular biology and evolution · 2024Article
- Harnessing deep learning for population genetic inference.Nature reviews. Genetics · 2024Review
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3 authors.
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Abstract
Understanding the impacts of selection pressures influencing modern-day genomic diversity is a major goal of evolutionary genomics. In particular, the contribution of selective sweeps to adaptation remains an open question, with persistent statistical limitations on the power and specificity of sweep detection methods. Sweeps with subtle genomic signals have been particularly challenging to detect. Although many existing methods powerfully detect specific types of sweeps and/or those with strong signals, their power comes at the expense of versatility. We present Flex-sweep, a machine learning-based tool designed to detect sweeps with a variety of subtle signals, including those thousands of generations old. It is especially valuable for nonmodel organisms, for which we have neither expectations about the overall characteristics of sweeps nor outgroups with population-level sequencing to otherwise facilitate detecting very old sweeps. We show that Flex-sweep has the power to detect sweeps with subtle signals, even in the face of demographic model misspecification, recombination rate heterogeneity, and background selection. Flex-sweep detects sweeps up to 0.125*4Ne generations old, including those that are weak, soft, and/or incomplete; it can also detect strong, complete sweeps up to 0.25*4Ne generations old. We apply Flex-sweep to the 1000 Genomes Yoruba data set and, in addition to recovering previously identified sweeps, show that sweeps disproportionately occur within genic regions and are close to regulatory regions. In addition, we show that virus-interacting proteins (VIPs) are strongly enriched for selective sweeps, recapitulating previous results that demonstrate the importance of viruses as a driver of adaptive evolution in humans.
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