ArticleMolecular biology and evolution2020
A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
- Allelic gene conversion softens selective sweeps.Genetics · 2026Article
- Haplotype and diversity signatures of ultra-soft selective sweeps in HIV-1.bioRxiv : the preprint server for biology · 2026Article
- Haplotype-Based Models Improve Sweep Detection in Ancient Populations with Complex Demography.bioRxiv : the preprint server for biology · 2026Article
- Detecting Positive Selection by Modeling Structure Within Images of Genetic Variation.Genome biology and evolution · 2026Article
- Selection scans and downstream analysis with selscan.Human population genetics and genomics · 2026Article
- Whole genome sequences of 289 native cattle from Finland, the Netherlands, and Portugal.Scientific data · 2025Article
- Fast and Memory-Efficient Dynamic Programming Approach for Large-Scale EHH-Based Selection Scans.Molecular biology and evolution · 2025Article
- Natural selection exerted by historical coronavirus epidemic(s): comparative genetic analysis in China Kadoorie Biobank and UK Biobank.BMC genomics · 2025Article
- Selection scans and downstream analysis with selscan.bioRxiv : the preprint server for biology · 2025Article
- Fast and Memory-Efficient Dynamic Programming Approach for Large-Scale EHH-Based Selection Scans.bioRxiv : the preprint server for biology · 2025Article
- Article
- An ancient origin of the naked grains of maize.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- HLA diversity and signatures of selection in the Maniq, a nomadic hunter-gatherer population in Southern Thailand.Immunogenetics · 2025Article
- Efficient Detection and Characterization of Targets of Natural Selection Using Transfer Learning.Molecular biology and evolution · 2025Article
- Convergent evolution of complex adaptive traits modulates angiogenesis in high-altitude Andean and Himalayan human populations.Communications biology · 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
- Article
- Population Genomic Scans for Natural Selection and Demography.Annual review of genetics · 2024Review
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2 authors.
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Abstract
Selective sweeps are frequent and varied signatures in the genomes of natural populations, and detecting them is consequently important in understanding mechanisms of adaptation by natural selection. Following a selective sweep, haplotypic diversity surrounding the site under selection decreases, and this deviation from the background pattern of variation can be applied to identify sweeps. Multiple methods exist to locate selective sweeps in the genome from haplotype data, but none leverages the power of a model-based approach to make their inference. Here, we propose a likelihood ratio test statistic T to probe whole-genome polymorphism data sets for selective sweep signatures. Our framework uses a simple but powerful model of haplotype frequency spectrum distortion to find sweeps and additionally make an inference on the number of presently sweeping haplotypes in a population. We found that the T statistic is suitable for detecting both hard and soft sweeps across a variety of demographic models, selection strengths, and ages of the beneficial allele. Accordingly, we applied the T statistic to variant calls from European and sub-Saharan African human populations, yielding primarily literature-supported candidates, including LCT, RSPH3, and ZNF211 in CEU, SYT1, RGS18, and NNT in YRI, and HLA genes in both populations. We also searched for sweep signatures in Drosophila melanogaster, finding expected candidates at Ace, Uhg1, and Pimet. Finally, we provide open-source software to compute the T statistic and the inferred number of presently sweeping haplotypes from whole-genome data.
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