ArticlePLoS genetics2022
A spatially aware likelihood test to detect sweeps from haplotype distributions.
Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Haplotype-Based Models Improve Sweep Detection in Ancient Populations with Complex Demography.bioRxiv : the preprint server for biology · 2026Article
- Genome Scans Reveal Species-Specific Selection in the Genus Lynx.Genome biology and evolution · 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
- Fast and Memory-Efficient Dynamic Programming Approach for Large-Scale EHH-Based Selection Scans.Molecular biology and evolution · 2025Article
- Accessible, Realistic Genome Simulation with Selection Using stdpopsim.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
- Archaic adaptive introgression in modern human reproductive genes.Communications biology · 2025Article
- Article
- Accessible, realistic genome simulation with selection using stdpopsim.bioRxiv : the preprint server for biology · 2025Article
- Sweeps in Space: Leveraging Geographic Data to Identify Beneficial Alleles in Anopheles gambiae.Molecular biology and evolution · 2025Article
- Complete sequencing of ape genomes.Nature · 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
- Genomic signatures of adaptation in native lizards exposed to human-introduced fire ants.Nature communications · 2025Article
- Adaptive introgression in modern human circadian rhythm genes.Npj biological timing and sleep · 2025Article
- Digital Image Processing to Detect Adaptive Evolution.Molecular biology and evolution · 2024Article
- Computational Genomics and Its Applications to Anthropological Questions.American journal of biological anthropology · 2024Review
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2 authors.
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Abstract
The inference of positive selection in genomes is a problem of great interest in evolutionary genomics. By identifying putative regions of the genome that contain adaptive mutations, we are able to learn about the biology of organisms and their evolutionary history. Here we introduce a composite likelihood method that identifies recently completed or ongoing positive selection by searching for extreme distortions in the spatial distribution of the haplotype frequency spectrum along the genome relative to the genome-wide expectation taken as neutrality. Furthermore, the method simultaneously infers two parameters of the sweep: the number of sweeping haplotypes and the "width" of the sweep, which is related to the strength and timing of selection. We demonstrate that this method outperforms the leading haplotype-based selection statistics, though strong signals in low-recombination regions merit extra scrutiny. As a positive control, we apply it to two well-studied human populations from the 1000 Genomes Project and examine haplotype frequency spectrum patterns at the LCT and MHC loci. We also apply it to a data set of brown rats sampled in NYC and identify genes related to olfactory perception. To facilitate use of this method, we have implemented it in user-friendly open source software.
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