ArticlePloS one
Detecting selection using extended haplotype homozygosity (EHH)-based statistics in unphased or unpolarized data.
Article in PloS one. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Local Trade-Offs Shape Flower Size Evolution Across Arabidopsis thaliana Distribution.Molecular ecology · 2026Article
- Characterization of Lipizzan Horse Population From Lipica Stud Using Molecular and Pedigree Data.Animal genetics · 2026Article
- Assessing the Evolutionary Potential of Endangered Populations Using Genomic Analyses of Selection in Ecologically Important Gene Regions.Molecular ecology · 2026Article
- Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Across Urban, Rural, and Forested Environments in Gabon.Molecular ecology · 2026Article
- Selection scans and downstream analysis with selscan.Human population genetics and genomics · 2026Article
- Selection scans and downstream analysis with selscan.bioRxiv : the preprint server for biology · 2025Article
- Archaic adaptive introgression in modern human reproductive genes.Communications biology · 2025Article
- Selection signature analysis using whole genome resequencing data reveals candidate genes for white plumage color in Korean native ducks.Animal bioscience · 2025Article
- Polaris: Polarization of ancestral and derived polymorphic alleles for inferences of extended haplotype homozygosity in human populations.Bioinformatics (Oxford, England) · 2025Article
- Selection signatures detection in Nelore, Gir, and Red Sindhi cattle breeds.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Population Genomics Reveals Demographic History and Climate Adaptation in Japanese Arabidopsis halleri.Plant & cell physiology · 2025Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Genome-wide study for signatures of selection identifies genomic regions and candidate genes associated with milk traits in sheep.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Adaptive introgression in modern human circadian rhythm genes.Npj biological timing and sleep · 2025Article
- Computational Genomics and Its Applications to Anthropological Questions.American journal of biological anthropology · 2024Review
- Article
- Genomic Reconstruction of the Successful Establishment of a Feralized Bovine Population on the Subantarctic Island of Amsterdam.Molecular biology and evolution · 2024Article
- Genomic Analyses Capture the Human-Induced Demographic Collapse and Recovery in a Wide-Ranging Cervid.Molecular biology and evolution · 2024Article
- Comparative genomic analyses provide new insights into evolutionary history and conservation genomics of gorillas.BMC ecology and evolution · 2024Review
- selscan 2.0: scanning for sweeps in unphased data.Bioinformatics (Oxford, England) · 2024Article
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2 authors.
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Abstract
Analysis of population genetic data often includes a search for genomic regions with signs of recent positive selection. One of such approaches involves the concept of extended haplotype homozygosity (EHH) and its associated statistics. These statistics typically require phased haplotypes, and some of them necessitate polarized variants. Here, we unify and extend previously proposed modifications to loosen these requirements. We compare the modified versions with the original ones by measuring the false discovery rate in simulated whole-genome scans and by quantifying the overlap of inferred candidate regions in empirical data. We find that phasing information is indispensable for accurate estimation of within-population statistics (for all but very large samples) and of cross-population statistics for small samples. Ancestry information, in contrast, is of lesser importance for both types of statistic. Our publicly available R package rehh incorporates the modified statistics presented here.
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