ArticleTheoretical population biology2015
Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps.
Article in Theoretical population biology, 2015. 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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28 citing papers in PubMed, 55 citations in OpenAlex.
- Article
- Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Across Urban, Rural, and Forested Environments in Gabon.Molecular ecology · 2026Article
- Genetic Footprints of Seasonal Fluctuating Selection: A Comparison With Established Selection Forms.Genome biology and evolution · 2026Article
- Distinct Genetic Footprint of Adaptation Observed WithinResearch and reports in tropical medicine · 2026Article
- Genome-wide analysis of genetic diversity in Anopheles darlingi from Rondônia State, Brazil.Communications biology · 2025Article
- Using mathematical constraints to explain narrow ranges for allele-sharing dissimilarities.Theoretical population biology · 2025Article
- Leveraging ancient DNA to uncover signals of natural selection in Europe lost due to admixture or drift.Nature communications · 2024Article
- Phenotypic evidence of deltamethrin resistance and identification of selective sweeps in Anopheles mosquitoes on the Bijagós Archipelago, Guinea-Bissau.Scientific reports · 2024Article
- Whole genome sequence analysis of population structure and insecticide resistance markers in Anopheles melas from the Bijagós Archipelago, Guinea-Bissau.Parasites & vectors · 2024Article
- Scans for Signatures of Selection in Genomes of Wagyu and Buryat Cattle Breeds Reveal Candidate Genes and Genetic Variants for Adaptive Phenotypes and Production Traits.Animals : an open access journal from MDPI · 2024Article
- Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species.Genetics · 2024Article
- Evidence for sweep signatures in antibiotic-resistant strains in three species of bacteria.PeerJ · 2024Article
- Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species.bioRxiv : the preprint server for biology · 2023Article
- Mathematical bounds on Shannon entropy given the abundance of the ith most abundant taxon.Journal of mathematical biology · 2023Article
- Transposons are important contributors to gene expression variability under selection in rice populations.eLife · 2023Article
- Understanding natural selection in Holocene Europe using multi-locus genotype identity scans.bioRxiv : the preprint server for biology · 2023Article
- On the origin and structure of haplotype blocks.Molecular ecology · 2023Article
- Enrichment of Hard Sweeps on the X Chromosome in Drosophila melanogaster.Molecular biology and evolution · 2023Article
- Whole-genome analysis reveals the hybrid formation of Chinese indigenous DHB pig following human migration.Evolutionary applications · 2022Article
- Article
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2 authors at 1 institution in 1 country.
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Abstract
Soft selective sweeps represent an important form of adaptation in which multiple haplotypes bearing adaptive alleles rise to high frequency. Most statistical methods for detecting selective sweeps from genetic polymorphism data, however, have focused on identifying hard selective sweeps in which a favored allele appears on a single haplotypic background; these methods might be underpowered to detect soft sweeps. Among exceptions is the set of haplotype homozygosity statistics introduced for the detection of soft sweeps by Garud et al. (2015). These statistics, examining frequencies of multiple haplotypes in relation to each other, include H12, a statistic designed to identify both hard and soft selective sweeps, and H2/H1, a statistic that conditional on high H12 values seeks to distinguish between hard and soft sweeps. A challenge in the use of H2/H1 is that its range depends on the associated value of H12, so that equal H2/H1 values might provide different levels of support for a soft sweep model at different values of H12. Here, we enhance the H12 and H2/H1 haplotype homozygosity statistics for selective sweep detection by deriving the upper bound on H2/H1 as a function of H12, thereby generating a statistic that normalizes H2/H1 to lie between 0 and 1. Through a reanalysis of resequencing data from inbred lines of Drosophila, we show that the enhanced statistic both strengthens interpretations obtained with the unnormalized statistic and leads to empirical insights that are less readily apparent without the normalization.
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