ArticleGenetics2013
Detecting signatures of selection through haplotype differentiation among hierarchically structured populations.
Article in Genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 181 papers, 2 of them syntheses that pooled it.
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Who cites it
181 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits.Genetics, selection, evolution : GSE · 2023Pooled it
- Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals.Nature genetics · 2018Pooled it
- Beyond two alleles: multiallelic genotypic selection and its estimation from time-series data.BMC genomics · 2026Article
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- Genetic basis of temporal variation in phenology in a woody perennial plant.NPJ systems biology and applications · 2026Article
- pyFLANK, a graph neural network based null distribution inference model for FBMC bioinformatics · 2026Article
- From selection signatures in cattle to functional validation in mice: HSPA12B negatively regulates adipose browning and thermogenesis.Journal of animal science · 2026Article
- Artificial and natural selection components reveal the mechanisms of tropical sheep populations against gastrointestinal parasites.PloS one · 2026Article
- Host-Associated Genetic Differentiation in the Face of Ongoing Gene Flow: Ecological Speciation in a Pathogenic Parasite of Freshwater Fish.Molecular biology and evolution · 2025Article
- Resequencing Composite Kazakh Whiteheaded Cattle: Insights into Ancestral Breed Contributions, Selection Signatures, and Candidate Genetic Variants.Animals : an open access journal from MDPI · 2025Article
- The Effect of Continuous Selection in KiwiCrossAnimals : an open access journal from MDPI · 2025Article
- Genomic insights into runs of homozygosity, effective population size and selection signatures in Iranian meat and dairy sheep breeds.PloS one · 2025Article
- Genome-wide scan for signatures of selection in Hanwoo and Angus cattle using whole-genome sequence data.PloS one · 2025Article
- Computational Genomics and Its Applications to Anthropological Questions.American journal of biological anthropology · 2024Review
- Genome-Wide Scan for Selective Sweeps Reveals Novel Loci Associated with Prolificacy in Iranian Sheep Breeds in Comparison with Highly Prolific Exotic Breed.Animals : an open access journal from MDPI · 2024Article
- Exome-wide comparative analyses revealed differentiating genomic regions for performance traits in Indian native buffaloes.Animal biotechnology · 2024Article
- Genomic profiling of selective sweeps through haplotype differentiation unravelled genes associated with production and reproduction traits in Indian goat breeds.Tropical animal health and production · 2024Article
- Adaptation of Fusarium Head Blight Pathogens to Changes in Agricultural Practices and Human Migration.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 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
121 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations and to look for genomic regions with outstanding genetic differentiation between these populations. Genetic differentiation is generally based on allele frequency differences between populations, which are measured by FST or related statistics. Here we introduce a new statistic, denoted hapFLK, which focuses instead on the differences of haplotype frequencies between populations. In contrast to most existing statistics, hapFLK accounts for the hierarchical structure of the sampled populations. Using computer simulations, we show that each of these two features-the use of haplotype information and of the hierarchical structure of populations-significantly improves the detection power of selected loci and that combining them in the hapFLK statistic provides even greater power. We also show that hapFLK is robust with respect to bottlenecks and migration and improves over existing approaches in many situations. Finally, we apply hapFLK to a set of six sheep breeds from Northern Europe and identify seven regions under selection, which include already reported regions but also several new ones. We propose a method to help identifying the population(s) under selection in a detected region, which reveals that in many of these regions selection most likely occurred in more than one population. Furthermore, several of the detected regions correspond to incomplete sweeps, where the favorable haplotype is only at intermediate frequency in the population(s) under selection.
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