ArticleHeredity2016
Using the variability of linkage disequilibrium between subpopulations to infer sweeps and epistatic selection in a diverse panel of chickens.
Article in Heredity, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- The population structure in the Baltic herring reflects natural selection and local adaptation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Large-scale genome-wide SNP analysis reveals the rugged (and ragged) landscape of global ancestry, phylogeny, and demographic history in chicken breeds.Journal of Zhejiang University. Science. B · 2024Article
- Parent-offspring genotyped trios unravelling genomic regions with gametic and genotypic epistatic transmission bias on the cattle genome.Frontiers in genetics · 2023Article
- Article
- Finding Hybrid Incompatibilities Using Genome Sequences from Hybrid Populations.Molecular biology and evolution · 2021Article
- Tracing the footprints of a moving hybrid zone under a demographic history of speciation with gene flow.Evolutionary applications · 2020Article
- Screening for epistatic selection signatures: A simulation study.Scientific reports · 2019Article
- MeSH-Informed Enrichment Analysis and MeSH-Guided Semantic Similarity Among Functional Terms and Gene Products in Chicken.G3 (Bethesda, Md.) · 2016Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A whole-genome scan for identifying selection acting on pairs of linked loci is proposed and implemented. The scan is based on , one of Ohta's 1982 measures of between-population linkage disequilibrium (LD). An approximate empirical null distribution for the statistic is suggested. Although the partitioning of LD into between-population components was originally used to investigate epistatic selection, we demonstrate that values of may also be influenced by single-locus selective sweeps with linkage but no epistasis. The proposed scan is implemented in a diverse panel of chickens including 72 distinct breeds genotyped at 538 298 single-nucleotide polymorphisms. In all, 1723 locus pairs are identified as putatively corresponding to a selective sweep or epistatic selection. These pairs of loci generally cluster to form overlapping or neighboring signals of selection. Known variants that were expected to have been under selection in the panel are identified, as well as an assortment of novel regions that have putatively been under selection in chickens. Notably, a promising pair of genes located 8 MB apart on chromosome 9 are identified based on as demonstrating strong evidence of dispersive epistatic selection between populations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.