Using the variability of linkage disequilibrium between subpopulations to infer sweeps and epistatic selection in a diverse panel of chickens
Open accessAbstract
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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Although a certain number of candidate genes were identified, the authors pointed out that single-locus selection could not be excluded as an alternative explanation since selective sweeps can generate similar patterns.
“Although a certain number of candidate genes were identified, the authors pointed out that single-locus selection could not be excluded as an alternative explanation since selective sweeps can generate similar patterns.”
From Finding Hybrid Incompatibilities Using Genome Sequences from Hybrid Populations (2021) · cites this paper as Beissinger et al. 2016
Beissinger et al. (2016) computed the DIS′2 statistic, a measure that partitions linkage disequilibrium between and within populations.
“Beissinger et al. (2016) computed the DIS′2 statistic (Ohta 1982a, 1982b), a measure that partitions linkage disequilibrium between and within populations.”
From Finding Hybrid Incompatibilities Using Genome Sequences from Hybrid Populations (2021) · cites this paper as Beissinger et al. 2016
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- Authors
- Beissinger, T. M., Gholami, M., Erbe, M., Weigend, S., Weigend, A., de Leon, N., Gianola, D., & Simianer, H.
- Affiliations
- University of Wisconsin–Madison (US)
- University of Göttingen (DE)
- Bavarian State Research Center for Agriculture (DE)
- Friedrich-Loeffler-Institut (DE)
- Corresponding author
- Simianer, H
- Venue
- Heredity
- Published
- 2015-09-09
- Volume
- 116
- Issue
- 2
- Pages
- 158-166
- ISSN
- 0018-067X (ISSN-L)
- 1365-2540
- PMC
- PMC4806882
- OpenAlex
- W1876509248
- Cited by
- 14
- References
- 41
- Citations by year
- 2026: 2 · 2024: 1 · 2023: 1 · 2022: 1 · 2021: 3 · 2020: 1 · 2019: 3 · 2016: 1 · 2015: 1
- FWCI
- 0.46
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Heredity (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- GRO (submittedVersion)
- OpenAgrar (submittedVersion)
- Funders
- National Science Foundation
- U.S. Department of Energy
- Wisconsin Alumni Research Foundation
- University of Wisconsin-Madison
- Bundesministerium für Bildung und Forschung (FKZ 0315528, 0315528)
- Office of Science
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- linkage disequilibrium, epistatic selection, selective sweeps, whole genome scan, chickens, chicken breeds, single nucleotide polymorphisms, empirical null distribution, chromosome 9
- MeSH terms
- Animals, Chickens, Epistasis, Genetic, Genetics, Population, Genotype, Genetic Linkage, Selection, Genetic, Linkage Disequilibrium, Polymorphism, Single Nucleotide
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