Detection of selective sweeps in structured populations: a comparison of recent methods
Open accessAbstract
Identifying genomic regions targeted by positive selection has been a long‐standing interest of evolutionary biologists. This objective was difficult to achieve until the recent emergence of next‐generation sequencing, which is fostering the development of large‐scale catalogues of genetic variation for increasing number of species. Several statistical methods have been recently developed to analyse these rich data sets, but there is still a poor understanding of the conditions under which these methods produce reliable results. This study aims at filling this gap by assessing the performance of genome‐scan methods that consider explicitly the physical linkage among SNP s surrounding a selected variant. Our study compares the performance of seven recent methods for the detection of selective sweeps ( iHS , nSL , EHHST , xp‐ EHH , XP ‐ EHHST , XPCLR and hap FLK ). We use an individual‐based simulation approach to investigate the power and accuracy of these methods under a wide range of population models under both hard and soft sweeps. Our results indicate that XPCLR and hap FLK perform best and can detect soft sweeps under simple population structure scenarios if migration rate is low. All methods perform poorly with moderate‐to‐high migration rates, or with weak selection and very poorly under a hierarchical population structure. Finally, no single method is able to detect both starting and nearly completed selective sweeps. However, combining several methods ( XPCLR or hap FLK with iHS or nSL ) can greatly increase the power to pinpoint the selected region.
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Combining methods for the detection of selection signature regions increases the power of the study compared to single analysis.
“Combining methods for the detection of selection signature regions has been suggested as a means of increasing the power of the study compared to single analysis (e.g. Ma et al., 2015; Vatsiou et al., 2016).”
From Identification of Candidate Signature Genes and Key Regulators Associated With Trypanotolerance in the Sheko Breed (2019) · cites this paper as Vatsiou et al., 2016
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Additional file 2 of Investigation of ancestral alleles in the Bovinae subfamily
Naji, M. M., Utsunomiya, Y. T., Sölkner, J., Rosen, B. D., & Mészáros, G. (2021) · Figshare · doi:10.6084/m9.figshare.13788232
Mahdabi, E. R., Esmailizadeh, A., Mehrgardi, A. A., & Fozi, M. A. (2021) · Figshare · doi:10.6084/m9.figshare.16599608
Additional file 1 of Investigation of ancestral alleles in the Bovinae subfamily
Naji, M. M., Utsunomiya, Y. T., Sölkner, J., Rosen, B. D., & Mészáros, G. (2021) · Figshare · doi:10.6084/m9.figshare.13788229
- Authors
- Vatsiou, A. I., Bazin, E., & Gaggiotti, O. E.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Laboratoire d'Ecologie Alpine UMR CNRS 5553 Université Joseph Fourier Grenoble France
- Corresponding author
- Gaggiotti, Oscar E.
- ORCID
- Gaggiotti, Oscar E.
- Venue
- Molecular Ecology
- Publisher
- Wiley
- Published
- 2015-10-12
- Volume
- 25
- Issue
- 1
- Pages
- 89-103
- ISSN
- 0962-1083 (ISSN-L)
- 1365-294X
- OpenAlex
- W2131888512
- Cited by
- 111
- References
- 53
- Citations by year
- 2026: 9 · 2025: 13 · 2024: 4 · 2023: 8 · 2022: 8 · 2021: 15 · 2020: 10 · 2019: 9 · 2018: 13 · 2017: 11 · 2016: 8 · 2015: 3
- FWCI
- 8.02
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Ecology (publishedVersion)
- PubMed (publishedVersion)
- St Andrews Research Repository (St Andrews Research Repository) (submittedVersion)
- Funders
- European Commission
- Marie-Curie Initial Training Network INTERCROSSING
- MASTS
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- selective sweeps, positive selection, structured populations, genome scan, hapFLK, hyperpolarization-activated current, XP-EHH, population structure, migration rate, statistical power, linkage disequilibrium
- MeSH terms
- Computer Simulation, Genetics, Population, Genotype, Haplotypes, Genetic Linkage, Models, Genetic, Selection, Genetic, Sequence Analysis, DNA, Evolution, Molecular, Polymorphism, Single Nucleotide
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