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Genome-wide scans for footprints of natural selection
Open accessAbstract
Detecting recent selected ‘genomic footprints’ applies directly to the discovery of disease genes and in the imputation of the formative events that molded modern population genetic structure. The imprints of historic selection/adaptation episodes left in human and animal genomes allow one to interpret modern and ancestral gene origins and modifications. Current approaches to reveal selected regions applied in genome-wide selection scans (GWSSs) fall into eight principal categories: (I) phylogenetic footprinting, (II) detecting increased rates of functional mutations, (III) evaluating divergence versus polymorphism, (IV) detecting extended segments of linkage disequilibrium, (V) evaluating local reduction in genetic variation, (VI) detecting changes in the shape of the frequency distribution (spectrum) of genetic variation, (VII) assessing differentiating between populations ( F ST ), and (VIII) detecting excess or decrease in admixture contribution from one population. Here, we review and compare these approaches using available human genome-wide datasets to provide independent verification (or not) of regions found by different methods and using different populations. The lessons learned from GWSSs will be applied to identify genome signatures of historic selective pressures on genes and gene regions in other species with emerging genome sequences. This would offer considerable potential for genome annotation in functional, developmental and evolutionary contexts.
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“in agreement with Rsb being a powerful method to detect selection signature when the selected allele has reached fixation (Tang et al., 2007; Oleksyk et al., 2010; Bahbahani et al., 2018).”
From Identification of Candidate Signature Genes and Key Regulators Associated With Trypanotolerance in the Sheko Breed (2019) · cites this paper as Oleksyk et al., 2010
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Metadata
- Authors
- Oleksyk, T. K., Smith, M. W., & O'Brien, S. J.
- Affiliations
- Biology Department, University of Puerto Rico at Mayaguez, Mayaguez 00681, Puerto Rico
- National Cancer Institute (US)
- Laboratory of Genomic Diversity, National Cancer Institute at Frederick, Frederick, MD 21702, USA
- ORCID
- Smith, Michael W.
- Venue
- Philosophical Transactions of the Royal Society B: Biological Sciences
- Publisher
- The Royal Society
- Published
- 2010-01-12
- Volume
- 365
- Issue
- 1537
- Pages
- 185-205
- ISSN
- 0962-8436 (ISSN-L)
- 1471-2970
- PMC
- PMC2842710
- OpenAlex
- W2143606043
- Cited by
- 340
- References
- 161
- Citations by year
- 2026: 11 · 2025: 18 · 2024: 12 · 2023: 18 · 2022: 19 · 2021: 27 · 2020: 17 · 2019: 18 · 2018: 31 · 2017: 28 · 2016: 20 · 2015: 28 · 2014: 27 · 2013: 21 · 2012: 18
- FWCI
- 1.41
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Philosophical Transactions of the Royal Society B Biological Sciences (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- NSUWorks (Nova Southeastern University) (submittedVersion)
- Funders
- U.S. Department of Health and Human Services
- National Institutes of Health
- National Cancer Institute (N01CO12400)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- natural selection, linkage disequilibrium, genetic variation, genetic differentiation, F(ST), admixture, disease-associated genes, phylogenetic footprinting, functional mutations, genome annotation, human genome, animal genomes
- MeSH terms
- Animals, Base Sequence, Humans, Phylogeny, Selection, Genetic, Genetic Variation, Genome, Human, Evolution, Molecular, Genome-Wide Association Study
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