Cited by 352Forensic and Genetic ResearchGenetic Associations and EpidemiologyGenetic diversity and population structure

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Genome-wide scans for footprints of natural selection

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Oleksyk, Taras K., Smith, Michael W., O'Brien, Stephen J.·2010·Philosophical Transactions of the Royal Society B: Biological Sciences

DOI 10.1098/rstb.2009.0219PMC PMC2842710

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Abstract

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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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
DOI: 10.1098/rstb.2009.0219
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
Licence: cc-by
royalsociety.org/journals/ethics-policies/data-sharing-mining/ (tdm)
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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Genome-wide scans for footprints of natural selection

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