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Cited by 461Forensic and Genetic ResearchGenetic diversity and population structureGenetic Associations and Epidemiology

A Practical Genome Scan for Population-Specific Strong Selective Sweeps That Have Reached Fixation.

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Kimura, Ryosuke, Fujimoto, Akihiro, Tokunaga, Katsushi, Ohashi, Jun·2007·PLoS ONE
DOI 10.1371/journal.pone.0000286PMC PMC1805687
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Abstract

Phenotypic divergences between modern human populations have developed as a result of genetic adaptation to local environments over the past 100,000 years. To identify genes involved in population-specific phenotypes, it is necessary to detect signatures of recent positive selection in the human genome. Although detection of elongated linkage disequilibrium (LD) has been a powerful tool in the field of evolutionary genetics, current LD-based approaches are not applicable to already fixed loci. Here, we report a method of scanning for population-specific strong selective sweeps that have reached fixation. In this method, genome-wide SNP data is used to analyze differences in the haplotype frequency, nucleotide diversity, and LD between populations, using the ratio of haplotype homozygosity between populations. To estimate the detection power of the statistics used in this study, we performed computer simulations and found that these tests are relatively robust against the density of typed SNPs and demographic parameters if the advantageous allele has reached fixation. Therefore, we could determine the threshold for maintaining high detection power, regardless of SNP density and demographic history. When this method was applied to the HapMap data, it was able to identify the candidates of population-specific strong selective sweeps more efficiently than the outlier approach that depends on the empirical distribution. This study, confirming strong positive selection on genes previously reported to be associated with specific phenotypes, also identifies other candidates that are likely to contribute to phenotypic differences between human populations.

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  • Analysis of SNP variation between diverse human populations shows evidence of selection of the EDAR locus in East Asian and American populations.

    “Analysis of SNP variation between diverse human populations shows evidence of selection of the EDAR locus in East Asian and American populations [56],[57].”

    From Zebrafish eda and edar Mutants Reveal Conserved and Ancestral Roles of Ectodysplasin Signaling in Vertebrates (2008) · cites this paper as [56]

    The Results section (page unavailable) identifies EDAR in a region with a strong signature of selection in East Asians compared with Yoruba and European-ancestry populations. The Results and Methods describe the populations analyzed but include no American population, so this source does not support that part of the claim. (LLM, conf=0.91)

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Cited by

Sorted by citations

Authors
Kimura, R., Fujimoto, A., Tokunaga, K., & Ohashi, J.
Affiliations
  • Japan Society for the Promotion of Science (JP)
  • The University of Tokyo (JP)
Corresponding author
Kimura, Ryosuke
ORCID
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2007-03-14
Volume
2
Issue
3
Pages
e286
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0000286
PMC
PMC1805687
OpenAlex
W2003781078
Cited by
461
References
2
Citations by year
2026: 1 · 2025: 1 · 2024: 3 · 2023: 2 · 2022: 2 · 2021: 20 · 2020: 32 · 2019: 21 · 2018: 12 · 2017: 13 · 2016: 22 · 2015: 15 · 2014: 15 · 2013: 12 · 2012: 24
FWCI
12.21
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Institutional Repositories DataBase (IRDB) (submittedVersion, cc-by-nc-nd)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
  • University of the Ryukyus academic repository (University of the Ryukyus) (submittedVersion, cc-by)
  • University oh the Ryukyus Repository (submittedVersion, cc-by-nc-nd)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords
positive selection, fixation, haplotype homozygosity, linkage disequilibrium, nucleotide diversity, detection power, phenotypic divergence, HapMap
MeSH terms
Animals, Chromosome Mapping, Computer Simulation, Genetics, Population, Haplotypes, Homozygote, Humans, Models, Genetic, Mutation, Pigmentation, Selection, Genetic, Linkage Disequilibrium, Genome, Human, Population Groups

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