Genome-wide detection and characterization of positive selection in human populations
Open accessAbstract
With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.
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Sabeti et al. and Voight et al. developed computationally efficient methods for detecting evidence of selection in whole genomes and applied them to the HapMap populations.
“Recently, Sabeti et al.99,100 and Voight et al.101 developed computationally efficient methods for detecting evidence of selection in whole genomes and have applied those methods to the HapMap populations.”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [100]
The Abstract (page unavailable) reports developing a new selection test and applying three methods to more than 3 million HapMap2 polymorphisms. The Methods section reports a computer program implementing those tests. Our copy does not establish that the methods were computationally efficient; the separate attribution to Voight et al. is outside the scope of this source. (LLM, conf=0.83)
Experimental — accuracy not yet measuredNo SNP-h2 enrichment for positive selection signatures was identified in East Asian and European analyses.
“Similar to other studies conducted in EUR [34, 35], we did not identify SNP-h2 enrichment for positive selection signatures in our EAS and EUR analyses (Additional file 1: Table S4).”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [35]
The Abstract (page unavailable) describes a positive-selection analysis that included European samples, supporting the reference to a study conducted in EUR. It does not report SNP-h2 enrichment or a lack of it; the absence of enrichment in the citing authors’ EAS and EUR analyses is their own result, not a finding established by this source. (LLM, conf=0.84)
Experimental — accuracy not yet measuredSLC30A9 encodes ZnT9, a ubiquitously expressed zinc transporter, and has been repeatedly reported as a top candidate region for positive selection in humans, mostly in East Asian populations.
“The SLC30A9 gene (chr4: 41,990,502–42,090,461; GRCh38) has been repeatedly reported as a top candidate region for positive selection in several genome-wide scans of selection, mostly in East Asian populations [14,16–20].”
From Human genetic adaptation related to cellular zinc homeostasis (2023) · cites this paper as [19]
The passage discussing the 22 strongest candidate regions (section labeled Abstract; page unavailable) lists SLC30A9 among genes with potentially functional variants in those regions. It does not identify the SLC30A9 signal as East Asian. The claim that several scans reported it is supported by the citations collectively, not established by this paper alone. (LLM, conf=0.84)
Experimental — accuracy not yet measuredMost pigmentation genes have geospatial patterns of genetic variation correlated with the geographic distribution of skin pigmentation and display strong evidence for selective sweeps in European and East Asian populations.
“Most of these genes have geospatial patterns of genetic variation that are correlated with the geographic distribution of skin pigmentation and display strong evidence for selective sweeps in European and East Asian populations (Izagirre et al. 2006;McEvoy et al. 2006;Soejima et al. 2006;Voight et al. 2006;Lao et al. 2007;Myles et al. 2007;Norton et al. 2007;Sabeti et al. 2007;Williamson et al. 2”
From The timing of pigmentation lightening in Europeans (2013) · cites this paper as Sabeti et al. 2007
The paper’s Abstract reports strong evidence of selection for two pigmentation genes, SLC24A5 and SLC45A2, in Europeans, and describes geographic differences in their variants. It does not establish the claim about most pigmentation genes or selective sweeps of pigmentation genes in East Asian populations; the Asian genes it highlights, EDAR and EDA2R, concern hair-follicle development. No page number is available in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredA defined allelic variant of EDAR within these populations leads to a coding change in the death domain of EDAR and is a candidate allele for altered gene function that could have led to the region being fixed in these populations.
“A defined allelic variant of EDAR within these populations leads to a coding change in the death domain of EDAR and is a candidate allele for altered gene function that could have lead to the region being fixed in these populations [34].”
From Zebrafish eda and edar Mutants Reveal Conserved and Ancestral Roles of Ectodysplasin Signaling in Vertebrates (2008) · cites this paper as [34]
None of the positive-selection annotations tested was significant in the two populations tested.
“However, similar to previous studies [34, 35], none of the positive-selection annotations tested was significant in the two populations tested.”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [35]
The Methods section on functional annotation describes classifying variants, while the Methods section on selection tests describes comparing populations to detect selective sweeps. Neither reports whether positive-selection annotations were statistically significant in the two populations mentioned by the citing sentence. I searched for annotation enrichment and significance results but found no passage addressing that claim. (LLM, conf=0.72)
Experimental — accuracy not yet measuredThe strongest dietary adaptive signal in the human genome is the highly structured global distribution and extended homozygosity around the lactase persistence allele in European genomes.
“The strongest dietary adaptive signal in the human genome is the highly structured global distribution and extended homozygosity around the lactase persistence allele in European genomes35.”
From Genome flux and stasis in a five millennium transect of European prehistory (2014) · cites this paper as [35]
Selection on the lactase persistence variant was driven by dairying.
“Selection on this variant was undoubtedly driven by dairying, but despite evidence for milk residues in ceramic vessels from a Körös context in the 6th millenium BC (ref. 36) this variant remains absent throughout the 10 Neolithic/Copper Age stages of our transect.”
From Genome flux and stasis in a five millennium transect of European prehistory (2014) · cites this paper as [35]
The ancient DNA-based simulation approach estimates selection coefficients over a defined period.
“Selection coefficients are estimated over a defined period”
From Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y (2014) · cites this paper as [1]
The ancient DNA-based simulation approach is insensitive to the frequently unaccounted for uncertainties associated with allele age estimation using molecular or recombination clocks.
“our approach is insensitive to the frequently unaccounted for uncertainties associated with allele age estimation using molecular or recombination clocks”
From Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y (2014) · cites this paper as [1]
The ancient DNA-based simulation approach can accommodate selection acting on standing variation.
“selection acting on standing variation can be accommodated”
From Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y (2014) · cites this paper as [1]
The low heritability of skin pigmentation in Europeans can be explained by reduced genetic variation at skin pigmentation loci due to strong positive selection for lighter skin in Europeans.
“Interestingly, the heritability of skin pigmentation is very low in Europeans (hg2 = 0.191; N = 1,231), which we think can be explained by reduced genetic variation at skin pigmentation loci due to strong positive selection for lighter skin in Europeans [17,21,38].”
From Investigating the case of human nose shape and climate adaptation (2017) · cites this paper as [38]
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- Authors
- The International HapMap Consortium, Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E. H., McCarroll, S. A., Gaudet, R., Schaffner, S. F., & Lander, E. S.
- Affiliations
- Broad Institute (US)
- Harvard University (US)
- ORCID
- Venue
- Nature
- Published
- 2007-10
- Volume
- 449
- Issue
- 7164
- Pages
- 913-918
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2687721
- OpenAlex
- W2156866331
- Cited by
- 2,131
- References
- 34
- Citations by year
- 2026: 96 · 2025: 106 · 2024: 155 · 2023: 98 · 2022: 129 · 2021: 154 · 2020: 125 · 2019: 104 · 2018: 138 · 2017: 109 · 2016: 92 · 2015: 119 · 2014: 100 · 2013: 95 · 2012: 106
- FWCI
- 53.01
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Funders
- Wellcome Trust (081682, 077011, 077008, 077046)
- 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 › Evolution and Genetic Dynamics
- Keywords
- positive selection, natural selection, human genetic variation, cross-population comparison, non-synonymous single nucleotide polymorphisms, Lassa virus, skin pigmentation, hair follicle development, LARGE, DMD, SLC24A5, SLC45A2, EDAR, EDA2R, candidate regions
- MeSH terms
- Gene Frequency, Genetics, Population, Geography, Haplotypes, Humans, Models, Molecular, Selection, Genetic, Genome, Human, Protein Structure, Tertiary, Antiporters, Polymorphism, Single Nucleotide, Edar Receptor
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