A scan for signatures of positive selection in candidate loci for skin pigmentation in humans
Open accessAbstract
Although the combination of pale skin and intense sun exposure results in an important health risk for the individual, it is less clear if at the population level this risk has possessed an evolutionary meaning. In this sense, a number of adaptive hypotheses have been put forward to explain the evolution of human skin pigmentation, such as photoprotection against sun-induced cancer, sexual selection, vitamin D synthesis or photoprotection of photolabile compounds, among others. It is expected that if skin pigmentation is adaptive, we might be able to see the signature of positive selection on some of the genes involved. In order to detect this signature, we analyze a battery of 81 candidate loci by means of phylogenetic and population genetic tests. Our results indicate that both light and dark skin may possess adaptive value. Of the main loci presenting this signature, TP53BP1 shows clear evidence of adaptive selection in Africans, whereas TYRP1 and SLC24A5 show evidence of adaptive selection in Caucasians. Although we cannot offer a mechanism that based on these genes explains the advantage of light skin, if TP53BP1, and perhaps RAD50, have truly conferred an adaptive value to the African population analyzed, photoprotection against sun-induced skin damage/cancer might be proposed as a mechanism that has driven the evolution of human skin pigmentation.
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Most 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 Izagirre et al. 2006
The EHH Test section reports significant selection signatures at only five of 32 tested loci after correction: three in Yorubans and two in Caucasians, with none in East Asians. The F ST Values section does report population-specific genetic differences at some loci, but it does not support the claim that most pigmentation genes show strong evidence of selective sweeps in European and East Asian populations. Page numbers are unavailable in our copy. (LLM, conf=0.90)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredThe SNP-haplotype structure around the derived alleles at all loci bears signals of Eurasian hard sweeps that are not expected under selection from standing variation.
“In any case, the SNP-haplotype structure around the derived alleles at all loci bear signals of Eurasian hard sweeps that are not expected under selection from standing variation (Hermisson and Pennings 2005;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. 2007;Pickrell et al. 2”
From The timing of pigmentation lightening in Europeans (2013) · cites this paper as Izagirre et al. 2006
The EHH Test section reports haplotype-based signatures of recent positive selection at two loci in Caucasians, TYRP1 and SLC24A5. It does not establish such signals at all loci or across Eurasian populations: three other significant loci showed signals only in Yorubans. The passages do not distinguish hard sweeps from selection on standing variation. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe SLC24A5 SNP rs1426654 is nearly fixed for one allele in all European groups.
“The SLC24A5 SNP rs1426654 is nearly fixed for one allele in all European groups.11,13,22,29,30,51”
From A Genomewide Association Study of Skin Pigmentation in a South Asian Population (2007) · cites this paper as [11]
Variants affecting skin pigmentation have previously been shown to be targets of selection.
“and variants affecting skin pigmentation have previously been shown to be targets of selection”
From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Izagirre et al. 2006
The C allele of rs1800414 has been associated with lighter skin pigmentation in East Asians.
“since this allele has been associated with lighter skin pigmentation in East Asians”
From A global view of the OCA2-HERC2 region and pigmentation (2012) · cites this paper as Izagirre et al. 2006
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Understanding the evolution of human pigmentation: recent contributions from population genetics
Rees, J. L., & Harding, R. M. (2012) · Journal of Investigative Dermatology · doi:10.1038/jid.2011.358 · Cited by 50 · see citing works
- Authors
- Izagirre, N., García, I., Junquera, C., de la Rúa, C., & Alonso, S.
- Affiliations
- University of the Basque Country (ES)
- Corresponding author
- Izagirre, Neskuts
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-06-06
- Volume
- 23
- Issue
- 9
- Pages
- 1697-1706
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2143088015
- Cited by
- 119
- References
- 72
- Citations by year
- 2026: 1 · 2024: 3 · 2023: 1 · 2022: 2 · 2021: 4 · 2020: 4 · 2019: 2 · 2018: 5 · 2017: 7 · 2016: 6 · 2015: 4 · 2014: 5 · 2013: 7 · 2012: 6
- FWCI
- 5.38
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Eusko Jaurlaritza
- Euskal Herriko Unibertsitatea
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › melanin and skin pigmentation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- human skin pigmentation, positive selection, candidate loci, 53BP1, RAD50, TRP-1, SLC24A5, photoprotection, vitamin D synthesis, sexual selection, adaptive evolution, phylogenetic analysis
- MeSH terms
- Adaptation, Biological, Biological Evolution, Genetics, Population, Homozygote, Humans, Phylogeny, Selection, Genetic, Skin Pigmentation, Reproducibility of Results
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