An Unexpectedly Complex Architecture for Skin Pigmentation in Africans

Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than pr...

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Published inCell Vol. 171; no. 6; pp. 1340 - 1353.e14
Main Authors Martin, Alicia R., Lin, Meng, Granka, Julie M., Myrick, Justin W., Liu, Xiaomin, Sockell, Alexandra, Atkinson, Elizabeth G., Werely, Cedric J., Möller, Marlo, Sandhu, Manjinder S., Kingsley, David M., Hoal, Eileen G., Liu, Xiao, Daly, Mark J., Feldman, Marcus W., Gignoux, Christopher R., Bustamante, Carlos D., Henn, Brenna M.
Format Journal Article
LanguageEnglish
Published United States Elsevier Inc 30.11.2017
Subjects
Africa
Africans
Black People - genetics
genes
heritability
human evolution
Humans
latitude
loci
phenotype
pigmentation
Polymorphism, Single Nucleotide
population genetics
Skin Pigmentation
Southern Africa
surveys
variance
Africa
Southern Africa
pigmentation
population genetics
human evolution
Africa
heritability
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Abstract Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures. [Display omitted] •Skin pigmentation in Africans is far more polygenic than light skin in Eurasians•Southern African KhoeSan populations have lighter skin compared to equatorial Africans•Highly heritable KhoeSan skin color variation is poorly explained by known genes•The study of African skin color identifies novel and canonical pigmentation genes The genetic architecture of skin pigmentation is highly complex, varies across human populations, and is subject to distinct geographical evolutionary pressures.
AbstractList Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures. [Display omitted] •Skin pigmentation in Africans is far more polygenic than light skin in Eurasians•Southern African KhoeSan populations have lighter skin compared to equatorial Africans•Highly heritable KhoeSan skin color variation is poorly explained by known genes•The study of African skin color identifies novel and canonical pigmentation genes The genetic architecture of skin pigmentation is highly complex, varies across human populations, and is subject to distinct geographical evolutionary pressures.
Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.
Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.
Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan, populations indigenous to southern Africa, who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5 , TYRP1, SMARCA2 / VLDLR , and SNX13 using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures. The genetic architecture of skin pigmentation is highly complex and varies across human populations subjected to distinct geographical evolutionary pressures
Author Lin, Meng
Granka, Julie M.
Henn, Brenna M.
Gignoux, Christopher R.
Martin, Alicia R.
Sandhu, Manjinder S.
Möller, Marlo
Kingsley, David M.
Hoal, Eileen G.
Liu, Xiaomin
Liu, Xiao
Daly, Mark J.
Feldman, Marcus W.
Myrick, Justin W.
Atkinson, Elizabeth G.
Werely, Cedric J.
Bustamante, Carlos D.
Sockell, Alexandra
AuthorAffiliation 3 Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141
6 Department of Biological Sciences, Stanford University, Stanford, CA, 94305
5 Department of Ecology and Evolution, SUNY Stony Brook, NY 11794
10 Wellcome Trust Sanger Institute, Genome Campus, Hinxton, England
1 Department of Genetics, Stanford University, Stanford, CA, 94305
4 Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02141
7 BGI-Shenzhen, Shenzhen, China
2 Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
8 Department of Developmental Biology, Stanford University, Stanford, California, USA
9 SA MRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/29195075$$D View this record in MEDLINE/PubMed
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Issue 6
Keywords pigmentation
population genetics
human evolution
Africa
heritability
Language English
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Snippet Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait....
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SubjectTerms Africa
Africans
Black People - genetics
genes
heritability
human evolution
Humans
latitude
loci
phenotype
pigmentation
Polymorphism, Single Nucleotide
population genetics
Skin Pigmentation
Southern Africa
surveys
variance
Title An Unexpectedly Complex Architecture for Skin Pigmentation in Africans
URI https://dx.doi.org/10.1016/j.cell.2017.11.015
https://www.ncbi.nlm.nih.gov/pubmed/29195075
https://www.proquest.com/docview/1971708155
https://www.proquest.com/docview/2131871281
https://pubmed.ncbi.nlm.nih.gov/PMC5884124
Volume 171
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