Mixed Race Studies

Skin Color and the Nature of Science

The American Biology Teacher
Volume 80, Number 3 (March 2018)
page 163
DOI: 10.1525/abt.2018.80.3.163

Douglas Allchin, Lecturer, History of Science and Technology
Minnesota Center for the Philosophy of Science
University of Minnesota

Skin color is the trait most commonly associated with race. Consider just the “black” in the Black Lives Matter name or the “white” in white nationalist rallies. Skin color and the concept of race are ideologically charged—and socially divisive. But scientifically, what is the nature of this relationship?

A study led by Sarah Tishkoff published not long ago in Science contradicts many widespread views of skin color and further dispels the very concept of human races in biology. The group identified at least eight genes for skin color, but the genes do not cluster neatly into predictable groups, or races. They further found that the genes do not align with conventional racial groups:

• The same depigmentation gene that led to “white” skin in the lineage of most Europeans (SLC24A5) is also common in East Africa, where skin color is much darker.
• Another pair of genes linked to lighter skin, hair, and eye color among Europeans actually originated in Africa, where among the San people in southern Africa, it also contributes to lighter skin tones.
• By contrast, a gene for darker pigmentation now common in Africa appears to be widespread in non-African groups as well: Indians, Melanesians, and Australian Aborigines.
• Some darker skin colors result not by increasing dark pigments but by reducing yellow and red pigments.

The routes to skin color are many and varied, and not exclusively determinant of any geographic or ancestral group. Trying to define race by skin color genetics is hardly “black and white.”…

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New gene variants reveal the evolution of human skin color

Science
2017-11-12

Ann Gibbons, Contributing Correspondent

Researchers have identified genes that help create diverse skin tones, such as those seen in the Agaw (left) and Surma (right) peoples of Africa. ALESSIA RANCIARO & DR. SIMON R. THOMPSON

Most people associate Africans with dark skin. But different groups of people in Africa have almost every skin color on the planet, from deepest black in the Dinka of South Sudan to beige in the San of South Africa. Now, researchers have discovered a handful of new gene variants responsible for this palette of tones.

The study, published online this week in Science, traces the evolution of these genes and how they traveled around the world. While the dark skin of some Pacific Islanders can be traced to Africa, gene variants from Eurasia also seem to have made their way back to Africa. And surprisingly, some of the mutations responsible for lighter skin in Europeans turn out to have an ancient African origin.

“This is really a landmark study of skin color diversity,” says geneticist Greg Barsh of the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama.

Researchers agree that our early australopithecine ancestors in Africa probably had light skin beneath hairy pelts. “If you shave a chimpanzee, its skin is light,” says evolutionary geneticist Sarah Tishkoff of the University of Pennsylvania, the lead author of the new study. “If you have body hair, you don’t need dark skin to protect you from ultraviolet [UV] radiation.”

Until recently, researchers assumed that after human ancestors shed most body hair, sometime before 2 million years ago, they quickly evolved dark skin for protection from skin cancer and other harmful effects of UV radiation. Then, when humans migrated out of Africa and headed to the far north, they evolved lighter skin as an adaptation to limited sunlight. (Pale skin synthesizes more vitamin D when light is scarce.)…

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Why Is Skin Color Different? Huge Genetic Study Reveals Prevailing Theory of Pigmentation is Wrong

Newsweek
2017-11-30

Kastalia Medrano, Staff Writer

These are South African individuals in a household that exemplify the substantial skin pigmentation variability in the Khomani and Nama populations. Brenna Henn

Scientists used to think that the same small handful of genes accounted for about half of all pigment variation in human skin. A new study shows the genetic picture behind skin color is far more complex.

Research supporting the prior, simpler conclusion was skewed by Eurocentrism. Because it focused almost exclusively on Northern Eurasian populations from higher latitudes, the data missed a huge swath of the globe. Now, scientists have factored in people of color living in lower latitudes—and found that the prevailing theory is wrong.

Scientists from the Broad Institute of MIT and Harvard, Stanford University, and Stony Brook University worked with groups of indigenous southern African peoples called the KhoeSan, notable to some for their use of “click” language. They interviewed them, measured their respective heights and weights, and used a tool called a reflectometer to measure their skin pigmentation.

After seven years of research, and data gathered from about 400 individuals, the researchers realized that the closer a population lives to the equator, the greater the number of genes play a part in determining skin pigmentation. A paper describing the research was published November 30 in the scientific journal Cell.

“Previous work has shown the biomedical consequences of ethnically biased studies. Over the past 10 years, approximately 80 percent of genetic association studies were performed in European-descent groups,” Alicia Martin, a postdoctoral scientist in the lab of Broad Institute member Mark Daly, told Newsweek by email. “What we find here is that the biology of pigmentation or ‘architecture’ can be very different in Africans.” Martin says the findings emphasize the need to fund more genetic work in diverse populations…

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Loci associated with skin pigmentation identified in African populations

Science
2017-10-12
eaan8433
DOI: 10.1126/science.aan8433

Nicholas G. Crawford, Derek E. Kelly, Matthew E. B. Hansen, Marcia H. Beltrame, Shaohua Fan, Shanna L. Bowman, Ethan Jewett, Alessia Ranciaro, Simon Thompson, Yancy Lo, Susanne P. Pfeifer, Jeffrey D. Jensen, Michael C. Campbell, William Beggs, Farhad Hormozdiari, Sununguko Wata Mpoloka, Gaonyadiwe George Mokone, Thomas Nyambo, Dawit Wolde Meskel, Gurja Belay, Jake Haut, NISC Comparative Sequencing Program, Harriet Rothschild, Leonard Zon, Yi Zhou, Michael A. Kovacs, Mai Xu, Tongwu Zhang, Kevin Bishop, Jason Sinclair, Cecilia Rivas, Eugene Elliot, Jiyeon Choi, Shengchao A. Li, Belynda Hicks, Shawn Burgess, Christian Abnet, Dawn E. Watkins-Chow, Elena Oceana, Yun S. Song, Eleazar Eskin, Kevin M. Brown, Michael S. Marks, Stacie K. Loftus, William J. Pavan, Meredith Yeager, Stephen Chanock, Sarah Tishkoff

Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in southern Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of UV response genes under selection in Eurasians.

Variation in epidermal pigmentation is a striking feature of modern humans. Human pigmentation is correlated with geographic and environmental variation (Fig. 1). Populations at lower latitudes have darker pigmentation than populations at higher latitudes, suggesting that skin pigmentation is an adaptation to differing levels of ultraviolet radiation (UVR) (1). Because equatorial regions receive more UVR than temperate regions, populations from these regions (including sub-Saharan Africans, South Asians, and Australo-Melanesians) have darker pigmentation (Fig. 1), which likely mitigates the negative impact of high UVR exposure such as skin cancer and folate degradation (1). In contrast, the synthesis of vitamin D3 in response to UVR, needed to prevent rickets, may drive selection for light pigmentation at high latitudes (1).

The basal layer of human skin contains melanocytes, specialized pigment cells that harbor subcellular organelles called melanosomes in which melanin pigments are synthesized and stored and then transferred to keratinocytes (2). Melanosome morphology and content differs between melanocytes that synthesize mainly eumelanins (black-brown pigments) or pheomelanins (pigments which range from yellow to reddish-brown) (3). Variation in skin pigmentation is due to the type and quantity of melanins generated, melanosome size, and the manner in which keratinocytes sequester and degrade melanins (4).

While over 350 pigmentation genes have been identified in animal models, only a subset of these genes have been linked to normal variation in humans (5). Of these, there is limited knowledge about loci that affect pigmentation in populations with African ancestry (6, 7).

Skin pigmentation is highly variable within Africa

To identify genes affecting skin pigmentation in Africa, we used a DSM II ColorMeter to quantify light reflectance from the inner arm as a proxy for melanin levels in 2,092 ethnically and genetically diverse Africans living in Ethiopia, Tanzania, and Botswana (table S1 and figs. S1 and S2) (8). Skin pigmentation levels vary extensively among Africans, with darkest pigmentation observed in Nilo-Saharan speaking pastoralist populations in Eastern Africa and lightest pigmentation observed in San hunter-gatherer populations from southern Africa (Fig. 2 and table S1)…

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Skin pigmentation is far more genetically complex than previously thought

Broad Institute
Massachusetts Institute of Technology, Cambridge, Massachusetts
2017-11-30

David Cameron, Director of Communications/Media Relations

Credit : Brenna Henn South African individuals in a household that exemplify the substantial skin pigmentation variability in the Khomani and Nama populations. Picture taken with consent for publication.

By studying an African population underrepresented in most datasets, researchers find genetic complexity of pigmentation varies by latitude

Many studies have suggested that the genetics of skin pigmentation are simple. A small number of known genes, it is thought, account for nearly 50 percent of pigment variation. However, these studies rely on datasets that heavily favor northern Eurasian populations—those that reside mostly in higher latitude regions.

Reporting in the November 30 issue of Cell, researchers from the Broad Institute of MIT and Harvard, Stanford University, and Stony Brook University report that while skin pigmentation is nearly 100 percent heritable, it is hardly a straightforward, Mendelian trait. By working closely with the KhoeSan, a group of populations indigenous to southern Africa, the researchers have found that the genetics of skin pigmentation become progressively complex as populations reside closer to the equator, with an increasing number of genes—known and unknown—involved, each making a smaller overall contribution.

“Africa has the greatest amount of phenotypic variability in skin color, and yet it’s been underrepresented in large scale endeavors,” said Alicia Martin, a postdoctoral scientist in the lab of Broad Institute member Mark Daly. “There are some genes that are known to contribute to skin pigmentation, but by and large there are many more new genes that have not been discovered.”

“We need to spend more time focusing on these understudied populations in order to gain deeper genetic insights,” said Brenna Henn, assistant professor in the Department of Ecology and Evolution at Stony Brook University who, along with Martin, is a co-corresponding author…

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An Unexpectedly Complex Architecture for Skin Pigmentation in Africans

Cell
Volume 171, Issue 6, 2017-11-30
pages 1340–1353.e14
DOI: 10.1016/j.cell.2017.11.015

Alicia R. Martin, Meng Lin, Julie M. Granka, Justin W. Myrick, Xiaomin Liu, Alexandra Sockell, Elizabeth G. Atkinson, Cedric J. Werely, Marlo Möller, Manjinder S. Sandhu, David M. Kingsley, Eileen G. Hoal, Xiao Liu, Mark J. Daly, Marcus W. Feldman, Christopher R. Gignoux, Carlos D. Bustamante, Brenna M. Henn

Highlights

• 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

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.

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