The Complex History of the Genes That Color Our Skin

Few human traits are more variable, more obvious, and more historically divisive than the color of our skin. And yet, for all its social and scientific importance, we know very little about how our genes influence its pigment. What we do know comes almost entirely from studying people of European descent.

To Sarah Tishkoff, a geneticist at the University of Pennsylvania, that’s a ridiculous state of affairs. “It gives you a very incomplete perspective,” she says.

To redress that imbalance, Tishkoff and her team looked to Africa—the continent where humanity is at its most physically and genetically diverse. They recruited 1,570 volunteers from 10 ethnic groups in Ethiopia, Tanzania, and Botswana, and measured the amount of the dark pigment melanin in the skin of their inner arms. Then the team looked at more than 4 million spots in the volunteers’ genomes where DNA can vary by a single letter, to identify which variations are associated with their skin color.

They found several, clustered around six specific genes: SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2. And they showed that these variants collectively account for 29 percent of the variation in skin color in the three countries studied. That’s a big proportion! For comparison, a similar and much bigger study identified hundreds of genes that affect one’s height, but that collectively account for just 16 percent of the variation that you see in large populations.

Tishkoff says that her results complicate the traditional evolutionary story of human skin. In this view, humanity began with dark skin in Africa to protect against the harmful effects of the sun’s ultraviolet radiation. As people migrated to other continents, some groups evolved lighter skin, to more effectively produce vitamin D in areas where sunlight is scarce.

But most of the variants that Tishkoff’s team identified, for both light and dark skin, have an ancient African origin. They likely arose in hominids like Homo erectus long before the dawn of our own species, and have coexisted in balance for hundreds and thousands of years. In many cases, the older variant is responsible for lighter skin, not darker. That’s consistent with an idea from Nina Jablonski, an anthropologist from Pennsylvania State University, who thinks that the ancient ancestors of humans—much like other primates—had pale skin. “As our ancestors moved out of the forest and into the savannah, they lost their hair and evolved darker skin,” says Nick Crawford, a researcher in Tishkoff’s lab.

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But that wasn’t an all-encompassing change. Different groups of people adapted to their own particular environments, not just around the world, but within Africa, too. “Africa is not some homogenous place where everyone has dark skin,” Tishkoff says. “There’s huge variation.” For example, her team’s measurements showed that the Nilotic peoples in eastern Africa have some of the darkest skin around, while the San of southern Africa have light skin, comparable to some East Asians.

This physical diversity is mirrored in these groups’ genes. The first gene identified as affecting human skin color—MC1R—is very diverse in European populations but remarkably similar across African ones. Based on that pattern, says Tishkoff, some geneticists have concluded that the evolutionary pressure for dark skin in Africa is so strong that any genetic variants that altered skin color were ruthlessly weeded out by natural selection. “That’s not true,” says Tishkoff—but it’s what happens when you only study skin color in Western countries. “When you look at this African-centered perspective, there’s a lot of variation.”

For example, a gene called MFSD12 has variants that are linked to darker skin; these are common in dark-skinned people from East Africa, but rare among the lighter-skinned San. MFSD12 also shows how the search for pigmentation genes can reveal new insights about the basic biology of our skin. Two years ago, the gene didn’t even have a name, but it was linked to vitiligo—a condition where people develop white patches on dark skin. By deleting the gene in fish and mice, Tishkoff’s colleagues confirmed that it controls the balance between light and dark pigments.

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Another gene called SLC24A5 has a variant that has traditionally been seen as “European,” because it is so starkly associated with lighter skin in Western European populations. But Tishkoff’s team showed that the variant entered the East African gene pool from the Middle East several millennia ago and well before the era of colonization. Today, it is common in Ethiopian and Tanzanian groups, but rare in other areas.

Critically, in East African groups, the variant doesn’t lighten skin color to the same degree that it does in Europeans. It’s a stark reminder that “a person can carry a gene that confers a particular trait in one population and yet not obviously show evidence of that trait themselves,” says Jablonski. “It reminds us that we can’t be cavalier about stating that a particular crime suspect has a particular skin color based on the presence of a single genetic variant in their DNA.”

Sandra Beleza, from the University of Leicester, has done one of the only other genetic studies of skin color to include people of mixed African ancestry. She says that neither her work nor Tishkoff’s have come close to identifying all the genes behind this trait. Further studies, involving other African populations that haven’t been included in genetic studies yet, may help to plug that gap.

While many have used skin color as a means of dividing people, Tishkoff sees the potential for unity and connectedness. “One of the traits that most people would associate with race—skin color—is a terrible classifier,” she says. Even without supposedly “dark” skin, there is a lot of hidden variation. “The study really discredits the idea of a biological construct of race,” she adds. “There are no discrete boundaries between groups that are consistent with biological markers.”

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Jedidiah Carlson from the University of Michigan, who has been keeping tabs on how white-supremacist groups misappropriate genetic studies, agrees. “Because visually distinguishable traits common in present-day Europeans, such as light skin color, are also assumed to have arisen within European populations, white supremacists treat these traits as a proxy for superior intelligence,” he says. The history of SLC24A5 reminds us that “light skin pigmentation, and likely other ‘European’ traits, are not unique to Europeans. Human populations have been interbreeding for as long as we have existed as a species.”

White-supremacist communities “often rally around the demonstrably false claim that Africans are more genetically similar to ancestral hominids than Europeans—and these results turn the tables,” Carlson adds. At several genes that influence skin pigments, “Europeans are actually more likely to be genetically similar to great apes.”

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