The Complex History of the Genes That Color Our Skin

 In Health
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.

“When you look at this African-centered perspective, there’s a lot of variation.”

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.

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.”

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