The surprising reason why some Latin Americans have light skin

Walk down a busy street in most Latin American cities today and you’ll see a palette of skin colors from dark brown to sepia to cream. For 500 years, people have assumed this variation comes from the meeting and mixing of Native Americans, Europeans, and Africans during colonial times and later. People with lighter skin are thought to have more European ancestry, whereas those with darker skin are taken to have more Native American or African ancestry—and are often targeted for discrimination.

Now, a new study of the genes of more than 6000 people from five Latin American countries undercuts the simplistic racial assumptions often made from skin color. An international team discovered a new genetic variant associated with lighter skin found only in Native American and East Asian populations. That means that in Latin America, lighter skin can reflect Native American as well as European ancestry.

“It’s a really important study,” especially because little genetic research has been done on Latin American populations, says human geneticist Sarah Tishkoff of the University of Pennsylvania Perelman School of Medicine. Most work on skin pigmentation genes “has been done on Europeans, where ironically we don’t see a lot of variation,” she says. “One of the last frontiers has been, ‘What about East Asians and Native Americans?’”

Latin America is fertile ground for such studies. People there often have Native American, European, and African ancestors, and because Native American populations are closely related to those from East Asia, researchers can also spot East Asian variants in Latin American genomes. “You get, in one place, the genetic variation from four different continents,” says statistical geneticist Kaustubh Adhikari of University College London.

He and Javier Mendoza-Revilla, a geneticist at the Pasteur Institute in Paris, analyzed the genomes of 6357 people from Brazil, Colombia, Chile, Mexico, and Peru, collected by the Consortium for the Analysis of the Diversity and Evolution of Latin America (CANDELA). The consortium also measured how much light reflected off participants’ skin, a way of gauging their levels of the dark pigment melanin. That allowed Adhikari and Mendoza-Revilla to look for genetic variants linked to skin tone.

One variant was on MFSD12. Tishkoff recently linked reduced expression of this gene with darker skin in Africans. The new MFSD12 variant, however, is associated with lighter skin, and might instead enhance the gene’s expression, Adhikari and Mendoza-Revilla report this week in Nature Communications. When they looked for the variant in other populations, they found it only in Native Americans and East Asians.

So the new variant sheds light on the genes underlying pale skin in East Asia. People at high latitudes in Europe and East Asia seem to have independently evolved lighter skin to produce vitamin D more efficiently with less sunlight, says Nina Jablonski, a biological anthropologist at Pennsylvania State University in University Park. But, “People have been scratching their heads” about which variants do this in East Asians. Now, researchers know MFSD12 is one. The ancestors of Native Americans presumably carried that variant over the Bering Strait into the Americas. “There was variation [in skin tone] present in Latin America long before Europeans got there,” Jablonski says.

The larger lesson, says geneticist Andrés Ruiz-Linares of Fudan University in Shanghai, China, chair of CANDELA, is the pitfalls of a Eurocentric view. “Our study shows that going beyond Europeans one can find additional genes, even for well-studied traits. Clearly the bias towards Europeans has led to a restricted view of human diversity."