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

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.

Skin pigmentation is still almost 100-percent heritable, meaning the shade of your skin is overwhelmingly determined by your parents, grandparents, and so forth. The KhoeSan’s ancestry doesn’t lighten or darken their skin, just increases genetic variation. Their genetic diversity makes for a fruitful source of study, and they’ve participated in similar research projects in the past.

Before the inclusion of the new data from the KhoeSan, the body of research on skin pigmentation showed it was controlled by a dynamic called “directional selection.” This refers to pigmentation being pushed in one unified direction—either lighter or darker—depending on the latitude of the population in question. Higher altitudes became lighter; lower latitudes became darker.

Directional selection held up for so long because it works in high latitudes, and high latitudes were the only ones ever really considered. But populations closer to the equator follow a different process, known as stabilization selection. In these geographic regions, more genes are involved in pigmentation, which means each one is making a smaller contribution to the end result. Instead of a few known genes contributing about 50 percent of skin pigmentation, each one accounts for about 10 percent. The researchers stated that the field needed to see a greater focus on diverse, understudied populations in order to get a complete picture of the true genetic architecture of skin pigmentation.

"In terms of next steps, we would like to create an online database where scientists can share pigmentation data from populations around the world," said co-author Brenna Henn, assistant professor in the Department of Ecology and Evolution at Stony Brook University. "We are actively working to collect more samples across Africa."