Researchers from the Broad Institute of MIT and Harvard, Stanford University, and Stony Brook University, they described that the study suggests that the genetics of skin pigmentation are simple. A small number of known genes, it is thought, However, these studies rely on datasets consisting almost entirely of information from northern Eurasian populations–those that reside mostly in higher latitude regions. This study has been published in Cell.
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. "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.
The researchers genotyped each sample looking at hundreds of thousands of sites across the genome to identify genetic markers linked with pigmentation measures and sequenced areas of interest. They took this information and compared it to a dataset that comprised nearly 5,000 individuals representing globally diverse populations throughout Africa, Asia, and Europe.
The prevailing theory is that "directional selection" pushes pigmentation in a single direction, from dark to light in high latitudes and from light to dark in lower latitudes. But Martin and Henn's data showed that the trajectory is more complex. In addition, the researchers found some unexpected insights into particular genes associated with pigmentation.
A derived mutation in one gene, SLC24A5, is thought to have arisen in Europe roughly 10,000 to 20,000 years ago. However, in the KhoeSan populations it appears in a much higher frequency than recent European admixture alone would suggest, indicating that it has either been positively selected in this population, arose in this population, or entered the population through gene flow thousands of years ago.
"We're still teasing this apart," said Martin. "Southern African KhoeSan ancestry appears to neither lighten nor darken skin," said Martin. "Rather, it just increases variation. In fact, the KhoeSan are approximately fifty percent lighter than equatorial Africans. Ultimately, in northern latitudes pigmentation is more homogenous, while in lower latitudes, it's more diverse both genetically and phenotypically."