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New genetic findings help explain different skin colors in humans

Alessia Ranciaro, a senior research scientist at the University of Pennsylvania, collects a skin reflectance reading from a study participant from a Nilo-Saharan population. Photo: Tishkoff lab

Scientists have discovered new genetic variations in some African populations that influence skin color and suggest our earliest ancestors may have had a medium skin tone that later evolved to both darker and lighter tones seen in modern humans, per a five-year study published in Science Thursday.

Why this matters: Not only do the results alter the assumption that lighter skin evolved from the dark skin of ancestral humans, but they also help explain the vast range of skin color, identify possible patterns of human evolution and migration, and add to our understanding of human skin conditions like cancer and aging.

"To me, it has really changed some of the story about the evolution of skin color," Sarah Tishkoff, a geneticist at the University of Pennsylvania and leader of the international team, told Axios. Some of the variations in pigmentation genes appear to have originated roughly 1 million years ago, well before the emergence of modern humans, she said.

The study: The team used a color meter to read the level of melanin in the inner-arm skin of more than 2,000 people from Ethiopia, Tanzania and Botswana and sequenced genes from almost 1,600 of them. Later, a team confirmed their findings by testing the variations in zebrafish and mouse models.

The team found several novel variations (called alleles) in genes associated with pigmentation:

  • DDB1– repairs DNA damage done by ultraviolet light radiation and could be key to understanding melanoma.
  • SLC24A5 and OCA2 – these genes are implicated in albinism
  • HERC2 – regulates the OCA2 gene
  • MFSD12 – Study author Nicholas Crawford told Axios "I remember I was very excited" when we found this gene is associated with vitiligo (an autoimmune disease that creates patches of light-colored skin on dark-skinned people). Tishkoff said their study found MFSD12 also contributes to the production of a protein that plays a role in optimizing nutrition and fighting infection. "This may be key to figuring out how to manipulate skin pigmentation for therapeutic means," she said.

Migration implications: The data collected is consistent with there being an early migration event of modern humans out of Africa along the southern coast of Asia and into Australo-Melanesia, Tishkoff said.

Africa is key: "Many variances rose in Africa and some [of those] went to 100% frequency in Europe so it was only by going to Africa and looking at these variables" that they discovered some of these new genes, said Tishkoff, who calls herself a "major advocate" to increase all studies of genetics in Africa.

  • Rick Sturm, molecular geneticist at the University of Queensland who was not part of the study, agreed. "I had made a simple assumption that selection was happening on multiple genes in European populations as skin pigmentation was lightening, but I hadn't thought that similar process was happening in Africa for darkening."
  • Sturm said there is more research to be done: "The identified [genetic variations] still only explain about 28.9% of the variance seen in pigmentation, so other genes remain to be discovered."

Go deeper: Listen to Tishkoff talk about the study on this Science podcast (9:55).

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