Abstract: Despite the wide range of skin pigmentation in humans, little is known about its genetic basis in global populations. Examining ethnically diverse African genomes, we identify variants in or near SLC24A5, MFSD12, DDB1, TMEM138, OCA2 and HERC2 that are significantly associated with skin pigmentation. Genetic evidence indicates that the light pigmentation variant at SLC24A5 was introduced into East Africa by gene flow from non-Africans. At all other loci, variants associated with dark pigmentation in Africans are identical by descent in southern Asian and Australo-Melanesian populations. Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte-specific regulatory regions near DDB1/TMEM138 correlate with expression of UV response genes under selection in Eurasians.
A related story:
New gene variants reveal the evolution of human skin color
Most people associate Africans with dark skin. But different groups of people in Africa have almost every skin color on the planet, from deepest black in the Dinka of South Sudan to beige in the San of South Africa. Now, researchers have discovered a handful of new gene variants responsible for this palette of tones.
The study, published online this week in Science, traces the evolution of these genes and how they traveled around the world. While the dark skin of some Pacific Islanders can be traced to Africa, gene variants from Eurasia also seem to have made their way back to Africa. And surprisingly, some of the mutations responsible for lighter skin in Europeans turn out to have an ancient African origin.
“This is really a landmark study of skin color diversity,” says geneticist Greg Barsh of the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama. ...
But Tishkoff ’s team found that the story of skin color evolution isn’t so black and white. Her team, including African researchers, used a light meter to measure skin reflectance in 2092 people in Ethiopia, Tanzania, and Botswana. They found the darkest skin in the Nilo-Saharan pastoralist populations of eastern Africa, such as the Mursi and Surma, and the lightest skin in the San of southern Africa, as well as many shades in between, as in the Agaw people of Ethiopia.
At the same time, they collected blood samples for genetic studies. They sequenced more than 4 million single nucleotide polymorphisms (SNPs)—places where a single letter of the genetic code varies across the genomes of 1570 of these Africans. They found four key areas of the genome where specific SNPs correlate with skin color.
The first surprise was that SLC24A5, which swept Europe, is also common in East Africa—found in as many as half the members of some Ethiopian groups. This variant arose 30,000 years ago and was probably brought to eastern Africa by people migrating from the Middle East, Tishkoff says. But though many East Africans have this gene, they don’t have white skin, probably because it is just one of several genes that shape their skin color.
The team also found variants of two neighboring genes, HERC2 and OCA2, which are associated with light skin, eyes, and hair in Europeans but arose in Africa; these variants are ancient and common in the light-skinned San people. The team proposes that the variants arose in Africa as early as 1 million years ago and spread later to Europeans and Asians. “Many of the gene variants that cause light skin in Europe have origins in Africa,” Tishkoff says.
If I recall discussion here a while back--this new study would seem to shed some light on the topic. In particular the genes associated with skin color are far more complex and far older than some would admit.
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