"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."
http://www.sciencemag.org/news/2017/10/new-gene-variants-reveal-evolution-human-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.
The most dramatic discovery concerned a gene known as 
MFSD12. Two mutations that decrease expression of this gene were found in high frequencies in people with the darkest skin. These variants arose about a half-million years ago, suggesting that human ancestors before that time may have had moderately dark skin, rather than the deep black hue created today by these mutations.
These same two variants are found in Melanesians, Australian Aborigines, and some Indians. These people may have inherited the variants from ancient migrants from Africa who followed a “southern route” out of East Africa, along the southern coast of India to Melanesia and Australia, Tishkoff says. That idea, however, counters three genetic studies that concluded last year that Australians, Melanesians, and Eurasians all descend from a single migration out of Africa. Alternatively, this great migration may have included people carrying variants for both light and dark skin, but the dark variants later were lost in Eurasians.
To understand how the 
MFSD12 mutations help make darker skin, the researchers reduced expression of the gene in cultured cells, mimicking the action of the variants in dark-skinned people. The cells produced more eumelanin, the pigment responsible for black and brown skin, hair, and eyes. The mutations may also change skin color by blocking yellow pigments: When the researchers knocked out 
MFSD12 in zebrafish and mice, red and yellow pigments were lost, and the mice’s light brown coats turned gray. “This new mechanism for producing intensely dark pigmentation is really the big story,” says Nina Jablonski, an anthropologist at Pennsylvania State University in State College.
The study adds to established research undercutting old notions of race. You can’t use skin color to classify humans, any more than you can use other complex traits like height, Tishkoff says. “There is so much diversity in Africans that there is no such thing as an African race.”