The genetics of skin colour

For centuries, skin colour has held powerful social meaning — a defining characteristic of race, and a starting point for racism. “If you ask somebody on the street, ‘What are the main differences between races?’ they’re going to say skin colour,” said Sarah A Tishkoff, a geneticist at the University of Pennsylvania. Recently, Sarah and her colleagues showed this to be a profound error. In the journal Science, the researchers published the first large-scale study of the genetics of skin colour in Africans. The researchers pinpointed eight genetic variants in four narrow regions of the human genome that strongly influence pigmentation — some making skin darker, and others making it lighter.

These genes are shared across the globe, it turns out; one of them, for example, lightens skin in both Europeans and hunter-gatherers in Botswana. The gene variants were present in humanity’s distant ancestors, even before our species evolved in Africa 3,00,000 years ago. The widespread distribution of these genes and their persistence over millenniums show that the old colour lines are essentially meaningless, the scientists said.

The research “dispels a biological concept of race,” Sarah said. Humans develop colour much as other mammals do. Special cells in the skin contain pouches, called melanosomes, packed with pigment molecules. The more pigment, the darker the skin. Skin colour also varies with the kind of pigments: melanosomes may contain mixtures of a brown-black called eumelanin and a yellow-red called pheomelanin.

Pigment-producing genes

To find the genes that help produce pigments, scientists began by studying people of European ancestry and found that mutations in a gene called SLC24A5 caused cells to make less pigment, leading to paler skin. Unsurprisingly, almost all Europeans have this variant. “We knew quite a lot about why people have pale skin if they had European ancestry,” said Nicholas G Crawford, a postdoctoral researcher at the University of Pennsylvania, USA and a co-author of the new study. “But there was very little known about why people have dark skin.” Since the early 2000s, Sarah has studied genes in Africa, discovering variants important to everything from resistance to malaria to height. African populations vary tremendously in skin colour, and Sarah reasoned that powerful genetic variants must be responsible.

Studying 1,570 people in Ethiopia, Tanzania and Botswana, she and her colleagues discovered a set of genetic variants that account for 29% of the variation in skin colour. One variant, MFSD12, was particularly mysterious: no one knew what it did anywhere in the body. To investigate its function, the researchers altered the gene in reddish lab mice. Giving them the variant found in darker-skinned Africans turned the mice grey.

As it turned out, MFSD12 can affect the production of brown-black eumelanin, producing a darker skin colour. The eight gene variants Sarah and her colleagues discovered in Africans turned out to be present in many populations outside the continent. By comparing the DNA of these people, the researchers were able to estimate how long ago the genes appeared.

They turned out to be immensely old. A variant for light skin — found in both Europeans and the San hunter-gatherers of Botswana — arose about 9,00,000 years ago, for example. Even before there were Homo sapiens, then, our distant forebears had a mix of genes for light and dark skin. Some populations may have been dark-skinned and others light-skinned; or maybe they were all the same colour, produced by a blend of variants.

Neanderthals split off from our own ancestors an estimated 6,00,000 years ago, spreading across Europe and eastern Asia. While they became extinct about 40,000 years ago, some of their DNA has survived. These hominins inherited the same combination of variants determining skin colour, Sarah and her colleagues also discovered. It’s possible that some populations of Neanderthals, too, were light-skinned, and others dark-skinned.

Unexpected complexity

Living humans come packaged in a wide range of hues — from pale and freckly in Ireland to dark brown in southern India, Australia and New Guinea. Researchers have argued that these varying colours evolved partly in response to sunlight. The idea is that people who live with intense ultraviolet light benefited from dark colour, pigments that shielded important molecules in their skin. In places with less sunlight, people needed lighter skin, because they were able to absorb more sunlight to make vitamin D.

The new genetic evidence supports this explanation but adds unexpected
complexity. The dark-skinned people of southern India, Australia and New Guinea, for example, did not independently evolve their colour simply because evolution favoured it. They inherited the ancestral dark variants Sarah’s team found in Africans. “They had to be introduced from an African population,” Sarah said. Yet, the same is true for some of the genes that produce light skin in Asia and Europe. They also originated in Africa and were carried from the continent with early migrants. As Africans moved into Europe and Asia, they interbred with Neanderthals on several occasions. Michael Dannemann and Janet Kelso of the Max Planck Institute for Evolutionary Anthropology in Germany reported recently that people in Britain still carry a number of Neanderthal variants that colour skin.

Some of the newly discovered genes appeared relatively recently in our evolution. The pale-skin variant of SLC24A5 that’s overwhelmingly common in Europe, for example, is a recent addition to the genome, arising just 29,000 years ago, according to the new study. It became widespread only in the past few thousand years. Sarah and her colleagues found it frequently not just in Europe, but in some populations of lighter-skinned Africans in East Africa and Tanzania. Studies of ancient
DNA recently discovered in Africa point to an explanation. Several thousand years ago, it seems, a migration of early Near Eastern farmers swept into East Africa. Over many generations of interbreeding, the pale variant of SLC24A5 became common in some African populations.

In all, the new study provides “a deeper appreciation of the genetic palette that has been mixed and matched through evolution,” said Nina Jablonski, an expert on skin colour at Pennsylvania State University, USA.