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One route to lighter skin, two different continents

January, 2019

Three men are pictured: a light-skinned older European man on the left; a brown-skinned KhoeSan tribesman in the center; and a dark-skinned Maasai tribesman on the right

The lighter skin tones of Europeans (left) and the KhoeSan (middle) are explained by the same gene. Other African populations that lack that "light" version of this gene, like the Maasai (right), typically have much darker skin. L to R images courtesy of: Pixabay, WikiMedia Commons, and Pixabay

Skin color is one of the most obvious physical characteristics that distinguishes one person's appearance from another's. However, the trait itself, its genetic basis, and its evolutionary history are complex. Human skin color ranges, not just between dark and light on a single axis, but over a whole landscape of shades and hues. Even within a single region, like Africa, skin color varies widely among different populations. Fittingly, many different genes are known to affect a person's skin tone. Last month, scientists announced that a gene version usually thought of as a "European" gene, for playing a major role in explaining the light skin of Europeans, was also favored among KhoeSan, populations native to South Africa that have relatively light skin in comparison to many other Africans. How and why did these geographically and physically distinct populations wind up with the same snippet of DNA?

Where's the evolution?

The evolutionary history of modern humans' range of skin tones seems to have been shaped by competing varieties of natural selection. Melanin, the pigment responsible for darkening human skin, protects us from UV radiation, which can cause skin cancer and degrade the essential vitamin folate. However, we need some amount of UV radiation for our bodies to synthesize vitamin D, which is also important — e.g., for preventing the disease rickets. Hence, skin color represents an evolutionary trade-off. When selection favoring the production of vitamin D is stronger, gene versions that produce less melanin and lighter skin become more common. When selection against UV damage is stronger, gene versions producing more melanin and darker skin become more common. Which form of natural selection wins out is broadly influenced by geography. Near the equator, UV radiation levels are high and sun damage can be severe, so darker skin tones are generally favored. Nearer the poles, lack of vitamin D is the more serious problem, so lighter tones are favored.

Since the KhoeSan live about as far from the equator as one can get in Africa, it's no surprise that gene versions conferring lighter skin became common among this group. Indeed, scientists think that when the KhoeSan's ancestors shifted from eating vitamin-D-rich fish to herding, the drop in vitamin D might have further favored lighter skin shades, which let in a little more sun and boosted vitamin D production. What was surprising was that the KhoeSan's lighter skin traces back to the exact same gene as European’s light skin does: the gene SLC24A5. What evolutionary process explains this similarity?

One possibility is that the common ancestor of all modern humans had the "light-skin" version of SLC24A5. Perhaps both the KhoeSan and Europeans simply inherited it from the ancestral human population they both shared. In the two populations, the gene version would have gone up and down in frequency over time depending on the balance of selection as the two populations migrated to different areas, until finally winding up where they are today. 

This would be a plausible hypothesis; however, researchers discovered a key piece of evidence that argues against it. It's not only the "light" gene version itself that is identical between people of European descent and the KhoeSan; the stretches of DNA that come before and after this gene are also remarkably similar across the two populations. This is not due to random chance. When gene copies are passed from parent to child, one gene version is physically linked to another on a chromosome. Generation by generation, these associations are broken up (and new ones are formed) by the process of recombination. It's a bit like shuffling a deck of cards. If you just shuffle once, some mixing will occur, but many cards will still be next to the same cards as they were in the original stack. With each additional shuffle (i.e., generation of recombination), the fewer cards (i.e., genes) will remain adjacent to their original neighbors. So when two individuals have long, identical stretches of DNA, it indicates that not many generations of recombination have occurred and that they descended from a recent common ancestor. The DNA surrounding SLC24A5 is so similar between Europeans and KhoeSan with the "light version of the gene that researchers concluded they must share a recent ancestor. However, we know that the KhoeSan split from other human populations quite early in our evolutionary history: 100,000-150,000 years ago. If each population had simply inherited the same gene from a common ancestor that lived 100,000 years ago, we wouldn't observe the identical genetic backgrounds surrounding the gene in the two populations; they would have long since been broken up by recombination. What else could explain this extensive similarity?

The biologists hypothesized that relatively recent migrants to South Africa brought the "light" version of SLC24A5 (and its adjacent genetic baggage) with them. Interbreeding would then have introduced the gene to the KhoeSan — and after that, natural selection favoring increased vitamin D production would have pushed the gene to high frequency in the South African population. But which immigrants? The "light" gene version is so common among the KhoeSan that it is unlikely to trace to the influx of European colonists to Africa, which began about 300 years ago. Instead, the researchers traced the genetic source of the KhoeSan's light skin back 2000 years to migrants from East Africa (who themselves got the gene version from mixing with Near Eastern populations). These migrants brought the SLC24A5 "light" gene version (as well as domestic sheep and goats) to South Africa, and that version then quickly rose to high frequency through natural selection. In this population, individuals that did not carry the new gene version and had darker skin left behind fewer offspring than individuals that did carry it.

The history of human skin color clearly illustrates that evolution is not a march of "progress" towards any particular end. Our earliest human ancestors in Africa probably had light skin (just as chimpanzees do underneath their fur). As these ancestors moved from forests to the open savannah and evolved reduced hair covering, natural selection favored gene variants for darker skin and protection from sun damage — but this was not a uniform process purging all "light" gene versions out of existence. This ancestral population still had a lot of genetic variation for a range of skin tones, even if the ones producing darker skin were more common. Then, as modern human populations split off from one another and fanned out over the globe, different gene versions rose to high frequency in different populations according to the balance between selection favoring UV protection and selection favoring vitamin D production. Several different groups evolved lighter skin as ancient gene versions for this trait were favored (e.g., in Europeans) — and as we've seen, at least one of these gene versions made it back to Africa where it became common among the KhoeSan. The twists and turns of this story illustrate, not a grand plan towards a specified goal, but a dynamic process, responding to the vagaries of history and migration, enabling so many diverse human populations to thrive in their unique environments.

Read more about it

Primary literature:

  • Crawford, N. G., Kelly, D. E., Hansen, M. E. B., Beltrame, M. H., Fan, S., Bowman, S. L., ... Tishkoff, S. A. (2017). Loci associated with skin pigmentation identified in African populations. Science. 358: eaan8433. read it
  • Meng, L., Siford, R. L., Martin, A. R., Nakagome, S., Möller, M., Hoal, E. G., ... Henn, B. M. (2018). Rapid evolution of a skin-lightening allele in southern African KhoeSan. Proceedings of the National Academy of Sciences USA. 115: 13324-13329. read it
News articles:

Understanding Evolution resources:

Discussion and extension questions

  1. List some ways in which melanin could be helpful for human survival and reproduction. List some ways in which melanin could be bad for human survival and reproduction.
  2. In your own words, describe the concept of an evolutionary trade-off.
  3. Review some background information on natural selection. Explain how the "light" version of SLC24A5 could have spread through the KhoeSan in South Africa once introduced there. Make sure to include the concepts of variation, selection, and inheritance in your explanation.
  4. If the KhoeSan and Europeans had both inherited the "light" version of SLC24A5 from the common ancestral population of all modern humans, what would you expect to observe in the chromosomal region around SLC24A5 in the two populations? Explain your reasoning.
  5. Is one version of SLC24A5 (the "light" or "dark") overall better than the other? Make an argument to support your conclusion.
  6. Advanced: This article describes how extensive areas of similarity on chromosomes in a population indicate the presence of an advantageous mutation in that region of the chromosome. Explain the relationship between this line of evidence and the reasoning the researchers in the article above applied to figuring out where the KhoeSan got the "light" version of SLC24A5. Do they rely on the same underlying process or different ones? Explain your answer.
Related lessons and teaching resources

  • Teach about natural selection: In this classroom activity for grades 9-16, students experience one mechanism of evolution through a simulation that models the principles of natural selection and helps answer the question: how might biological change have occurred and been reinforced over time?
  • Teach about recent human evolution: This research profile for grades 13-16 follows statistician and population geneticist Emilia Huerta-Sánchez as she studies the adaptations that allow Tibetan highlanders to live 13,000 feet above sea level without developing altitude sickness.
  • Teach about the genetics of human skin color: This news brief for grades 9-16 describes the remarkably ancient roots of the gene SLC24A5.


  • Crawford, N. G., Kelly, D. E., Hansen, M. E. B., Beltrame, M. H., Fan, S., Bowman, S. L., ... Tishkoff, S. A. (2017). Loci associated with skin pigmentation identified in African populations. Science. 358: eaan8433.
  • Mallick, C. B., Iliescu, F. M., Möls, M., Hill, S., Tamang, R., Chaubey, G., ... Kivisild, T. (2013). The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent. PLoS Genetics. 9: e1003912.
  • Meng, L., Siford, R. L., Martin, A. R., Nakagome, S., Möller, M., Hoal, E. G., ... Henn, B. M. (2018). Rapid evolution of a skin-lightening allele in southern African KhoeSan. Proceedings of the National Academy of Sciences USA. 115: 13324-13329.