Why Do Humans Have Different Skin Colours?

Map the average skin pigmentation of Indigenous populations across the world and lay it over a map of ultraviolet radiation, and the two line up remarkably well. Near the equator, where UV is intense year-round, skin is darkest. Towards the poles, where UV is weak and seasonal, it is lightest. That correlation, first mapped systematically by Nina Jablonski and George Chaplin in 2000, is the key to the whole story.

Skin colour is not a random marker of ancestry. It is a finely tuned compromise between two vitamins that UV light affects in opposite ways.

Step one: losing the fur

Chimpanzees have pale skin under dark hair. The fur does the sun-blocking. Our ancestors’ skin became exposed when they lost most of their body hair, probably as an adaptation for cooling by sweat during long days of walking and running in open African landscapes.

Naked skin under an equatorial sun needed its own protection. The answer was eumelanin, the dark-brown pigment produced by cells called melanocytes. Everyone has roughly the same number of melanocytes; what differs is how much pigment they make and what kind.

A clue to the timing comes from the gene MC1R, which controls the switch between dark eumelanin and reddish pheomelanin. In Africans it is highly conserved — almost any change is weeded out — suggesting strong selection to keep skin dark. Alan Rogers and colleagues used variation in the gene to estimate that this constraint has been in place for around 1.2 million years, roughly the era of Homo erectus.

Why dark skin: folate

Melanin prevents skin cancer, but skin cancers usually strike after the reproductive years, so they are a weaker evolutionary force than it seems. Jablonski and Chaplin pointed to something with direct effects on reproduction: folate, a B vitamin essential for DNA synthesis and cell division.

UV radiation breaks down folate circulating in blood vessels near the skin surface. Low folate in pregnancy causes neural tube defects such as spina bifida and it impairs sperm production. In high-UV regions, dark skin protects fertility itself.

Why light skin: vitamin D

UV also does something essential. UVB light striking the skin converts a cholesterol precursor into vitamin D, which the body needs to absorb calcium. Without it, children develop rickets — soft, bent bones — and in women, a deformed pelvis can make childbirth deadly.

At high latitudes, UVB is weak for much of the year, and in winter it can be almost absent. Heavily pigmented skin blocks too much of what little arrives. Lighter skin lets more through. The trade-off shifts, and selection favours depigmentation.

Light skin evolved more than once

If lighter skin were a single ancient mutation, Europeans and East Asians would share it. They largely do not.

• Europe and West Asia: The main variants are in SLC24A5 (discovered through a pale “golden” zebrafish mutant) and SLC45A2. The SLC24A5 variant is carried by nearly all Europeans and many people in the Middle East and South Asia.
• East Asia: Lighter skin involves different changes, including a variant in OCA2 common in East Asians but rare in Europeans.

That is convergent evolution: different populations reached a similar solution through different genetic routes, just as with lactose tolerance.

Africa holds the most diversity

It is a mistake to picture “African skin” as one shade. A 2017 study led by Nicholas Crawford and Sarah Tishkoff measured pigmentation in over 2,000 people across Ethiopia, Tanzania and Botswana and found enormous variation — from the very dark skin of Nilo-Saharan pastoralists to the relatively light skin of San peoples in the Kalahari.

Many of the variants involved are old. Some alleles associated with lighter skin arose in Africa hundreds of thousands of years ago, long before anyone left the continent. Some associated with darker skin in Melanesians and South Asians also trace back to African origins. Pigmentation evolution has moved in both directions, repeatedly.

What ancient DNA revealed about Europe

Modern Europeans are not descended from one population but from three main ancestral groups: Mesolithic hunter-gatherers, early farmers from Anatolia, and herders from the Pontic steppe who arrived in the Bronze Age. Their genomes carry different pigmentation variants.

Western European hunter-gatherers such as La Braña in Spain (about 7,000 years old) and Loschbour in Luxembourg (about 8,000 years old) carried the gene variants for blue eyes but not the main European light-skin variants. Cheddar Man, a British skeleton about 10,000 years old, was reconstructed in 2018 with dark skin and pale eyes. (Such predictions carry real uncertainty, especially for intermediate tones.)

The SLC24A5 and SLC45A2 variants arrived largely with Anatolian farmers and steppe herders, then continued to rise under selection. Ancient DNA surveys suggest that pale skin became the majority in much of Europe only within the last several thousand years — after farming and in some places not until the Bronze or Iron Age.

The exceptions that prove the rule

Indigenous Arctic peoples such as the Inuit have darker skin than their latitude would predict. The likely reason is diet: a traditional diet of fish, seal and whale is rich in vitamin D, relaxing selection for light skin while strong UV reflected off snow and ice still favours protection.

Neanderthals, too, adapted to northern light. One Neanderthal MC1R variant, not found in living people, reduced the gene’s function and may have produced pale skin and red hair in some individuals.

What skin colour does — and doesn’t — tell us

Because it tracks sunlight so closely, skin colour is a poor guide to ancestry. Populations with similar pigmentation can be only distantly related, and closely related populations can differ markedly. Pigmentation genes are a tiny fraction of the genome, shaped by strong local selection.

That is the strongest lesson from the evolution of skin colour: the most eye-catching human difference is one of the most superficial, in the most literal sense.