Published online 25 October 2007 | Nature | doi:10.1038/news.2007.197

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Ancient DNA contains clues about complexion.

Pale complexions may have evolved many times over. Digital Vision

An analysis of 50,000-year-old Neanderthal DNA suggests that at least some of the ancient hominids probably had pale skin and red hair.

The findings, published this week in Science1, are based on the sequence of a single gene, called mc1r. Humans with a less functional form of the MC1R protein are more likely to be fair skinned — an adaptation that may have helped inhabitants of high latitudes synthesize vitamin D more efficiently in limited sunlight.

Analyses of Neanderthal DNA are always subject to the problem of fossil samples being contaminated with modern human DNA in the lab or the field. But Carles Lalueza-Fox of the University of Barcelona, Spain, with Holger Römpler of the University of Leipzig in Germany and colleagues, found that the mc1r gene in two European Neanderthal fossils they studied contained a single base-pair change that seems to be unique to Neanderthals.

“We were lucky we found a variant that had not been described in modern humans,” says co-author Michael Hofreiter of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “That made it unlikely to be human contamination.”

The researchers re-sequenced the applicable region of the gene multiple times, then asked two additional labs to repeat the experiments using fresh extracts. They also sequenced fragments of the mc1r gene from the researchers in each lab, as well as the archaeologists and palaeontologists who had handled the fossils. And they searched databases containing mc1r sequence from 2,800 humans and tested several hundred additional samples.

In the end, they had surveyed more than 3,700 humans, and none contained the Neanderthal sequence. “If it is in the modern human population, it’s at an extremely low frequency,” says Hofreiter.

Fair test

The researchers inserted the Neanderthal mc1r gene into human cells grown in the lab, and found that it had roughly the same low functionality as seen in mc1r genes from fair-skinned people with red hair.

It’s impossible to determine the precise frequency of pallid, red-haired Neanderthals that once populated Europe. But the researchers estimate that at least 1% of the population would have carried two copies of this less-active gene, giving them roughly the same pigmentation seen in modern red-heads.

Scientists have estimated that there should be at least a million nucleotides (single letters in the genome) that differ between humans and Neanderthals, says Lalueza-Fox. But little research has been done as yet to identify these. Recent work shows that Neanderthals have the same version of a speech gene as modern humans (see Modern speech gene found in Neanderthals). “This is the first functional difference in the genome between Neanderthals and modern humans,” says Lalueza-Fox.

Independent evolution

Lalueza-Fox and Hofreiter note that the absence of the Neanderthal-specific mc1r sequence in modern humans suggests that pale skin evolved independently in Neanderthals and humans, rather than from interbreeding between the two.

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That's interesting but not entirely unexpected, says Rachel Caspari, an anthropologist at Central Michigan University in Mount Pleasant. The regulation of skin colour in humans is very complex, she notes; so she would expect evolution to have come up with many different ways to generate lighter skin.

Caspari cautions against ruling out genetic exchange between the two populations just yet. It is still possible that the allele was present in humans 50,000 years ago, but was later replaced by a different mutation, she says. “It certainly doesn’t support gene flow between Neanderthals and humans,” says Caspari, “but it doesn’t refute the idea either.”