When you think of Neandertals, freckles probably aren't the first facial features that come to mind.

But, a new analysis of genetic material from the remains of two Neandertals indicates that some members of the ancient hominid population may well have been pale-skinned redheads. An international team of researchers reached that conclusion after studying a segment of the gene MC1R that controls melanin, which is responsible for skin and hair color.

"In modern humans, this gene is under a strong selective constraint in Africa, but has experienced a relaxation of this constraint in European populations coming out from Africa 40,000 years ago and, therefore, it has accumulated quite a lot of variation on it," says Carles Lalueza-Fox, an associate professor of animal biology at Spain's University of Barcelona and a co-author of the new study appearing in Science. "I thought that Neandertal's ancestors, having experienced something similar, but half a million years ago, would have accumulated lots of variation in this gene also. But, of course, the mutations were going to be at different places of the gene."

The two Neandertal samples the researchers examined were found in separate locations: Monti Lessini, Italy, and El Sidrón Cave in northern Spain. A 128–base pair fragment of MC1R was isolated from the Italian sample. (For reference, there are estimated to be 250,000,000 base pairs in the entire Neandertal genome.) The researchers found a single base substitution that was unique when compared with the same section of DNA from 3,700 people (indicating that it was not contaminated by human DNA); the Spanish Neandertal sample contained the same mutation.

To determine the skin and hair color this mutation would have caused, the scientists created a copy of the human version of gene with the Neandertal substitution in it and then injected it into a culture of pigment cells. They were particularly interested in observing how the MC1R protein expressed by the altered gene interacted with a second protein—α-MSH—which triggers melanin production.

When the two substances mixed, the researchers say, they had a relatively low level of interaction, indicating that low levels of melanin would be produced—a reaction that mirrors the results in genes of humans with red hair and fair complexions. Pale skin allows those living at higher latitudes and exposed to less frequent and weaker sunlight to more efficiently synthesize vitamin D. (This vitamin helps the body absorb calcium to keep bones strong and healthy; deficiencies can lead to bone disorders such as the childhood disease rickets, which softens bones.)

"Chances are that the gene was full of functional variants in the Neandertal populations that provoked quite a high prevalence of red-haired people," Lalueza-Fox says. "But of course, it still depends on if you are heterozygous [(have two different versions of the gene)] or homozygous for these variants [(like Neandertals and modern Europeans)], so I guess that we should expect the whole range of hair color variation [that is] observed in northern modern Europeans."

Lalueza-Fox says he and his team plan to examine other Neandertal genes to learn more about the species, with eye color, behavior, metabolism, immunity and physiology being of particular interest. As for the findings surrounding MC1R, "It was a big opportunity to have an inference of a trait," he says, "that will never be found in the fossil record."