Lalueza-Fox believes the variant his team discovered was likely one of many that spread through ancient Neandertal populations by processes of natural selection.
"European [humans] have quite a lot of variation in this gene—not only red hair variants but also others," he explained, adding that humans have been in Europe for only about 40,000 years.
"The Neandertals, being there at least 400,000 [years], likely accumulated ten times more variation."
Neandertals are believed to have roamed Europe between 28,000 and 400,000 years ago.
James Noonan, a geneticist at the Yale University School of Medicine who was unaffiliated with the research, said Lalueza-Fox's conclusions were convincing.
"It's not surprising that there would be a Neandertal-specific MC1R variant that results in a partial loss of function (and thus lighter skin and hair)," he said. "Similar mutations have arisen independently in different modern human populations."
Another scientist who was not involved with the research, Henry Harpending, an anthropologist at the University of Utah in Salt Lake City, added that a number of genes that affect human skin color are still changing and spreading through Europe and Asia.
The particular genes that affects skin color are different in Europe and Asia, he said, but in both places, fairer complexions appear to be the result of broken versions of these genes.
"This paper suggests that Neandertals were light, or were getting light, in the same way, i.e., by selection for slightly broken genes," he said.
Scientists are not sure why the broken gene—and fairer complexions—would be spread by natural selection.
Yale's Noonan said geography was the likeliest explanation for the endurance of this trait in both modern humans and Neandertals—pigment advantage was likely less relevant in darker places.
Northern latitudes have "less sunlight and so less need for darker skin pigmentation to protect against UV-induced damage," Noonan said.
Though the genetic processes that helped to lighten their complexions may have worked similarly, humans have never displayed the same sequence seen in the ancient Neandertal gene samples.
"Both processes took place independently—that's the reason the Neandertal variant is not present in modern humans," Lalueza-Fox said.
The new find offers no evidence of interbreeding between humans and Neandertals, he added.
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