After several failed attempts, they managed to reconstruct the man’s entire genome from DNA found in the root of a third molar. It is the first time researchers have obtained the complete genome of a modern European who lived before the Neolithic revolution.

The DNA threw up a series of surprises. When Lalueza-Fox looked at the genome, he found that rather than having light skin, the man had gene variants that tend to produce much darker skin. “This guy had to be darker than any modern European, but we don’t know how dark,” the scientist said.

Another surprise finding was that the man had blue eyes. That was unexpected, said Lalueza-Fox, because the mutation for blue eyes was thought to have arisen more recently than the mutations that cause lighter skin colour. The results suggest that blue eye colour came first in Europe, with the transition to lighter skin ongoing through Mesolithic times.

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The Spanish team went on to compare the genome of the hunter-gatherer to those of modern Europeans from different regions to see how they might be related. They found that the ancient DNA most closely matched the genetic makeup of people living in northern Europe, in particular Sweden and Finland.

The discovery of mutations that bolstered the immune system against bacteria and viruses suggests that the shift to a farming culture in Neolithic times did not drive all of the changes in immunity genes that Europeans carry today. At least some of those genetic changes have a history that stretches further back. “One thing we don’t know is what sort of pathogens were affecting these people,” said Lalueza-Fox.

Martin Jones, professor of archaeological science at Cambridge University, said the immunity genes were the most striking result. “There is a no doubt oversimplified grand narrative that the move from a hunter-gatherer lifestyle to settled farming was initially bad for our health. A number of factors contributed, particularly living closely together with other humans and animals, shrinking the food web, and crowding-out water supplies. The authors are drawing attention to the role of pathogens in pre-agricultural lives, and that is interesting.”

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