BERLIN — A hunter-gatherer who lived in Europe some 7,000 years ago probably had blue eyes and dark skin, a combination that has largely disappeared from the continent in the millennia since, scientists said Tuesday.

The discovery, published in the journal Nature this week, was made by scientists from the United States, Europe and Australia who analyzed ancient DNA extracted from a male tooth found in a cave in northern Spain.

“We have the stereotype that blue eyes are found only in light-skinned people but that’s not necessarily the case,” lead researcher Carles Lalueza-Fox said in a telephone interview Tuesday with The Associated Press.

Lalueza-Fox, who works at the Institute of Evolutionary Biology in Barcelona, Spain, said the man’s skin would have been darker than most modern Europeans, while his eyes may have resembled those of Scandinavians, his closest genetic relatives today. The combination of blue eyes and dark skin, which is sometimes seen in people with mixed European and African ancestry, may once have been common among ancient European hunter-gatherers, he said.

The researchers also found the man had genes that indicated he was poor at digesting milk and starch, an ability which only spread among Europeans with the arrival of Neolithic farmers from the Middle East. The arrival of this group was also believed to have introduced several diseases associated with proximity to animals — and the genes that helped resist them.

But the hunter-gatherer whose remains were found in the La Brana caves, near Spanish city of Leon, already had some genes that would have helped him fight diseases such as measles, flu and smallpox. This came as a surprise to researchers, indicating that the genetic transition was already under way 7,000 years ago, Lalueza-Fox said.

The lack of such genes among pre-Columbian populations in the Americas was one of the reasons they were so susceptible to these diseases when the Europeans arrived.

Researchers are hoping to make further discoveries from a second skeleton found at the site, said Lalueza-Fox.

Beth Shapiro, an associate professor of ecology and evolutionary biology at the University of California Santa Cruz, said the paper showed how old DNA could be used to learn more about the appearance and traits of ancient populations.

“I anticipate that this is just the beginning and am excited to see these sorts of analyses taking place,” said Shapiro, who wasn’t involved in the study. “I look forward to what else we will learn once we have population samples of paleogenomes (ancient DNA).”