Europe’s oldest known humans mated with Neandertals surprisingly often

When some of the earliest human migrants to Europe encountered Neandertals already living there around 45,000 years ago, hookups flourished.

Analyses of DNA found in human fossils from around that time — the oldest known human remains in Europe — suggest that interbreeding between Homo sapiens and Neandertals, who were on the fast track to extinction, occurred more commonly than has often been assumed, two new studies suggest. Both reports appear April 7 in Nature Ecology & Evolution.

Genetic evidence in the new reports indicates for the first time that distinct human populations reached Europe shortly after 50,000 years ago. Neandertals interbred with all the groups detected so far, ensuring that some of their genes live on today in our DNA.

Remains of three H. sapiens individuals unearthed in Bulgaria’s Bacho Kiro Cave yielded nuclear DNA containing Neandertal contributions of about 3 to 4 percent, says a team led by evolutionary geneticist Mateja Hajdinjak of the Francis Crick Institute in London. The ancient DNA came from a tooth and two bone fragments radiocarbon dated to between around 43,000 and 46,000 years ago. Stone tools typical of late Stone Age humans were found in the same sediment as the fossils.

“All of the Bacho Kiro individuals had recent Neandertal ancestors, as few as five to seven generations back in their family trees,” Hajdinjak says.

Further evidence of ancient interbreeding comes from a nearly complete human skull discovered in 1950 in a cave in what’s now the Czech Republic. About 2 percent of the genes in DNA from that fossil, identified as a female’s, also come from Neandertals, say evolutionary geneticist Kay Prüfer of the Max Planck Institute for the Science of Human History in Jena, Germany, and his colleagues. Analysis of those DNA segments suggest she also lived around 45,000 years ago.

The H. sapiens fossils in Bulgaria and the Czech Republic aren’t the first ones found with bits of Neandertal DNA in their genomes, but they are most likely the oldest. The long Neandertal DNA segments in the eastern European woman, which would have broken into shorter segments in later human generations, suggest she lived a few hundred to a few thousand years earlier than a previously reported 45,000-year-old Siberian man who shared 2.3 percent of his genes with Neandertals (SN: 10/22/14). That find indicated that interbreeding outside of Europe dated to as early as 60,000 years ago. And a Romanian man who lived roughly 40,000 years ago also possessed long stretches of Neandertal DNA, indicating he was four to six generations removed from a Neandertal relative (SN: 5/11/15).

Neandertals went extinct around 40,000 years ago, though their genetic remnants remain — today, non-African people carry, on average, nearly 2 percent Neandertal DNA. Present-day Africans possess a smaller Neandertal genetic legacy (SN: 1/30/20).

Taken together, the new studies suggest that some early human entrants to Europe had a long-lasting impact on our DNA while others hit genetic dead-ends. Bacho Kiro humans represent a newly identified population of ancient Europeans with genetic ties to present-day East Asians and Native Americans, but not western Eurasians, Hajdinjak’s group says. Like the ancient Romanian and Siberian men, the Czech Republic woman contributed no genes to H. sapiens that lived after around 40,000 years ago.

“It is remarkable that the Bacho Kiro finds could represent a population that was spreading 45,000 years ago at least from Bulgaria to China,” says evolutionary geneticist Carles Lalueza-Fox of the Institute of Evolutionary Biology in Barcelona, who did not participate in either new investigation.

If H. sapiens and Neandertals regularly interbred as the latter population neared its demise, then relatively large numbers of incoming humans accumulated a surprising amount of DNA from smaller Neandertal populations, Lalueza-Fox suspects. After 40,000 years ago, additional migrations into Europe by people with little or no Neandertal ancestry would have further diluted Neandertal DNA from the human gene pool, he says.

Those humans made distinctive stone and bone tools and served as ancestors of present-day Europeans, Hajdinjak suggests. At Bacho Kiro Cave, for instance, newly recovered DNA from a roughly 35,000-year-old H. sapiens bone fragment displays a different makeup than that of the cave’s earlier human inhabitants. This individual contributed genes mainly to later populations in Europe and western Asia, Hajdinjak says.