The four-story labyrinth of galleries in Bulgaria’s Bacho Kiro cave has long been a magnet for all sorts of humans. Neanderthals came first, more than 50,000 years ago, and left their characteristic Mousterian stone tools among the stalagmites. Next came modern humans in at least two waves; the first littered the cave floor with beads and stone blades stained with ochre, about 45,000 years ago. Another group settled in about 36,000 years ago with even more sophisticated artifacts.
Now, a new ancient DNA study shows the first group of modern humans at Bacho Kiro carried a recent legacy from Neanderthals: Those people’s ancestors had interbred with our extinct cousins as recently as six generations, or 160 to 180 years, previously.
However, another study out today, of what may be the oldest modern human in Europe, shows the first wave of moderns had diverse Neanderthal legacies. The genome of a dark-skinned, brown-haired, brown-eyed woman from Zlatý kůň cave in the Czech Republic included only 3% Neanderthal DNA, which likely came from a long-ago tryst in the Middle East, not from recent contact, the study suggests.
Taken together, these genomic snapshots offer a glimpse into the identities of the mysterious modern humans who first set foot in Europe and their relationship to Neanderthals, who vanished about 40,000 years ago. “You’re talking about multiple waves of modern humans,” says paleoanthropologist Chris Stringer of the Natural History Museum in London. “Some groups mixed with Neanderthals, and some didn’t. Some are related to later humans and some are not.”
The new revelations fill out the story of these ancient encounters, says Mateja Hajdinjak, a postdoc at the Max Planck Institute for Evolutionary Anthropology (MPI) and an author of the Bacho Kiro study. “For the first time, we’re getting ancient DNA from multiple early modern humans that tells us so much about their interactions with some of the very last Neanderthals in Europe,” she says.
After modern humans trekked out of Africa 60,000 to 80,000 years ago, they interbred at least once with Neanderthals, most likely in the Middle East about 50,000 years ago, previous ancient DNA research has shown. Those studies include analyses of two early modern humans from Eurasia: a 45,000-year-old thigh bone of a man from Ust’-Ishim in Siberia, and the jawbone of a young man from Petştera cu Oase cave in Romania, dated to between 37,000 and 42,000 years ago. The Oase man inherited as much as 6.4% of his DNA from a recent Neanderthal ancestor. But he lived at least 5000 years after modern humans had arrived in Europe. Today’s studies offer a genetic glimpse of an earlier time, when modern humans first ventured into Neanderthal territory.
Hajdinjak and MPI paleogeneticist Svante Paabo analyzed genomes from Bacho Kiro, where last year researchers used a new protein-based method to show that bone fragments in a middle layer of cave sediments came from modern humans. In the new study, the researchers sequenced genomes from a molar and bone fragments from that middle layer and directly dated them to 42,580 to 45,930 years ago. They also sequenced DNA from bone found in a younger layer and dated it to 35,000 years ago. Remains from both layers were modern humans, but from different populations, they report in Nature today.
The genomes show the three oldest modern humans at Bacho Kiro were distantly related to a 40,000-year-old partial skeleton from Tianyuan in China, as well as to other ancient and living East Asians and Native Americans. That suggests they all descended from an early population that once spread across Eurasia, but whose descendants in Europe seem to have died out. The lineage survived in Asia, later giving rise to people who migrated to America.