• Daniyar Kylyzhov

More than 45,000 years ago, modern humans entered Neanderthal territory. Here's what happened next

This skull from Zlatý kůň cave near Prague belonged to the earliest known modern human in Europe. MAREK JANTAČ

The four-story maze of galleries in the Bacho Kiro cave in Bulgaria has long been a magnet for a variety of people. Neanderthals came first, more than 50,000 years ago, and left their distinctive Mousterian stone tools among the stalagmites. Then came modern humans, in at least two waves; the first was dotted with the cave floor with beads and ochre-colored stone blades about 45,000 years ago. Another group settled about 36,000 years ago with even more complex artifacts.

A new study of ancient DNA shows that the first group of modern humans in Bacho Kiro inherited the recent legacy of Neanderthals: the ancestors of these people interbred with our extinct cousins in just six generations, or from 160 to 180 years ago.

However, another study conducted today of what may be the oldest modern human in Europe shows that the first wave of modern humans had a diverse Neanderthal heritage. The genome of a dark-skinned, dark-haired, and brown-eyed woman from the Zlaty Ku Cave in the Czech Republic included only 3% of Neanderthal DNA, which was likely derived from a long-ago encounter in the Middle East, rather than from recent contact, the study suggests.

Taken together, these genomic images provide a glimpse into the identities of the mysterious modern humans who first set foot in Europe and their relationship to the Neanderthals who disappeared 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 did not. Some of them are related to later people, and some are not."

"The new revelations add to the story of these ancient encounters," says Mateja Hajdinjak, a postdoc at the Max Planck Institute for Evolutionary Anthropology (MPI) and author of the Bacho Kiro study. "For the first time, we are getting ancient DNA from several early modern humans, which tells us so much about their interactions with some of the most recent Neanderthals in Europe," she says.

After modern humans left Africa 60,000-80,000 years ago, they interbred with Neanderthals at least once, most likely in the Middle East around 50,000 years ago, as previous studies of ancient DNA have shown. These studies include an analysis of two early modern humans from Eurasia: a 45,000-year-old femur from Ust-Ishim in Siberia, and a young man's jawbone from the Petshtera-Ku-Oase cave in Romania, dating from about 37,000 years ago and 42,000 years ago. The oasis man inherited 6.4% of the DNA from a recent Neanderthal ancestor. But he lived at least 5,000 years after modern humans arrived in Europe. Today's research offers a genetic glimpse of an earlier time when modern humans first ventured into Neanderthal territory.

Haidinjak 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 the middle layer of cave sediments belong to modern humans. In the new study, the researchers sequenced the molar genomes and bone fragments from this middle layer and directly dated them from 42,580 to 45,930 years ago. They also sequenced DNA from a bone found in a younger layer and dated it to 35,000 years ago. The remains of both layers belonged to modern humans, but, as reported today in Nature, belong to different populations.

Genomes show that the three oldest modern humans in Bacho Kiro were distantly related to a 40,000-year-old partial skeleton from Tianyuan in China, as well as other ancient and living East Asians and Native Americans. This suggests that they all descended from an ancient population that once spread across Eurasia, but whose descendants in Europe seem to have become extinct. The lineage survived in Asia, later giving rise to people who migrated to the Americas.

Modern people on the move

The new genomes from the two sites (red) complement a handful of ancient DNA studies of the mysterious modern humans who first traveled to Eurasia and the heartland of the Neanderthals. These modern humans also inherited between 3% and 3.8% of their DNA from Neanderthal ancestors. The pieces of Neanderthal DNA were long, suggesting that they had originated from mixing only six generations earlier, because, with each new generation, recombination breaks sections of DNA into shorter fragments. This marriage must have been different from what gave the young man Oase his larger Neanderthal heritage. This "suggests that such mixing was common," says Haidinjak.

Genomic analysis of a female skull found in the cave of Zlaty ke (which means "golden horse" in Czech), near Prague, says something else, according to a report today in Nature Ecology & Evolution published by the team of paleogeneticists Johannes Krause and Kai Prufer from MPI. According to Krause, the woman's Neanderthal DNA probably originated from the first known interbreeding between Neanderthals and the ancestors of all living Eurasians, when modern humans spread out of Africa and migrated to Eurasia.

The researchers were unable to directly date the Czech skull, which was discovered in the 1950s because the bovine glue used to repair it had contaminated the bones. So Krause and Prufer turned to a clever dating method that uses the ancestral link to Neanderthals as a timestamp. They conclude that fragments of Neanderthal DNA in the genome of the Golden Ku skull suggest that the woman was born 60-80 generations (approximately 2000 years) after her ancestors mated with Neanderthals. The 45,000-year-old Siberian male inherited his shorter Neanderthal DNA fragments from about 85 to 100 generations after the same encounter. This suggests that the Czech woman lived earlier than the Siberian man and could be older than 47,000 years - the oldest known modern in Europe, Krause says.

According to population geneticist John Novembre of the University of Chicago, the authors cite "compelling" evidence that the female lived at least 45,000 years ago.

Krause's team also found that, unlike the Bacho Kiro people, the Zlata-Ku skull was not more closely related to ancient Asians than to Europeans. This suggests that she came from an ancient population that had not yet differentiated genetically into Asians and Europeans, Krause says.

Novembre suggests that the differences in how often modern humans mate with Neanderthals may reflect the small population size of each group at the time. And Zlaty-Ku is located, perhaps, on the northern edge of Neanderthal territory, whereas the Balkan Mountains of Bulgaria were a known refuge for Neanderthals when modern humans invaded Europe.

New data shows that all modern human bloodlines disappeared with the onset of the last Ice Age, which peaked about 20,000 years ago. After the ice melted, other modern humans from Eurasia repopulated the continent. "A lot of groups went [to Eurasia], but it looks like only a fraction of these early modern humans left offspring," Novembre says.


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