Mysterious human relatives moved into ‘penthouse’ Siberian cave 100,000 years earlier than thought

With its light-filled main gallery and sweeping views of the Altai Mountains of southern Russia, Denisova Cave was a Stone Age version of a Manhattan penthouse. Overlooking the Anui River, where herds of animals came to drink, it offered an unparalleled vantage for spotting game and other humans, as well as refuge from Siberian storms. Generations of Neanderthals, their Denisovan cousins, and modern humans enjoyed the view.

But when did each group reside there? The timing could yield clues to how these diverse humans interacted and shed new light on the most enigmatic of the three, the Denisovans, who are known only from DNA and scrappy fossils from this cave. Denisova's human fossils and artifacts have been notoriously difficult to date because of the complex layering of sediments in its three chambers. Now, two teams have combined state-of-the-art dating methods to create a timeline of the cave's occupants.

For the Denisovans, the results—reported in Nature this week—paint a portrait of endurance. They first moved in 287,000 years ago, more than 100,000 years earlier than had been thought, and then occupied the cave off and on through shifting climates until 55,000 years ago, a period when Neanderthals also came and went. "The general picture is now clear," says archaeologist Robin Dennell of the University of Sheffield in the United Kingdom, who was not a member of the teams.

Ever since DNA extracted from a girl's tiny pinkie bone found in the cave revealed that she belonged to a formerly unknown type of human, researchers have been trying to nail down when the Denisovans lived. In 2015, several samples of cut-marked animal bones and charcoal found near the pinkie bone yielded radiocarbon dates of at least 50,000 years, at the oldest limit of the method. But that was a minimum age because bone fragments, teeth, and DNA from four other Denisovans and from a young woman whose DNA shows she had a Neanderthal mother and a Denisovan father have also been found in the cave, some in deeper, older layers. One tooth might have been as old as 170,000 years.

Those older dates had wide margins of error. So, Russian Academy of Sciences archaeologists who have been excavating at Denisova for 40 years invited geochronologists Zenobia Jacobs and Richard Roberts of the University of Wollongong in Australia to try state-of-the-art optical dating methods. Optical dating reveals when single grains of quartz or potassium feldspar in a sample of sediment were last exposed to sunlight and, thus, when the sediment was deposited. By measuring 280,000 individual grains of these minerals in more than 100 samples collected near stone tools or fossils, the Wollongong team calculated the average age of every layer of the cave's deposits.

The team checked its dates for the most recent layers against radiocarbon dates that geochronologists Tom Higham and Katerina Douka at the University of Oxford in the United Kingdom determined from 50 new cut-marked bone and charcoal samples. The Oxford team also developed a new statistical model that merges data from several dating methods, as well as from genetic sequencing, which can reveal the relative ages of fossils. By evaluating all the data and their range of errors, the model determines which dates are most reliable. "There's a huge value in using multiple techniques," says Ed Rhodes of the University of Sheffield, who was not involved in the work. The resulting dates, he adds, are "fully convincing."

The oldest stone tools in the cave date back to at least 287,000 years, according to the optical methods. These so-called Middle Paleolithic tools look subtly different from those associated with Neanderthals in other caves in Siberia, suggesting they are the first artifacts ever linked to the Denisovans. Direct evidence of Denisovans—so-called environmental DNA found in the sediments—also appears a bit before DNA from Neanderthals, who occupied the cave on and off from 193,000 to 97,000 years ago.

The Denisovans were "evidently a hardy bunch," Jacobs says. They apparently persisted at the site through multiple episodes of cold Siberian climate, based on analysis of fossil pollen. In contrast, when the Neanderthals showed up, the pollen shows that the forest around the cave had hornbeam, oak, and Eurasian linden trees, which thrive in a relatively warm and humid climate.

The dates also suggest a new puzzle: Who made so-called Initial Upper Paleolithic artifacts, such as ornaments of bone, animal teeth, mammoth ivory, and ostrich eggshell, that date to between 43,000 to 49,000 years at the site? Higham's Russian collaborators propose they were made by Denisovans, like the tools from older layers. No modern human fossils have been found in the cave, they note. But others say the artifacts resemble the handiwork of modern humans in Eurasia, suggesting the newcomers arrived just after the Denisovans vanished—or even hastened the disappearance of this lost group.

"My money would be on early modern humans, who can be mapped elsewhere at this date, for example at Ust'-Ishim in Siberia," says paleoanthropologist Chris Stringer of the Natural History Museum in London, not a member of the team. "Only more discoveries and more research can resolve that question."