Denisova Cave (Russie): New DNA tests on ancient Denisovan people 'shows them occupying Altai cave 170,000 years ago'

Ann Gibbons 

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In 2010, scientists discovered a new kind of human by sequencing DNA from a girl’s pinky finger found in Denisova Cave in Siberia. Ever since, researchers have wondered when the girl lived, and if her people, called Denisovans, lingered in the cave or just passed through. But the elusive Denisovans left almost no fossil record—only that bit of bone and a handful of teeth—and they came from a site that was notoriously difficult to date.

Now, state-of-the-art DNA analysis on the Denisovan molars and new dates on cave material show that Denisovans occupied the cave surprisingly early and came back repeatedly. The data suggest that the girl lived at least 50,000 years ago and that two other Denisovan individuals died in the cave at least 110,000 years ago and perhaps as early as 170,000 years ago, according to two talks here last week at the meeting of the European Society for the study of Human Evolution. Although the new age estimates have wide margins of error, they help solidify our murky view of Denisovans and provide “really convincing evidence of multiple occupations of the cave,” says paleoanthropologist Fred Spoor of University College London. “You can seriously see it’s a valid species.”

Most of the cave’s key fossils come from a thick band of sandstone called layer 11. When researchers first dated animal bones and artifacts in this layer, the results varied widely, between 30,000 to 50,000 years ago. So Siberian researchers invited geochronologist Tom Higham of the University of Oxford in the United Kingdom to re-date the sequence. Higham’s team collected and radiocarbon-dated about 20 samples of artifacts and animal bones with cut marks, which presumably were discarded by ancient humans. Sediments holding the finger bone, at the bottom of layer 11, came out right at the limit of radiocarbon dating, and are likely older than 48,000 to 50,000 years, reported postdoc and archaeologist Katerina Douka of Oxford.

Another dating expert at the meeting was cautious about these results. “How secure is the association of the Denisovans with the [dated] animal remains?” asked geochronologist Daniel Richter of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and Leuphana University in Lüneburg. But Douka stressed that the dates were from cut-marked animal bones and ornaments, and were consistent across three cave chambers.

The dates also fit with genetic evidence presented at the meeting that Denisovans were in the cave early. Researchers sequenced nuclear DNA from three molars from layer 11 and a child’s molar from a deeper layer, 22, according to a talk by graduate student Viviane Slon, who works in the lab of paleogeneticist Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology. (A dating method considered experimental for caves, thermoluminescence dating, had suggested that layer 22 is 170,000 years old.)

Slon and her colleagues managed to analyze a significant amount of nuclear DNA from three teeth that turned out to be Denisovan. (A fourth was Neandertal.) By comparing key sites on the tooth DNA with corresponding sites in the high-quality genomes of the Denisova girl, Neandertals, and modern humans, they revealed that the Denisovan inhabitants in that one cave were not closely related. They had more genetic variation among them than all the Neandertals so far sequenced, although Neandertals are known to be similar genetically.

Sn denisovanembedDenisovans were discovered when their genome was sequenced from this pinky finger bone from a young girl. Max Planck Institute for Evolutionary Anthropology

To find out when the Denisovans were in the cave, the team also sequenced their entire mitochondrial DNA (mtDNA)  genomes and placed them on a family tree. Then they counted the number of mtDNA differences between individuals and used the modern human mutation rate to estimate how long it might have taken those mutations to appear. They concluded that the girl with the pinky finger was in the cave roughly 65,000 years after the oldest Denisovan, who was there at least 110,000 years ago and possibly earlier.

Neandertals were in Denisova Cave, too—Pääbo’s team has sequenced their DNA from a toe bone and molar found there. And modern humans also were apparently drawn to the large, light-filled cave, given the more recent artifacts found there. “What I found fascinating is the interdigitization of the Neandertals and Denisovans—that both groups were in and out of the cave,” says paleoanthropologist Leslie Aiello of the Wenner-Gren Foundation in New York City.

The challenge now is to get more fossils to flesh out the still-mysterious Denisovans. To that end, Oxford grad student Samantha Brown reported in a poster that she discovered a human bone fragment by using a new technique, called ZooMS, to scan 2315 bones from the cave for uniquely human proteins. Anything she finds will be welcome. “This is a real lineage, and we have to work out what the hell it looks like,” says paleoanthropologist Bernard Wood of George Washington University in Washington. D.C.