In a new study published this week in the journal Nature, an international team of researchers analyzed DNA from more than 700 sediment samples that were collected from the Pleistocene layers of Denisova Cave in Siberia and detected ancient hominin and mammalian mitochondrial DNA (mtDNA) in 685 and 175 samples, respectively; the earliest evidence for hominin mtDNA is of Denisovans, and is associated with the stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period; the authors also detected a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly — possibly until, or after, the onset of the Initial Upper Paleolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.
Denisova Cave in the Altai Mountains of southern Siberia. Image credit: Alex Demin / CC BY-SA 4.0.
Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals.
The cave consists of three chambers (designated Main, East and South Chambers) that contain deposits from the Middle Pleistocene to the Holocene epoch.
The dozen hominin remains recovered from the deposits also include Neanderthals and the child of a Neanderthal and a Denisovan, which suggests that the cave was a contact zone between these archaic hominins.
However, uncertainties exist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological finds.
“Just collecting hundreds of samples from all three chambers in the cave, and documenting their precise locations, took us more than a week, but we obtained a comprehensive set of samples spanning more than 300,000 years of Siberian history,” said Professor Zenobia Jacobs, a researcher at the University of Wollongong.
“The chronology generated previously for the cave sediments allowed us to choose the best places to collect the DNA samples and make the most of the extraordinary insights from sediment DNA.”
In the new study, Professor Jacobs and colleagues extracted and sequenced small traces of ancient human and animal (such as cave-dwelling bears, hyenas and wolves) mtDNA from 728 sediment samples.
When matching the DNA profiles with the ages of the layers, the researchers found the first humans to visit the site were Denisovans about 250,000 years ago, followed by Neanderthals about 200,000 years ago.
Only Neanderthal DNA was found in sediments deposited between 130,000 and 80,000 years ago.
Denisovans who came back after this time carried a different mtDNA to Denisovans who were there earlier, suggesting a different population had arrived in the region.
The ancient DNA of anatomically modern Homo sapiens first shows up in layers deposited between about 60,000 and 45,000 years ago, which contained pendants and other ornaments made from animal bones and teeth, mammoth ivory, ostrich eggshell, marble and gemstones.
“This provides not only the first evidence of modern humans at the site, but also suggests that they may have brought new technology into the region with them,” said Elena Zavala, a Ph.D. student at the Max Planck Institute for Evolutionary Anthropology.
The scientists also found animal DNA in nearly all samples, and identified two time periods when changes occurred in both animal and human populations.
The first, around 190,000 years ago, coincided with a shift from relatively warm to relatively cold conditions, when hyena and bear populations changed and Neanderthals first appeared in the cave.
The second major change occurred between 130,000 and 100,000 years ago, along with a shift in climate from relatively cold to relatively warm conditions.
During this period, animal populations changed again, Denisovans vanished, and Neanderthals were left as the only human occupants of the cave.
“The coincidence of these population turnovers with climatic transitions between interglacial and glacial periods suggests that environmental factors played a key role in shaping the human and faunal history of this region,” Professor Roberts said.
“Being able to generate such dense genetic data from an archaeological site is like a dream come true,” said Professor Matthias Meyer, a researcher at the Max Planck Institute for Evolutionary Anthropology.
“There is so much information hidden in sediments — it will keep us and many other geneticists busy for a lifetime.”
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E.I. Zavala et al. Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave. Nature, published online June 23, 2021; doi: 10.1038/s41586-021-03675-0
