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Archaic Hominin History, Interactions Revealed With Denisova Cave Sediment Sequences

NEW YORK – By digging into mitochondrial DNA sequences in sediment samples from the southern Siberia cave where Denisovan remains were first found, an international research team has retraced hominin history going back hundreds of thousands of years in the region, while highlighting the other animals and artifacts found there over time.

As they reported in Nature on Wednesday, the researchers used shotgun sequencing to delve into more than 700 Pleistocene sediments from three chambers of Denisova Cave, found in the Altai Mountains. The search uncovered mitochondrial DNA, or mtDNA, from Denisovans, Neanderthals, or ancient modern humans in 175 of the samples considered, while ancient mammalian mtDNA turned up in almost 700 of the samples.

Together, the team explained, the available data provided a look at the archaic hominin dynamics at the Denisova Cave in the Altai Mountains going back some 250,000 years or more, along with the arrival and disappearance of other animals in the context of climate features found in southern Siberia.

"This study provides us with insights for when Neanderthals, Denisovans, and modern humans were present in Denisova Cave and when they may have overlapped in time," co-first author Elena Zavala, a Ph.D. student at the Max Planck Institute for Evolutionary Anthropology, said in an email. "Importantly, it also places these occupational periods into context with environmental conditions such as the climate and the presence of different animals, as well as the different types of artifacts found in the cave."

For their study, the investigators systematically collected teaspoon-sized sediment samples in a grid pattern in the cave, subsequently extracting DNA from each subsample and preparing these molecules for single-stranded DNA library sequencing using a library preparation method designed to deal with fragmented ancient DNA, Zavala explained. From there, they enriched for not only human mtDNA but also mtDNA spanning more than 200 other mammalian species.

"This last step is especially critical for sediment DNA because of the variety of potential DNA contributors in each sample," she said, noting that the process took more than two years, even with automated DNA extraction, preparation, and enrichment steps.

The team's results pointed to the presence of Denisovan mtDNA going back 170,000 to 250,000 years, overlapping with stone tool artifacts dated to the early Middle Paleolithic. On the other hand, mtDNA sequences from Neanderthals started to turn up roughly 190,000 years ago, when the climate transitioned from relatively warm to cooler conditions. At around the same time, brown bear mtDNA became more common, while the mtDNA from cave bears and other animals became less common.

"This is the first study to use high-density sediment sampling and demonstrates that this technique can be used to provide a more comprehensive understanding of a single site," Zavala said. "If applied at more sites, it has the potential to provide new insights into the migration patterns of different hominin groups through time and space while linking these patterns to the spread of different types of artifacts and technologies, mammalian migration patterns, and climatic changes."

Within the past 170,000 years, Denisova Cave appeared to be home to both Denisovans and Neanderthals, the sequences suggested, though a gap in Denisovan habitation turned up during a warming period between 100,000 and 130,000 years ago, followed by the arrival of Denisovans with a distinct mitochondrial lineage.

Still other tools turned up more recently, during the Initial Upper Paleolithic, around the same time that mtDNA from ancient modern humans began appearing in sediment layers from the cave, suggesting that humans not only inhabited the cave for a time, but also introduced new tools to the site.

"We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA," the authors reported, "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."