Archaeologists Discover Who Really Lived in Siberia's Denisova Cave

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Denisova Cave
The view from Denisova CaveCredit: Dr. Richard G. Roberts

Denisova Cave, nestled deep in the Altai Mountains of Siberia, is a crossroads of human evolution. Over tens of thousands of years it was inhabited by different species of hominins, not necessarily in this order: Homo sapiens, Neanderthals and of course Denisovans – an elusive group only recently discovered at this very site.

Now, researchers have used a new technique that allows them to extract ancient DNA strands from soil samples to determine the cave’s occupational history – in other words, who lived there first, and which species lived there throughout prehistory.

Spoiler alert: the Denisovans were the original residents. In fact, the analysis published Wednesday in Nature found Denisovan DNA dating back to some 250,000 years ago, much older than actual fossils discovered at the cave.

About a decade ago, DNA extracted from a tiny finger bone unearthed at the site revealed the existence of an entire new branch of the Homo evolutionary tree, which researchers dubbed the Denisovan after the name of this Russian site. Since then, a handful more human fossils have emerged at the cave, some identified as Neanderthal, as well as the 90,000-year-old remains of a teenage girl who had a Denisovan father and a Neanderthal mother

It became clear that the cave had changed hands over time and was located on the edge of the territories of these two hominin groups, with the Neanderthals living in Western Eurasia and the Denisovans occupying at least parts of East Asia. But the timing and order of these occupancies were not known.

To answer this question, researchers led by Elena Zavala of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, collected more than 700 sediment samples dated from 300,000 to 20,000 years ago. In 175 of these samples, hominin DNA was found, the study reports.

Denisova CaveCredit: Dr. Richard G. Roberts

Denisovans, we hardly knew ye

The mere number of positive hits illustrates the promise of this new method as opposed to relying solely on skeletal remains. Human bones are exceedingly rare in prehistoric digs. For example, the Denisovans are only known to us from the fragmentary finds at the Siberian cave and a single jawbone found in Tibet. This, for now, is all we have left of a hominin that evidently occupied large swaths of Asia for tens of thousands of years. It did however manage to leave traces of its existence in people living today, by interbreeding with our distant ancestry

Stone tools are more frequently unearthed in archaeological digs, but because different hominins often made the same utensils, it’s hard to know who was living where based solely on artifacts.

By extracting DNA from cave sediments we can have a much clearer picture of who was inhabiting a site at any given point in time, says Viviane Slon, a paleogeneticist from Tel Aviv University who has been among the method’s pioneers. 

Because researchers have sequenced the genome of humans, Neanderthals and Denisovans, they can compare the DNA strands found in archaeological layers and figure out who they belong to, says Slon, who also took part in the latest study at Denisova Cave. For this analysis, the experts looked at mitochondrial DNA, which is the genetic material found in the mitochondria, the organelles that power our cells. This DNA is usually inherited solely from the mother’s side and is much shorter than our nuclear genome, with some 16,500 base pairs versus three billion.

That means that mitochondrial DNA tends to evolve much faster and is therefore more variable, making it easier to use as a tool to differentiate between species, Slon explains.

Zenobia Jacobs, Bo Li and Kieran O'Gorman collecting sediment samples in the South Chamber of Denisova CaveCredit: Dr. Richard G. Roberts

“Most of these 16,500 base pairs will be similar for all hominins but there are few hundred differences in the genome,” she says. “So if you have fragments that overlap these specific bases then you can say who this DNA belonged to.”

Coexistence, or alternation?

At the Siberian cave, the oldest hominin DNA, going back 250,000 years, belonged to the Denisovans.

Neanderthal genetic material begins to appear in layers dated to around 170,000 years ago, the study reports. After that, control of the cave appears to have seesawed between the two groups.

Because there is a margin of error on dating the samples, we don’t know if the two hominins were occupying the cave at alternating times, perhaps a few centuries apart, or if they were actually there contemporaneously, as was probably the case with the family of “Denny,” the above-mentioned Neanderthal-Denisovan hybrid.

It is also not clear what might have caused the cave to change hands. Some of the more clear-cut occupational changes were also accompanied by a significant change in the composition of the animal DNA found in the cave, so it is possible that environmental factors were at play, Slon notes.

Matthias Meyer at work in the clean laboratory at the Max Planck Institute for Evolutionary AnthropologyCredit: Max Planck / Institute for Evol

“I don’t know if we should blame the Neanderthals for the Denisovans being out of the cave for a while,” she says. “This is an era when the climate is shifting between warm and cold periods, so it may be linked to that.”

Interestingly, the hominin lineages that appear in this later period, around 80,000 years ago, are different than those of the earlier inhabitants of the cave, both for Neanderthals and Denisovans. This suggests that the local populations of both hominins disappeared at some point – again, possibly in connection to climate change – and were then replaced by new groups, Slon tells Haaretz.

Denis the genetic menace

Whether in harmony or not, Neanderthals and Denisovans continued to live in the cave possibly until around 45,000 years ago, when modern human DNA appears for the first time in the sediments.

These strands of sapiens genetic material can be associated with the appearance in the cave of a more advanced stone tool culture, the Initial Upper Paleolithic, which some researchers have linked to the dispersal of our direct human ancestors from Africa.

No sapiens fossils have been found in Denisova Cave, which again highlights how much this new method can contribute to the study of human evolution.

One reasonable question would be how experts can distinguish between prehistoric DNA and genetic material that may have been left by more recent human visitors. After all, Denisova Cave (“of Denis” in Russian) is named after a hermit who lived there in the 18th century. And archaeologists themselves most likely have contaminated the site with their own DNA.

The answer is that ancient DNA is found in much shorter strands and undergoes molecular changes that make it distinguishable from more recent material, Slon says. So, we can be reassured that, most probably, scientists have not been mistakenly studying the DNA of Denis the Russian hermit.

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