At various points in the last 300,000 years, Denisova Cave has sheltered three different species of hominins. But with fossils from only eight individuals—four Denisovans, three Neanderthals, and the daughter of a Neanderthal/Denisovan pairing—it’s hard to tell a detailed story about when each species lived in the cave. According to a recent genetic study, however, the Denisovans were the first, arriving around 250,000 years ago. And they may still have been there when the first members of our species arrived around 45,000 years ago.

 

That timeline is the result of a recent study of mitochondrial DNA (genetic material passed directly from mother to child) mixed into the deep layers of sediment covering the cave floor. The fragments of ancient DNA probably came from a mixture of feces, decomposing remains, and shed skin and hair that ended up mixed with the dirt of the cave floor, according to archaeologist Elena Zavala of the Max Planck Institute for Evolutionary Anthropology, lead author of the study.

 

"We know that DNA can bind to the minerals found in the sediments and we have also seen microfossils when examining the sediments under a microscope," she told Ars in an email. "Future studies linking specific elements of the sediment to DNA preservation will help increase our understanding of this process."

 

Zavala and her colleagues sampled sediment from every layer of the cave, in all three chambers, at 10-15 centimeter intervals. Then they isolated the sequences of mitochondrial DNA from hominins and other mammal species, like mammoths, bears, and hyenas. To identify which hominin each of the 175 hominin mtDNA samples belonged to, they compared the fragments of DNA to specific parts of the genome that differ among Denisovans, Neanderthals, and us.

New hominins on the block

In a sediment layer that began piling up on the cave floor 250,000 ago, they found the earliest traces of Denisovan mtDNA. That's substantially older than the earliest Denisovan fossil from the cave, which dated to between 194,000 and 123,000 years ago. The earliest Neanderthals showed up in the cave sometime before 170,000 years ago, and for about 40,000 years, the two hominin groups seem to have shared the cave more or less. It’s hard to say for sure, because the layers of sediment only break time down into chunks of several thousand years. That means archaeologists can’t say whether the two species were roommates or whether they alternated possession of the cave every few years, decades, or centuries.

 

“The resolution of the chronology is too coarse-grained to distinguish events at even 1000-year resolution, so we can’t say whether Denisovans and Neanderthals were cohabiting in the cave at times during the Middle Palaeolithic,” University of Wollongong archaeologist Richard Roberts, a coauthor of the study, told Ars.

 

In any case, the arrival of the Neanderthals came on the heels of a major change in the climate. Around 190,000 years ago, the climate in the Altai Mountains turned colder as the world moved out of a relatively warm interglacial period and into another Ice Age. We know this from chemical records locked in ice sheets, cave formations, and marine sediments around the world. The floor of Denisova Cave holds its own record of changing life in the Altai. In layers from this period, Zavala and her colleagues found less mitochondrial DNA from bears and wolves, and more from hyenas and the ancient relatives of modern cattle.

 

Then 130,000 years ago, the climate shifted back into a warmer interglacial period. Deer and wild horses become more common in the mitochondrial DNA record, and the last traces of the Denisovans disappear from the cave by 120,000 years ago. We have no way to know whether they died out or just left. That answer, according to Zavala, probably lies buried at other sites in the region.

 

“To better understand these questions we need to find more sites with Denisovan and Neanderthal remains across this time period,” she told Ars. “It’s possible that the movement or disappearance of the earlier Denisovan was due to climate, but to determine this we would need to identify similar changes in other locations with Denisovan remains. More sites from this time period are needed to track the movements (and disappearances) of different populations of both Neanderthals and Denisovans.”

Who gets credit for these end-scrapers?

These questions matter, in part, because archaeologists want to know who made the stone tools they’ve unearthed at Denisova Cave and other sites around Eurasia. The oldest tools at Denisova Cave date to a period called the early Middle Paleolithic, which spans roughly 200,000 to 170,000 years ago. Denisovans had the cave to themselves for most of that period, and Neanderthals showed up just in time for the last bit of it.

 

The evidence seems to suggest that the “first and principal makers” of the cave’s early Middle Paleolithic scrapers, notched tools, and cores were Denisovans. But since Neanderthals arrived shortly before 170,000 years ago, they may have made at least some of the stone tools from later in the period. That leaves archaeologists with the question of whether Neanderthals learned these manufacturing techniques from Denisovans, contributed some ideas of their own, or developed similar technology independently. Again, the answers probably won’t come from Denisova Cave itself.

 

“What we need are other sites that contain distinctive artefacts and only Denisovan or Neanderthal fossils/DNA deposited alongside them, so that we can link each hominin group to a specific artifact assemblage,” Roberts told Ars.

 

Similar questions linger about bone tools and ornaments dating to a much more recent 45,000 years old, a period called the Initial Upper Paleolithic. Our species arrived in Eurasia sometime between 50,000 and 45,000 years ago, and it’s tempting to give ourselves credit for the relatively advanced suite of bone tools and jewelry that litter these layers of Denisova Cave and other sites across Europe. But there’s evidence to suggest that we probably traded some technology back and forth with the Neanderthals.

Return of the Denisovans

The Neanderthals living in Denisova Cave around 80,000 years ago probably had no cultural memory left of sharing the cave with another hominin group; after all, Denisovans had been absent from Denisova Cave for the last 40,000 years at that point. So it’s interesting to wonder what both sides thought when a group of Denisovans, genetically distinct from the first population to call the cave home, showed up at least 80,000 years ago.

 

“Denisova 11—the bone fragment of the daughter of a Neanderthal mother and Denisovan father—bears witness to Denisovans and Neanderthals becoming very cosy at least once!” Roberts told Ars.

 

The Denisovan mitochondrial DNA in these layers of the cave floor is similar to that from another Denisovan whose DNA archaeologists recovered from a 70,000 to 45,000-year-old site on the Tibetan Plateau. And that could hint at where the second Denisovan population to arrive in the Altai originally came from. Paleontologists studying animal remains from this time period suggest that some large mammals from southeast Asia migrated along the foothills of the Himalayas into the Altai Mountains.

 

“These faunal migrations may have spurred the dispersal of Denisovans into the region in which their remains were first discovered,” Zavala and her colleagues wrote.

When worlds collided

This second wave of Denisovans was still around 45,000 years ago when another hominin species—us—began shedding mitochondrial DNA into the floor of Denisova Cave.

 

In their samples from one chamber of the cave, Zavala and her colleagues found mitochondrial DNA sequences from Denisovans, Neanderthals, and Homo sapiens in a layer dating between 45,000 and 22,000 years ago. Altogether, that suggests that Denisovans, as well as Neanderthals, may still have been living in the Altai Mountains when the first members of our species arrived.

 

That’s not terribly surprising; the location of the Altai Mountains, including Denisova Cave, makes it a geographical meeting point for species moving around among Africa, Europe, and Asia. Bones and mitochondrial DNA from the cave include hyena species from Africa and East Asia as well as extinct European hyena species. But it could also mean that the bone tools of the Initial Upper Paleolithic may have been a multispecies effort.

 

Nature, 2021 DOI: 10.1020874/2071-0437-2021-53-2-1  (About DOIs).