A cave nestled in the Russian mountains could solve an ancient human mystery

In a remote cave nestled in the Altai Mountains of southern Russia, scientists are uncovering the secrets of ancient human life. Here in this cave, ancient peoples like the Neanderthals found shelter from the bitter chill of the Ice Age.

According to new research, Neanderthals also shared this cave with another, little-known group of ancient humans: the Denisovans. Furthermore, the Denisovans were likely there first.

This finding was published Wednesday in the journal Nature and was made by extracting and analyzing DNA from ancient sediment. Previous to this study, it was unclear which ancient human originally made this site their home. Now, evidence suggests the Denisovans appeared first — before occupying the site repeatedly, alongside Neanderthals, until around 45,000 years ago.

It’s a clarifying detail in the vague story of human history, and the even vaguer story of the Denisovans.

“This is a group we know very little about,” lead author Elena Zavala tells Inverse. Zavala is a researcher at the Max Planck Institute for Evolutionary Anthropology.

“By increasing our knowledge, we are provided with another perspective or reference for understanding what are the elements that make us modern humans ‘human.’”

Who were the Denisovans?

Our understanding of who exactly the Denisovans were is still murky, but it’s one that’s steadily becoming improved.

Denisovans and Neanderthals — the ancient sister kin of humans — both belong to the same Homo genus, but we knew little about these ancient peoples until 2010. This is when scientists discovered their fossilized remains in what’s known called Denisova Cave, the three-chambered site in the Altai Mountains.

“... our results have wider implications for understanding the human past.”

Since then, scientists have learned Denisovans interbred with ancient humans. As a result, their DNA lingers on in billions of people living today in East and Southeast Asia. Their genes may even help explain the renowned athleticism of the people of Tibet.

“Denisovans are an extinct hominin group whose DNA makes up about 1 to 3 percent of the genomes of some modern-day human populations,” Zavala says.

Using DNA sequencing of the cave fossils, two studies published in 2019 suggested Denisovans likely lived sometime between 50,000 and 200,000 years ago.

However, thanks to this new Nature study, scientists have a more accurate estimated timeline of the Denisovans’ life on Earth. And their lineage may stretch further back than we previously realized.

What’s new — A team of researchers, led by the Max Planck Institute for Evolutionary Anthropology in Germany, sequenced the mitochondrial DNA of Denisovans, Neanderthals, and animals to provide a more complete picture regarding:

• The timeline of when Denisovans and Neanderthals lived in the cave
• How Denisovans and Neanderthals interacted
• The possible migration of Denisovans

Scientists had previously discovered a dozen remains of Neanderthals and Denisovans in the cave, as well as a hybrid child with a mix of Denisovan and Neanderthal DNA, suggesting that the two groups mated with each other.

However, the researchers didn’t fully understand when and how these different groups of ancient humans overlapped.

That’s where the new study comes into play. Contrary to what we previously thought, Denisovans may have actually predated the Neanderthals.

The team discovered three key findings:

• The oldest and earliest hominin DNA found in the cave is Denisovan
• Neanderthals and Denisovans likely overlapped — possibly living together in the cave — between 130,0000 to 190,000 years ago and 45,000 to 80,000 years ago
• DNA shifts in ancient peoples mirrors changes in animal populations and ecological fluctuations

Denisovan remains were associated with the use of stone tools from the Middle Paleolithic period roughly 170,000 to 250,000 years ago, implying Denisovans may have been one of the earliest stone tool users.

Neanderthal DNA didn’t start appearing until the tail end of this period. From then on, both Neanderthals and Denisovans interacted and occupied the cave site until 45,000 years ago, when modern humans first arrived on the scene.

Even though no modern human fossils were previously found in the cave, the researchers successfully detected the DNA of the ancestors of modern humans, suggesting that our ancient ancestors may have overlapped with Denisovans during the late Stone Age.

The scientists also discovered changes in the types of animals that were found in the caves — like wooly mammoths, hyenas, and canines — over time.

For example, the animal DNA shifted from cave bears to brown bears roughly 190,000 years ago, which is roughly when Neanderthals first appeared in the cave. It’s also when Earth began shifting from an interglacial period to a fully glacial period, which may have catalyzed the migration of ancient peoples to Siberia.

How they did it — Previously scientists used fossil records from the cave to understand when Denisovans and Neanderthals lived and how they interacted. However, fragmented fossils can’t always paint a full picture of ancient humans, especially when you don’t have enough of them.

In this study, researchers turned to another method to depict the timeline of ancient peoples living in the cave: sediment records. In other words, they collected dirt to conduct their research.

The researchers collected 728 sediment samples from the three chambers of Denisova cave, finding Neanderthal and Denisovan DNA in 47 and 79 samples, respectively. The scientists then sequenced the DNA to date when the ancient hominins lived in the cave.

“In order to recover Denisovan DNA, we extracted DNA directly from the sediment,” Zavala explains. “This allowed us to have a more holistic view of when they were present in the cave.”

Why it matters — Little by little, archaeologists are putting together the puzzle pieces that comprise Denisovan life.

The researchers write that their findings provide the “earliest genetic evidence for hominin occupation in Denisova Cave.”

The findings also help us understand how Denisovans may have wound up in the Siberian cave where their remains were found: They may have been following in the footsteps of animals that migrated from southeast Asia into Siberia.

Denisovans’ potential interactions with Neanderthals in the cave also suggest that these two groups are more closely linked than we previously understood.

“We can't say for sure if they met often during these periods or cohabitated, but from a previous study on the child of a Neanderthal mother and Denisovan father, we know they met at least once,” Zavala says.

By better understanding the Denisovans, we’ll have a fuller appreciation for how they interacted with Neanderthals and possibly the ancestors of modern humans.

The researchers write that “our results have wider implications for understanding the human past.”

What’s next — These findings provide an exciting update to the timeline of ancient humans, but we should still be a little wary about gaps in the data, the study team writes.

For example, the sediment record doesn’t cover the periods between 80,000 to 97,000 years ago and 156,000 to 170,000 years ago, so we don't know what happened to the Denisovans during that time.

There’s also a chance that different soil layers may have become disturbed due to burrowing animals, possibly affecting the researchers’ suggested timeline.

However, the findings still point to the possibility of using improvements in archaeological technology to learn more about the evolution of ancient peoples like the Denisovans — and ourselves.

Abstract: Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals. The dozen hominin remains recovered from the deposits also include Neanderthals and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist 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 assemblages. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect 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 Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.