How a now-extinct people profoundly influenced human history

In 2019, in a cave high on the Tibetan Plateau, scientists discovered a chunk of a jawbone. At least 160,000 years old, its novelty has less to do with its age, than who it belonged to.

This half-mandible is the largest Denisovan fossil ever found — a physical memento of an elusive and long-extinct species of early humans.

But a new study proves what was originally only hypothesized. According to scientists, the jaw is just one part of a more robust Denisovan story.

To try and solve the mystery, the scientists returned to the Baishiya Karst Cave where the jaw was found. There, they extracted genetic material from cave sediments, proving Denisovans did occupy the cave. This paper, alongside another Denisovan study, adds to our ever-growing understanding of how Denisovans once lived — and how their DNA continues to influence humankind today.

The pair of studies were published Thursday in the journal Science.

Bo Li is an associate professor at the University of Wollongong in Australia and a co-author of the study examining the Tibetan cave. He was also involved in the dating project for the Denisova Cave in Siberia, the first site Denisovan remains were discovered.

Scientists assume Denisovans were widely distributed in Asia, but they have only ever been found at these two cave sites.

“Unlike Neanderthals, whose skeleton remains are abundant in Europe, the Denisovans are considered as ‘enigmatic’ because there are very few physical remains of them,” Li tells Inverse.

Apart from their DNA structure, we don’t really know what Denisovans looked like — a factor that contributes to their ambiguous reputation, Li explains. Their DNA has enabled scientists to produce a rough sketch of what they looked like — illustrating a wide jaw and skull — but these artistic renderings are still just a prediction of morphology, not the real thing.

The scarcity of this ancient human's remains shows why the jaw finding is so important to understanding how they lived.

“I felt so lucky to work on this unique and important site,” Li says. “I was very excited when I first heard that Denisovan DNA was successfully extracted from the sediments in this cave, as this confirms the Denisovan mandible from the same cave reported in the last year.”

The Tibetan cave study — In the first study, scientists analyzed the sediments found in the dirt floor of the cave. It is a testament to the power of technology that we know what the sediment contains, Li says. The samples look ordinary, but using tools to extract DNA from the dirt reveals stone artifacts and animal remains laced through every layer.

The researchers detected DNA from animal species that have not lived in the region for nearly 10,000 years — creatures like extinct hyenas and rhinoceros — as well as the mitochondrial DNA of Denisovans. Taken together, the different components of the analysis suggest Denisovans lived in this cave as far back as 100,000 years ago, and possibly as recently as 45,000 years ago.

The finding confirms that these ancient humans were widely distributed in Asia. It also reveals a little about how this enigmatic people lived. If they lived over the course of millennia on the Tibetan Plateau, then they likely adapted to the high altitude environment.

Gene variants found in modern-day Tibetans are linked to high-altitude advantages, like the ability to metabolize oxygen more efficiently and protect against Vitamin D deficiency. In 2014, scientists suggested this high altitude adaptation was made possible because of inherited Denisovan DNA — an unusual haplotype is only found in Denisovans and in Tibetans, for example. These data lend further credibility to this theory.

The ancient inheritance study — In the second study, the genetic legacy of Denisovans is again front and center. In this case, the findings trace who carries that legacy, rather than the advantages it prompts.

The main focus of the analysis is a fragment of a skull found more than a decade ago by miners in eastern Mongolia.

Initially, scientists thought the skullcap belonged to a Neanderthal, or a member of Homo erectus. But this study indicates it actually belonged to a Homo sapien woman who lived around 34,000 years ago.

When lead author Diyendo Massilani, a researcher at the Max-Planck Institute for Evolutionary Anthropology, traveled to Mongolia to sample the specimen, he thought it was a Denisovan individual, he tells Inverse. There was "a little disappointment" when he realized she was a modern human, he says. But it didn't last. Instead, he found himself thinking about her life — and fantasizing about what had happened to her. Why had they only found her skull?

"It is always fascinating for me that archeology and ancient DNA are, somehow, able to give a second life to these individuals tens of thousands of years after they lived," he says.

When Massilani and his team compared the DNA extracted from the skullcap to DNA belonging to a 40,000-year-old Homo sapien individual found outside of Beijing, the study team discovered both were more related to present-day East Eurasians and Native Americans than to West Eurasians. They also both carried genomic segments of Denisovan ancestry.

Together, the two individuals “provide direct evidence that ancestors of modern humans who lived in East Asia 40,000 years ago had met and mixed with Denisovans," the researchers write.

This finding also indicates the modern human communities living in East Asia around this time “were already quite cosmopolitan," Massilani explains. Distinct groups of people were frequently migrating and interacting in this region — and sometimes these interactions resulted in children.

"There is a nice message of inclusion between prehistoric people behind this finding."

In turn, while the modern human skullcap found is quite old, the analysis suggests that this woman’s ancestors had already mixed with Denisovans. Exactly when that happened is unclear, but the study authors theorize it’s possible it happened 10,000 years before she lived.

"I really like the idea of finding evidence of admixture between the two 'populations' in Asia so far back, meaning that some of these prehistorical men migrated long distances over time and interacted willingly with different people they would meet along the way," Massilani says.

"There is a nice message of inclusion between prehistoric people behind this finding, and maybe coming myself from an admixed background, it resonates even bigger for me."

Interestingly, the Denisovan DNA segments in the ancient East Asian genomes observed here overlap more with Denisovan segments found in the genomes of living populations in Asians than they do with the Denisovan segments found in the genomes of living Papuans and Aboriginal Australians. (These groups carry about 20 times more Denisovan DNA than mainland Asians.)

Ultimately, this supports the idea that there were multiple “independent mixture events” between Denisovans and modern humans, Massilani says. A two-wave event of this kind has been hypothesized before, hinting two distinct Denisovan populations mated with humans at different times in our early history.

But the story gets more complicated. In the mix was another ancient human, known only as D2, jumbling things up even further in Oceania. D2 is not a Denisovan, but a similar being whose genetic legacy is also found in living people. As little as we know about Denisovans, we know far less about this ancient hominin. But both their stories both reflect themes of dispersal, survival, and disappearance.

For the Denisovans, their history is now a bit more illuminated. For other unnamed species, we’re still a long way from understanding how they fit into the human family tree.

Study 1, Abstract: A late Middle Pleistocene mandible from Baishiya Karst Cave (BKC) on the Tibetan Plateau has been inferred to be from a Denisovan, an Asian hominin related to Neanderthals, on the basis of an amino acid substitution in its collagen. Here we describe the stratigraphy, chronology, and mitochondrial DNA extracted from the sediments in BKC. We recover Denisovan mitochondrial DNA from sediments deposited ~100 thousand and ~60 thousand years ago (ka) and possibly as recently as ~45 ka. The long-term occupation of BKC by Denisovans suggests that they may have adapted to life at high altitudes and may have contributed such adaptations to modern humans on the Tibetan Plateau.

Study 2, Abstract: We present analyses of the genome of a ~34,000-year-old hominin skull cap discovered in the Salkhit Valley in northeastern Mongolia. We show that this individual was a female member of a modern human population that, following the split between East and West Eurasians, experienced substantial gene flow from West Eurasians. Both she and a 40,000-year-old individual from Tianyuan outside Beijing carried genomic segments of Denisovan ancestry. These segments derive from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians