DNA study reveals fresh ties between humans and an enigmatic ancient people

Denisovans are an elusive, ancient population. They may not have the same name recognition as Neanderthals, but knowing their history is tantamount to understanding where we come from, too.

For years, the sole evidence we had of Denisovans was a single pinkie bone. Today, we have a few more remains to go on and new genetic tools to tease their fingerprint out from our own DNA. Now, a new study shows we still know so little about how they lived and died — but it also offers us some clues.

Previously, scientists thought Aboriginal Australians and people from Papua New Guinea had the greatest proportion of Denisovan DNA — just as Europeans have the greatest degree of Neanderthal DNA. But now anthropologists have just discovered that a group of people has some 30 to 40 percent more Denisovan ancestry than do Papuans and Aboriginal Australians.

The study, published Thursday in the journal Current Biology, shows that members of the Philippine ethnic group Ayta Magbukon have the highest level of Denisovan DNA of any living group on Earth.

Who are the Denisovans?

The Denisovans are an archaic, enigmatic group of hominins who lived in Asia for thousands of years — until they died out around 40,000 years ago. We know from older studies that these ancient people produced children with Neanderthals and that they are distantly related to Neanderthals themselves. We also know that they interbred with Homo sapiens, aka modern humans.

The name Denisovan stems from Siberia’s Denisova Cave, which is where paleoanthropologists discovered the pinkie bone of a Denisovan girl dating back to 50,000 years ago. From that bone, they managed to sequence the child’s genome and published it in 2010. Then, in 2019 researchers published fresh findings based on a Denisovan mandible found in Tibet — the first such fossil found outside of Siberia. Together, these fragments added to the mystery of who these people were and where they dwelled — and how they relate to us today.

The discovery — That’s what makes this new paper so exciting — in it, researchers show evidence that the Ayta Magbukon, an ethnolinguistic group in the Philippines, has the highest levels of Denisovan ancestry.

“They possess more Denisovan ancestry than anybody else on the planet today,” Mattias Jakobsson, a biologist at Uppsala University in Sweden and co-author on the study, tells Inverse. “So that was a surprise to us.”

What makes this discovery so shocking is that, since 2010 when the first Denisovan genome came to light, the prevailing theory had been that indigenous people from Papua New Guinea and Aboriginal Australians possessed the most Denisovan ancestry. Some 4 percent of their genome contained Denisovan DNA, but now we know that the Ayta Magbukon have about 5 percent Denisovan DNA in their genome.

From this, we gain a little more insight on how Denisovans in Southeast Asia mixed with modern humans — but just a little.

“When it comes to Southeast Asia and the Southeast Asian Islands, we have more questions than answers as we don’t have a good archaeological record,” Fernando Villanea says. Villanea is a population geneticist at the University of Colorado, Boulder, whose work focuses on ancient human ancestry. He was not involved in this study.

“Now we have these incredible genetic findings and we’re having a hard time putting together a cohesive story,” he adds.

How they did it — Jakobsson and his team actually fell upon their groundbreaking finding while working on a totally different study altogether — one that focused on the human history of the Philippines.

“We kind of stumbled upon this result,” Jakobsson tells Inverse.

For the other study, Jakobsson and his team had focused on the Philippines’ myriad ethnic populations — they examined some 2.3 million genotypes from 1,028 individuals who together represent 115 indigenous Filipino groups.

The Ayta Magbukon people are a subgroup within a larger ethnic population known as Negritos, a name originally coined by Spanish colonizers to refer to indigenous Southeast Asian islanders.

When Jakobsson and his team saw the Denisovan signal in their original investigation, they decided to dig deeper. In the new study, they take a concentrated look at 25 distinct Negrito groups, which, according to Jakobsson, is a much more comprehensive analysis of this particular population than can be found in older research.

“That’s why nobody has seen this result in the past,” Jakobsson says, “because there hasn’t really been a study of so many different Negrito groups.”

Why it matters — Our knowledge of how Denisovans arrived at the Southeast Asian islands — a chapter of humanity’s migration from Africa — is limited, to say the least. We also don’t know when, how often, or why they may have mixed with the Homo sapiens also living there. But this finding does add another piece to the puzzle of where Denisovans once lived.

“It becomes very likely that Denisovans were in Island Southeast Asia,” says Jakobsson.

“Because we have one unique group that mixed with them, it seems more likely that they actually came onto the islands when the sea levels were much lower,” he speculates.

For his part, Villanea wonders if “Denisovans” might at this point be a catchall term for a number of different hominin groups that once migrated to these islands. Once they arrived, they assimilated together and helped to create the fabric of the tapestry that is the modern gene pool of people indigenous to the Philippines today.

What’s next — For Jakobsson, a new line of inquiry is how Denisovan gene variants may have helped the Ayta Magbukon adapt to their surroundings. For example, certain genes that have come from ancient human species and are now found in people from Tibet appear to have helped them adapt to high altitudes.

Do people of the Ayta Magbukon have similar genetic adaptations as a result of their ancient ancestry? Only further research can tell.

“Is it random across the entire genome? Or is it specific genes or gene variants?” he asks.

Yet as important as what the next steps for the research may be is also who takes those steps. Villanea says the Filipino community should be involved in conducting this research, as it involves them directly.

“I think it’s time for them organize with researchers so that they maintain some control over defining their very unique genetic ancestry,” he says.

Anthropology at large is tasked with the broader quest of refining the term Denisovan as well.

“I think what we have been calling Denisovans has been overly simplistic, and maybe it’s time to revise that,” says Villanea. “It may be that we now need to invoke different species, or maybe even just more complex demographic scenarios.”

Abstract: Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ~2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world—~30%–40% greater than that of Australians and Papuans—consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.