Scientists Have Discovered a Hotspot of Denisovan Ancestors

Scientists Have Discovered a Hotspot of Denisovan Ancestors
Replica of the lone Denisovan finger bone, the only source of Denisovan DNA to date. (Image: Thilo Parg/Wikimedia)

A demographic study shows that the Ayta Magbukun — a Philippine ethnic group — has the highest known level of Denisovan ancestry in the world. The finding shows that the history of archaic and modern humans living on the islands of southeast Asia during the Pleistocene is more complex than we imagined.

New research published in Current Biology shows that the Ayta Magbukun have retained around 5% of their Denisovan ancestry, which is around 30% to 40% higher than rates found in indigenous Papuans — an ethnic group previously known to possess high rates of Denisovan DNA. Most mainland Asian individuals, by contrast, have less than 0.05% Denisovan ancestry, while individuals of European and African descent have none.

That the Ayta Magbukun — a Philippine Negrito ethnic group — has retained so much Denisovan DNA is nothing short of astounding (Negritos comprise several diverse ethnic groups from southeast Asia and the Andaman Islands). The Ayta Magbukun have largely kept to themselves over the millennia, but the new finding suggests the occurrence of a distinct interbreeding event, or events, in the Philippines, as modern humans flowed into a region occupied by Denisovans.

Not much is known about the Denisovans, but what is known comes from a finger bone and some teeth pulled from a Siberian cave in 2010 (dated to 80,000 years ago) and a mandible recently discovered on the Tibetan Plateau (dated to 160,000 years ago). Scientists were able to extract DNA from the finger bone, revealing a close relation to Neanderthals and even hinting at certain physical characteristics. Importantly, and perhaps incredibly, no Denisovan fossil has been found elsewhere — including in the Philippines.

Community fieldwork in Luzon Island, Philippines.  (Image: Ophelia Persson)Community fieldwork in Luzon Island, Philippines. (Image: Ophelia Persson)

Denisovans branched off from Neanderthals some 390,000 to 440,000 years ago and possibly as recently as 200,000 years ago. Modern humans share a common ancestor with both groups, but that divergence dates back some 800,000 years. That said, all three groups belong to the Homo genus, meaning they’re all humans. Importantly, Neanderthals and Denisovans interbred with modern humans, and we can see evidence of this in our DNA. All living humans have some Neanderthal ancestry to varying degrees, including individuals of African descent, but only Pacific Islander populations and southeast Asians have Denisovan ancestry. Denisovans went extinct around 50,000 years ago, but the lack of fossil evidence means we cannot be sure. Neanderthals exited the scene around 40,000 years ago.

Going into the new study, scientists already knew that Papuan Highlanders had high levels of Denisovan ancestry, but the new results came as a shock, even to the researchers.

“The most surprising finding is the very high levels of Denisovan ancestry among Philippine Negritos, especially the Ayta Magbukon,” Maximilian Larena, population geneticist from Uppsala University, Sweden, explained in an email. “This led us to speculate that there may have been resident Denisovans within the Philippines.”

The Ayta Magbukon, according to the National Commission on Indigenous Peoples, have occupied the Bataan Peninsula of the Philippines “since time immemorial owing to the origin of its name which means ‘to separate’ from the rest of the Ayta language groups.”

The new study was an effort to document the demographic history of the Philippines — a big job requiring contributions from Uppsala University, the National Commission for Culture and the Arts of the Philippines, indigenous communities, local universities and governments, among other groups and institutions. The first phase of this project was published earlier this year, in which the team reported at least five major migrations of modern humans into the Philippines.

Community assembly with a Negrito ethnic group in Luzon Island, Philippines. (Image: Ophelia Persson)Community assembly with a Negrito ethnic group in Luzon Island, Philippines. (Image: Ophelia Persson)

“As a follow up study, we intended to look at the distant past by assessing the levels of archaic ancestry among the populations, especially that some populations in these region were previously shown to have elevated levels of Denisovan ancestry and that Island Southeast Asia is known to be inhabited by various archaic species of Homo,” wrote Larena.

The analysis included 2.3 million genotypes belonging to 118 ethnic groups of the Philippines, including 25 self-identified Negrito populations. The researchers found that, the higher the Negrito ancestry in an individual, the higher their Denisovan ancestry.

As the study points out, Negritos recently mixed with groups closely related to east Asians. Larena and his colleagues accounted for this, and, when excluding this recent influx of DNA, the researchers found that the Denisovan ancestry among Negritos is upwards of 46% greater than rates seen in native Australians and Papuans. And among the Ayta Magbukun, it’s even higher.

These findings “are consistent with a model of an independent interbreeding event between Negritos and Denisovans within the Philippines, suggesting that Denisovans may have been in the islands long before the presence of any modern human ethnic group,” Larena said. These interbreeding events happened at multiple locations and at various points in time, leading to “variable levels of Denisovan ancestry in the genomes of Philippine Negritos and Papuans,” as Mattias Jakobsson, a study co-author and researcher at Uppsala University, said in a press release. Accordingly, “our findings unveil a [more] complex intertwined history between modern and archaic humans in the Asia-Pacific region than previously appreciated,” Larena explained in his email.

The picture gets even more complicated considering that other archaic humans existed in this part of the world during the Pleistocene, including Homo erectus and the recently discovered diminutive human, Homo luzonensis. More evidence is needed to know if these groups interbred with modern humans and their potential relation to Denisovans.

“This is a fascinating piece of work that really rounds out the existing knowledge about Denisovan introgression [the transfer of genetic information] into modern human populations,” Sharon Browning, a professor of biostatistics from the University of Washington who wasn’t involved in the study, said in an email.

The conclusion that an additional interbreeding event occurred between Denisovans and the ancestors of Negritos “seems hard to dispute,” she added. Populations of Denisovans were spread out among the islands of southeast Asia, as the new research suggests, yet existing fossils from this region have failed to yield DNA or proteins for analysis, according to Browning. That said, “it is tempting to suppose that some of these fossils may be derived from Denisovan populations,” she said.

Browning said that future work could include even more genetic sequencing of Negrito individuals, as this would “provide higher resolution to detect the level of divergence between the Denisovan populations that contributed to their ancestry.” And of course, the discovery of Denisovan fossils in the region would likewise be helpful.

Indeed, the evidence is continuing to mount that Denisovans most certainly occupied the islands of southeast Asia. But man, it would be so nice to finally find some actual Denisovan fossils in the Philippines, and elsewhere in the region. So the big question: Where the heck are they?

More: Researchers may have found the true identity of ancient ‘Hobbit’ species.