New clue to human evolution’s biggest mystery emerges in Philippines

The only definitive fossil evidence that points to the existence of Denisovans — an enigmatic group of early humans first identified in 2010 — comes from five bones from the Denisova cave in the foothills of Siberia’s Altai mountains.

The fragments are so tiny that they can all fit in the palm of one person’s hand.

Now, DNA from 3,000 miles (4,828 kilometers) away in the Philippines is shedding more light on human evolution’s biggest mystery.

New research published Thursday has found that a Philippine ethnic group known as the Ayta Magbukon has the highest known level of Denisovan ancestry in the world.

Denisovan DNA lives on in some humans today because, once our Homo sapien ancestors encountered the Denisovans, they had sex with them and gave birth to babies — something geneticists call admixture. By analyzing current-day genetic data, we can look back into human history.

The “admixing” happened more than 50,000 years ago, as modern humans moved out of Africa and likely crossed paths with both Neanderthals and Denisovans. But pinning down exactly where it happened has proven difficult — particularly in the case of Denisovans.

It’s especially puzzling that the only Denisovan fossils were found in Siberia (with the potential exception of a jaw bone on the Tibetan plateau). Genetic evidence has tied the archaic humans most closely to places much farther south.

“The fact that Ayta Magbukon have the highest amount of Denisovan ancestry of anywhere in the world is unexpected, and I am intrigued, as previous studies did not report such high amounts in other Philippines populations,” said João Teixeira, a visiting fellow at the Australian Centre for Ancient DNA at The University of Adelaide. He was not involved in the study.

Researchers from the Philippines and Sweden stumbled on the new findings as part of a wider study on human history in the Philippines that involved studying the genetic makeup of 118 different groups in the country. The study was published in the journal Current Biology on Thursday.

The study found that the Ayta Magbukon had around 5% Denisovan ancestry, more than Aboriginal Australians and Papuans, whom previous research found to have around 4%, said Mattias Jakobsson, a geneticist at Uppsala University in Sweden and an author of the study.

Denisovan ancestory is also present in many East Asian people — although at a much lower level, other studies have found.

Ayta Magbukon belong to a wider group of people in the Philippines that identify as Negritos, Jakobsson said.

The findings are further evidence that Denisovans once lived all throughout Asia and were likely living in the Philippines long before any Homo sapiens arrived, the authors said. It also suggests that different Denisovan populations mixed and intermingled with Homo sapiens in multiple locations and various points in time.

“If the results are accurate, then human colonizations of the Philippines and surrounding regions were even more complex than we thought up to now,” said Chris Stringer, a professor and research leader in Human Origins at The Natural History Museum in London. He was not involved in research.

It also appears that our ancestors may have interacted more widely with Denisovans than Neanderthals — a much more deeply studied early human who lived in Europe and some parts of Asia until about 40,000 years ago, Stringer said.

“Relatively small groups of early modern humans interbred with Neanderthals in western Eurasia and then spread across Eurasia and beyond, passing on that level of acquired Neanderthal DNA to descendant populations,” he said.

“In the case of the Denisovans, it looks like they were genetically much more diverse, and they intermixed separately in different locations with differentiating early modern populations, hence the more varied patterns we see today.”

Why so few Denisovan fossils?

Denisovan DNA, along with Neanderthal DNA, was sequenced completely for the first time in 2010, which led to the initial discovery that they were interbreeding with our Homo sapien ancestors.

DNA sequenced from the few fossilized bones found in the Siberian cave they were named after has allowed us to learn more about the Denisovans. But we still don’t know what these extinct hominins looked like.

It’s not clear why we have so few fossilized remains of Denisovans, but several factors could be at play. Unlike Europe, southeast Asia isn’t a region that’s been well studied by archaeologists. Also, some locations in the region that might harbor a rich fossil record are now submerged under the sea.

Tantalizingly, the fossils could also be hiding in plain sight — in museum or university collections — but misidentified because we know so little about Denisovan morphology. There are remains in China, Taiwan and other places that could be Denisovan, but it has not yet been possible to extract any DNA, which does not preserve well in tropical heat, from those fossils.

“What if we have been looking at them all along and calling them something else? The recognized fossil evidence for Denisovans includes fossils for which DNA or proteins have confirmed it to be the case. But how can we tell for sure what a Denisovan is supposed to look like?” Teixeira said.

This finding — along with the recent discoveries of new types of archaic humans in the Philippines and Indonesia — suggest that Southeast Asia may play a key role in untangling the human story.

“Island Southeast Asia is still relatively underrepresented. However this may change in the future given the increased interest in the region. Our study, together with the recent discoveries on Homo luzonensis and Homo floresiensis, brings Island Southeast Asia at the forefront of research in human evolutionary history,” said Maximilian Larena, study author and researcher at Uppsala University.

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