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Press release: DNA study reveals evidence for the presence of Islander Denisovans in the Philippines

Updated: Aug 24, 2021

Photos by Ophelia Persson

The enigmatic group of extinct hominins known as Denisovans were previously shown to have interbred with the ancestors of modern humans. This left an indelible trace in the DNA of present-day populations, including the Papuan Highlanders who until recently possess the highest level of Denisovan ancestry in the world.

However, an international team of researchers reported anew on August 12 in Current Biology that a Philippine Negrito population, the Ayta Magbukon, now holds the record of possessing the highest level of Denisovan ancestry in the world — levels that are considerably greater than that of Australians and Papuans.

“We made this observation despite the fact that Philippine Negritos were recently admixed with East Asian-related groups—who carry little Denisovan ancestry, and which consequently diluted their levels of Denisovan ancestry,” said Maximilian Larena of Uppsala University, Sweden. “If we account for and mask away the East Asian-related ancestry in Philippine Negritos, their Denisovan ancestry can be up to 46 percent greater than that of Australians and Papuans.”

The remarkable observation is 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.

The researchers note that their findings unveil a likely complex intertwined history between modern and archaic humans in the Asia-Pacific region, where distinct resident Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time.

“This admixture led to variable levels of Denisovan ancestry in the genomes of Philippine Negritos and Papuans,” said Mattias Jakobsson of Uppsala University, Sweden. “In Island Southeast Asia, Philippine Negritos later admixed with East Asian migrants who possess little Denisovan ancestry, which subsequently diluted their archaic ancestry. Some groups, though, such as the Ayta Magbukon, minimally admixed with the more recent incoming migrants. For this reason, the Ayta Magbukon retained most of their inherited archaic tracts and were left with the highest level of Denisovan ancestry in the world.”

The pattern of historical admixture is supported by the genomic evidence observed in Philippine populations today, where Negrito ancestry is strongly correlated with Denisovan ancestry. Hence, the higher an individual’s Negrito ancestry, the higher is his or her Denisovan ancestry.

The authors further suggest that, together with the recent discovery of Homo luzonensis, there may have been multiple archaic species inhabiting the Philippines prior to the arrival of modern humans, and that these archaic groups may have been genetically related.

“The identification of a lineage of Homo in Luzon provides one possible fossil for Denisovans in this region,” says Phillip Endicott of Musee de l’Homme, Paris, France. “If not, it is necessary to have a minimum of two lineages co-existing in this region around 60,000 years ago. This means that these hominins were capable of multiple sea crossings to reach New Guinea and the Philippines. Previously, these journeys were explained away as accidental but it is becoming increasingly likely that these distant cousins of humans possessed many of the technical abilities once reserved for ourselves.”

Altogether the study brings Southeast Asia, especially the Philippines, at the forefront of research in human evolutionary history. “Knowing more about the populations underrepresented in most genetic studies, like the Philippine Negritos, appears to be an important key in advancing our understanding of our distant past,” says Larena.

The seminal study was made possible through the partnership between Uppsala University, led by Larena and Jakobsson, and the National Commission for Culture and the Arts of the Philippines (NCCA) through the office of then NCCA chairperson Felipe M. de Leon Jr., and aided by the involvement of indigenous cultural communities and various local institutions. In a recent publication in PNAS earlier this year, the same collaborative network shed light on the demographic history of the Philippines for the past 50,000 years, where it was shown that the Philippine Negritos are the first modern human inhabitants of the archipelago.

“Having been influenced by Austronesian-speaking peoples of East Asian descent for many centuries now, the Negritos have lost their original languages and now speak one or the other Austronesian language. Additionally, they unfortunately have often been relegated to the margins of society,” says Felipe M. de Leon Jr. “With these new genetic findings that the Philippine Negritos are the First Filipinos and have the highest level of Denisovan ancestry in the world, their profound importance in human history and advancing our understanding of who we are as a species will be highlighted. These can lift them out of relative obscurity in the eyes of the world and earn them the proper respect that they truly deserve.”


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