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Ethnic Group in the Philippines Have Highest Level of Denisovan DNA in the World

Ethnic Group in the Philippines Have Highest Level of Denisovan DNA in the World content piece image
Community fieldwork in Luzon Island, Philippines. Credit: Ophelia Persson
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A study analyzing the genomes of nearly 120 ethnic groups in the Philippines has identified that one population, the Ayta Magbukon, have the highest level of DNA derived from Denisovans, an extinct human subspecies, recorded to date.

Denisovans, unlike the better-studied Neanderthals, were only discovered by modern science around a decade ago, when mysterious remains found in a cave in Siberia turned out to be from the previously unidentified subspecies.

From Siberia to Southeast Asia

Since that finding, scientists have only found Denisovan DNA in one other location, the Baishiya Karst Cave site of the Tibetan Plateau. Computational analysis using the genome found in Siberia has enabled researchers to quantify the contribution of Denisovan DNA to the genomes of modern-day humans. Previous research had identified that Australasians have the highest level of Denisovan DNA relative to any other population.

But the Australasian population covers a vast area of Island Southeast Asia (ISEA), including the complex ethnic melting pot of the Philippines. Here, well over 100 distinct ethnic groups occupy 2,000 inhabited islands. In the new study, a team of Filipino and international researchers examined DNA from 1,107 individuals across 118 ethnic groups with 2.3 million different genetic point variations.

Who are the Philippine Negritos?

Philippine Negritos are thought to be the
earliest human population to have migrated to the Philippines. At least 30 self-identified Negrito groups speak different Malayo-Polynesian languages. The researchers noted that the 25 groups who were contacted in this study were spread across hunting and gathering, subsistence and urbanized lifestyles, with many of their languages regarded as severely endangered. 

The in-depth analysis highlighted that the Ayta Magbukon Negrito genome contains the highest proportion of Denisovan DNA. The Ayta Magbukon population, who the authors believe have not previously been investigated in any genomic study, occupy the Central Luzon province of Bataan. There was evidence that many of the Negrito populations had previously mixed with East Asian populations, who have much less genetic contribution from Denisovans in their genome. Using a genomic tool called masking, the researchers, including Uppsala University’s Maximilian Larena, were able to pinpoint the significant differences in genomic contribution. “If we account for and masked away the East Asian-related ancestry in Philippine Negritos, their Denisovan ancestry can be up to 46% greater than that of Australians and Papuans,” said Larena, in a press release.

A complex history

The findings were surprising to the team. Previous studies suggested that a relatively simple, one-off mixing event had occurred between Australasians and Denisovans, but these new findings imply multiple mixing events have occurred across different locations and timepoints. “In [ISEA], 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 authors explain in the publication. 

The new findings pair with the recent discovery of the remains of another previously unidentified extinct human species, Homo luzonensis, in Luzon, the Philippines’ largest island. Together, the authors suggest that there is a rich tapestry of ancient human interaction waiting to be discovered in ISEA. Piecing that picture together could reveal secrets of the entire human race. “By sequencing more genomes in the future, we will have better resolution in addressing multiple questions, including how the inherited archaic tracts influenced our biology and how it contributed to our adaptation as a species,” Larena concluded.


Larena M, McKenna J, Sanchez-Quinto F, et al. Philippine Ayta possess the highest level of Denisovan ancestry in the world. Current Biology. 2021;31:1-12. doi:10.1016/j.cub.2021.07.022