Indigenous Filipino Group Has Highest Known Denisovan Ancestry

Researchers found the relatively high proportion of DNA from a hominin cousin—nearly 5 percent—when they scanned more than 1,000 genomes from 118 distinct ethnic groups.

by Annie Melchor, The Scientist

Until recently, scientists thought the modern humans with the highest proportion of Denisovan ancestry lived in Papua New Guinea and Australia. According to a new study published yesterday (August 12) in Current Biology, however, an Indigenous group in the Philippines called the Ayta Magbukon have 30 to 40 percent more Denisovan DNA than these other frontrunners, for a total of nearly 5 percent of their genomes.

Denisovans were a group of archaic humans first identified from a single pinkie bone in a Siberian cave. They coexisted with modern humans and other archaic human species, such as Neanderthals, for hundreds of thousands of years, until they went extinct an estimated 30,000 to 50,000 years ago. According to Gizmodo, only Pacific Islanders and Southeast Asians have substantial Denisovan ancestry. By comparison, most people in other parts of mainland Asia have less than 0.05 percent Denisovan ancestry, and people of African and European descent don’t have any.

“[The Ayta Magbukon] possess more Denisovan ancestry than anybody else on the planet today,” Uppsala University biologist and study coauthor Mattias Jakobsson tells Inverse. “So that was a surprise to us.”

According to Gizmodo, the researchers were originally interested in studying the human history of the Philippines as part of a massive collaborative effort with Indigenous communities, local governments, the National Commission for Culture and the Arts of the Philippines, and researchers at Uppsala University.

As a follow-up study to an earlier one studying human migrations to the Philippines, “we intended to look at the distant past by assessing the levels of archaic ancestry among the populations, especially that some populations in these regions 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,” population geneticist and study coauthor Maximilian Larena tells Gizmodo. 

To do this, the researchers analyzed the genomes of 1,107 individuals belonging to 118 distinct ethnic groups in the Philippines—including 25 groups self-identifying as “Negritos,” who are regarded as the earliest modern human inhabitants of the Philippines, according to the study’s authors. By comparing these genomes to Denisovan and Neanderthal genomes, they found that while the degree of Neanderthal ancestry was fairly uniform in their study population (and comparable to modern humans in other parts of the world), the degree of Denisovan ancestry was highly variable, and substantially higher among Negritos than in other groups.

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 tells Gizmodo. 

University of Tübingen paleogeneticist Cosimo Posth, who was not involved in the study, tells Science News the new report suggests that “still today there are populations that have not been fully genetically described and that Denisovans were geographically widespread.”

Currently, the Denisovan fossil record is sparse, and according to Science News, Denisovan fossils can’t be identified by morphology alone. They have to be genetically sequenced, which can be difficult when extracting fossils from tropical climates where the ancient DNA degrades more quickly. 

The findings “further increase my suspicions that Denisovan fossils are hiding in plain sight,” among previously excavated discoveries on Southeast Asian islands, University of Adelaide population geneticist João Teixeira tells Science News. Teixeira was not involved with the current study. 

“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,” University of Colorado Boulder population geneticist Fernando Villanea tells Inverse. Villanea, who was not involved with the study, adds, “Now we have these incredible genetic findings and we’re having a hard time putting together a cohesive story.”

“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 says in the press release.