New research led by Uppsala University scientists suggests that there were multiple archaic human species that inhabited the Philippines prior to the arrival of anatomically modern Homo sapiens and that these archaic groups may have been genetically related.
Since their exit out of Africa, anatomically modern humans have overlapped and interbred with archaic hominins across time and space.
Interactions with Neanderthals, Denisovans, and possibly other archaic hominins, have left an indelible genetic trace in the genomes of present-day populations.
All Eurasians possess uniform levels of Neanderthal ancestry, whereas Australasians uniquely have elevated levels of Denisovan ancestry relative to any other population.
Some present-day populations of the Philippines, who self-identify as ‘Negritos’ and who are genetically related to Australopapuans, display significant levels of Denisovan ancestry.
In the new study, Dr. Maximilian Larena, a researcher in the Department of Organismal Biology at Uppsala University, and his colleagues aimed to establish the demographic history of the Philippines.
They comprehensively investigated the archaic ancestry of 1,107 individuals from 118 distinct ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos.
The results show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world, consistent with an independent admixture event into Negritos from Denisovans.
“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,” Dr. Larena said.
“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.”
Together with the recent discovery of Homo luzonensis, the data suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans.
“The admixture led to variable levels of Denisovan ancestry in the genomes of Philippine Negritos and Papuans,” said Dr. Mattias Jakobsson, a researcher in the Department of Organismal Biology at Uppsala University and the Palaeo-Research Institute at the University of Johannesburg.
“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 findings were published in the journal Current Biology.
Maximilian Larena et al. Philippine Ayta possess the highest level of Denisovan ancestry in the world. Current Biology, published online August 12, 2021; doi: 10.1016/j.cub.2021.07.022