Philippine Ayta possess the highest level of Denisovan ancestry in the world

Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified Negrito populations, along with high-coverage genomes of Australopapuans and Ayta Magbukon Negritos. We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world—∼30%–40% greater than that of Australians and Papuans—consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time. •Comprehensive analyses of archaic ancestry among 118 Philippine ethnic groups•Ayta Magbukon display ∼30%–40% greater Denisovan ancestry than Australopapuans•The model is explained by a distinct admixture event into Negritos from Denisovans•Prior to modern humans, Islander Denisovans may have been present in the Philippines Larena et al. reveal Philippine Ayta to possess the highest level of Denisovan ancestry in the world—∼30%–40% greater than that of Australopapuans—consistent with an independent admixture event into Negritos from Denisovans. The Philippine archipelago is thus likely inhabited by multiple archaic groups prior to the arrival of modern humans.