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.

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

Maximilian Larena, James McKenna, Federico Sanchez-Quinto, Carolina Bernhardsson, Carlo Ebeo, Rebecca Reyes, Ophelia Casel, Jin-Yuan Huang, Kim Pullupul Hagada, Dennis Guilay, Jennelyn Reyes, Fatima Pir Allian, Virgilio Mori, Lahaina Sue Azarcon, Alma Manera, Celito Terando, Lucio Jamero Jr., Gauden Sireg, Renefe Manginsay-Tremedal, Maria Shiela Labos, Richard Dian Vilar, Acram Latiph, Rodelio Linsahay Saway, Erwin Marte, Pablito Magbanua, Amor Morales, Ismael Java, Rudy Reveche, Becky Barrios, Erlinda Burton, Jesus Christopher Salon, Ma. Junaliah Tuazon Kels, Adrian Albano, Rose Beatrix Cruz-Angeles, Edison Molanida, Lena Granehäll, Mário Vicente, Hanna Edlund, Jun-HunLoo, Jean Trejaut, Simon Y.W.Ho, Lawrence Reid, Kurt Lambeck, Helena Malmström, Carina Schlebusch, Phillip Endicott, Mattias Jakobsson

DOI: 10.1016/j.cub.2021.07.022