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Larena M, McKenna J, Sanchez-Quinto F, Bernhardsson C, Ebeo C, Reyes R, Casel O, Huang JY, Hagada KP, Guilay D, Reyes J, Allian FP, Mori V, Azarcon LS, Manera A, Terando C, Jamero L, Sireg G, Manginsay-Tremedal R, Labos MS, Vilar RD, Latiph A, Saway RL, Marte E, Magbanua P, Morales A, Java I, Reveche R, Barrios B, Burton E, Salon JC, Kels MJT, Albano A, Cruz-Angeles RB, Molanida E, Granehäll L, Vicente M, Edlund H, Loo JH, Trejaut J, Ho SYW, Reid L, Lambeck K, Malmström H, Schlebusch C, Endicott P, Jakobsson M. Philippine Ayta possess the highest level of Denisovan ancestry in the world. Curr Biol 2021; 31:4219-4230.e10. [PMID: 34388371 PMCID: PMC8596304 DOI: 10.1016/j.cub.2021.07.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/04/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022]
Abstract
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.
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Affiliation(s)
- Maximilian Larena
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden.
| | - James McKenna
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Federico Sanchez-Quinto
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico
| | - Carolina Bernhardsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Carlo Ebeo
- National Committee on Cultural Education, National Commission for Culture and the Arts, Intramuros, Manila, Philippines; National Museum of the Philippines, Padre Burgos Avenue, Rizal Park, Ermita, Manila, Philippines
| | - Rebecca Reyes
- Ayta Magbukon Cultural Bearer, Ayta Magbukon Indigenous Cultural Community, Abucay, Bataan, Philippines; National Commission on Indigenous Peoples, Philippines
| | - Ophelia Casel
- Mindanao Doctors Hospital and Cancer Center, Kabacan, Cotabato, Philippines
| | - Jin-Yuan Huang
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City 10449, Taiwan
| | - Kim Pullupul Hagada
- National Commission on Indigenous Peoples, Philippines; Young Indigenous Peoples Empowered to Act in Community Engagement, Diffun, Quirino
| | - Dennis Guilay
- Balangao Indigenous Cultural Community, Paracelis, Mountain Province, Cordillera Administrative Region, Philippines
| | - Jennelyn Reyes
- Department of Education - Bataan Division, Bataan, Philippines
| | - Fatima Pir Allian
- Nisa Ul Haqq fi Bangsamoro, Zamboanga City, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines; Tarbilang Foundation, Inc., Bongao, Tawi-Tawi, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines
| | - Virgilio Mori
- Tarbilang Foundation, Inc., Bongao, Tawi-Tawi, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines
| | - Lahaina Sue Azarcon
- Center for Language and Culture, Quirino State University, Barangay Andres Bonifacio, Diffun, Quirino, Philippines
| | - Alma Manera
- Center for Language and Culture, Cagayan State University - Andrews Campus, Caritan Highway, Tuguegarao, Cagayan, Philippines
| | - Celito Terando
- Tagakaulo Indigenous Cultural Community, Malungon, Sarangani, Philippines; Sulong Tribu Program, Provincial Government of Sarangani, Glan, Sarangani, Philippines
| | - Lucio Jamero
- Ayta Magbukon Cultural Bearer, Ayta Magbukon Indigenous Cultural Community, Abucay, Bataan, Philippines
| | - Gauden Sireg
- Subanen Indigenous Cultural Community, Lakewood, Zamboanga del Sur, Philippines; Dumendingan Arts Guild Inc., Pagadian City, Zamboanga del Sur, Philippines
| | | | - Maria Shiela Labos
- Ateneo Institute of Anthropology, Ateneo de Davao University, Roxas Avenue, 8016 Davao City, Philippines; Museo Dabawenyo, Andres Bonifacio Rotunda, Poblacion District, Davao City, Philippines
| | - Richard Dian Vilar
- Cultural Outreach Program, Kaliwat Performing Artists Collective, Gumamela St., Lanang, Davao City, Philippines; Culture, Heritage, and Arts Office, Local Government Unit of Butuan, Butuan City, Philippines
| | - Acram Latiph
- Institute for Peace and Development in Mindanao, Mindanao State University - Marawi Campus, Marawi City, Lanao del Sur, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines
| | | | - Erwin Marte
- Legal Affairs Office, Indigenous People's Mandatory Representative - Sangguniang Panlalawigan, Bukidnon, Northern Mindanao, Philippines
| | - Pablito Magbanua
- National Commission on Indigenous Peoples, Philippines; Cuyonon Indigenous Cultural Community, Cuyo Island, Palawan, Philippines
| | - Amor Morales
- Surigaonon Heritage Center, Surigao City, Surigao del Norte, Philippines
| | - Ismael Java
- Kabankalan City Cultural and Tourism Foundation, Inc., Kabankalan City, Negros Occidental, Philippines; Cultural Research and Documentation, Negros Museum, Gatuslao St., Bacolod, Negros Occidental, Philippines
| | - Rudy Reveche
- Cultural Research and Documentation, Negros Museum, Gatuslao St., Bacolod, Negros Occidental, Philippines; Culture and Arts Program, Colegio San Agustin, BS Aquino Drive, Bacolod, Negros Occidental, Philippines
| | - Becky Barrios
- Panaghiusa Alang Sa Kaugalingnan Ug Kalingkawasan, Inc., Bunawan, Agusan del Sur, Philippines; Agusan Manobo Indigenous Cultural Community, La Paz, Agusan del Sur, Philippines
| | - Erlinda Burton
- Museo de Oro, Xavier University - Ateneo de Cagayan, Corrales Avenue, Cagayan de Oro City, Philippines
| | - Jesus Christopher Salon
- Museo de Oro, Xavier University - Ateneo de Cagayan, Corrales Avenue, Cagayan de Oro City, Philippines; City Museum of Cagayan de Oro, Fernandez St., Cagayan de Oro City, Philippines
| | - Ma Junaliah Tuazon Kels
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Adrian Albano
- Kalanguya Indigenous Cultural Community, Tinoc, Ifugao, Cordillera Administrative Region, Philippines; Office of Tinoc Campus Administrator, Ifugao State University, Tinoc, Ifugao, Cordillera Administrative Region, Philippines
| | | | - Edison Molanida
- Heritage Office, National Commission for Culture and the Arts, Intramuros, Manila, Philippines; Office of the Executive Director, National Commission for Culture and the Arts, Intramuros, Manila, Philippines
| | - Lena Granehäll
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Mário Vicente
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Hanna Edlund
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Jun-Hun Loo
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City 10449, Taiwan
| | - Jean Trejaut
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City 10449, Taiwan
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Lawrence Reid
- Department of Linguistics, University of Hawai'i at Mānoa, Mānoa, HI, USA; National Museum of the Philippines, Padre Burgos Avenue, Rizal Park, Ermita, Manila, Philippines
| | - Kurt Lambeck
- Research School of Earth Sciences, The Australian National University, Canberra, ACT 0200, Australia
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Palaeo-Research Institute, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Palaeo-Research Institute, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa; SciLifeLab, Stockholm and Uppsala, Sweden
| | - Phillip Endicott
- Department Hommes Natures Societies, Musée de l'Homme, 75016 Paris, Ile de France, France
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Palaeo-Research Institute, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa; SciLifeLab, Stockholm and Uppsala, Sweden.
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