.2021 Oct 11;31(19):4219-4230.e10.

doi: 10.1016/j.cub.2021.07.022. Epub 2021 Aug 12.

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

Maximilian Larena¹, James McKenna², Federico Sanchez-Quinto³, Carolina Bernhardsson², Carlo Ebeo⁴, Rebecca Reyes⁵, Ophelia Casel⁶, Jin-Yuan Huang⁷, Kim Pullupul Hagada⁸, Dennis Guilay⁹, Jennelyn Reyes¹⁰, Fatima Pir Allian¹¹, Virgilio Mori¹², Lahaina Sue Azarcon¹³, Alma Manera¹⁴, Celito Terando¹⁵, Lucio Jamero Jr¹⁶, Gauden Sireg¹⁷, Renefe Manginsay-Tremedal¹⁸, Maria Shiela Labos¹⁹, Richard Dian Vilar²⁰, Acram Latiph²¹, Rodelio Linsahay Saway²², Erwin Marte²³, Pablito Magbanua²⁴, Amor Morales²⁵, Ismael Java²⁶, Rudy Reveche²⁷, Becky Barrios²⁸, Erlinda Burton²⁹, Jesus Christopher Salon³⁰, Ma Junaliah Tuazon Kels², Adrian Albano³¹, Rose Beatrix Cruz-Angeles³², Edison Molanida³³, Lena Granehäll², Mário Vicente², Hanna Edlund², Jun-Hun Loo⁷, Jean Trejaut⁷, Simon Y W Ho³⁴, Lawrence Reid³⁵, Kurt Lambeck³⁶, Helena Malmström³⁷, Carina Schlebusch³⁸, Phillip Endicott³⁹, Mattias Jakobsson⁴⁰

Affiliations

¹ Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden. Electronic address: maximilian.larena@ebc.uu.se.
² Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden.
³ Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico.
⁴ 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.
⁵ Ayta Magbukon Cultural Bearer, Ayta Magbukon Indigenous Cultural Community, Abucay, Bataan, Philippines; National Commission on Indigenous Peoples, Philippines.
⁶ Mindanao Doctors Hospital and Cancer Center, Kabacan, Cotabato, Philippines.
⁷ Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City 10449, Taiwan.
⁸ National Commission on Indigenous Peoples, Philippines; Young Indigenous Peoples Empowered to Act in Community Engagement, Diffun, Quirino.
⁹ Balangao Indigenous Cultural Community, Paracelis, Mountain Province, Cordillera Administrative Region, Philippines.
¹⁰ Department of Education - Bataan Division, Bataan, Philippines.
¹¹ 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.
¹² Tarbilang Foundation, Inc., Bongao, Tawi-Tawi, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines.
¹³ Center for Language and Culture, Quirino State University, Barangay Andres Bonifacio, Diffun, Quirino, Philippines.
¹⁴ Center for Language and Culture, Cagayan State University - Andrews Campus, Caritan Highway, Tuguegarao, Cagayan, Philippines.
¹⁵ Tagakaulo Indigenous Cultural Community, Malungon, Sarangani, Philippines; Sulong Tribu Program, Provincial Government of Sarangani, Glan, Sarangani, Philippines.
¹⁶ Ayta Magbukon Cultural Bearer, Ayta Magbukon Indigenous Cultural Community, Abucay, Bataan, Philippines.
¹⁷ Subanen Indigenous Cultural Community, Lakewood, Zamboanga del Sur, Philippines; Dumendingan Arts Guild Inc., Pagadian City, Zamboanga del Sur, Philippines.
¹⁸ Dumendingan Arts Guild Inc., Pagadian City, Zamboanga del Sur, Philippines.
¹⁹ Ateneo Institute of Anthropology, Ateneo de Davao University, Roxas Avenue, 8016 Davao City, Philippines; Museo Dabawenyo, Andres Bonifacio Rotunda, Poblacion District, Davao City, Philippines.
²⁰ 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.
²¹ Institute for Peace and Development in Mindanao, Mindanao State University - Marawi Campus, Marawi City, Lanao del Sur, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines.
²² Talaandig Indigenous Cultural Community, Lantapan, Bukidnon, Philippines.
²³ Legal Affairs Office, Indigenous People's Mandatory Representative - Sangguniang Panlalawigan, Bukidnon, Northern Mindanao, Philippines.
²⁴ National Commission on Indigenous Peoples, Philippines; Cuyonon Indigenous Cultural Community, Cuyo Island, Palawan, Philippines.
²⁵ Surigaonon Heritage Center, Surigao City, Surigao del Norte, Philippines.
²⁶ Kabankalan City Cultural and Tourism Foundation, Inc., Kabankalan City, Negros Occidental, Philippines; Cultural Research and Documentation, Negros Museum, Gatuslao St., Bacolod, Negros Occidental, Philippines.
²⁷ 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.
²⁸ Panaghiusa Alang Sa Kaugalingnan Ug Kalingkawasan, Inc., Bunawan, Agusan del Sur, Philippines; Agusan Manobo Indigenous Cultural Community, La Paz, Agusan del Sur, Philippines.
²⁹ Museo de Oro, Xavier University - Ateneo de Cagayan, Corrales Avenue, Cagayan de Oro City, Philippines.
³⁰ 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.
³¹ Kalanguya Indigenous Cultural Community, Tinoc, Ifugao, Cordillera Administrative Region, Philippines; Office of Tinoc Campus Administrator, Ifugao State University, Tinoc, Ifugao, Cordillera Administrative Region, Philippines.
³² Heritage Office, National Commission for Culture and the Arts, Intramuros, Manila, Philippines.
³³ 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.
³⁴ School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.
³⁵ 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.
³⁶ Research School of Earth Sciences, The Australian National University, Canberra, ACT 0200, Australia.
³⁷ 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.
³⁸ 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.
³⁹ Department Hommes Natures Societies, Musée de l'Homme, 75016 Paris, Ile de France, France.
⁴⁰ 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. Electronic address: mattias.jakobsson@ebc.uu.se.

PMID:34388371
PMCID: PMC8596304
DOI: 10.1016/j.cub.2021.07.022

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

Maximilian Larena et al. Curr Biol.2021.

.2021 Oct 11;31(19):4219-4230.e10.

doi: 10.1016/j.cub.2021.07.022. Epub 2021 Aug 12.

Authors

Affiliations

¹ Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden. Electronic address: maximilian.larena@ebc.uu.se.
² Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden.
³ Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden; Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico.
⁴ 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.
⁵ Ayta Magbukon Cultural Bearer, Ayta Magbukon Indigenous Cultural Community, Abucay, Bataan, Philippines; National Commission on Indigenous Peoples, Philippines.
⁶ Mindanao Doctors Hospital and Cancer Center, Kabacan, Cotabato, Philippines.
⁷ Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City 10449, Taiwan.
⁸ National Commission on Indigenous Peoples, Philippines; Young Indigenous Peoples Empowered to Act in Community Engagement, Diffun, Quirino.
⁹ Balangao Indigenous Cultural Community, Paracelis, Mountain Province, Cordillera Administrative Region, Philippines.
¹⁰ Department of Education - Bataan Division, Bataan, Philippines.
¹¹ 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.
¹² Tarbilang Foundation, Inc., Bongao, Tawi-Tawi, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines.
¹³ Center for Language and Culture, Quirino State University, Barangay Andres Bonifacio, Diffun, Quirino, Philippines.
¹⁴ Center for Language and Culture, Cagayan State University - Andrews Campus, Caritan Highway, Tuguegarao, Cagayan, Philippines.
¹⁵ Tagakaulo Indigenous Cultural Community, Malungon, Sarangani, Philippines; Sulong Tribu Program, Provincial Government of Sarangani, Glan, Sarangani, Philippines.
¹⁶ Ayta Magbukon Cultural Bearer, Ayta Magbukon Indigenous Cultural Community, Abucay, Bataan, Philippines.
¹⁷ Subanen Indigenous Cultural Community, Lakewood, Zamboanga del Sur, Philippines; Dumendingan Arts Guild Inc., Pagadian City, Zamboanga del Sur, Philippines.
¹⁸ Dumendingan Arts Guild Inc., Pagadian City, Zamboanga del Sur, Philippines.
¹⁹ Ateneo Institute of Anthropology, Ateneo de Davao University, Roxas Avenue, 8016 Davao City, Philippines; Museo Dabawenyo, Andres Bonifacio Rotunda, Poblacion District, Davao City, Philippines.
²⁰ 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.
²¹ Institute for Peace and Development in Mindanao, Mindanao State University - Marawi Campus, Marawi City, Lanao del Sur, Bangsamoro Autonomous Region in Muslim Mindanao, Philippines.
²² Talaandig Indigenous Cultural Community, Lantapan, Bukidnon, Philippines.
²³ Legal Affairs Office, Indigenous People's Mandatory Representative - Sangguniang Panlalawigan, Bukidnon, Northern Mindanao, Philippines.
²⁴ National Commission on Indigenous Peoples, Philippines; Cuyonon Indigenous Cultural Community, Cuyo Island, Palawan, Philippines.
²⁵ Surigaonon Heritage Center, Surigao City, Surigao del Norte, Philippines.
²⁶ Kabankalan City Cultural and Tourism Foundation, Inc., Kabankalan City, Negros Occidental, Philippines; Cultural Research and Documentation, Negros Museum, Gatuslao St., Bacolod, Negros Occidental, Philippines.
²⁷ 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.
²⁸ Panaghiusa Alang Sa Kaugalingnan Ug Kalingkawasan, Inc., Bunawan, Agusan del Sur, Philippines; Agusan Manobo Indigenous Cultural Community, La Paz, Agusan del Sur, Philippines.
²⁹ Museo de Oro, Xavier University - Ateneo de Cagayan, Corrales Avenue, Cagayan de Oro City, Philippines.
³⁰ 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.
³¹ Kalanguya Indigenous Cultural Community, Tinoc, Ifugao, Cordillera Administrative Region, Philippines; Office of Tinoc Campus Administrator, Ifugao State University, Tinoc, Ifugao, Cordillera Administrative Region, Philippines.
³² Heritage Office, National Commission for Culture and the Arts, Intramuros, Manila, Philippines.
³³ 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.
³⁴ School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.
³⁵ 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.
³⁶ Research School of Earth Sciences, The Australian National University, Canberra, ACT 0200, Australia.
³⁷ 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.
³⁸ 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.
³⁹ Department Hommes Natures Societies, Musée de l'Homme, 75016 Paris, Ile de France, France.
⁴⁰ 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. Electronic address: mattias.jakobsson@ebc.uu.se.

PMID:34388371
PMCID: PMC8596304
DOI: 10.1016/j.cub.2021.07.022

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.

Keywords: Australasian; Denisovans; Island Southeast Asia; Negrito; Philippines; admixture; archaic introgression; genomics.

PubMed Disclaimer

Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Figures

**Figure 1**
Indigenous Negrito ethnic groups of the Philippines (A) Location of the 118 Philippine ethnic groups analyzed in this study. Negrito ethnic groups are labeled with red circular markers, whereas all other non-Negrito populations are labeled with yellow circular markers. Philippine Negritos are classified based on their genetic and/or geographical clusters: Northeast Luzon Negrito; Central Luzon Negrito; Southern Luzon Negrito; Southeast Luzon Negrito; and Southern Negrito. (B) Principal-component analysis (PCA) of West Eurasians, Australasians, and East Asians. Philippine Negritos lie between the axis defined by East Asian and Australasian-related ancestries. (C) Subset PCA showing the five distinct population clusters of Philippine Negritos. (D) Proportion of Australasian-related versus East-Asian-related ancestries among Philippine Negritos estimated using qpAdm. See also Figures S1 and S2.

**Figure 2**
Ayta Negritos exhibit the highest levels of Denisovan ancestry (A) Map showing distribution of populations with the indicative levels of Denisovan ancestry estimated by f4-ratio (Mbuti;Neanderthal,EastAsian,X)/(Mbuti,Neanderthal,EastAsian, Denisovan) (see Data S1 for the complete list of Denisovan ancestry estimates among 118 ethnic groups of the Philippines). (B) Asia-Pacific populations, represented by five least admixed individuals per group, with the highest levels of Denisovan ancestry estimated by f4-ratio statistics. Thick and thin error bars represent 1 and 1.96 standard error of the estimate, respectively. See also Figures S2–S5 and Data S1.

**Figure 3**
Ancestral Philippine Negritos exhibit higher levels of Denisovan ancestry than Australopapuans (A) Correlation between Denisovan ancestry and Australasian ancestry. Philippine Negritos fall outside the slope formed by populations with Papuan-related ancestry. (B and C) Denisovan ancestry in Northern Negritos versus Papuans (B) or Australians (C), before and after accounting for East Asian admixture. Masked or unmasked labels indicate removal or non-removal of East Asian ancestry following RFMix analysis (see STAR Methods). (D) Extrapolation on the level of Denisovan ancestry in an ancestral “unadmixed” Negrito population by plotting Denisovan ancestry and East-Asian-related ancestry. (E) Ratio of Denisovan ancestry over Australasian-related ancestry where Philippine Negritos display significantly higher values over near Oceanians or remote Oceanians (Mann-Whitney U test). Thick and thin error bars represent 1 and 1.96 standard error of the estimate, respectively. See also Figures S2–S5 and Data S1.

**Figure 4**
Analyses of high-coverage genomes confirm higher levels of Denisovan ancestry in Ayta Magbukon relative to Australopapuans (A) Using high-coverage genomes of Ayta Magbukon, Papuans, Australians, Bougainville Islanders, and East Asians, percentage Denisovan ancestry were estimated using the statistic f4-ratio (Mbuti;Neanderthal,Han,X)/ (Mbuti;Neanderthal,Han,Denisovan). (B) Percentage difference in Denisovan ancestry based on f4-ratio statistics. (C) Direct comparison of Denisovan ancestry between Australians, Papuans, and Ayta Magbukon, using the statistic D(Mbuti;Denisovan,Y1,Y2) (see Data S2C). (D) Mean plus SEM of Denisovan sequence detected per individual using S’ approach. Inferred model of Denisovan introgression events into Philippine Negritos and Papuans is shown (see STAR Methods). (E) Topology of East Asians and Australasians indicating the pulses of Denisovan introgression into Papuans and East Asians as previously reported in Browning et al. and Jacobs et al. and an independent pulse of Denisovan introgression into Philippine Negritos reported here. Time of divergence between East Asians and Australasians was previously reported in Malaspinas et al. Divergence time between Philippine Negritos and Papuans was estimated using the Two-plus-Two method (see STAR Methods; Sjödin et al.²⁵). Mean date of admixture between Philippine Negritos and East Asians was inferred using Malder. Values between brackets represent 95% confidence interval. Thick and thin error bars represent 1 and 1.96 standard error of the estimate, respectively. See also Figures S6 and S7 and Data S2.

**Figure 5**
Contour density plots showing the affiliation of S’-detected introgressed segments to the reference archaic genomes Contour density plots of match rate to the reference Vindija Neanderthal and Altai Denisovan genomes, using the S’-detected introgressed segments in Ayta Magbukon Negritos (A) and Papuans (B). The numbers within the plots correspond to the height of the density for each contour line, and contour lines are shown for multiples of 1 (solid lines) and multiples of 0.1 between 0.3 and 0.9 (dashed lines). See also Figure S6.

**Figure 6**
Admixture graph models of Denisovan introgression into Philippine Negritos and Papuans Admixture graphs for the null, alternative 1, and alternative 2 models indicating the number of archaic introgression events into Ayta Negritos and Papuans. (A) Null model depicts a single Denisovan introgression event into the ancestral populations of Ayta Negritos and Papuans. (B) Alternative 1 model depicts an additional admixture event into Ayta Negritos coming from a distinct and unsampled Denisovan population, after an admixture event in the shared ancestral population of Ayta Negritos and Papuans. (C) Alternative 2 model depicts two completely separate Denisovan introgression events into the ancestral populations of Ayta Negritos and Papuans. Only alternative 1 and 2 models are not rejected (Z score= −1.181). See also STAR Methods.

**Figure 7**
Evidence for independent Denisovan introgression event into Philippine Negritos (A and B) Empirical evidence for higher Denisovan ancestry in Ayta relative to Papuans estimated by f4-ratio statistics on genotyped data (A) and S’ method on sequence data (B). (C) Mean Denisovan tracts lengths in Ayta Magbukon versus Papuans. (D) Ratio of Denisovan ancestry over Australasian ancestry in Ayta-related and Papuan-related populations. (E) Correlation between Denisovan ancestry and Australasian ancestry, where Negritos (red line) fall outside the slope of the Papuan cline (blue line). (F–Ad) Diagram for the null (F), alternative models 1–4 (K, P, U, and Z) indicating the number and the time of archaic introgression events into Ayta Negritos and Papuans, simulated using msprime (see STAR Methods), with the respective estimated levels of Denisovan ancestry (G, L, Q, V, and Aa), mean Denisovan tract length (H, M, R, W, and Ab), ratio of Denisovan ancestry over Australasian ancestry (I, N, S, X, and Ac), and correlation between Denisovan ancestry and Australasian ancestry (J, O, T, Y, and Ad). Australasian ancestry was estimated using qpAdm. All pairwise comparisons were tested for significance using the Mann-Whitney U test with Holm-Bonferroni correction. Error bars represent standard error of the mean. See also Tables S1 and S2.

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

MeSH terms

LinkOut - more resources

Full Text Sources