1
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Sohail M, Palma-Martínez MJ, Chong AY, Quinto-Cortés CD, Barberena-Jonas C, Medina-Muñoz SG, Ragsdale A, Delgado-Sánchez G, Cruz-Hervert LP, Ferreyra-Reyes L, Ferreira-Guerrero E, Mongua-Rodríguez N, Canizales-Quintero S, Jimenez-Kaufmann A, Moreno-Macías H, Aguilar-Salinas CA, Auckland K, Cortés A, Acuña-Alonzo V, Gignoux CR, Wojcik GL, Ioannidis AG, Fernández-Valverde SL, Hill AVS, Tusié-Luna MT, Mentzer AJ, Novembre J, García-García L, Moreno-Estrada A. Mexican Biobank advances population and medical genomics of diverse ancestries. Nature 2023; 622:775-783. [PMID: 37821706 PMCID: PMC10600006 DOI: 10.1038/s41586-023-06560-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/22/2023] [Indexed: 10/13/2023]
Abstract
Latin America continues to be severely underrepresented in genomics research, and fine-scale genetic histories and complex trait architectures remain hidden owing to insufficient data1. To fill this gap, the Mexican Biobank project genotyped 6,057 individuals from 898 rural and urban localities across all 32 states in Mexico at a resolution of 1.8 million genome-wide markers with linked complex trait and disease information creating a valuable nationwide genotype-phenotype database. Here, using ancestry deconvolution and inference of identity-by-descent segments, we inferred ancestral population sizes across Mesoamerican regions over time, unravelling Indigenous, colonial and postcolonial demographic dynamics2-6. We observed variation in runs of homozygosity among genomic regions with different ancestries reflecting distinct demographic histories and, in turn, different distributions of rare deleterious variants. We conducted genome-wide association studies (GWAS) for 22 complex traits and found that several traits are better predicted using the Mexican Biobank GWAS compared to the UK Biobank GWAS7,8. We identified genetic and environmental factors associating with trait variation, such as the length of the genome in runs of homozygosity as a predictor for body mass index, triglycerides, glucose and height. This study provides insights into the genetic histories of individuals in Mexico and dissects their complex trait architectures, both crucial for making precision and preventive medicine initiatives accessible worldwide.
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Affiliation(s)
- Mashaal Sohail
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico.
| | - María J Palma-Martínez
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Amanda Y Chong
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Consuelo D Quinto-Cortés
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Carmina Barberena-Jonas
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Santiago G Medina-Muñoz
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Aaron Ragsdale
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Luis Pablo Cruz-Hervert
- Instituto Nacional de Salud Pública (INSP), Cuernavaca, Mexico
- División de Estudios de Posgrado e Investigación, Facultad de Odontología, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | | | | | | | | | - Andrés Jimenez-Kaufmann
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
| | - Hortensia Moreno-Macías
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas UNAM/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Carlos A Aguilar-Salinas
- Division de Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Kathryn Auckland
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adrián Cortés
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | | | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Selene L Fernández-Valverde
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico
- School of Biotechnology and Biomolecular Sciences and the RNA Institute, The University of New South Wales, Sydney, New South Wales, Australia
| | - Adrian V S Hill
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, University of Oxford, Oxford, UK
| | - María Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto de Investigaciones Biomédicas UNAM/Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Alexander J Mentzer
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | | | - Andrés Moreno-Estrada
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), Irapuato, Mexico.
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2
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Liu YC, Hunter-Anderson R, Cheronet O, Eakin J, Camacho F, Pietrusewsky M, Rohland N, Ioannidis A, Athens JS, Douglas MT, Ikehara-Quebral RM, Bernardos R, Culleton BJ, Mah M, Adamski N, Broomandkhoshbacht N, Callan K, Lawson AM, Mandl K, Michel M, Oppenheimer J, Stewardson K, Zalzala F, Kidd K, Kidd J, Schurr TG, Auckland K, Hill AVS, Mentzer AJ, Quinto-Cortés CD, Robson K, Kennett DJ, Patterson N, Bustamante CD, Moreno-Estrada A, Spriggs M, Vilar M, Lipson M, Pinhasi R, Reich D. Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers. Science 2022; 377:72-79. [PMID: 35771911 PMCID: PMC9983687 DOI: 10.1126/science.abm6536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Micronesia began to be peopled earlier than other parts of Remote Oceania, but the origins of its inhabitants remain unclear. We generated genome-wide data from 164 ancient and 112 modern individuals. Analysis reveals five migratory streams into Micronesia. Three are East Asian related, one is Polynesian, and a fifth is a Papuan source related to mainland New Guineans that is different from the New Britain-related Papuan source for southwest Pacific populations but is similarly derived from male migrants ~2500 to 2000 years ago. People of the Mariana Archipelago may derive all of their precolonial ancestry from East Asian sources, making them the only Remote Oceanians without Papuan ancestry. Female-inherited mitochondrial DNA was highly differentiated across early Remote Oceanian communities but homogeneous within, implying matrilocal practices whereby women almost never raised their children in communities different from the ones in which they grew up.
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Affiliation(s)
- Yue-Chen Liu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
| | - Joanne Eakin
- Independent Researcher, Albuquerque, NM 87107, USA
| | - Frank Camacho
- Department of Biology, University of Guam, Mangilao 96923, Guam
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - J. Stephen Athens
- International Archaeological Research Institute, Inc., Honolulu, HI 96826, USA
| | | | | | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan J. Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kenneth Kidd
- Department of Genetics, Yale Medical School, New Haven, CT 06520, USA
| | - Judith Kidd
- Department of Genetics, Yale Medical School, New Haven, CT 06520, USA
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK,The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK
| | - Consuelo D. Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato 36821, Mexico
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Douglas J. Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carlos D. Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.,Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA 94305, USA,Current Address: Galatea Bio, Inc. 975 W 22nd St. Hialeah, FL 33010, USA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato 36821, Mexico
| | - Matthew Spriggs
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT 2601, Australia,Vanuatu National Museum, Vanuatu Culture Centre, P.O. Box 184, Port Vila, Vanuatu
| | - Miguel Vilar
- Department of Anthropology, University of Maryland, College Park, MD 20742, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria,Human Evolution and Archaeological Sciences, University of Vienna, Vienna 1030, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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3
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Bastard P, Hsiao KC, Zhang Q, Choin J, Best E, Chen J, Gervais A, Bizien L, Materna M, Harmant C, Roux M, Hawley NL, Weeks DE, McGarvey ST, Sandoval K, Barberena-Jonas C, Quinto-Cortés CD, Hagelberg E, Mentzer AJ, Robson K, Coulibaly B, Seeleuthner Y, Bigio B, Li Z, Uzé G, Pellegrini S, Lorenzo L, Sbihi Z, Latour S, Besnard M, Adam de Beaumais T, Jacqz Aigrain E, Béziat V, Deka R, Esera Tulifau L, Viali S, Reupena MS, Naseri T, McNaughton P, Sarkozy V, Peake J, Blincoe A, Primhak S, Stables S, Gibson K, Woon ST, Drake KM, Hill AV, Chan CY, King R, Ameratunga R, Teiti I, Aubry M, Cao-Lormeau VM, Tangye SG, Zhang SY, Jouanguy E, Gray P, Abel L, Moreno-Estrada A, Minster RL, Quintana-Murci L, Wood AC, Casanova JL. A loss-of-function IFNAR1 allele in Polynesia underlies severe viral diseases in homozygotes. J Exp Med 2022; 219:213170. [PMID: 35442418 PMCID: PMC9026234 DOI: 10.1084/jem.20220028] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/15/2022] [Accepted: 03/21/2022] [Indexed: 12/11/2022] Open
Abstract
Globally, autosomal recessive IFNAR1 deficiency is a rare inborn error of immunity underlying susceptibility to live attenuated vaccine and wild-type viruses. We report seven children from five unrelated kindreds of western Polynesian ancestry who suffered from severe viral diseases. All the patients are homozygous for the same nonsense IFNAR1 variant (p.Glu386*). This allele encodes a truncated protein that is absent from the cell surface and is loss-of-function. The fibroblasts of the patients do not respond to type I IFNs (IFN-α2, IFN-ω, or IFN-β). Remarkably, this IFNAR1 variant has a minor allele frequency >1% in Samoa and is also observed in the Cook, Society, Marquesas, and Austral islands, as well as Fiji, whereas it is extremely rare or absent in the other populations tested, including those of the Pacific region. Inherited IFNAR1 deficiency should be considered in individuals of Polynesian ancestry with severe viral illnesses.
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Affiliation(s)
- Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Assistance Publique – Hôpitaux de Paris, Paris, France
| | - Kuang-Chih Hsiao
- Starship Child Health, Auckland, New Zealand
- Department of Paediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Murdoch Children’s Research Institute, Melbourne, Australia
- Clinical Immunogenomics Research Consortium Australasia, Sydney, Australia
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
| | - Jeremy Choin
- Institut Pasteur, Université de Paris, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
- Chair of Human Genomics and Evolution, Collège de France, Paris, France
- Paris Cité University, Paris, France
| | - Emma Best
- Starship Child Health, Auckland, New Zealand
- Department of Paediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Jie Chen
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Department of Infectious Diseases, Shanghai Sixth Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Adrian Gervais
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Lucy Bizien
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Marie Materna
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Christine Harmant
- Institut Pasteur, Université de Paris, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
| | - Maguelonne Roux
- Institut Pasteur, Université de Paris, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, Paris, France
| | - Nicola L. Hawley
- Department of Chronic Disease Epidemiology, Yale University School of Public Health, New Haven, CT
- International Health Institute, Department of Epidemiology, School of Public Health, Brown University, Providence, RI
| | - Daniel E. Weeks
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Stephen T. McGarvey
- International Health Institute, Department of Epidemiology, School of Public Health, Brown University, Providence, RI
- Department of Anthropology, Brown University, Providence, RI
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO) - UGA, CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Carmina Barberena-Jonas
- National Laboratory of Genomics for Biodiversity (LANGEBIO) - UGA, CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Consuelo D. Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO) - UGA, CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Boubacar Coulibaly
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Zhi Li
- Institut Pasteur, Université de Paris, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
- Unit of Cytokine Signaling, Pasteur Institute, INSERM U1224, Paris, France
| | - Gilles Uzé
- Institute for Regenerative Medicine and Biotherapy, Université Montpellier, INSERM, CNRS, Montpellier, France
| | - Sandra Pellegrini
- Unit of Cytokine Signaling, Pasteur Institute, INSERM U1224, Paris, France
| | - Lazaro Lorenzo
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
| | - Zineb Sbihi
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Sylvain Latour
- Paris Cité University, Imagine Institute, Paris, France
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR 1163, Imagine Institute, Paris, France
| | - Marianne Besnard
- Department of Neonatology, Centre Hospitalier de Polynésie Française, Papeete, French Polynesia
| | - Tiphaine Adam de Beaumais
- Precision Cancer Medicine Team, Institut Gustave Roussy, Villejuif, France
- Pharmacology - Pharmacogenetic Department, Hopital Saint-Louis, Assistance Publique – Hôpitaux de Paris, Paris, France
| | - Evelyne Jacqz Aigrain
- Paris Cité University, Paris, France
- Pharmacology - Pharmacogenetic Department, Hopital Saint-Louis, Assistance Publique – Hôpitaux de Paris, Paris, France
| | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
| | - Ranjan Deka
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH
| | | | | | | | - Take Naseri
- International Health Institute, Department of Epidemiology, School of Public Health, Brown University, Providence, RI
- Ministry of Health, Apia, Samoa
| | - Peter McNaughton
- Clinical Immunogenomics Research Consortium Australasia, Sydney, Australia
- Queensland Children’s Hospital and University of Queensland, Brisbane, Queensland, Australia
| | - Vanessa Sarkozy
- Tumbatin Developmental Services, Sydney Children’s Hospital, Randwick, New South Wales, Australia
- School of Women’s and Children’s Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Jane Peake
- Clinical Immunogenomics Research Consortium Australasia, Sydney, Australia
- Queensland Children’s Hospital and University of Queensland, Brisbane, Queensland, Australia
| | - Annaliesse Blincoe
- Starship Child Health, Auckland, New Zealand
- Clinical Immunogenomics Research Consortium Australasia, Sydney, Australia
| | - Sarah Primhak
- Starship Child Health, Auckland, New Zealand
- Department of Paediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Simon Stables
- Department of Forensic Pathology, Auckland City Hospital, Auckland, New Zealand
| | - Kate Gibson
- Clinical Geneticist, South Island Hub, Genetic Health Service, Christchurch, New Zealand
| | - See-Tarn Woon
- Department of Virology and Immunology, LabPLUS, Auckland City Hospital, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
| | - Kylie Marie Drake
- Molecular Pathology, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Adrian V.S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Cheng-Yee Chan
- Chemical Pathology and Genetics, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Richard King
- Chemical Pathology and Genetics, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Rohan Ameratunga
- Department of Virology and Immunology, LabPLUS, Auckland City Hospital, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
- Department of Clinical Immunology, Auckland City Hospital, Auckland, New Zealand
| | - Iotefa Teiti
- Laboratory of Research on Infectious Vector-borne Diseases, Institut Louis Malardé, Papeete, French Polynesia
| | - Maite Aubry
- Laboratory of Research on Infectious Vector-borne Diseases, Institut Louis Malardé, Papeete, French Polynesia
| | - Van-Mai Cao-Lormeau
- Laboratory of Research on Infectious Vector-borne Diseases, Institut Louis Malardé, Papeete, French Polynesia
| | - Stuart G. Tangye
- Clinical Immunogenomics Research Consortium Australasia, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- St Vincent’s Clinical School, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Shen-Ying Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
| | - Emmanuelle Jouanguy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
| | - Paul Gray
- Clinical Immunogenomics Research Consortium Australasia, Sydney, Australia
- School of Women’s and Children’s Health, University of New South Wales, Sydney, New South Wales, Australia
- Department of Immunology and Infectious Diseases, Sydney Children’s Hospital, Randwick, New South Wales, Australia
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO) - UGA, CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Ryan L. Minster
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Lluis Quintana-Murci
- Institut Pasteur, Université de Paris, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
- Chair of Human Genomics and Evolution, Collège de France, Paris, France
| | - Andrew C. Wood
- Starship Child Health, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
- Paris Cité University, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Assistance Publique – Hôpitaux de Paris, Paris, France
- Howard Hughes Medical Institute, New York, NY
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4
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Rodríguez-Rodríguez JE, Ioannidis AG, Medina-Muñoz SG, Barberena-Jonas C, Blanco-Portillo J, Quinto-Cortés CD, Moreno-Estrada A. The genetic legacy of the Manila galleon trade in Mexico. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200419. [PMID: 35430879 PMCID: PMC9014187 DOI: 10.1098/rstb.2020.0419] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The population of Mexico has a considerable genetic substructure due to both its pre-Columbian diversity and due to genetic admixture from post-Columbian trans-oceanic migrations. The latter primarily originated in Europe and Africa, but also, to a lesser extent, in Asia. We analyze previously understudied genetic connections between Asia and Mexico to infer the timing and source of this genetic ancestry in Mexico. We identify the predominant origin within Southeast Asia—specifically western Indonesian and non-Negrito Filipino sources—and we date its arrival in Mexico to approximately 13 generations ago (1620 CE). This points to a genetic legacy from the seventeenth century Manila galleon trade between the colonial Spanish Philippines and the Pacific port of Acapulco. Indeed, within Mexico we observe the highest level of this trans-Pacific ancestry in Acapulco, located in the state of Guerrero. This colonial Spanish trade route from East Asia to Europe was centred on Mexico and appears in historical records, but its legacy has been largely ignored. Identities and stories were suppressed due to slavery, assimilation of the immigrants as ‘Indios’ and incomplete historical records. Here we characterize this understudied Mexican ancestry. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
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Affiliation(s)
- Juan Esteban Rodríguez-Rodríguez
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | | | - Santiago G. Medina-Muñoz
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Carmina Barberena-Jonas
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | | | - Consuelo D. Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
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5
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Jiménez-Kaufmann A, Chong AY, Cortés A, Quinto-Cortés CD, Fernandez-Valverde SL, Ferreyra-Reyes L, Cruz-Hervert LP, Medina-Muñoz SG, Sohail M, Palma-Martinez MJ, Delgado-Sánchez G, Mongua-Rodríguez N, Mentzer AJ, Hill AVS, Moreno-Macías H, Huerta-Chagoya A, Aguilar-Salinas CA, Torres M, Kim HL, Kalsi N, Schuster SC, Tusié-Luna T, Del-Vecchyo DO, García-García L, Moreno-Estrada A. Imputation Performance in Latin American Populations: Improving Rare Variants Representation With the Inclusion of Native American Genomes. Front Genet 2022; 12:719791. [PMID: 35046991 PMCID: PMC8762266 DOI: 10.3389/fgene.2021.719791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 06/03/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Current Genome-Wide Association Studies (GWAS) rely on genotype imputation to increase statistical power, improve fine-mapping of association signals, and facilitate meta-analyses. Due to the complex demographic history of Latin America and the lack of balanced representation of Native American genomes in current imputation panels, the discovery of locally relevant disease variants is likely to be missed, limiting the scope and impact of biomedical research in these populations. Therefore, the necessity of better diversity representation in genomic databases is a scientific imperative. Here, we expand the 1,000 Genomes reference panel (1KGP) with 134 Native American genomes (1KGP + NAT) to assess imputation performance in Latin American individuals of mixed ancestry. Our panel increased the number of SNPs above the GWAS quality threshold, thus improving statistical power for association studies in the region. It also increased imputation accuracy, particularly in low-frequency variants segregating in Native American ancestry tracts. The improvement is subtle but consistent across countries and proportional to the number of genomes added from local source populations. To project the potential improvement with a higher number of reference genomes, we performed simulations and found that at least 3,000 Native American genomes are needed to equal the imputation performance of variants in European ancestry tracts. This reflects the concerning imbalance of diversity in current references and highlights the contribution of our work to reducing it while complementing efforts to improve global equity in genomic research.
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Affiliation(s)
- Andrés Jiménez-Kaufmann
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
| | - Amanda Y Chong
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Adrián Cortés
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Consuelo D Quinto-Cortés
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
| | - Selene L Fernandez-Valverde
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
| | | | | | - Santiago G Medina-Muñoz
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
| | - Mashaal Sohail
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico.,Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - María J Palma-Martinez
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
| | | | | | - Alexander J Mentzer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.,Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Hortensia Moreno-Macías
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), Mexico City, Mexico.,Departamento de Economía, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Alicia Huerta-Chagoya
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), Mexico City, Mexico
| | - Carlos A Aguilar-Salinas
- Departamento de Endocrinología y Metabolismo, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Unidad de Investigación de Enfermedades Metabólicas, Mexico City, Mexico.,Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Michael Torres
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
| | - Hie Lim Kim
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.,GenomeAsia 100K (GA100K) Consortium, Singapore.,School of Biological Science, Nanyang Technological University, Singapore
| | - Namrata Kalsi
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.,GenomeAsia 100K (GA100K) Consortium, Singapore
| | - Stephan C Schuster
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.,GenomeAsia 100K (GA100K) Consortium, Singapore.,School of Biological Science, Nanyang Technological University, Singapore
| | - Teresa Tusié-Luna
- Unidad de Biología Molecular y Medicina Genómica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (INCMNSZ), Mexico City, Mexico.,Instituto de Investigaciones Biomédicas de la UNAM, Mexico City, Mexico
| | - Diego Ortega Del-Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano (LIIGH), UNAM, Juriquilla, Mexico
| | | | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), Unidad de Genómica Avanzada, Irapuato, Mexico
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6
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Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman EC, Galloway JG, Gladstein AL, Gorjanc G, Guo B, Jeffery B, Kretzschmar WW, Lohse K, Matschiner M, Nelson D, Pope NS, Quinto-Cortés CD, Rodrigues MF, Saunack K, Sellinger T, Thornton K, van Kemenade H, Wohns AW, Wong Y, Gravel S, Kern AD, Koskela J, Ralph PL, Kelleher J. Efficient ancestry and mutation simulation with msprime 1.0. Genetics 2021; 220:6460344. [PMID: 34897427 PMCID: PMC9176297 DOI: 10.1093/genetics/iyab229] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [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: 09/22/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this, a large number of specialized simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and the tskit library. We summarize msprime’s many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.
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Affiliation(s)
- Franz Baumdicker
- Cluster of Excellence "Controlling Microbes to Fight Infections", Mathematical and Computational Population Genetics, University of Tübingen, 72076 Tübingen, Germany
| | - Gertjan Bisschop
- Institute of Evolutionary Biology,The University of Edinburgh, EH9 3FL, UK
| | - Daniel Goldstein
- Khoury College of Computer Sciences, Northeastern University, MA 02115, USA.,No affiliation
| | - Graham Gower
- Lundbeck GeoGenetics Centre, Globe Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Aaron P Ragsdale
- Department of Integrative Biology, University of Wisconsin-Madison, WI 53706, USA
| | - Georgia Tsambos
- Melbourne Integrative Genomics, School of Mathematics and Statistics, University of Melbourne, Victoria, 3010, Australia
| | - Sha Zhu
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| | - Bjarki Eldon
- Leibniz Institute for Evolution and Biodiversity Science,Museum für Naturkunde Berlin, 10115, Germany
| | | | - Jared G Galloway
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA.,Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98102, USA
| | - Ariella L Gladstein
- Department of Genetics, University of North Carolina at Chapel Hill, NC 27599-7264, USA.,Embark Veterinary, Inc., Boston, MA 02111, USA
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, EH25 9RG, UK
| | - Bing Guo
- Institute for Genome Sciences,University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ben Jeffery
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| | - Warren W Kretzschmar
- Center for Hematology and Regenerative Medicine, Karolinska Institute, 141 83 Huddinge, Sweden
| | - Konrad Lohse
- Institute of Evolutionary Biology,The University of Edinburgh, EH9 3FL, UK
| | | | - Dominic Nelson
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Nathaniel S Pope
- Department of Entomology, Pennsylvania State University, PA 16802, USA
| | - Consuelo D Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato, Mexico
| | - Murillo F Rodrigues
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA
| | - Kumar Saunack
- IIT Bombay, Powai, Mumbai 400 076, Maharashtra, India
| | - Thibaut Sellinger
- Professorship for Population Genetics, Department of Life Science Systems, Technical University of Munich, 85354 Freising, Germany
| | - Kevin Thornton
- Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | | | - Anthony W Wohns
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yan Wong
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
| | - Simon Gravel
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Andrew D Kern
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA
| | - Jere Koskela
- Department of Statistics, University of Warwick, CV4 7AL, UK
| | - Peter L Ralph
- Institute of Ecology and Evolution, Department of Biology, University of Oregon, OR 97403-5289, USA.,Department of Mathematics, University of Oregon, OR 97403-5289 USA
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, OX3 7LF, UK
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7
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Ioannidis AG, Blanco-Portillo J, Sandoval K, Hagelberg E, Barberena-Jonas C, Hill AVS, Rodríguez-Rodríguez JE, Fox K, Robson K, Haoa-Cardinali S, Quinto-Cortés CD, Miquel-Poblete JF, Auckland K, Parks T, Sofro ASM, Ávila-Arcos MC, Sockell A, Homburger JR, Eng C, Huntsman S, Burchard EG, Gignoux CR, Verdugo RA, Moraga M, Bustamante CD, Mentzer AJ, Moreno-Estrada A. Paths and timings of the peopling of Polynesia inferred from genomic networks. Nature 2021; 597:522-526. [PMID: 34552258 PMCID: PMC9710236 DOI: 10.1038/s41586-021-03902-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
Polynesia was settled in a series of extraordinary voyages across an ocean spanning one third of the Earth1, but the sequences of islands settled remain unknown and their timings disputed. Currently, several centuries separate the dates suggested by different archaeological surveys2-4. Here, using genome-wide data from merely 430 modern individuals from 21 key Pacific island populations and novel ancestry-specific computational analyses, we unravel the detailed genetic history of this vast, dispersed island network. Our reconstruction of the branching Polynesian migration sequence reveals a serial founder expansion, characterized by directional loss of variants, that originated in Samoa and spread first through the Cook Islands (Rarotonga), then to the Society (Tōtaiete mā) Islands (11th century), the western Austral (Tuha'a Pae) Islands and Tuāmotu Archipelago (12th century), and finally to the widely separated, but genetically connected, megalithic statue-building cultures of the Marquesas (Te Henua 'Enana) Islands in the north, Raivavae in the south, and Easter Island (Rapa Nui), the easternmost of the Polynesian islands, settled in approximately AD 1200 via Mangareva.
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Affiliation(s)
- Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico.
| | - Javier Blanco-Portillo
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Carmina Barberena-Jonas
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Adrian V S Hill
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Juan Esteban Rodríguez-Rodríguez
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Keolu Fox
- Department of Anthropology, University of California San Diego, La Jolla, CA, USA
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Consuelo D Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Abdul Salam M Sofro
- Department of Biochemistry, Faculty of Medicine, Yayasan Rumah Sakit Islam (YARSI) University, Cempaka Putih, Jakarta, Indonesia
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico
| | - Alexandra Sockell
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Julian R Homburger
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Celeste Eng
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Esteban G Burchard
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, USA
| | - Ricardo A Verdugo
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Translational Oncology Department, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mauricio Moraga
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Department of Anthropology, Faculty of Social Sciences, University of Chile, Santiago, Chile
| | - Carlos D Bustamante
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico.
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8
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Quinto-Cortés CD, Arriola LA, García-Hughes G, García-López R, Molina DP, Flores M, Palacios R, Piñero D. Genetic Characterization of Indigenous Peoples from Oaxaca, Mexico, and Its Relation to Linguistic and Geographic Isolation. Hum Biol 2010; 82:409-32. [DOI: 10.3378/027.082.0405] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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