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Capodiferro MR, Chero Osorio AM, Rambaldi Migliore N, Tineo Tineo DH, Raveane A, Xavier C, Bodner M, Simão F, Ongaro L, Montinaro F, Lindo J, Huerta-Sanchez E, Politis G, Barbieri C, Parson W, Gusmão L, Achilli A. The multifaceted genomic history of Ashaninka from Amazonian Peru. Curr Biol 2023; 33:1573-1581.e5. [PMID: 36931272 DOI: 10.1016/j.cub.2023.02.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/14/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Despite its crucial location, the western side of Amazonia between the Andes and the source(s) of the Amazon River is still understudied from a genomic and archaeogenomic point of view, albeit possibly harboring essential information to clarify the complex genetic history of local Indigenous groups and their interactions with nearby regions,1,2,3,4,5,6,7,8 including central America and the Caribbean.9,10,11,12 Focusing on this key region, we analyzed the genome-wide profiles of 51 Ashaninka individuals from Amazonian Peru, observing an unexpected extent of genomic variation. We identified at least two Ashaninka subgroups with distinctive genomic makeups, which were differentially shaped by the degree and timing of external admixtures, especially with the Indigenous groups from the Andes and the Pacific coast. On a continental scale, Ashaninka ancestors probably derived from a south-north migration of Indigenous groups moving into the Amazonian rainforest from a southeastern area with contributions from the Southern Cone and the Atlantic coast. These ancestral populations diversified in the variegated geographic regions of interior South America, on the eastern side of the Andes, differentially interacting with surrounding coastal groups. In this complex scenario, we also revealed strict connections between the ancestors of present-day Ashaninka, who belong to the Arawakan language family,13 and those Indigenous groups that moved further north into the Caribbean, contributing to the early Ceramic (Saladoid) tradition in the islands.14,15.
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Affiliation(s)
- Marco Rosario Capodiferro
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy; Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland.
| | - Ana María Chero Osorio
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Dean Herman Tineo Tineo
- Laboratorio de Biología Forense, Instituto de Medicina Legal y Ciencias Forenses, Ministerio Público, Lima 15033, Perú
| | | | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4099-002 Porto, Portugal
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Filipa Simão
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 23968-000, Brazil
| | - Linda Ongaro
- Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, 70125 Bari, Italy; Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Emilia Huerta-Sanchez
- Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland; Ecology and Evolutionary Biology and Center for Computational and Molecular Biology, Brown University, Providence, RI 02906, USA
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland; Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; Forensic Science Program, Pennsylvania State University, State College, PA 16801, USA
| | - Leonor Gusmão
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 23968-000, Brazil
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy.
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Fernandes DM, Sirak KA, Ringbauer H, Sedig J, Rohland N, Cheronet O, Mah M, Mallick S, Olalde I, Culleton BJ, Adamski N, Bernardos R, Bravo G, Broomandkhoshbacht N, Callan K, Candilio F, Demetz L, Carlson KSD, Eccles L, Freilich S, George RJ, Lawson AM, Mandl K, Marzaioli F, McCool WC, Oppenheimer J, Özdogan KT, Schattke C, Schmidt R, Stewardson K, Terrasi F, Zalzala F, Antúnez CA, Canosa EV, Colten R, Cucina A, Genchi F, Kraan C, La Pastina F, Lucci M, Maggiolo MV, Marcheco-Teruel B, Maria CT, Martínez C, París I, Pateman M, Simms TM, Sivoli CG, Vilar M, Kennett DJ, Keegan WF, Coppa A, Lipson M, Pinhasi R, Reich D. A genetic history of the pre-contact Caribbean. Nature 2021; 590:103-110. [PMID: 33361817 PMCID: PMC7864882 DOI: 10.1038/s41586-020-03053-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 11/10/2020] [Indexed: 12/27/2022]
Abstract
Humans settled the Caribbean about 6,000 years ago, and ceramic use and intensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago1-3. Here we report genome-wide data from 174 ancient individuals from The Bahamas, Haiti and the Dominican Republic (collectively, Hispaniola), Puerto Rico, Curaçao and Venezuela, which we co-analysed with 89 previously published ancient individuals. Stone-tool-using Caribbean people, who first entered the Caribbean during the Archaic Age, derive from a deeply divergent population that is closest to Central and northern South American individuals; contrary to previous work4, we find no support for ancestry contributed by a population related to North American individuals. Archaic-related lineages were >98% replaced by a genetically homogeneous ceramic-using population related to speakers of languages in the Arawak family from northeast South America; these people moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools that reflect small effective population sizes, which we estimate to be a minimum of 500-1,500 and a maximum of 1,530-8,150 individuals on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the individuals who we analysed lived. Census sizes are unlikely to be more than tenfold larger than effective population sizes, so previous pan-Caribbean estimates of hundreds of thousands of people are too large5,6. Confirming a small and interconnected Ceramic Age population7, we detect 19 pairs of cross-island cousins, close relatives buried around 75 km apart in Hispaniola and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically differentiated groups from the mainland, but instead reflected interactions within an interconnected Caribbean world1,8.
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Affiliation(s)
- Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Kendra A Sirak
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Harald Ringbauer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Jakob Sedig
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Guillermo Bravo
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Department of Legal Medicine, Toxicology and Physical Anthropology, University of Granada, Granada, Spain
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Anthropology, University of California, Santa Cruz, CA, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Francesca Candilio
- Superintendency of Archaeology, Fine Arts and Landscape for the city of Cagliari and the provinces of Oristano and South Sardinia, Cagliari, Italy
| | - Lea Demetz
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Laurie Eccles
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Richard J George
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Fabio Marzaioli
- Department of Mathematics and Physics, Campania University 'Luigi Vanvitelli', Caserta, Italy
| | - Weston C McCool
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Kadir T Özdogan
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Constanze Schattke
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Ryan Schmidt
- CIBIO-InBIO, University of Porto, Vairão, Portugal
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Filippo Terrasi
- Department of Mathematics and Physics, Campania University 'Luigi Vanvitelli', Caserta, Italy
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | | | - Roger Colten
- Peabody Museum of Natural History, Yale University, New Haven, CT, USA
| | - Andrea Cucina
- Facultad de Ciencias Antropológicas, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Francesco Genchi
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Claudia Kraan
- National Archaeological-Anthropological Memory Management (NAAM), Willemstad, Curaçao
| | | | - Michaela Lucci
- DANTE Laboratory of Diet and Ancient Technology, Sapienza University of Rome, Rome, Italy
| | | | | | | | | | - Ingeborg París
- Instituto de Investigaciones Bioantropológicas y Arqueológicas, Universidad de Los Andes, Mérida, Venezuela
| | - Michael Pateman
- Turks and Caicos National Museum Foundation, Cockburn Town, Turks and Caicos Islands
- AEX Bahamas Maritime Museum, Freeport, Bahamas
| | - Tanya M Simms
- Department of Biology, University of The Bahamas, Nassau, Bahamas
| | - Carlos Garcia Sivoli
- Instituto de Investigaciones Bioantropológicas y Arqueológicas, Universidad de Los Andes, Mérida, Venezuela
| | - Miguel Vilar
- National Geographic Society, Washington, DC, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, USA
| | - William F Keegan
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Alfredo Coppa
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy.
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
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