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Ferraz T, Suarez Villagran X, Nägele K, Radzevičiūtė R, Barbosa Lemes R, Salazar-García DC, Wesolowski V, Lopes Alves M, Bastos M, Rapp Py-Daniel A, Pinto Lima H, Mendes Cardoso J, Estevam R, Liryo A, Guimarães GM, Figuti L, Eggers S, Plens CR, Azevedo Erler DM, Valadares Costa HA, da Silva Erler I, Koole E, Henriques G, Solari A, Martin G, Serafim Monteiro da Silva SF, Kipnis R, Müller LM, Ferreira M, Carvalho Resende J, Chim E, da Silva CA, Borella AC, Tomé T, Müller Plumm Gomes L, Barros Fonseca D, Santos da Rosa C, de Moura Saldanha JD, Costa Leite L, Cunha CMS, Viana SA, Ozorio Almeida F, Klokler D, Fernandes HLA, Talamo S, DeBlasis P, Mendonça de Souza S, de Paula Moraes C, Elias Oliveira R, Hünemeier T, Strauss A, Posth C. Genomic history of coastal societies from eastern South America. Nat Ecol Evol 2023; 7:1315-1330. [PMID: 37524799 PMCID: PMC10406606 DOI: 10.1038/s41559-023-02114-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 06/08/2023] [Indexed: 08/02/2023]
Abstract
Sambaqui (shellmound) societies are among the most intriguing archaeological phenomena in pre-colonial South America, extending from approximately 8,000 to 1,000 years before present (yr BP) across 3,000 km on the Atlantic coast. However, little is known about their connection to early Holocene hunter-gatherers, how this may have contributed to different historical pathways and the processes through which late Holocene ceramists came to rule the coast shortly before European contact. To contribute to our understanding of the population history of indigenous societies on the eastern coast of South America, we produced genome-wide data from 34 ancient individuals as early as 10,000 yr BP from four different regions in Brazil. Early Holocene hunter-gatherers were found to lack shared genetic drift among themselves and with later populations from eastern South America, suggesting that they derived from a common radiation and did not contribute substantially to later coastal groups. Our analyses show genetic heterogeneity among contemporaneous Sambaqui groups from the southeastern and southern Brazilian coast, contrary to the similarity expressed in the archaeological record. The complex history of intercultural contact between inland horticulturists and coastal populations becomes genetically evident during the final horizon of Sambaqui societies, from around 2,200 yr BP, corroborating evidence of cultural change.
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Affiliation(s)
- Tiago Ferraz
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rita Radzevičiūtė
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Renan Barbosa Lemes
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
| | - Domingo C Salazar-García
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Verônica Wesolowski
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Marcony Lopes Alves
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Murilo Bastos
- Departamento de Antropologia, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Jéssica Mendes Cardoso
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
- Géosciences Environnement Toulouse, Observatoire Midi Pyrénées, UMR 5563, CNRS, Toulouse, France
| | - Renata Estevam
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Andersen Liryo
- National Museum, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Geovan M Guimarães
- Grupo de Pesquisa em Educação Patrimonial e Arqueologia (Grupep), Universidade do Sul de Santa Catarina, Santa Catarina, Brazil
| | - Levy Figuti
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | - Cláudia R Plens
- Laboratory of Archaeological Studies, Department of History, Federal University of São Paulo, São Paulo, Brazil
| | | | | | | | | | | | - Ana Solari
- Fundação Museu do Homem Americano, Piauí, Brazil
| | | | | | | | - Letícia Morgana Müller
- Scientia Consultoria Científica, São Paulo, Brazil
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Mariane Ferreira
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
- Scientia Consultoria Científica, São Paulo, Brazil
| | - Janine Carvalho Resende
- Instituto Goiano de Pré-história e Arqueologia, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Eliane Chim
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | - Ana Claudia Borella
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | - Tiago Tomé
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lisiane Müller Plumm Gomes
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | | | - João Darcy de Moura Saldanha
- Universidade de Évora, Évora, Portugal
- Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Macapá, Brazil
| | - Lúcio Costa Leite
- Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá (IEPA), Macapá, Brazil
| | - Claudia M S Cunha
- Federal University of Piauí, Piauí, Brazil
- Centro de Investigação em Antropologia e Saúde, Universidade de Coimbra, Coimbra, Portugal
| | - Sibeli Aparecida Viana
- Instituto Goiano de Pré-história e Arqueologia, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Fernando Ozorio Almeida
- Programa de Pós-Graduação em Arqueologia, Universidade Federal de Sergipe, Sergipe, Brazil
- Departamento de Arqueologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daniela Klokler
- Programa de Pós-Graduação em Arqueologia, Universidade Federal de Sergipe, Sergipe, Brazil
- Departamento de Antropologia e Arqueologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Henry Luydy Abraham Fernandes
- Programa de Pós-Graduação em Arqueologia e Patrimônio Cultural, Universidade Federal do Recôncavo da Bahia, Bahia, Brazil
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paulo DeBlasis
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil
| | | | | | - Rodrigo Elias Oliveira
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil
| | - Tábita Hünemeier
- Institute of Biosciences, Genetics Department, University of São Paulo, São Paulo, Brazil.
- Institut de Biologia Evolutiva, CSIC/Universitat Pompeu Fabra, Barcelona, Spain.
| | - André Strauss
- Museum of Archaeology and Ethnology, University of São Paulo, São Paulo, Brazil.
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany.
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.
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Posth C, Nakatsuka N, Lazaridis I, Skoglund P, Mallick S, Lamnidis TC, Rohland N, Nägele K, Adamski N, Bertolini E, Broomandkhoshbacht N, Cooper A, Culleton BJ, Ferraz T, Ferry M, Furtwängler A, Haak W, Harkins K, Harper TK, Hünemeier T, Lawson AM, Llamas B, Michel M, Nelson E, Oppenheimer J, Patterson N, Schiffels S, Sedig J, Stewardson K, Talamo S, Wang CC, Hublin JJ, Hubbe M, Harvati K, Nuevo Delaunay A, Beier J, Francken M, Kaulicke P, Reyes-Centeno H, Rademaker K, Trask WR, Robinson M, Gutierrez SM, Prufer KM, Salazar-García DC, Chim EN, Müller Plumm Gomes L, Alves ML, Liryo A, Inglez M, Oliveira RE, Bernardo DV, Barioni A, Wesolowski V, Scheifler NA, Rivera MA, Plens CR, Messineo PG, Figuti L, Corach D, Scabuzzo C, Eggers S, DeBlasis P, Reindel M, Méndez C, Politis G, Tomasto-Cagigao E, Kennett DJ, Strauss A, Fehren-Schmitz L, Krause J, Reich D. Reconstructing the Deep Population History of Central and South America. Cell 2018; 175:1185-1197.e22. [PMID: 30415837 PMCID: PMC6327247 DOI: 10.1016/j.cell.2018.10.027] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/15/2018] [Accepted: 10/11/2018] [Indexed: 01/16/2023]
Abstract
We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.
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Affiliation(s)
- Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany.
| | - Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA.
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Francis Crick Institute, London NW1 1AT, UK
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Thiseas C Lamnidis
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Emilie Bertolini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia 27100, Italy
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Brendan J Culleton
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Kelly Harkins
- UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Jakob Sedig
- Department of Genetics, 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
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Chuan-Chao Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Anthropology and Ethnology, Xiamen University, Xiamen 361005, China
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Mark Hubbe
- Department of Anthropology, The Ohio State University, Columbus, OH 43210, USA; Instituto de Arqueología y Antropología, Universidad Católica del Norte, San Pedro de Atacama, Región de Antofagasta, Antofagasta CP 1410000, Chile
| | - Katerina Harvati
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; DFG Center for Advanced Studies, "Words, Bones, Genes, Tools," University of Tübingen, Tübingen 72070, Germany
| | | | - Judith Beier
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany
| | - Michael Francken
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany
| | - Peter Kaulicke
- Pontifical Catholic University of Peru, San Miguel, Lima 32, Peru
| | - Hugo Reyes-Centeno
- Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; DFG Center for Advanced Studies, "Words, Bones, Genes, Tools," University of Tübingen, Tübingen 72070, Germany
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | - Willa R Trask
- Central Identification Laboratory, Defense POW/MIA Accounting Agency, Department of Defense, Joint Base Pearl Harbor-Hickam, HI 96853, USA
| | - Mark Robinson
- Department of Archaeology, Exeter University, Exeter EX4 4QJ, UK
| | | | - Keith M Prufer
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA; Center for Stable Isotopes, University of New Mexico, Albuquerque, NM 87131, USA
| | - Domingo C Salazar-García
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany; Grupo de Investigación en Prehistoria IT-622-13 (UPV-EHU), IKERBASQUE-Basque Foundation for Science, Vitoria, Spain
| | - Eliane N Chim
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | | | - Marcony L Alves
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Andersen Liryo
- Museu Nacional da Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940-040, Brazil
| | - Mariana Inglez
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil
| | - Rodrigo E Oliveira
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Departamento de Estomatologia, Faculdade de Odontologia, Universidade de São Paulo, São Paulo 05508-000, Brazil
| | - Danilo V Bernardo
- Laboratório de Estudos em Antropologia Biológica, Bioarqueologia e Evolução Humana, Instituto de Ciências Humanas e da Informação, Universidade Federal do Rio Grande, Rio Grande do Sul 96203-900, Brazil
| | - Alberto Barioni
- Faculdade de Filosofia Ciencias e Letras, Universidade de São Paulo, São Paulo 05508-080, Brazil
| | - Veronica Wesolowski
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Nahuel A Scheifler
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Mario A Rivera
- Comité Chileno del Consejo Internacional de Monumentos y Sitios, Santiago 8320000, Chile; Field Museum of Natural History, Chicago, IL 60605, USA; Universidad de Magallanes, Punta Arenas 6200000, Chile
| | - Claudia R Plens
- Escola De Filosofia, Letras E Ciências Humanas, Universidade Federal de São Paulo, São Paulo 07252-312, Brazil
| | - Pablo G Messineo
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Levy Figuti
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires y CONICET, Ciudad Autonoma de Buenos Aires, Junin 954, Argentina
| | - Clara Scabuzzo
- CONICET-División Arqueología, Facultad de Ciencias Naturales y Museo, La Plata 1900, Argentina
| | - Sabine Eggers
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Naturhistorisches Museum Wien, Vienna 1010, Austria
| | - Paulo DeBlasis
- Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil
| | - Markus Reindel
- German Archaeological Institute, Commission for Archaeology of Non-European Cultures, Bonn 53173, Germany
| | - César Méndez
- Centro de Investigación en Ecosistemas de la Patagonia, Coyhaique 5951601, Chile
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | | | - Douglas J Kennett
- Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - André Strauss
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany; Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil; Centro de Arqueologia Annette Laming Emperaire, Miguel A Salomão, Lagoa Santa, MG 33400-000, Brazil
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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