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Cell. 2018 Nov 15;175(5):1185-1197.e22. doi: 10.1016/j.cell.2018.10.027. Epub 2018 Nov 8.

Reconstructing the Deep Population History of Central and South America.

Author information

1
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. Electronic address: posth@shh.mpg.de.
2
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA. Electronic address: nathan_nakatsuka@hms.harvard.edu.
3
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
4
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Francis Crick Institute, London NW1 1AT, UK.
5
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.
6
Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany.
7
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
8
Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia 27100, Italy.
9
Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia.
10
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.
11
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.
12
Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany.
13
UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
14
Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA.
15
Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil.
16
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.
17
Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
18
Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
19
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.
20
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.
21
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.
22
Centro de Investigación en Ecosistemas de la Patagonia, Coyhaique 5951601, Chile.
23
Institute for Archaeological Sciences, Palaeoanthropology and Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tuebingen, Tübingen 72070, Germany.
24
Pontifical Catholic University of Peru, San Miguel, Lima 32, Peru.
25
Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA.
26
Central Identification Laboratory, Defense POW/MIA Accounting Agency, Department of Defense, Joint Base Pearl Harbor-Hickam, HI 96853, USA.
27
Department of Archaeology, Exeter University, Exeter EX4 4QJ, UK.
28
Ya'axché Conservation Trust, Punta Gorda Town, Belize.
29
Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA; Center for Stable Isotopes, University of New Mexico, Albuquerque, NM 87131, USA.
30
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.
31
Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo 05508-070, Brazil.
32
Museu Nacional da Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940-040, Brazil.
33
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.
34
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.
35
Faculdade de Filosofia Ciencias e Letras, Universidade de São Paulo, São Paulo 05508-080, Brazil.
36
INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina.
37
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.
38
Escola De Filosofia, Letras E Ciências Humanas, Universidade Federal de São Paulo, São Paulo 07252-312, Brazil.
39
Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, Universidad de Buenos Aires y CONICET, Ciudad Autonoma de Buenos Aires, Junin 954, Argentina.
40
CONICET-División Arqueología, Facultad de Ciencias Naturales y Museo, La Plata 1900, Argentina.
41
Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo 05508-090, Brazil; Naturhistorisches Museum Wien, Vienna 1010, Austria.
42
German Archaeological Institute, Commission for Archaeology of Non-European Cultures, Bonn 53173, Germany.
43
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.
44
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.
45
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. Electronic address: reich@genetics.med.harvard.edu.

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.

KEYWORDS:

Central America; South America; anthropology; archaeology; population genetics

PMID:
30415837
DOI:
10.1016/j.cell.2018.10.027
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