A Paleogenomic Reconstruction of the Deep Population History of the Andes

Nathan Nakatsuka; Iosif Lazaridis; Chiara Barbieri; Pontus Skoglund; Nadin Rohland; Swapan Mallick; Cosimo Posth; Kelly Harkins-Kinkaid; Matthew Ferry; Éadaoin Harney; Megan Michel; Kristin Stewardson; Jannine Novak-Forst; José M Capriles; Marta Alfonso Durruty; Karina Aranda Álvarez; David Beresford-Jones; Richard Burger; Lauren Cadwallader; Ricardo Fujita; Johny Isla; George Lau; Carlos Lémuz Aguirre; Steven LeBlanc; Sergio Calla Maldonado; Frank Meddens; Pablo G Messineo; Brendan J Culleton; Thomas K Harper; Jeffrey Quilter; Gustavo Politis; Kurt Rademaker; Markus Reindel; Mario Rivera; Lucy Salazar; José R Sandoval; Calogero M Santoro; Nahuel Scheifler; Vivien Standen; Maria Ines Barreto; Isabel Flores Espinoza; Elsa Tomasto-Cagigao; Guido Valverde; Douglas J Kennett; Alan Cooper; Johannes Krause; Wolfgang Haak; Bastien Llamas; David Reich; Lars Fehren-Schmitz

doi:10.1016/j.cell.2020.04.015

A Paleogenomic Reconstruction of the Deep Population History of the Andes

Cell. 2020 May 28;181(5):1131-1145.e21. doi: 10.1016/j.cell.2020.04.015. Epub 2020 May 7.

Authors

Nathan Nakatsuka¹, Iosif Lazaridis², Chiara Barbieri³, Pontus Skoglund⁴, Nadin Rohland², Swapan Mallick⁵, Cosimo Posth⁶, Kelly Harkins-Kinkaid⁷, Matthew Ferry⁸, Éadaoin Harney⁸, Megan Michel⁸, Kristin Stewardson⁸, Jannine Novak-Forst⁷, José M Capriles⁹, Marta Alfonso Durruty¹⁰, Karina Aranda Álvarez¹¹, David Beresford-Jones¹², Richard Burger¹³, Lauren Cadwallader¹⁴, Ricardo Fujita¹⁵, Johny Isla¹⁶, George Lau¹⁷, Carlos Lémuz Aguirre¹⁸, Steven LeBlanc¹⁹, Sergio Calla Maldonado¹⁸, Frank Meddens²⁰, Pablo G Messineo²¹, Brendan J Culleton²², Thomas K Harper⁹, Jeffrey Quilter¹⁹, Gustavo Politis²¹, Kurt Rademaker²³, Markus Reindel²⁴, Mario Rivera²⁵, Lucy Salazar¹², José R Sandoval¹⁵, Calogero M Santoro²⁶, Nahuel Scheifler²¹, Vivien Standen²⁷, Maria Ines Barreto²⁸, Isabel Flores Espinoza²⁸, Elsa Tomasto-Cagigao²⁹, Guido Valverde³⁰, Douglas J Kennett³¹, Alan Cooper³⁰, Johannes Krause⁶, Wolfgang Haak⁶, Bastien Llamas³⁰, David Reich³², Lars Fehren-Schmitz³³

Affiliations

¹ Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA. Electronic address: nathan_nakatsuka@hms.harvard.edu.
² Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
³ Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland.
⁴ Francis Crick Institute, London NW1 1AT, UK.
⁵ Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
⁶ Max Planck Institute for the Science of Human History, Jena 07745, Germany.
⁷ UCSC Paleogenomics, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
⁸ Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA.
⁹ Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA.
¹⁰ Department of Sociology, Anthropology and Social Work, Kansas State University, Manhattan, KS 66506, USA.
¹¹ Sociedad de Arqueología de La Paz, 5294 La Paz, Bolivia.
¹² McDonald Institute for Archaeological Research, University of Cambridge, Downing St., Cambridge, CB2 3ER, UK.
¹³ Department of Anthropology, Yale University, New Haven, CT 06511, USA.
¹⁴ Office of Scholarly Communication, Cambridge University Library, Cambridge CB3 9DR, UK.
¹⁵ Centro de Genética y Biología Molecular, Facultdad de Medicina, Universidad de San Martín de Porres, Lima 15011, Peru.
¹⁶ Peruvian Ministry of Culture, DDC Ica, Directos of the Nasca-Palpa Management Plan, Calle Juan Matta 880, Nasca 11401, Peru.
¹⁷ Sainsbury Research Unit, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
¹⁸ Carrera de Arqueología, Universidad Mayor de San Andrés, Edificio Facultad de Ciencias Sociales 3er Piso, La Paz 1995, Bolivia.
¹⁹ Harvard Peabody Museum, Harvard University, Cambridge, MA 02138, USA.
²⁰ School of Archaeology, Geography and Environmental Sciences, University of Reading, Reading, Berkshire, RG6 6AH, UK.
²¹ INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina.
²² Institutes for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA.
²³ Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA.
²⁴ Commission for Archaeology of Non-European Cultures, German Archaeological Institute, Berlin 14195, Germany.
²⁵ Universidad de Magallanes, Punta Arenas 6210427, Chile; Field Museum Natural History 1400 S Lake Shore Dr., Chicago, IL 60605, USA.
²⁶ Instituto de Alta Investigation, Universidad de Tarapaca, Antafogasta 1520, Arica, 1000000, Chile.
²⁷ Departamento de Antropología, Universidad de Tarapacá, Antafogasta 1520, Arica, 1000000, Chile.
²⁸ Museo de Sitio Huaca Pucllana, Calle General Borgoño, Cuadra 8, Miraflores, Lima 18, Peru.
²⁹ Department of Humanities, Pontifical Catholic University of Peru, San Miguel 15088, Peru.
³⁰ Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia.
³¹ Institutes for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
³² Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02446, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: reich@genetics.med.harvard.edu.
³³ 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. Electronic address: lfehrens@ucsc.edu.

Abstract

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.

Keywords: Andes; ancient DNA; anthropology; archaeology; population genetics.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Anthropology / methods*
Central America
DNA, Ancient / analysis*
DNA, Mitochondrial / genetics
Gene Flow / genetics*
Gene Flow / physiology
Genetics, Population / methods
Haplotypes
Humans
Sequence Analysis, DNA
South America

Substances

DNA, Ancient
DNA, Mitochondrial

Abstract

Publication types

MeSH terms

Substances

Grants and funding