1. Evolutionary Biology
  2. Genetics and Genomics
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Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes

  1. Paloma Fernández Diaz-Maroto  Is a corresponding author
  2. Alba Rey-Iglesia
  3. Isabel Cartajena
  4. Lautaro Núñez
  5. Michael Vincent Westbury
  6. Valeria Varas
  7. Mauricio Moraga
  8. Paula F Campos
  9. Pablo Orozco-terWengel  Is a corresponding author
  10. Juan Carlos Marin  Is a corresponding author
  11. Anders Johannes Hansen
  1. University of Copenhagen, Denmark
  2. Universidad de Chile, Chile
  3. Universidad Católica del Norte, Chile
  4. Austral University of Chile, Chile
  5. University of Chile, Chile
  6. University of Porto, Portugal
  7. Cardiff University, United Kingdom
  8. Bio-Bio University, Chile
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Cite this article as: eLife 2021;10:e63390 doi: 10.7554/eLife.63390

Abstract

The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca and llama) in archaeological sites based solely on morphological data is challenging due to their similarity with respect to their wild ancestors. Using genetic methods also presents challenges due to the hybridization history of the domestic species, which are thought to have extensively hybridized following the Spanish conquest of South America that resulted in camelids slaughtered en-masse. In this study we generated mitochondrial genomes for 61 ancient South American camelids dated between 3,500 - 2,400 years before the present (Early Formative period) from two archaeological sites in Northern Chile (Tulán-54 and Tulán-85), as well as 66 modern camelid mitogenomes and 815 modern mitochondrial control region sequences from across South America. In addition, we performed osteometric analyses to differentiate big and small body size camelids. A comparative analysis of these data suggests that a substantial proportion of the ancient vicuña genetic variation has been lost since the Early Formative period as it is not present in modern specimens. Moreover, we propose a domestication hypothesis that includes an ancient guanaco population that no longer exists. Finally, we find evidence that interbreeding practices were widespread during the domestication process by the early camelid herders in the Atacama during the Early Formative period and predating the Spanish conquest.

Data availability

Sequencing data have been deposited in GenBank under accession codes:BankIt2325854 C10mito MT254135BankIt2325854 C11mito MT254136BankIt2325854 C12mito MT254137BankIt2325854 c13mito MT254138BankIt2325854 C14mito MT254139BankIt2325854 C15mito MT254140BankIt2325854 C16mito MT254141BankIt2325854 C18mito MT254142BankIt2325854 c1mito MT254143BankIt2325854 C20mito MT254144BankIt2325854 C21mito MT254145BankIt2325854 C22mito MT254146BankIt2325854 C24mito MT254147BankIt2325854 C25mito MT254148BankIt2325854 C27mito MT254149BankIt2325854 C28mito MT254150BankIt2325854 C29mito MT254151BankIt2325854 C30mito MT254152BankIt2325854 C31mito MT254153BankIt2325854 C32mito MT254154BankIt2325854 C33mito MT254155BankIt2325854 C34mito MT254156BankIt2325854 C35mito MT254157BankIt2325854 C36mito MT254158BankIt2325854 C37mito MT254159BankIt2325854 C38mito MT254160BankIt2325854 C39mito MT254161BankIt2325854 C41mito MT254162BankIt2325854 C42mito MT254163BankIt2325854 C43mito MT254164BankIt2325854 C44mito MT254165BankIt2325854 C46mito MT254166BankIt2325854 C47mito MT254167BankIt2325854 C48mito MT254168BankIt2325854 C49mito MT254169BankIt2325854 C50mito MT254170BankIt2325854 C52mito MT254171BankIt2325854 C54mito MT254172BankIt2325854 C55mito MT254173BankIt2325854 C57mito MT254174BankIt2325854 C59mito MT254175BankIt2325854 C5mito MT254176BankIt2325854 C60mito MT254177BankIt2325854 C61mito MT254178BankIt2325854 C62mito MT254179BankIt2325854 C63mito MT254180BankIt2325854 C64mito MT254181BankIt2325854 C65mito MT254182BankIt2325854 C66mito MT254183BankIt2325854 C67mito MT254184BankIt2325854 C68mito MT254185BankIt2325854 C69mito MT254186BankIt2325854 C6mito MT254187BankIt2325854 C70mito MT254188BankIt2325854 C71mito MT254189BankIt2325854 C72mito MT254190BankIt2325854 C73mito MT254191BankIt2325854 C74mito MT254192BankIt2325854 C75mito MT254193BankIt2325854 C76mito MT254194BankIt2325854 C77mito MT254195

The following previously published data sets were used

Article and author information

Author details

  1. Paloma Fernández Diaz-Maroto

    Globe Institute, University of Copenhagen, Copenhagen, Denmark
    For correspondence
    palomafdm@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3937-6609
  2. Alba Rey-Iglesia

    Globe Institute, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    The authors declare that no competing interests exist.
  3. Isabel Cartajena

    Facultad de Ciencias Sociales, Universidad de Chile, Santiago de Chile, Chile
    Competing interests
    The authors declare that no competing interests exist.
  4. Lautaro Núñez

    Instituto de Investigaciones Arqueológicas y Museo, Universidad Católica del Norte, San Pedro de Atacama, Chile
    Competing interests
    The authors declare that no competing interests exist.
  5. Michael Vincent Westbury

    Globe Institute, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    The authors declare that no competing interests exist.
  6. Valeria Varas

    Faculty of Sciences, Austral University of Chile, Valdivia, Chile
    Competing interests
    The authors declare that no competing interests exist.
  7. Mauricio Moraga

    Human Genetics Program, Institute of Biomedical Sciences, University of Chile, Santiago de Chile, Chile
    Competing interests
    The authors declare that no competing interests exist.
  8. Paula F Campos

    CIIMAR, University of Porto, Matosinhos, Portugal
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1285-4671
  9. Pablo Orozco-terWengel

    School of Biosciences, Cardiff University, Cardiff, United Kingdom
    For correspondence
    Orozco-terWengelPA@cardiff.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
  10. Juan Carlos Marin

    Faculty of Sciences, Bio-Bio University, Chillán, Chile
    For correspondence
    dromiciops@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
  11. Anders Johannes Hansen

    Globe Institute, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    The authors declare that no competing interests exist.

Funding

Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica (1070040)

  • Paloma Fernández Diaz-Maroto

Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica (1020316)

  • Paloma Fernández Diaz-Maroto

Fondo Nacional de Desarrollo Científico y Tecnológico (1130917)

  • Paloma Fernández Diaz-Maroto

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Jessica C Thompson, Yale University, United States

Publication history

  1. Received: September 23, 2020
  2. Accepted: March 15, 2021
  3. Accepted Manuscript published: March 16, 2021 (version 1)
  4. Version of Record published: April 8, 2021 (version 2)

Copyright

© 2021, Diaz-Maroto et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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