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Authentication and Assessment of Contamination in Ancient DNA

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Ancient DNA

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1963))

Abstract

Contamination from both present-day humans and postmortem microbial sources is a common challenge in ancient DNA studies. Here we present a suite of tools to assist in the assessment of contamination in ancient DNA data sets. These tools perform standard tests of authenticity of ancient DNA data including detecting the presence of postmortem damage signatures in sequence alignments and quantifying the amount of present-day human contamination.

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Acknowledgments

We would like to thank Fernando Racimo for comments and suggestions and José Victor Moreno Mayar and Thorfinn Sand Korneliussen for their insights into the contamination method using the X chromosome. This work was supported by the Danish Council for Independent Research, Natural Sciences (Grant 4002-00152B); the Danish National Research Foundation (Grant DNRF94); Initiative d’Excellence Chaires d’attractivité, Université de Toulouse (OURASI); the Villum Fonden miGENEPI research project; and the European Research Council (ERC-CoG-2015-681605).

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Authors and Affiliations

  1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark

    Gabriel Renaud, Mikkel Schubert, Susanna Sawyer & Ludovic Orlando

  2. Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier, Toulouse, France

    Ludovic Orlando

Authors
  1. Gabriel Renaud
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  2. Mikkel Schubert
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  3. Susanna Sawyer
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  4. Ludovic Orlando
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Corresponding author

Correspondence to Ludovic Orlando .

Editor information

Editors and Affiliations

  1. Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA

    Beth Shapiro

  2. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Axel Barlow

  3. Tromsø University Museum, UiT—The Arctic University of Norway, Tromsø, Norway

    Peter D. Heintzman

  4. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Michael Hofreiter

  5. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany

    Johanna L. A. Paijmans

  6. Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil

    André E. R. Soares

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Renaud, G., Schubert, M., Sawyer, S., Orlando, L. (2019). Authentication and Assessment of Contamination in Ancient DNA. In: Shapiro, B., Barlow, A., Heintzman, P., Hofreiter, M., Paijmans, J., Soares, A. (eds) Ancient DNA. Methods in Molecular Biology, vol 1963. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9176-1_17

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  • DOI: https://doi.org/10.1007/978-1-4939-9176-1_17

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