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Ancient DNA pp 163-194 | Cite as

Authentication and Assessment of Contamination in Ancient DNA

  • Gabriel Renaud
  • Mikkel Schubert
  • Susanna Sawyer
  • Ludovic OrlandoEmail author
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Contamination Ancient DNA Postmortem damage Schmutzi DICE mapDamage2.0 

Notes

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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Gabriel Renaud
    • 1
  • Mikkel Schubert
    • 1
  • Susanna Sawyer
    • 1
  • Ludovic Orlando
    • 1
    • 2
    Email author
  1. 1.Centre for GeoGenetics, Natural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
  2. 2.Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de SynthèseCNRS UMR 5288, Université de Toulouse, University Paul SabatierToulouseFrance

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