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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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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