Authentication and Assessment of Contamination in Ancient DNA

Gabriel Renaud; Mikkel Schubert; Susanna Sawyer; Ludovic Orlando

doi:10.1007/978-1-4939-9176-1_17

Authentication and Assessment of Contamination in Ancient DNA

Methods Mol Biol. 2019:1963:163-194. doi: 10.1007/978-1-4939-9176-1_17.

Authors

Gabriel Renaud¹, Mikkel Schubert¹, Susanna Sawyer¹, Ludovic Orlando^{2

3}

Affiliations

¹ Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark.
² Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark. ludovic.orlando@univ-tlse3.fr.
³ Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier, Toulouse, France. ludovic.orlando@univ-tlse3.fr.

PMID: 30875054
DOI: 10.1007/978-1-4939-9176-1_17

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.

Keywords: Ancient DNA; Contamination; DICE; Postmortem damage; Schmutzi; mapDamage2.0.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cell Nucleus / genetics*
DNA Contamination*
DNA, Ancient / analysis*
DNA, Mitochondrial / genetics*
Genome, Mitochondrial
Humans
Sequence Analysis, DNA / methods*

Substances

DNA, Ancient
DNA, Mitochondrial