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MBE Advance Access published online on June 29, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl047
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted June 23, 2006

Research Article

Tracking Down Human Contamination in Ancient Human Teeth

María Lourdes Sampietro 1, M. Thomas P. Gilbert 2, Oscar Lao 3, David Caramelli 4, Martina Lari 4, Jaume Bertranpetit 1, and Carles Lalueza-Fox 5 *

1 Unitat de Biologia Evolutiva, Dept. Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
2 Ancient DNA, Niels Bohr Institute, Juliane Maries vej 30, DK-2100 Copenhagen Ø, Denmark
3 Department of Forensic Molecular Biology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
4 Dipartimento di Biologia Animale e Genetica, Laboratori di Antropologia, Università di Florence, Italy
5 Unitat d'Antropologia, Dept. de Biologia Animal, Universitat de Barcelona, Barcelona, Spain

* To whom correspondence should be addressed.
Carles Lalueza-Fox, E-mail: clalueza{at}ub.edu


  Abstract

DNA contamination arising from the manipulation of ancient calcified tissue samples is a poorly understood, yet fundamental problem that affects the reliability of ancient DNA studies. We have typed the mitochondrial DNA hypervariable region I (HVR1) of the only six people involved in the excavation, washing and subsequent anthropological and genetic study of 23 Neolithic remains excavated from Granollers (Barcelona, Spain), and examined for their presence among the 572 clones generated during the aDNA analyses of teeth from these samples. 17.13% of the cloned sequences could be unambiguously identified as contaminants, with those derived from the people involved in the retrieval and washing of the remains present in higher frequencies than those of the anthropologist and genetic researchers. This finding confirms for the first time previous hypotheses that teeth samples are most susceptible to contamination at their initial excavation. More worrying, the cloned contaminant sequences exhibit substitutions that can be attributed to DNA damage after the contamination event, and we demonstrate that the level of such damage increases with time; contaminants that are >10 years old have approximately five times more damage than those that are recent. Furthermore, we demonstrate that in this dataset, the damage rate of the old contaminant sequences is indistinguishable from that of the endogenous DNA sequences. As such, the commonly used argument that miscoding lesions observed among cloned aDNA sequences can be used to support data authenticity, is misleading in scenarios where the presence of old contaminant sequences is possible. We argue therefore that the typing of those involved in the manipulation of the ancient human specimens is critical in order to ensure that generated results are accurate.

Keywords: ancient DNA; contamination; human; teeth; post mortem damage.
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