DNA contamination of ancient teeth

Genetic studies of ancient human populations usually rely on amplification of DNA preserved in dental samples. Two main problems plague such studies. First, DNA suffers damage after death and until it is studied by scientists. Therefore, it is not clear which parts of a DNA sequence are due to the genetic makeup of the ancient individual, and which ones have been modified after his/her death.

The second problem is due to the fact that skeletal remains are usually handled by many people, e.g., excavators, archaeologists, anthropologists, after they are taken off the ground. This may introduce the handlers' DNA on them. Then, when DNA is amplified, it is not clear whether the observed sequence is from the ancient individual or the more recent handlers. During recent excavations, people take care not to contaminate samples. Moreover, they tend to record meticulously the group of individuals handling the remains, since this is useful to check whether a DNA sequence may belong to one of them. Unfortunately, many useful ancient skeletons were excavated before such precautions were in place.

The identification of these two problems does not, in itself, quantify their severity. How much faith should we have in DNA sequences amplified from ancient teeth? This new paper is a welcome contribution to tackling this important problem.

Molecular Biology and Evolution (Advance Access)

Tracking Down Human Contamination in Ancient Human Teeth

María Lourdes Sampietro et al.

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.

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