Real-time quantitative PCR to assess the authenticity of ancient DNA amplification

Molecular analysis of DNA preserved in archaeological bone allows bypassing of certain palaeontological biases. Studies of DNA in fossils are based on the PCR amplification of the small number of molecules that have not been destroyed over time by diagenetic processes. The sensitivity of the method, the presence of polymerase inhibitors in the fossil extracts, the small number of authentic ancient DNA molecules, and their numerous chemical modifications render this powerful approach unreliable and have led to many controversies. Here we show that real-time PCR is the method of choice to assess the initial number of genuine ancient DNA molecules in the extracts, the effect of inhibitors and the presence of low concentrations of contaminating modern target molecules. We suggest that this methodology will help to identify contaminations, to better interpret PCR results and to render ancient DNA studies more reliable. (C) 2004 Elsevier Ltd. All rights reserved.