Ancient DNA studies: new perspectives on old samples

The field of ancient DNA studies began twenty-eight years ago with the extraction and sequencing of DNA material from the quagga, a South African equid (Equus quagga quagga) that went extinct in the 19th century [1] and from an Egyptian mummy [2]. These studies used bacterial cloning to amplify small DNA sequences (retrieved from skin fragments of these specimens) and showed that the origin of the extracted genetic material was mainly microbial or fungal. In general, endogenous DNA was composed of very low concentrations of short and damaged fragments of multi-copy loci, such as mitochondrial DNA (mtDNA).A few years later, with the development of PCR (polymerase chain reaction) it became possible to routinely amplify and study surviving ancient DNA molecules even if only in a single copy, resulting in a rapid increase and diversification of ancient DNA research [3-5]. However, due to the enormous power of PCR to amplify even a few copies of DNA sequences, modern DNA contamination has become a crucial problem. For this reason, many of the most extravagant reports on ancient DNA, including claims of DNA sequences surviving for millions of years in plants [6-8] and dinosaur bones [9], have been disputed and actually disregarded. Studies on ancient DNA need to deal with technical problems that are specific to this field. The first difficulty is the production of sufficient quantities of authentic DNA sequences to make a study conclusive. This difficulty is a consequence of post-mortem DNA degradation processes, which can cause miscoding lesions, potentially leading to sequence errors, or physical destruction of the DNA molecule, thus increasing the risk for preferential amplification of exogenous contaminant sequences (Table？1). To deal with this issue, researchers have outlined a series of guidelines to ensure the quality of ancient DNA data and the reliability of consequent conclusions [5]. Over the years, these guidelines have gradually evolved into a more detailed a