Ancient DNA: Problems and perspectives for molecular microbial palaeoecology

DNA can be extracted from a variety of human, animal and plant archaeologic al, palaeontological, and museum specimens. We can use sequence information from an old or ancient double helix to address questions ranging from the sex determination of a Bronze Age human skeleton to the assignment of a stu ffed bird to its proper systematic position. While the methods employed to isolate, replicate and sequence ancient and modem DNA are basically the sam e, manipulation and analysis of the former requires more stringent approach es. DNA in archaeological deposits is affected by hydrolytic and oxidative damage, resulting in base loss, base modification and strand cleavage. The chances of DNA surviving over long periods is low, unless the environment o ffers particularly favourable conditions. Theoretical calculations and empi rical observations suggest that DNA may not be able to survive for more tha n 50,000-100,000 years. Because of the tiny amounts of DNA which can be ext racted from an archaeological specimen and the sensitivity of the detection methods employed, stringent laboratory precautions and systematic controls are required to avoid contamination. In addition, several criteria of auth enticity have to be met. The use of the DNA technology to describe ancient bacterial communities is discussed, including particular problems in their study mainly due to contamination by modem microorganisms. Despite these pr oblems, thanks to an accurate archaeometrical evaluation of the specimens a nd the application of appropriate criteria ("palaeoecological consistency") , it is possible, at least under some circumstances, to determine the compo sition of the original microbial flora of an ancient human or animal body.