Novel methodology for distinguishing between ancient and contaminating DNA in human archaeological remains

Since the late 1980s it has been known that DNA is sometimes preserved in the bones and other remains of humans and other animals, and that in some cases this 'ancient' DNA can be retrieved from specimens up to 50,000 years in age. The study of ancient DNA has had a huge impact in zoology, enabling researchers to obtain DNA sequences from extinct species such as mammoths and cave bears, leading to new discoveries about the evolutionary relationships between these animals and their living relatives, and providing insights into the reasons why these species failed to survive the climate changes of the last 50,000 years. Potentially, ancient DNA could have an equally great impact in archaeology, for example by enabling the family relationships between groups of human skeletons to be traced and by charting the migrations of prehistoric human populations. Sadly, this potential has not been realized, for the simple reason that specimens such as bones are easily contaminated with modern human DNA by handling, and it is difficult to distinguish this contamination from the genuine ancient DNA in a specimen. A number of researchers, including us, have suggested solutions to this problem, but none of these 'solutions' have been completely successful. Our best attempt so far is based on the fact that ancient DNA is chemically different from modern DNA because the ancient molecules have become partially degraded. Identifying the degraded molecules in a bone extract should therefore pinpoint which ones are ancient DNA. But there is a complication: it turns out that even the contaminating DNA is degraded to a certain extent, because usually it is deposited on a specimen during excavation, and this can be months or years before the DNA in the specimen is examined, enough time for the contaminating DNA to begin to degrade. Identifying the ancient DNA therefore becomes more difficult because, rather than simply identifying which molecules are degraded, we must distinguish the ones which are most degraded (and which could therefore be ancient DNA) from the ones that are only slightly degraded (and are therefore likely to be modern contaminants). We have tried to do this with the standard methods used to study ancient DNA, with some success, but these methods are not really suitable for this type of analysis. In this project we plan to test a new method, called single primer extension (SPEX), which was recently developed as a tool for obtaining more accurate DNA sequences from extinct species such as the moa and Tasmanian wolf. Unlike the standard ancient DNA methods, SPEX does allow accurate comparisons of the amounts of damage in different DNA molecules, and we therefore believe that SPEX will enable us to distinguish the genuine ancient DNA in a human specimen from the contaminants. The objective of the project is therefore to apply SPEX to analysis of the DNA in a human bone, to see if our expectations are fulfilled.