Poor preservation is a highly constraining factor in ancient DNA research. In the majority of ancient specimens, endogenous DNA molecules represent a minor fraction of the total amount of DNA, rendering shotgun sequencing inefficient for obtaining genomic data. It is therefore necessary to be extremely selective during the sampling process, ideally relying on published data and comparative analyses. Such data are, however, in short supply.
NGS data offer an excellent means to obtain detailed insigths into the molecular preservation of a given specimen. As a convenient "by-product" of shotgun sequencing, it is possible to estimate the endogenous DNA content, the average fragment lenght, the DNA decay rate and half-life, and the deamination damage fraction.
Using NGS data from hundreds of ancient skeletons we compare these signatures of molecular preservation in different skeletal elements, and in skeletons that differ in respect to age, preservation environment, and burial temperature. We support the findings with similar data from in situ burial experiments. While some degree of uncertainty persists, our results show that factors such as preservation state, burial temperature, and age can indeed provide grounds for predicting molecular preservation in ancient biological remains and the potential for genome-scale research.