Comparing ancient DNA preservation in petrous bone and tooth cementum

Large-scale genomic analyses of ancient human populations have become feasiblepartly due to refined sampling methods. The inner part of petrous bones and thecementum layer in teeth roots are currently recognized as the best substrates for suchresearch. We here present a comparative analysis of DNA preservation in these twosubstrates obtained from the same human skulls, across a range of different ages andpreservation environments. Both substrates display significantly higher endogenousDNA content (average of 16.4% and 40.0% for teeth and petrous bones, respectively)than parietal skull bone (average of 2.2%). Despite sample-to-sample variation,petrous bone overall performs better than tooth cementum (p = 0.001). This difference,however, is driven largely by a cluster of viking skeletons from one particular locality,showing relatively poor molecular tooth preservation (<10% endogenous DNA). In theremaining skeletons there is no systematic difference between the two substrates. Acrude preservation label (good/bad) applied to each sample prior to DNA-extractionpredicted the above/below 10% endogenous DNA threshold in 80% of the cases.Interestingly, we observe signficantly higher levels of cytosine to thymine deaminationdamage and lower proportions of mitochondrial/nuclear DNA in petrous bonecompared to tooth cementum. Lastly, we show that petrous bones from ancientcremated individuals contain no measurable levels of authentic human DNA. Based onthese findings we discuss the pros and cons of sampling the different elements.