Large-scale genomic analyses of ancient human populations have become feasible 
partly due to refined sampling methods. The inner part of petrous bones and the 
cementum layer in teeth roots are currently recognized as the best substrates 
for such research. We present a comparative analysis of DNA preservation in 
these two substrates obtained from the same human skulls, across a range of 
different ages and preservation environments. Both substrates display 
significantly higher endogenous DNA 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 the remaining 
skeletons there is no systematic difference between the two substrates. A crude 
preservation (good/bad) applied to each sample prior to DNA-extraction predicted 
the above/below 10% endogenous DNA threshold in 80% of the cases. Interestingly, 
we observe signficantly higher levels of cytosine to thymine deamination damage 
and lower proportions of mitochondrial/nuclear DNA in petrous bone compared to 
tooth cementum. Lastly, we show that petrous bones from ancient cremated 
individuals contain no measurable levels of authentic human DNA. Based on these 
findings we discuss the pros and cons of sampling the different elements.