Abstract
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.
Highlights
With the introduction of next-generation sequencing (NGS), ancient DNA studies on humans have progressed from analyses of a few hundred basepairs of mitochondrial DNA to large-scale population genomic studies [1,2,3]
We present a comparative analysis of DNA preservation in tooth cementum and petrous bone obtained from ancient human skulls, from across a range of different ages and preservation environments
Plotting paired values of endogenous DNA content on a 2-dimensinal plot (Fig 2), we see that the endogenous content in petrous bone is not a good predictor of endogenous content in teeth according to a linear model
Summary
With the introduction of next-generation sequencing (NGS), ancient DNA (aDNA) studies on humans have progressed from analyses of a few hundred basepairs of mitochondrial DNA to large-scale population genomic studies [1,2,3]. The feasibility of such projects rely on having access to many ancient samples with sufficient biomolecule preservation. Owing to the indiscriminate nature of ’shotgun’ sequencing, the proportion of DNA that derives from the target species—the endogenous DNA content—is a crucial factor. Ancient DNA Preservation in Tooth and Petrous Bone collection and analysis, decision to publish, or preparation of the manuscript
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