title: Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum.
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.
authors.affiliation: Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Henrik B
authors.initials: HB
authors.lastname: Hansen
authors.affiliation: Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Peter B
authors.initials: PB
authors.lastname: Damgaard
authors.affiliation: Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Ashot
authors.initials: A
authors.lastname: Margaryan
authors.affiliation: Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Jesper
authors.initials: J
authors.lastname: Stenderup
authors.affiliation: Unit of Forensic Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Niels
authors.initials: N
authors.lastname: Lynnerup
authors.affiliation: Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.|Department of Zoology, University of Cambridge, Cambridge, United Kingdom.|Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.affiliation: Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Morten E
authors.initials: ME
authors.lastname: Allentoft
mesh_terms: D000072441:DNA, Ancient / Q000737:chemistry* / Q000302:isolation & purification; D004272:DNA, Mitochondrial / Q000737:chemistry* / Q000235:genetics; D003739:Dental Cementum / Q000737:chemistry*; D006801:Humans; D010579:Petrous Bone / Q000737:chemistry*; D014070:Tooth / Q000737:chemistry
chemical_list: D000072441:DNA, Ancient; D004272:DNA, Mitochondrial