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Abstract
Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007–0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003–70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.
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1 Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany; Department of Anthropology, University of Oklahoma, Norman, Oklahoma, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, USA
2 Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
3 Faculty of Archaeology, Leiden University, Leiden, The Netherlands
4 Faculty of Archaeology, Leiden University, Leiden, The Netherlands; Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
5 Department of Anthropology, University of Oklahoma, Norman, Oklahoma, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, USA; Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
6 Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, USA; Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
7 Department of Anthropology, University of Oklahoma, Norman, Oklahoma, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, USA
8 Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany; Grupo de Investigación en Prehistoria IT-622-13 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain
9 Department of Anthropology, Dartmouth College, Hanover, New Hampshire, USA; Department of Anthropology, Smithsonian Institution, Washington DC, USA
10 School of Social Sciences, Humanities, and Arts, University of California Merced, Merced, California, USA
11 Institute of Technology Sligo, Sligo, Ireland
12 Department of Anthropology, Penn State University, University Park, Pennsylvania, USA
13 Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA; School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA; Institute of Human Origins, Arizona State University, Tempe, Arizona, USA