The efficacy of whole human genome capture on ancient dental calculus and dentin

Bibliographic Data

ID8316239
AuthorsKirsten A Ziesemer (0000-0001-7783-1126, Faculty of Archaeology Leiden University Leiden The Netherlands), Jazmín Ramos‐Madrigal (0000-0002-1661-7991, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark), Allison E Mann (0000-0001-7170-6017, Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology University of Oklahoma Norman Oklahoma), Bernd W Brandt (0000-0002-1155-1989, Department of Preventive Dentistry Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam Amsterdam The Netherlands), Krithivasan Sankaranarayanan (0000-0002-4767-311X, Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology University of Oklahoma Norman Oklahoma), Andrew T Ozga (0000-0003-4540-7106, School of Human Evolution and Social Change Arizona State University Tempe Arizona), M L P Hoogland (0000-0002-6355-1278, Leiden University), Menno Hoogland (Faculty of Archaeology Leiden University Leiden The Netherlands), Courtney A Hofman (0000-0002-6808-3370, Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology University of Oklahoma Norman Oklahoma), Domingo C Salazar‐garcía (0000-0002-8017-0194, Department of Archaeogenetics Max Planck Institute for the Science of Human History Jena Germany), B Frohlich (0000-0003-4444-5733, Dartmouth College), Bruno Frøhlich (Department of Anthropology Hanover New Hampshire), G R Milner (0000-0002-3330-0726, Pennsylvania State University), Anne C Stone (0000-0001-8021-8314, School of Human Evolution and Social Change Arizona State University Tempe Arizona), M Aldenderfer (0000-0002-7033-4319, University of California, Merced), Cecil M Lewis (0000-0002-2198-3427, Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology University of Oklahoma Norman Oklahoma), C L Hofman (0000-0003-4447-5019, Leiden University), Christina Warinner (0000-0002-4528-5877, Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology University of Oklahoma Norman Oklahoma), H Schroeder (0000-0002-6743-0270, Faculty of Archaeology Leiden University Leiden The Netherlands, corresponding author)
Year2019
Volume168
Issue3
Pages496-509
Publication date2019-03-01
Peer ReviewedYes
Open AccessYes
TypeARTICLE
VenueAmerican Journal of Physical Anthropology (JOURNAL)
Journal identifiersISSN: 0002-9483 • E-ISSN: 1096-8644
PublisherWiley (PUBLISHER • GB)
DOI10.1002/ajpa.23763
PMID30586168
OpenAlexW2905622830
LanguageEN
Citations received9
References cited57

OBJECTIVES: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. MATERIALS AND METHODS: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing. RESULTS: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction. DISCUSSION: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples

Ancient DNA · Biology · Calculus (dental) · Computational biology · Dentin · DNA · DNA sequencing · Gene · Genome · Human genome · Population · Dentistry · Forensic and Genetic Research · Forensic Anthropology and Bioarchaeology Studies · Genetics · Medicine · Race, Genetics, and Society