A minimally destructive protocol for DNA extraction from ancient teeth
- Éadaoin Harney1,2,3,4,28,
- Olivia Cheronet5,28,
- Daniel M. Fernandes5,6,
- Kendra Sirak3,4,
- Matthew Mah3,7,8,
- Rebecca Bernardos3,8,
- Nicole Adamski3,8,
- Nasreen Broomandkhoshbacht3,8,
- Kimberly Callan3,8,
- Ann Marie Lawson3,8,
- Jonas Oppenheimer3,8,
- Kristin Stewardson3,8,
- Fatma Zalzala3,8,
- Alexandra Anders9,
- Francesca Candilio10,
- Mihai Constantinescu11,
- Alfredo Coppa3,5,12,
- Ion Ciobanu13,14,
- János Dani15,
- Zsolt Gallina16,
- Francesco Genchi12,
- Emese Gyöngyvér Nagy15,
- Tamás Hajdu17,18,
- Magdolna Hellebrandt19,
- Antónia Horváth19,
- Ágnes Király20,
- Krisztián Kiss17,18,
- Barbara Kolozsi15,
- Péter Kovács21,
- Kitti Köhler20,
- Michaela Lucci22,
- Ildikó Pap18,
- Sergiu Popovici23,
- Pál Raczky9,
- Angela Simalcsik14,24,
- Tamás Szeniczey17,18,
- Sergey Vasilyev25,26,
- Cristian Virag27,
- Nadin Rohland3,7,
- David Reich2,3,4,7,8 and
- Ron Pinhasi5
- 1Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA;
- 2The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, Massachusetts 02138, USA and Jena D-07745, Germany;
- 3Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
- 4Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA;
- 5Department of Evolutionary Anthropology, University of Vienna, Vienna 1090, Austria;
- 6CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal;
- 7Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA;
- 8Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA;
- 9Institute of Archaeological Sciences, Eötvös Loránd University, 1088 Budapest, Hungary;
- 10Superintendency of Archaeology, Fine Arts and Landscape for the City of Cagliari and the Provinces of Oristano and South Sardinia, 09121 Cagliari, Italy;
- 11Fr. I. Rainer Institute of Anthropology, Bucharest 050711, Romania;
- 12Department of Environmental Biology, Sapienza University, 00185 Rome, Italy;
- 13Cultural-Natural Reserve “Orheiul Vechi”, 3552 Orhei, Republic of Moldova;
- 14Institute of Bioarchaeological and Ethnocultural Research, 2012 Chișinău, Republic of Moldova;
- 15Déri Museum, 4026 Debrecen, Hungary;
- 16Ásatárs Kulturális, Régészeti Szolgáltató és Kereskedelmi Limited, 6000 Kecskemét, Hungary;
- 17Department of Biological Anthropology, Eötvös Loránd University, 1171 Budapest, Hungary;
- 18Department of Anthropology, Hungarian Natural History Museum, 1083 Budapest, Hungary;
- 19Herman Ottó Museum, 3529 Miskolc, Hungary;
- 20Institute of Archaeology, Research Centre for the Humanities, 1097 Budapest, Hungary;
- 21Damjanich János Museum, 5000 Szolnok, Hungary;
- 22Department of History, Anthropology, Religion, Arts and Performing Arts, Sapienza University, 00185 Rome, Italy;
- 23National Agency for Archaeology, 2012 Chișinău, Republic of Moldova;
- 24Olga Necrasov Center for Anthropological Research, Romanian Academy, 700481 Iasi, Romania;
- 25Institute of Ethnology and Anthropology of the Russian Academy of Sciences, 119991 Moscow, Russia;
- 26Center for Egyptological Studies of the Russian Academy of Sciences, 119071 Moscow, Russia;
- 27Satu Mare County Museum, 440031 Satu Mare, Romania
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↵28 These authors contributed equally to this work.
Abstract
Ancient DNA sampling methods—although optimized for efficient DNA extraction—are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.267534.120.
- Received June 17, 2020.
- Accepted December 14, 2020.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
