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Preservation of ancient DNA in thermally damaged archaeological bone

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Abstract

Evolutionary biologists are increasingly relying on ancient DNA from archaeological animal bones to study processes such as domestication and population dispersals. As many animal bones found on archaeological sites are likely to have been cooked, the potential for DNA preservation must be carefully considered to maximise the chance of amplification success. Here, we assess the preservation of mitochondrial DNA in a medieval cattle bone assemblage from Coppergate, York, UK. These bones have variable degrees of thermal alterations to bone collagen fibrils, indicative of cooking. Our results show that DNA preservation is not reliant on the presence of intact collagen fibrils. In fact, a greater number of template molecules could be extracted from bones with damaged collagen. We conclude that moderate heating of bone may enhance the retention of DNA fragments. Our results also indicate that ancient DNA preservation is highly variable, even within a relatively recent assemblage from contexts conducive to organic preservation, and that diagenetic parameters based on protein diagenesis are not always useful for predicting ancient DNA survival.

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Acknowledgements

We wish to thank Professor O’Connor (University of York) for providing the archaeological samples from Coppergate, York. We thank Dr. Tom Gilbert for his useful advice for designing the qPCR and sequencing reactions. We also thank the European Commission (Marie Curie Mobility Actions; MEIF-CT-2004-0100) and the Ministero dell’Istruzione, dell’Università e della Ricerca (Programmi di Ricerca Scientifica di Rilevante Interesse Nazionale; prot. # 2005057557, allotted to O.R.) for supporting this work as well as NERC (GR9/4760; NERC/S/A/2002/12028) and the Wellcome Trust for supporting the amino acid and collagen analyses and three anonymous referees for their useful comments. The experiments reported in this study comply with the current laws of Italy and the United Kingdom where they were performed.

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Authors and Affiliations

  1. Centro di Antropologia Molecolare per lo studio del DNA antico, Dipartimento di Biologia, Università di Roma “Tor Vergata”, Via della Ricerca Scientifica 1, 00133, Rome, Italy

    Claudio Ottoni, Olga Rickards & Oliver E. Craig

  2. BioArCh, Department of Biology, University of York, Biology S Block, P.O. Box 373, York, YO10 5YW, UK

    Hannah E. C. Koon & Matthew J. Collins

  3. BioArCh, Department of Chemistry, University of York, Biology S Block, P.O. Box 373, York, YO10 5DD, UK

    Kirsty E. H. Penkman

  4. Department of Archaeology, University of York, The King’s Manor York, YO1 7EP, UK

    Oliver E. Craig

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  1. Claudio Ottoni
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  2. Hannah E. C. Koon
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  3. Matthew J. Collins
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  4. Kirsty E. H. Penkman
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  5. Olga Rickards
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  6. Oliver E. Craig
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Correspondence to Oliver E. Craig.

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Ottoni, C., Koon, H.E.C., Collins, M.J. et al. Preservation of ancient DNA in thermally damaged archaeological bone. Naturwissenschaften 96, 267–278 (2009). https://doi.org/10.1007/s00114-008-0478-5

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