Skip to main content

Methods for the Study of Ancient DNA

  • Protocol
Forensic DNA Typing Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 297))

Abstract

Whereas the analysis of ancient DNA (aDNA) has become an increasingly popular mode of investigation in both archaeological and evolutionary studies, this approach is complicated by the degraded nature of ancient nucleic acids, the presence of enzymatic inhibitors in aDNA extracts, as well as the risk of contamination during either excavation or manipulation of samples. Despite these difficulties, numerous methods have been developed to optimize the recovery, study, and authentication of aDNA. In this article, we describe the procedures used in our laboratory to extract and amplify informative DNA segments from prehistoric or protohistoric human samples, as well as the precautions and strategies implemented to avoid or at least detect contaminations.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 159.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Higuchi, R., Bowman, B., Freiberger, M., Ryder, O. A., and Wilson, A. C. (1984) DNA sequences from the quagga an extinct member of the horse family. Nature 312, 282–284.

    Article  PubMed  CAS  Google Scholar 

  2. Pääbo, S. (1985) Molecular cloning of Ancient Egyptian mummy DNA. Nature 314, 644–645.

    Article  PubMed  Google Scholar 

  3. Stone, A. C., and Stoneking, M. (1998) mtDNA analysis of a prehistoric Oneta population: implications for the peopling of the New World. Am. J. Hum. Genet. 62, 1153–1170.

    Article  PubMed  CAS  Google Scholar 

  4. Raoult, D., Aboudharam, G, Crubézy, E., Larrouy, G., Ludes, B., and Drancourt, M. (2000) Molecular identification by “suicide PCR” of Yersinia pestis as the agent of Medieval Black Death. Proc. Natl. Acad. Sci. USA 97, 12800–12803.

    Article  PubMed  CAS  Google Scholar 

  5. Clisson, I., Keyser, C., Francfort, H.-P., Crubézy, E., Samashev, K., and Ludes B. (2002) Genetic analysis of human remains from a frozen kurgan in Kazakhstan (Berel site, 200-300 B.C.). Int. J. Legal Med. 116, 304–308.

    PubMed  CAS  Google Scholar 

  6. Keyser-Tracqui, C., Crubézy, E., and Ludes B. (2003) Nuclear and mitochondrial DNA analysis a 2,000-year-old necropolis in the Egyin Gol valley of Mongolia. Am. J. Hum. Genet. 73, 247–260.

    Article  PubMed  CAS  Google Scholar 

  7. Mullis, K. B., and Faloona, F. A. (1987) Specific synthesis of DNA in vitro via a polymerase-catalysed chain reaction. Methods Enzymol. 155, 335–350.

    Article  PubMed  CAS  Google Scholar 

  8. Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature 362, 709–715.

    Article  PubMed  CAS  Google Scholar 

  9. Pääbo, S. (1989) Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc. Natl. Acad. Sci. USA 86, 1939–1943.

    Article  PubMed  Google Scholar 

  10. Scholtz, M., Giddings, I., and Pusch, C.M. (1998) A polymerase chain reaction inhibitor of ancient hard and soft tissue DNA extracts is determined as human collagen type I. Anal. Biochem. 92, 463–471.

    Google Scholar 

  11. Handt, O., Höss, M., Krings M., and Pääbo S. (1994) Ancient DNA: methodological challenges. Experientia 50, 521–619.

    Article  Google Scholar 

  12. Cooper, A., and Poinar, H. N. (2000) Ancient DNA: do it right or not at all. Science 289, 1139.

    Article  PubMed  CAS  Google Scholar 

  13. Yang, D. G., Eng, B., Waye, J. S., Dudar, J. C., and Saunders, S. R. (1998) Technical note: improved DNA extraction from ancient bones using silica-based spin columns. Am. J. Phys. Anthropol. 105, 539–543.

    Article  PubMed  CAS  Google Scholar 

  14. Kolman, C. J. and Tuross, N. (2000) Ancient DNA analysis of human populations. Am. J. Phys. Anthropol. 111, 5–23.

    Article  PubMed  CAS  Google Scholar 

  15. Gill, P., Ivanov, P. L., Kimpton, C., Piercy, R., Benson, N., and Tully, G. (1994) Identification of the remains of the Romanov family by DNA analysis. Nat. Genet. 6, 130–135.

    Article  PubMed  CAS  Google Scholar 

  16. Schmerer, W. M., Hummel, S., and Herrmann, B. (1999) Optimized DNA extraction to improve reproducibility of short tandem repeat genotyping with highly degraded DNA as target. Electrophoresis 20, 1712–1716.

    Article  PubMed  CAS  Google Scholar 

  17. Hummel, S., Bramanti, B., Schultes, T., Kahle, M., Haffner, S., and Herrmann, B. (2000) Megaplex DNA typing can provide a strong indication of the authenticity of ancient DNA amplifications by clearly recognizing any possible type of modern contamination. Anthrop. Anz 58, 15–21.

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Humana Press Inc., Totowa, NJ

About this protocol

Cite this protocol

Keyser-Tracqui, C., Ludes, B. (2005). Methods for the Study of Ancient DNA. In: Carracedo, A. (eds) Forensic DNA Typing Protocols. Methods in Molecular Biology, vol 297. Humana Press. https://doi.org/10.1385/1-59259-867-6:253

Download citation

  • DOI: https://doi.org/10.1385/1-59259-867-6:253

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-264-3

  • Online ISBN: 978-1-59259-867-0

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics