Ancient DNA: Recovery and Analysis


Ancient deoxyribonucleic acid (DNA) can be recovered from any preserved organic remains of both dead and living organisms and is characterized by degradation down to a few hundred base pairs. The analysis requires especially adapted parameters for DNA extraction, PCR (polymerase chain reaction)‐based amplification and specific strategies for data validation.

Keywords: ancient DNA; DNA preservation; DNA extraction; contamination; authentification

Figure 1.

Thin cross‐sections of two medieval femoral bones. (a) The specimen shows large areas that have been destroyed by so‐called bore‐channels as a result of microorganisms colonizing the bone. If the biogenic decay is highly advanced, then the chance of extracting DNA indigenous to the specimen is very low. (b) An almost intact specimen. Given an effective purification of the ancient DNA extract that removes possible enzyme inhibitors, specimens such as this are usually highly suitable for successful PCR analysis.

Figure 2.

Electropherograms of multiplex autosomal STR amplifications (‘genetic fingerprinting’) of three medieval bone specimens (WG 342 in lane 12, WG 631 in lane 17 and WG 134 in lane 15). The amplification products generated by dye‐labelled primers occur in different colours (B=blue, G=green and Y=yellow). Typically, genetic fingerprinting of degraded DNA shows significantly lower peak heights (vertical scale in dimensionless fluorescence units) for fragments exceeding 200 bp (horizontal scale). This indicates that comparatively few long intact templates were present in the ancient DNA extract, although many templates contained fragment lengths smaller than 200 bp.



Bailey JF, Henneberg M and Colson IB (1999) Monkey business in Pompeii–unique find of a juvenile barbary macaque skeleton in Pompeii identified using osteology and ancient DNA techniques. Molecular Biology of Evolution 16: 1410–1414.

Barnes I, Matheus P, Shapiro B, Jensen D and Cooper A (2002) Dynamics of pleistocene population extinctions in Beringian brown bears. Science 295: 2267–2270.

Baron H, Hummel S and Herrmann B (1996) Mycobacterium tuberculosis complex DNA in ancient human bones. Journal of Archaeological Science 23: 667–671.

Beauval C, Maureille B, Lacrampe‐Cuyaubere F et al. (2005) A late Neanderthal femur from Les Rochers‐de‐Villeneuve, France. Proceedings of the National Academy of Sciences of the USA 102: 7085–7090.

Binladen J, Wiuf C, Gilbert MTP et al. (2006) Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics 172: 733–741.

Burger J, Hummel S, Herrmann B and Henke W (1999) DNA preservation: a microsatellite‐DNA study on ancient skeletal remains. Electrophoresis 20: 1722–1728.

Gerstenberger J, Hummel S, Schultes T, Häck B and Herrmann B (1999) Reconstruction of a historical genealogy by means of STR analysis and Y‐haplotyping of ancient DNA. European Journal of Human Genetics 7: 469–477.

Hansen AJ, Mitchell DL, Wiuf C et al. (2006) Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics 173: 1175–1179.

Hofreiter M, Jaenicke V, Serre D, von Haesler A and Pääbo S (2001) DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Research 29: 4793–4799.

Höss M and Pääbo S (1993) DNA extraction from Pleistocene bones by a silica‐based purification method. Nucleic Acids Research 21: 3913–3914.

Hummel S (2003) Ancient DNA Typing. Methods, Strategies and Applications. Heidelberg: Springer.

Hummel S (2006) Ancient DNA. In: Henke W and Tattersal I (eds) Handbook of Palaeoanthropology. Heidelberg: Springer.

Hummel S, Schmidt D, Kremeyer B, Herrmann B and Oppermann M (2005) Detection of the CCR5 delta 32 HIV resistance gene in Bronze Age skeletons. Genes and Immunity 6: 371–374.

Hummel S, Schultes T, Bramanti B and Herrmann B (1999) Ancient DNA profiling by megaplex amplifications. Electrophoresis 20: 1717–1721.

Krings M, Stone A and Schmitz RW (1997) Neandertal DNA sequences and the origin of modern humans. Cell 90: 19–30.

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

Loreille O, Orlando L and Patou‐Mathies M (2001) Ancient DNA analysis reveals divergence of cave bear Ursus spelaeus, and brown bear, Ursus arctos, lineages. Current Biology 11: 200–203.

Meijer H, Perizonius WRK and Geraedts JPM (1992) Recovery and identification of DNA sequences harboured in preserved ancient human bones. Biochemical and Biophysical Research Communications 183: 367–374.

Orlando L, Bonjean D, Bocherens H et al. (2002) Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time. Molecular Biology of Evolution 19: 1920–1933.

Ovchinnikov IV, Gotherstrom A and Romanova GP (2000) Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404: 490–493.

Rogaev EI, Moliaka YK, Malyarchuk BA et al. (2006) Complete mitochondrial genome and Phylogeny of Pleistocene mammoth Mammuthus primigenius. PLoS Biology 4(3). Epub February 7.

Römpler H, Rohland N, Lalueza‐Fox C et al. (2006) Nuclear gene indicates coat‐color polymorphism in mammoths. Science 313: 62.

Schilz F (2006) Molekulargenetische Verwandtschaftsanalysen am prähistorischen Skelettkollektiv der Lichtensteinhöhle. Dissertation, Göttingen.

Schilz F, Schmidt D and Hummel S (2005) Automated purification of DNA from bones of a Bronze Age family using the BioRobot® EZ1 workstation. Qiagen Application Note.

Schmidt T, Hummel S and Herrmann B (1995) Evidence of contamination in PCR laboratory disposables. Naturwissenschaften 82: 423–431.

Scholz M, Hengst S, Broghammer M and Pusch CM (2001) Intrapopulational relationships in ancient societies: a multidisciplinary study. Zeitschrift für Morphologie und Anthropologie 83: 5–21.

Schultes T, Hummel S and Herrmann B (2000) Ancient DNA‐typing approaches for the determination of kinship in a disturbed collective burial site. Anthropologischer Anzeiger 58: 37–44.

Yang H, Golenberg EM and Shoshani J (1997) Proboscidean DNA from museum and fossil specimens: an assessment of ancient DNA extraction and amplification techniques. Biochemical Genetics 35: 165–179.

Further Reading

Bramanti B, Hummel S, Schultes T and Herrmann B (2000) Genetic characterization of a historical human society by means of aDNA analysis of autosomal STRs. Biennial Books of EAA 1: 147–163.

Briggs AW, Stenzel U, Johnson PL et al. (2007) Patterns of damage in genomic DNA sequences from a Neanderthal. Proceedings of the National Academy of Sciences of the USA 104: 14616–14621.

Brotherton P, Edicott P, Sanchez JJ et al. (2007) Novel high‐resolution characterization of ancient DNA reveals C>U‐type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Research 35: 5717–5728.

Di Bernado G, Del Gaudio S, Cammarota M et al. (2002) Enzymatic repair of selected cross‐linked homoduplex molecules enhances nuclear gene rescue from Pompeii and Herculaneum remains. Nucleic Acids Research 30: e16.

Dixon RA and Roberts CA (2001) Modern and ancient scourges: the application of ancient DNA to the analysis of tuberculosis and leprosy from archaeologically derived human remains. Ancient Biomolecules 3: 181–193.

Gill P, Ivanov PL and Kimpton C (1994) Identification of the remains of the Romanov family by DNA analysis. Nature Genetics 6: 130–135.

Greenblatt CL (ed.) (1998) Digging for Pathogens. Rehovot, Israel: Balaban Publishers.

Herrmann B and Hummel S (eds) (1994) Ancient DNA. New York: Springer.

Hofreiter M, Serre D, Poinar HN, Kuch M and Pääbo S (2001) Ancient DNA. Nature Reviews. Genetics 2: 353–359.

Hummel S (2002) Ancient DNA Typing. Methods, Strategies and Applications. Heidelberg: Springer.

Hummel S and Schultes T (2000) From skeletons to fingerprints – STR typing of ancient DNA. Ancient Biomolecules 3: 103–116.

Jehaes E, Decorte R and Peneau A (1998) Mitochondrial DNA analysis on remains of a putative son of Louis XVII, King of France and Marie‐Antoinette. European Journal of Human Genetics 6: 383–395.

Kaestle FA and Smith DG (2001) Ancient mitochondrial DNA evidence for prehistoric population movement: the Numic expansion. American Journal of Physical Anthropology 115: 1–12.

Lalueza‐Fox C, Römpler H, Caramelli D et al. (2007) A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science 318: 1453–1454.

Lambert DM, Ritchie PA, Millar CD et al. (2002) Rates of evolution in ancient DNA from Adélie penguins. Science 295: 2270–2273.

Poinar HN, Kuch M and Sobolik KD (2001) A molecular analysis of dietary diversity for three archaic Native Americans. Proceedings of the National Academy of Sciences of the USA 98: 4317–4322.

Rollo F, Ubaldi M, Ermini L and Marota I (2002) Ötzi's last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Alps. Proceedings of the National Academy of Sciences of the USA 99: 12594–12599.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Hummel, Susanne(Jul 2008) Ancient DNA: Recovery and Analysis. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0005342.pub2]