21 Ancient DNA

  • Susanne Hummel
Reference work entry


Ancient DNA research, defined as the retrieval and analysis of DNA sequences from various degraded biological source materials, has promoted many biological and medical research fields during the last two decades. In particular, historical anthropology and paleoanthropology stand to benefit from direct access to back-dating genetic data, as has already been shown through applications ranging from individual identification, reconstruction of kinship and marriage patterns to human phylogeny. The DNA-based prerequisites and basic methodological strategies for access to the various types of information are explained, as well as the characteristics of ancient DNA that limit the different approaches. Major restrictions arise from the degradation of ancient DNA down to fragment sizes of at the most only a few hundred base pairs. This fact links ancient DNA analysis almost exclusively to the PCR technique that enables us to deduce genetic information from degraded nucleic acids. Futhermore, ancient DNA extracts regularly consist of only a few intact target sequences, which may additionally reveal sequence deviations due to the degradation process. Both these factors make the analysis vulnerable to the generation of nonauthentic results. These pitfalls of ancient DNA analysis are explained and discussed in detail with reference to the most recent relevant literature. Wherever possible and available, suggestions for strategies to overcome commonly experienced obstacles in ancient DNA analysis are highlighted and evaluated.


Short Tandem Repeat Mass Grave Product Carryover Cambridge Reference Sequence Short Tandem Repeat Typing 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Altschuler EL (2000) Plague as HIV vaccine adjuvant. Med Hypotheses 54: 1003–1004CrossRefPubMedGoogle Scholar
  2. Anderson S, Bankier A, Barrell B, De Bruijn M, Coulson A, Drouin J, Eperon I, Nierlich D, Roe B, Sanger F, Schreier P, Smith A, Staden R, Young I (1981) Sequence and organization of the human mitochondrial genome. Nature 290: 457–465CrossRefPubMedGoogle Scholar
  3. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23: 147CrossRefPubMedGoogle Scholar
  4. Bandelt HJ (2005) Mosaics of ancient mitochondrial DNA: Positive indicators for nonauthenticity. Eur J Hum Genet 13: 1106–1112CrossRefPubMedGoogle Scholar
  5. Barbujani G, Bertorelle G (2001) Genetics and the population history of Europe. Proc Natl Acad Sci USA 98: 22–25PubMedCentralCrossRefPubMedGoogle Scholar
  6. Beauval C, Maureille B, Lacrampe-Cuyaubere F, Serre D, Peressinotto D, Bordes JG, Cochard D, Couchoud I, Dubrasquet D, Laroulandie V, Lenoble A, Mallye JB, Pasty S, Primault J, Rohland N, Paabo S, Trinkaus E (2005) A late Neandertal femur from Les Rochers-de-Villeneuve, France. Proc Natl Acad Sci USA 102: 7085–7090PubMedCentralCrossRefPubMedGoogle Scholar
  7. Binladen J, Wiuf C, Gilbert MTP, Bunce M, Barnett R, Larson G, Greenwood A, Haile J, Ho SYW, Hansen AJ, Willerslev E (2006) Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics 172: 733–741PubMedCentralCrossRefPubMedGoogle Scholar
  8. Bramanti B, Sineo L, Vianello M, Caramelli D, Hummel S, Chiarelli B, Herrmann B (2000) The selective advantage of cystic fibrosis heterocygotes tested by aDNA analysis. Int J Anthropol 15: 255–262CrossRefGoogle Scholar
  9. Brenner CH, Morris JW (1990) Paternity index calculations in single locus hypervariable DNA probes: Validation and other studies. In: Proceedings of the international symposium on human identity 1989, Promega Corporation, pp 21–53Google Scholar
  10. Budowle B, Allard MW, Wilson MR, Chakraborty R (2003) Forensics and mitochondrial DNA: Applications, debates, and foundations. Annu Rev Genomics Hum Genet 4: 119–141CrossRefPubMedGoogle Scholar
  11. Budowle B, Bieber FR, Eisenberg AJ (2005) Forensic aspects of mass disasters: Strategic considerations for DNA-based human identification. Leg Med 7: 230–243CrossRefGoogle Scholar
  12. Burger J, Hummel S, Herrmann B, Henke W (1999) DNA preservation: A microsatellite-DNA study on ancient skeletal remains. Electrophoresis 20: 1722–1728CrossRefPubMedGoogle Scholar
  13. Butler JM (2001) Forensic DNA typing. Biology and technology behind STR markers. Academic Press, San DiegoGoogle Scholar
  14. Cann RL (2001) Genetic clues to dispersal in human populations: Retracing the past from the present. Science 291(5509): 1742–1748CrossRefPubMedGoogle Scholar
  15. Carracedo A, Sanchez-Diz P (2005) Forensic DNA-typing technologies: A review. Methods Mol Biol 297: 1–12PubMedGoogle Scholar
  16. Cavalli-Sforza LL, Feldman MW (2003) The application of molecular genetic approaches to the study of human evolution. Nat Genet 33(Suppl.): 266–275CrossRefPubMedGoogle Scholar
  17. Chakraborty R, Jin L (1993) Determination of relatedness between individuals using DNA fingerprinting. Hum Biol 65: 875–895PubMedGoogle Scholar
  18. Cooper A, Poinar H (2000) Ancient DNA: Do it right or not at all. Science 289: 1139CrossRefPubMedGoogle Scholar
  19. Currat M, Excoffier L (2004) Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biol 2(e421): 2264–2274CrossRefGoogle Scholar
  20. Drancourt M, Raoult D (2005) Palaeomicrobiology: Current issues and perspectives. Nat Rev Microbiol 3: 23–35CrossRefPubMedGoogle Scholar
  21. Fulge M (2005) Laktosetoleranz in der bronzezeitlichen Lichensteinhöhle—Molekulargenetischer Nachweis des Polymorphismus C/T 13910 an prähistorischer DNA. Staatsexamensarbeit, GöttingenGoogle Scholar
  22. Gilbert MTP, Hansen A, Willerslev E, Rudbeck L, Barnes I, Lynnerup N, Cooper A (2003) Characterization of genetic miscoding lesions caused by post-mortem damage. Am J Hum Genet 72: 48–61PubMedCentralCrossRefPubMedGoogle Scholar
  23. Gilbert MTP, Bandelt HJ, Hofreiter M, Barnes I (2005) Assessing ancient DNA studies. Trends Ecol Evol 20: 542–544CrossRefGoogle Scholar
  24. Gill P, Ivanov PL, Kimpton C, Piercy R, Benson N, Tully G, Evett I, Hagelberg E, Sullivan K (1994) Identification of the remains of the Romanov family by DNA analysis. Nat Genet 6: 130–135CrossRefPubMedGoogle Scholar
  25. Greenblatt C, Spigelman M, Vernon K (2003) The impact of “ancient pathogen” studies on the practice of public health. Public Health Rev 31: 81–91PubMedGoogle Scholar
  26. Gugerli F, Parducci L, Petit RJ (2005) Ancient plant DNA: Review and prospects. New Phytol 166: 409–418CrossRefPubMedGoogle Scholar
  27. Haak W, Forster P, Bramanti B, Matsumura S, Brandt G, Tanzer M, Villems R, Renfrew C, Gronenborn D, Alt KW, Burger J (2005) Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science 310: 1016–1018PubMedGoogle Scholar
  28. Hagelberg E, Sykes B, Hedges R (1989) Ancient bone DNA amplified. Nature 342: 485CrossRefPubMedGoogle Scholar
  29. Hauswirth WW (1994) Ancient DNA. Experientia 50: 521–523CrossRefPubMedGoogle Scholar
  30. Herrmann B, Hummel S (1993) Ancient DNA. Recovery and analysis of genetic material from palaeontological, archaeological, museum, medical and forensic specimens. Springer, New YorkGoogle Scholar
  31. Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC (1984) DNA sequences from the quagga, an extinct member of the horse family. Nature 312: 282–284CrossRefPubMedGoogle Scholar
  32. Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S (2001) Ancient DNA. Nat Rev Genet 2: 353–359CrossRefPubMedGoogle Scholar
  33. Hummel S (2003a) Ancient DNA typing: Methods, strategies and applications. Springer, HeidelbergCrossRefGoogle Scholar
  34. Hummel S (2003b) Ancient DNA: Recovery and analysis. Encyclopedia of the human genome. Nature Publ Group (Ref. 342)Google Scholar
  35. Hummel S, Herrmann B (1991) Y-chromosome-specific DNA amplified in ancient human bone. Naturwissenschaften 78: 266–267CrossRefPubMedGoogle Scholar
  36. Hummel S, Bramanti B, Schultes T, Kahle M, Haffner S, 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. Anthropol Anz 58: 15–21PubMedGoogle Scholar
  37. Hummel S, Schmidt D, Kremeyer B, Herrmann B, Oppermann M (2005) Detection of the CCR5 delta 32 HIV resistance gene in Bronze Age skeletons. Genes Immun 6: 371–374CrossRefPubMedGoogle Scholar
  38. Iwamura ES, Soares-Vieira JA, Munoz DR (2004) Human identification and analysis of DNA in bones. Rev Hosp Clin Fac Med Sao Paulo 59: 383–388CrossRefPubMedGoogle Scholar
  39. Jeffreys AJ, Allen MJ, Hagelberg E, Sonnberg A (1992) Identification of the skeletal remains of Josef Mengele by DNA analysis. Forensic Sci Int 56: 65–76CrossRefPubMedGoogle Scholar
  40. Kaessmann H, Pääbo S (2004) The genetical history of humans and the great apes. J Intern Med 251: 1–18CrossRefGoogle Scholar
  41. Kato H, Saito K, Kimura T (2005) A perspective on DNA microarray technology in food and nutritional science. Curr Opin Clin Nutr Metab Care 8: 516–522CrossRefPubMedGoogle Scholar
  42. Keyser-Tracqui C, Crubezy E, Ludes B (2003) Nuclear and mitochondrial DNA analysis of a 2,000-year-old Necropolis in the Egyin Gol Valley of Mongolia. Am J Hum Genet 73: 247–260PubMedCentralCrossRefPubMedGoogle Scholar
  43. Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo S (1997) Neanderthal DNA sequences and the origin of modern humans. Cell 90: 19–30CrossRefPubMedGoogle Scholar
  44. Krings M, Capelli C, Tschentscher F, Geisert H, Meyer S, von Haeseler A, Grossschmidt K, Possnert G, Paunovic M, Paabo S (2000) A view of Neandertal genetic diversity. Nat Genet 26: 144–146CrossRefPubMedGoogle Scholar
  45. Leiva IM, Emmert-Buck MR, Gillespie JW (2003) Handling of clinical tissue specimens for molecular profiling studies. Curr Issues Mol Biol 5: 27–35PubMedGoogle Scholar
  46. Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362: 709–715CrossRefPubMedGoogle Scholar
  47. Malik S, Sudoyo H, Pramoonjago P, Suryadi H, Sukarna T, Njunting M, Sahiratmadja E, Marzuki S (2002) Nuclear mitochondrial interplay in the modulation of the homopolymeric tract length heteroplasmy in the control (D-loop) region of the mitochondrial DNA. Hum Genet 110: 402–411CrossRefPubMedGoogle Scholar
  48. Mariappan MR, Zehnder J, Arber DA, Lay M, Fadare O, Schrijver I (2005) Identification of mislabeled specimen by molecular methods: Case report and review. Int J Surg Pathol 13: 253–258CrossRefPubMedGoogle Scholar
  49. Miraglia M, Berdal KG, Brera C, Corbisier P, Holst-Jensen A, Kok EJ, Marvin HJ, Schimmel H, Rentsch J, van Rie JP, Zagon J (2004) Detection and traceability of genetically modified organisms in the food production chain. Food Chem Toxicol 42: 1157–1180CrossRefPubMedGoogle Scholar
  50. Ovchinnikov IV, Gotherstrom A, Romanova GP, Kharitonov VM, Liden K, Goodwin W (2000) Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404: 490–493CrossRefPubMedGoogle Scholar
  51. Pääbo S (1984) Über den Nachweis von DNA in altägyptischen Mumien. Das Altertum 30: 213–218Google Scholar
  52. Paik S, Kim CY, Song YK, Kim WS (2005) Technology insight: Application of molecular techniques to formalin-fixed paraffin-embedded tissues from breast cancer. Nat Clin Pract Oncol 2: 246–254CrossRefPubMedGoogle Scholar
  53. Pakendorf B, Stoneking M (2005) Mitochondrial DNA and human evolution. Annu Rev Genomics Hum Genet 6: 165–183CrossRefPubMedGoogle Scholar
  54. Puder Y (2005) Molekulargenetische Identifikation der Allelhäufigkeit eines immungenetischen Markers der IL16-Promotorregion bei bronzezeitlichen Individuen aus Mitteleuropa. Diplomarbeit, GöttingenGoogle Scholar
  55. Rannala B, Bertorelle G (2001) Using linked markers to infer the age of a mutation. Hum Mutat 18: 87–100CrossRefPubMedGoogle Scholar
  56. Richards MB, Macaulay VA, Bandelt H-J, Sykes BC (1998) Phylogeography of mitochondrial DNA in western Europe. Ann Hum Genet 62: 241–260CrossRefPubMedGoogle Scholar
  57. Rowold DJ, Herrera RJ (2005) On human STR sub-population structure. Forensic Sci Int 151: 59–69CrossRefPubMedGoogle Scholar
  58. Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N (1985) Enzymatic amplification of P-globulin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230: 1350–1354CrossRefPubMedGoogle Scholar
  59. Schmidt T, Hummel S, Herrmann B (1995) Evidence of contamination in PCR laboratory disposables. Naturwissenschaften 82: 423–431CrossRefPubMedGoogle Scholar
  60. Scott S, Duncan CJ (2001) Biology of plagues: Evidence from historical populations. Cambridge University Press, Cambridge New YorkCrossRefGoogle Scholar
  61. Sipoli Marques MA, Pinto Damasceno LM, Gualberto Pereira HM, Caldeira CM, Pereira Dias BF, de Giacomo Vargens D, Amoedo ND, Volkweis RO, Volkweis Viana RO, Rumjanek FD, Aquino Neto FR (2005) DNA typing: An accessory evidence in doping control. J Forensic Sci 50: 587–592PubMedGoogle Scholar
  62. Stephens JC, Reich DE, Goldstein DB, Shin HD, Smith MW, Carrington M, Winkler C, Huttley GA, Allikmets R, Schriml L, Gerrard B, Malasky M, Ramos MD, Morlot S, Tzetis M, Oddoux C, di Giovine FS, Nasioulas G, Chandler D, Aseev M, Hanson M, Kalaydjieva L, Glavac D, Gasparini P, Kanavakis E, Claustres M, Kambouris M, Ostrer H, Duff G, Baranov V, Sibul H, Metspalu A, Goldman D, Martin M, Duffy D, Schmidtke J, Estivill X, O'Brien S, Dean M (1998) Dating the origin of the CCR5-δ32 AIDS-resistance allele by the coalescence of haplotypes. Am J Hum Genet 62: 1507–1515PubMedCentralCrossRefPubMedGoogle Scholar
  63. Tamaki K, Jeffreys AJ (2005) Human tandem repeat sequences in forensic DNA typing. Leg Med 7: 244–250CrossRefGoogle Scholar
  64. Teletchea F, Laudet V, Hänni C (2005) Food and forensic molecular identification: Update and challenges. Trends Biotechnol 23: 359–366CrossRefPubMedGoogle Scholar
  65. Torroni A, Schurr TG, Yang CC, Szathmary EJ, Williams RC, Schanfield MS, Troup GA, Knowler WC, Lawrence DN, Weiss KM, Wallace DC (1992) Native American mitochondrial DNA analysis indicates that the Amerind and the Nadene populations were founded by two independent migrations. Genetics 130: 153–162PubMedCentralPubMedGoogle Scholar
  66. Torroni A, Schurr TG, Cabell MF, Brown MD, Neel JV, Larsen M, Smith DG, et al (1993) Asian affinities and continental radiation of the four founding Native American mtDNAs. Am J Hum Genet 53: 563–590PubMedCentralPubMedGoogle Scholar
  67. Valenstein PN, Sirota RL (2004) Identification errors in pathology and laboratory medicine. Clin Lab Med 24: 979–996CrossRefPubMedGoogle Scholar
  68. Watson E, Forster P, Richards M, Bandelt H-J(1997) Mitochondrial footprints of human expansions in Africa. Am J Hum Genet 61: 691–704PubMedCentralCrossRefPubMedGoogle Scholar
  69. Willerslev E, Cooper A (2005) Ancient DNA. Proc R Soc B 272: 3–16PubMedCentralCrossRefPubMedGoogle Scholar
  70. Zink AR, Reischl U, Wolf H, Nerlich AG (2002) Molecular analysis of ancient microbial infections. FEMS Microbiol Lett 213: 141–147CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg New York 2007

Authors and Affiliations

  • Susanne Hummel

There are no affiliations available

Personalised recommendations