Advertisement

Journal of Molecular Evolution

, Volume 65, Issue 1, pp 92–102 | Cite as

A Statistical Approach to Identify Ancient Template DNA

  • Agnar HelgasonEmail author
  • Snæbjörn Pálsson
  • Carles Lalueza-Fox
  • Shyamali Ghosh
  • Sigrún Sigurðardóttir
  • Adam Baker
  • Birgir Hrafnkelsson
  • Lilja Árnadóttir
  • Unnur Þorsteinsdóttir
  • Kári Stefánsson
Article

Abstract

One of the key problems in the study of ancient DNA is that of authenticating sequences obtained from PCR amplifications of highly degraded samples. Contamination of ancient samples and postmortem damage to endogenous DNA templates are the major obstacles facing researchers in this task. In particular, the authentication of sequences obtained from ancient human remains is thought by many to be rather challenging. We propose a novel approach, based on the c statistic, that can be employed to help identify the sequence motif of an endogenous template, based on a sample of sequences that reflect the nucleotide composition of individual template molecules obtained from ancient tissues (such as cloned products from a PCR amplification). The c statistic exploits as information the most common form of postmortem damage observed among clone sequences in ancient DNA studies, namely, lesion-induced substitutions caused by cytosine deamination events. Analyses of simulated sets of templates with miscoding lesions and real sets of clone sequences from the literature indicate that the c-based approach is highly effective in identifying endogenous sequence motifs, even when they are not present among the sampled clones. The proposed approach is likely to be of general use to researchers working with DNA from ancient tissues, particularly from human remains, where authentication of results has been most challenging.

Keywords

Ancient DNA Authentication Postmortem damage Statistical method 

Notes

Acknowledgment

C.L.-F. was supported by grant CGL2006-03987 from the Spanish Ministry of Education and Science.

References

  1. Abbott A (2003) Anthropologists cast doubt on human DNA evidence. Nature 423:468PubMedGoogle Scholar
  2. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48PubMedGoogle Scholar
  3. Binladen J, Wiuf C, Gilbert MT, Bunce M, Barnett R, Larson G, Greenwood AD, Haile J, Ho SY, Hansen AJ, Willerslev E (2006) Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics 172:733–741PubMedCrossRefGoogle Scholar
  4. Bower MA, Spencer M, Matsumura S, Nisbet RE, Howe CJ (2005) How many clones need to be sequenced from a single forensic or ancient DNA sample in order to determine a reliable consensus sequence? Nucleic Acids Res 33:2549–2556PubMedCrossRefGoogle Scholar
  5. Caramelli D, Lalueza-Fox C, Condemi S, Longo L, Milani L, Manfredini A, de Saint Pierre M, Adoni F, Lari M, Giunti P, Ricci S, Casoli A, Calafell F, Mallegni F, Bertranpetit J, Stanyon R, Bertorelle G, Barbujani G (2006) A highly divergent mtDNA sequence in a Neandertal individual from Italy. Curr Biol 16:R630–R632PubMedCrossRefGoogle Scholar
  6. Gilbert MT, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, Carlson JE, Leebens-Mack JH, Schuster SC (2007) Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res 35:1–10PubMedCrossRefGoogle Scholar
  7. Gilbert MT, Hansen AJ, Willerslev E, Rudbeck L, Barnes I, Lynnerup N, Cooper A (2003) Characterization of genetic miscoding lesions caused by postmortem damage. Am J Hum Genet 72:48–61PubMedCrossRefGoogle Scholar
  8. Gilbert MTP, Bandelt HJ, Hofreiter M, Barnes I (2005) Assessing ancient DNA studies. Trends Ecol Evol 20:541–544PubMedCrossRefGoogle Scholar
  9. Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, Simons JF, Du L, Egholm M, Rothberg JM, Paunovic M, Paabo S (2006) Analysis of one million base pairs of Neanderthal DNA. Nature 444:330–336PubMedCrossRefGoogle Scholar
  10. 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
  11. Handt O, Krings M, Ward RH, Pääbo S (1996) The retrieval of ancient human DNA sequences. Am J Hum Genet 59:368–376PubMedGoogle Scholar
  12. Hansen A, Willerslev E, Wiuf C, Mourier T, Arctander P (2001) Statistical evidence for miscoding lesions in ancient DNA templates. Mol Biol Evol 18:262–265PubMedGoogle Scholar
  13. Hansen AJ, Mitchell DL, Wiuf C, Paniker L, Brand TB, Binladen J, Gilichinsky DA, Ronn R, Willerslev E (2006) Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics 173:1175–1179PubMedCrossRefGoogle Scholar
  14. Hebsgaard MB, Phillips MJ, Willerslev E (2005) Geologically ancient DNA: Fact or artefact? Trends Microbiol 13:212–220PubMedCrossRefGoogle Scholar
  15. Hofreiter M, Jaenicke V, Serre D, Haeseler Av A, Pääbo S (2001a) DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res 29:4793–4799CrossRefGoogle Scholar
  16. Hofreiter M, Serre D, Poinar HN, Kuch M, Pääbo S (2001b) Ancient DNA. Nat Rev Genet 2:353–359CrossRefGoogle Scholar
  17. Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo S (1997) Neandertal DNA sequences and the origin of modern humans. Cell 90:19–30PubMedCrossRefGoogle Scholar
  18. Mitchell D, Willerslev E, Hansen A (2005) Damage and repair of ancient DNA. Mutat Res 571:265–276PubMedGoogle Scholar
  19. Pääbo S (1989) Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci USA 86:1939–1943PubMedCrossRefGoogle Scholar
  20. Pääbo S, Irwin DM, Wilson AC (1990) DNA damage promotes jumping between templates during enzymatic amplification. J Biol Chem 265:4718–4721PubMedGoogle Scholar
  21. Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38:645–679PubMedCrossRefGoogle Scholar
  22. Rollo F, Ermini L, Luciani S, Marota I, Olivieri C, Luiselli D (2006) Fine characterization of the Iceman’s mtDNA haplogroup. Am J Phys Anthropol 130:557–564PubMedCrossRefGoogle Scholar
  23. Rudbeck L, Gilbert MT, Willerslev E, Hansen AJ, Lynnerup N, Christensen T, Dissing J (2005) mtDNA analysis of human remains from an early Danish Christian cemetery. Am J Phys Anthropol 128:424–429PubMedCrossRefGoogle Scholar
  24. Sampietro ML, Gilbert MT, Lao O, Caramelli D, Lari M, Bertranpetit J, Lalueza-Fox C (2006) Tracking down human contamination in ancient human teeth. Mol Biol Evol 23:1801–1807PubMedCrossRefGoogle Scholar
  25. Schmitz RW, Serre D, Bonani G, Feine S, Hillgruber F, Krainitzki H, Pääbo S, Smith FH (2002) The Neandertal type site revisited: interdisciplinary investigations of skeletal remains from the Neander Valley, Germany. Proc Natl Acad Sci USA 99:13342–13347PubMedCrossRefGoogle Scholar
  26. Serre D, Langaney A, Chech M, Teschler-Nicola M, Paunovic M, Mennecier P, Hofreiter M, Possnert GG, Pääbo S (2004) No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol 2:E57PubMedCrossRefGoogle Scholar
  27. Smith CI, Chamberlain AT, Riley MS, Cooper A, Stringer CB, Collins MJ (2001) Neanderthal DNA. Not just old but old and cold? Nature 410:771–772Google Scholar
  28. Stiller M, Green RE, Ronan M, Simons JF, Du L, He W, Egholm M, Rothberg JM, Keats SG, Ovodov ND, Antipina EE, Baryshnikov GF, Kuzmin YV, Vasilevski AA, Wuenschell GE, Termini J, Hofreiter M, Jaenicke-Despres V, Pääbo S (2006) Patterns of nucleotide misincorporations during enzymatic amplification and direct large–scale sequencing of ancient DNA. Proc Natl Acad Sci USA 103:13578–13584PubMedCrossRefGoogle Scholar
  29. Topf AL, Gilbert MT, Dumbacher JP, Hoelzel AR (2006) Tracing the phylogeography of human populations in Britain based on 4th–11th century mtDNA genotypes. Mol Biol Evol 23:152–161PubMedCrossRefGoogle Scholar
  30. Willerslev E, Cooper A (2005) Ancient DNA. Proc Biol Sci 272:3–16PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Agnar Helgason
    • 1
    Email author
  • Snæbjörn Pálsson
    • 1
    • 2
  • Carles Lalueza-Fox
    • 3
  • Shyamali Ghosh
    • 1
  • Sigrún Sigurðardóttir
    • 1
  • Adam Baker
    • 1
  • Birgir Hrafnkelsson
    • 4
  • Lilja Árnadóttir
    • 5
  • Unnur Þorsteinsdóttir
    • 1
  • Kári Stefánsson
    • 1
  1. 1.deCODE GeneticsReykjavikIceland
  2. 2.Department of BiologyUniversity of IcelandReykjavikIceland
  3. 3.Department of BiologyUniversity of BarcelonaBarcelonaSpain
  4. 4.Faculty of EngineeringUniversity of IcelandReykjavikIceland
  5. 5.National Museum of IcelandReykjavikIceland

Personalised recommendations