Achievements and Peculiarities in Studies of Ancient DNA and DNA from Complicated Forensic Specimens

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Abstract

Studies of ancient DNA specimens started 25 years ago. At that time short mitochondrial DNA (mtDNA) fragments were the main targets in ancient DNA studies. The last three years were especially productive in the development of new methods of DNA purification and analysis. Complete mtDNA molecules and relatively large fragments of nuclear DNA are the targets of ancient DNA studies today. Ancient DNA studies allowed us to study organisms that went extinct more than ten thousand years ago, to reconstruct their phenotypic traits and evolution. Ancient DNA analyses can help understand the development of ancient human populations and how they migrated. A new evolutionary hypothesis and reconstruction of the biota history have been re-created from recent ancient DNA data. Some peculiarities and problems specific to the study of ancient DNA were revealed, such as very limited amounts of DNA available for study, the short length of the DNA fragments, breaks and chemical modifications in DNA molecules that result in “postmortem” mutations or complete blockage of DNA replication in vitro. The same specific features of DNA analysis were revealed for specimens from complicated forensic cases that result in the lack of experimental data or interpretation problems.. Here, we list the specific features of ancient DNA methodology and describe some achievements in fundamental and applied research of ancient DNA, including our own work in the field.

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Ancient DNA studies allow to empirically verify evolutionary hypotheses and contribute to the complex reconstruction of historical changes in biota. The analysis of DNA from human archeological samples reveals information on the genetic traits of ancient inhabitants of various geographical regions. The first published reports on the study of ancient DNA appeared 25 years ago. Researchers managed to extract a DNA fragment from a museum sample of dried muscle tissue taken from a quagga – a South-African odd-toed ungulate animal that disappeared in the 19th century. The extracted DNA fragment was cloned in a phage vector and sequenced. Phylogenetic analysis showed that the determined sequence of the mitochondrial DNA (mtDNA) was related to zebra species [1, 2]. The next study described the extraction, cloning, and sequencing of DNA fragment from a ~2,400-thousandyearold Egyptian mummy [3]. After these, attempts were made to extract DNA from the remains of animals, plants and microorganisms whose ages ranged from several hundreds to more than a million years (see review in [4]). As the data accumulated, it became clear that the age of the remains that could still have analyzable templates, calculated using kinetics of DNA decay, was not greater than 0.1–1.0 Myr, and that the level of DNA preservation depended on the age and type of the biological sample, and also on the conditions in which it was preserved [5, 6].
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About the authors

A P Grigorenko

Vavliov Institute of General Genetics, Russian Academy of Sciences; Research Center of Mental Health, Russian Academy of Medical Sciences; University of Massachusetts Medical School, Worcester, U.S.A

S A Borinskaya

Vavliov Institute of General Genetics, Russian Academy of Sciences

N K Yankovsky

Vavliov Institute of General Genetics, Russian Academy of Sciences

E I Rogaev

Vavliov Institute of General Genetics, Russian Academy of Sciences; Research Center of Mental Health, Russian Academy of Medical Sciences; University of Massachusetts Medical School, Worcester, U.S.A

Email: rogaev@vigg.ru

References

  1. Higuchi R., Bowman B., Freiberger M., Ryder O.A., Wilson A.C. // Nature. 1984. 312 (5991). P. 282–284.
  2. Higuchi R.G., Wrischnik L.A., Oakes E. et al. // J. Mol. Evol. 1987. 25 (4). P. 283–287.
  3. Paabo S. // Nature. 1985. 314. P. 644–645.
  4. Willerslev E., Cooper A. Ancient DNA. // Proc. Biol. Sci. 2005. 272 (1558). P. 3–16.
  5. Poinar H.N., Hoss M., Bada J.L., Paabo S. // Science. 1996. 272 (5263). P. 864–866.
  6. Smith C.I., Chamberlain A.T., Riley M.S. et al. // Nature. 2001. 410 (6830). P. 771–772.
  7. Gilbert M.T., Wilson A.S., Bunce M. et al. // Curr. Biol. 2004. 14. P. R463–R464.
  8. Shapiro B., Drummond A.J., Rambaut A. et al. // Science. 2004. 306 (5701). P. 1561–1565.
  9. Willerslev E., Hansen A.J., Brand T.B. et al. // Science. 2003. 300 (5620). P. 792–795.
  10. Willerslev E., Hansen A.J., Brand T.B. et al. // Curr. Biol. 2004. 14 (1). P. R9–R10.
  11. Barnes I., Matheus P., Shapiro B., Jensen D., Cooper A. // Science. 2002. 295. P. 2267–2270.
  12. Lambert D.M., Ritchie P.A., Millar C.D. et al. // Science. 2001. 295 (5563). P. 2270–2273.
  13. Rogaev E.I., Moliaka Y.K., Malyarchuk B.A. et al. // PLoS Biol. 2006. 4 (3). P. e73.
  14. Saiki R.K., Scharf S., Faloona F. et al. // Science. 1985. 230 (4732). P. 1350–1354.
  15. Mullis K., Faloona F., Scharf S. et al. // Cold Spring Harb Symp Quant Biol. 1986. 51 Pt 1. P.263–373.
  16. Saiki R.K., Gelfand D.H., Stoffel S. et al. // Science. 1988. 239 (4839). P. 487–491.
  17. Paabo S., Poinar H., Serre D. et al. // Annu. Rev. Genet. 2004. 38. P. 645–679.
  18. Ho S.Y., Gilbert M.T. Ancient mitogenomics. // Mitochondrion. 2010. 10 (1). P. 1–11.
  19. Ramakrishnan U., Hadly E.A.. // Mol Ecol. 2009. 18 (7). P. 1310–1330.
  20. Hofreiter M., Stewart J. // Curr Biol. 2009. 19 (14). P. R584–R594.
  21. Woodward S.R., Weyand N.J., Bunell M. // Science. 1994. 266 (5188). P. 1229–1232.
  22. Collura R.V., Stewart C.B. // Nature. 1995. 378 (6556). P. 485-489.
  23. Cooper A., Wayne R. // Current Opinion in Biotechnology. 1998. 9. P. 49–53.
  24. Noonan J.P., Coop G., Kudaravalli S. et al. // Science. 2006. 314 (5802). P. 1113–1118.
  25. Green R.E., Krause J., Ptak S.E. et al. // Nature. 2006. 444 (7117). P. 330–336
  26. Wall J.D., Kim S.K. // PLoS Genet. 2007. 3 (10). P. 1862–1866.
  27. Green R.E., Malaspinas A.S., Krause J. et al. // Cell. 2008. 134 (3). P. 416–426.
  28. Pennisi E. // Science. 2009. 323 (5916). P. 866–871.
  29. Krings M., Stone A., Schmitz R.W. et al. // Cell. 1997. 90. P. 19–30.
  30. Schmitz R.W., Serre D., Bonani G. Et al. // Proc. Natl. Acad. Sci. USA. 2002. 99 (20). P. 13342–13347
  31. Noonan J.P., Hofreiter M., Smith D. et al. // Science. 2005. 309 (5734). P. 597–599.
  32. Poinar H.N., Schwarz C., Qi J. et al. // Science. 2006. 311 (5759). P.392–394.
  33. Schwarz C., Debruyne R., Kuch M. et al. // Nucleic Acids Res. 2009. 37 (10). P. 3215–3129.
  34. Cooper A., Poinar H.N. // Science. 2000. 289 (5482). P. 1139
  35. Binladen J., Wiuf C., Gilbert M.T. et al. Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. // Genetics. 2006. 172 (2). P. 733–741.
  36. Endicott P., Sanchez J.J., Pichler I. et al. // BMC Genet. 2009. 10. P. 29.
  37. Pusch C.M., Broghammer M., Nicholson G.J. et al. //Mol. Biol. Evol. 2004. 21 (11). P. 2005–2011.
  38. Gilbert M.T., Hansen A.J., Willerslev E. et al. // Am J. Hum. Genet. 2003. 72 (1). P. 48–61.
  39. Lamers R., Hayter S., Matheson C.D. // J. Mol. Evol. 2009. 68 (1). P.40–55.
  40. Krause J., Dear P.H., Pollack J.L. // Nature. 2006.439 (7077). P. 724–727.
  41. Shendure J., Ji H. // Nat. Biotechnol. 2008.;6 (10). P. 1135–1145.
  42. Gill P., Ivanov P.L., Kimpton C. et al. // Nat. Genet. 1994. 6 (2). P. 130–135.
  43. Ivanov P.L., Wadhams M.J., Roby R.K. et al. // Nat. Genet. 1996. 12 (4). P. 417–420.
  44. Rogaev E.I. Analysis of mitochondrial DNA of the alleged remains of Nicholas II and his nephew. // In.: “Repentance”. Government commission materials: Moscow, 1998. P. 171-182.
  45. Rogaev E.I., Grigorenko A.P., Moliaka Y.K. et al // Proc. Natl. Acad. Sci U S A. 2009a.(13). P. 5258–5263.
  46. Grigorenko A.P., Andreeva T.V., Rogaev E.I. // Medical Genetics. 2009. 8 (4). P. 45-46
  47. Irwin J.A., Saunier J.L., Niederstatter H. et al. // J. Mol. Evol. 2009.68. P. 516–527.
  48. Wai T., Teoli D., Shoubridge E.A. // Nat. Genet. 2008. 40 (12). P. 1484–1488.
  49. Rogaev E.I., Grigorenko A.P., Faskhutdinova G., Kittler E.L., Moliaka Y.K. // Science. 2009b. 326 (5954). P. 817.
  50. White G.C., Rosendaal F., Aledort L.M. et al. // Thromb. Haemost. 2001. 85 (3). P. 560.

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Copyright (c) 2009 Grigorenko A.P., Borinskaya S.A., Yankovsky N.K., Rogaev E.I.

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