Molecular Biology and Evolution 18:262-265 (2001)
© 2001 Society for Molecular Biology and Evolution
LETTER |
Statistical Evidence for Miscoding Lesions in Ancient DNA Templates
*Department of Evolutionary Biology, Zoological Institute, University of Copenhagen Denmark, Copenhagen, Denmark; and
Department of Statistics, Oxford University, Oxford, England
It is generally believed that sequence heterogeneity in PCR products from fossil remains are due to regular DNA polymerase errors as well as miscoding lesions compounded by damage in the template DNA (Pääbo 1990
; Handt et al. 1994b, 1996
; Höss et al. 1996
; Krings et al. 1997
). However, it has been difficult to test the frequency with which this assumption holds. First, DNA extractions from fossil remains rarely produce a yield large enough for pre-PCR analysis of postmortem modifications (Höss et al. 1996
). Second, in most cases, it is not possible to determine whether nucleotide misincorporations by the DNA polymerase enzyme during amplification are caused by regular DNA polymerase errors or miscoding lesions in the template DNA sequences (Greenwood et al. 1999
). Finally, the error rates of the DNA polymerase enzymes for PCR have proved to be highly unpredictable, making it difficult to
Acknowledgements
Footnotes
literature cited
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  E. Axelsson, E. Willerslev, M. T. P. Gilbert, and R. Nielsen The Effect of Ancient DNA Damage on Inferences of Demographic Histories Mol. Biol. Evol., October 1, 2008; 25(10): 2181 - 2187. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. M. Mateiu and B. H. Rannala Bayesian Inference of Errors in Ancient DNA Caused by Postmortem Degradation Mol. Biol. Evol., July 1, 2008; 25(7): 1503 - 1511. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Brotherton, P. Endicott, J. J. Sanchez, M. Beaumont, R. Barnett, J. Austin, and A. Cooper 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 Res., September 27, 2007; 35(17): 5717 - 5728. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. S. Johnson, M. B. Hebsgaard, T. R. Christensen, M. Mastepanov, R. Nielsen, K. Munch, T. Brand, M. T. P. Gilbert, M. T. Zuber, M. Bunce, et al. Ancient bacteria show evidence of DNA repair PNAS, September 4, 2007; 104(36): 14401 - 14405. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Y. W. Ho, T. H. Heupink, A. Rambaut, and B. Shapiro Bayesian Estimation of Sequence Damage in Ancient DNA Mol. Biol. Evol., June 1, 2007; 24(6): 1416 - 1422. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Haile, R. Holdaway, K. Oliver, M. Bunce, M. T. P. Gilbert, R. Nielsen, K. Munch, S. Y. W. Ho, B. Shapiro, and E. Willerslev Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions Possible and Is DNA Leaching a Factor? Mol. Biol. Evol., April 1, 2007; 24(4): 982 - 989. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Burger, M. Kirchner, B. Bramanti, W. Haak, and M. G. Thomas Absence of the lactase-persistence-associated allele in early Neolithic Europeans PNAS, March 6, 2007; 104(10): 3736 - 3741. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. T. P. Gilbert, J. Binladen, W. Miller, C. Wiuf, E. Willerslev, H. Poinar, J. E. Carlson, J. H. Leebens-Mack, and S. C. Schuster Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis Nucleic Acids Res., January 12, 2007; 35(1): 1 - 10. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Stiller, R. E. Green, M. Ronan, J. F. Simons, L. Du, W. He, M. Egholm, J. M. Rothberg, S. G. Keates, N. D. Ovodov, et al. Inaugural Article: Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA PNAS, September 12, 2006; 103(37): 13578 - 13584. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. L. Sampietro, M. T. P. Gilbert, O. Lao, D. Caramelli, M. Lari, J. Bertranpetit, and C. Lalueza-Fox Tracking down Human Contamination in Ancient Human Teeth Mol. Biol. Evol., September 1, 2006; 23(9): 1801 - 1807. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Binladen, C. Wiuf, M. T. P. Gilbert, M. Bunce, R. Barnett, G. Larson, A. D. Greenwood, J. Haile, S. Y. W. Ho, A. J. Hansen, et al. Assessing the Fidelity of Ancient DNA Sequences Amplified From Nuclear Genes Genetics, February 1, 2006; 172(2): 733 - 741. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. L. Erickson, B. D. Smith, A. C. Clarke, D. H. Sandweiss, and N. Tuross An Asian origin for a 10,000-year-old domesticated plant in the Americas PNAS, December 20, 2005; 102(51): 18315 - 18320. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Rohland, J. L. Pollack, D. Nagel, C. Beauval, J. Airvaux, S. Paabo, and M. Hofreiter The Population History of Extant and Extinct Hyenas Mol. Biol. Evol., December 1, 2005; 22(12): 2435 - 2443. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Malmstrom, J. Stora, L. Dalen, G. Holmlund, and A. Gotherstrom Extensive Human DNA Contamination in Extracts from Ancient Dog Bones and Teeth Mol. Biol. Evol., October 1, 2005; 22(10): 2040 - 2047. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Salamon, N. Tuross, B. Arensburg, and S. Weiner Relatively well preserved DNA is present in the crystal aggregates of fossil bones PNAS, September 27, 2005; 102(39): 13783 - 13788. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. M. Pusch, M. Broghammer, G. J. Nicholson, A. G. Nerlich, A. Zink, I. Kennerknecht, L. Bachmann, and N. Blin PCR-Induced Sequence Alterations Hamper the Typing of Prehistoric Bone Samples for Diagnostic Achondroplasia Mutations Mol. Biol. Evol., November 1, 2004; 21(11): 2005 - 2011. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. M. Pusch and L. Bachmann Spiking of Contemporary Human Template DNA with Ancient DNA Extracts Induces Mutations Under PCR and Generates Nonauthentic Mitochondrial Sequences Mol. Biol. Evol., May 1, 2004; 21(5): 957 - 964. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. T. P. Gilbert, J. Cuccui, W. White, N. Lynnerup, R. W. Titball, A. Cooper, and M. B. Prentice Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims Microbiology, February 1, 2004; 150(2): 341 - 354. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Willerslev, A. J. Hansen, J. Binladen, T. B. Brand, M. T. P. Gilbert, B. Shapiro, M. Bunce, C. Wiuf, D. A. Gilichinsky, and A. Cooper Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments Science, May 2, 2003; 300(5620): 791 - 795. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Gutierrez, D. Sanchez, and A. Marin A Reanalysis of the Ancient Mitochondrial DNA Sequences Recovered from Neandertal Bones Mol. Biol. Evol., August 1, 2002; 19(8): 1359 - 1366. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Hofreiter, V. Jaenicke, D. Serre, A. v. Haeseler, and S. Paabo DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA Nucleic Acids Res., December 1, 2001; 29(23): 4793 - 4799. [Abstract] [Full Text] [PDF]
|
|