Nucleic Acids Research, 2001, Vol. 29, No. 23 4793-4799
© 2001 Oxford University Press
DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA
Max Planck Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103 Leipzig, Germany
We show that DNA molecules amplified by PCR from DNA extracted from animal bones and teeth that vary in age between 25 000 and over 50 000 years carry C
T and GA substitutions. These substitutions can reach high proportions among the molecules amplified and are due to the occurrence of modified deoxycytidine residues in the template DNA. If the template DNA is treated with uracil N-glycosylase, these substitutions are dramatically reduced. They are thus likely to result from deamination of deoxycytidine residues. In addition, ‘jumping PCR’, i.e. the occurrence of template switching during PCR, may contribute to these substitutions. When DNA sequences are amplified from ancient DNA extracts where few template molecules initiate the PCR, precautions such as DNA sequence determination of multiple clones derived from more than one independent amplification are necessary in order to reduce the risk of determination of incorrect DNA sequences. When such precautionary measures are taken, errors induced by damage to the DNA template are unlikely to be more frequent than 
0.1% even under the unlikely scenario where each amplification starts from a single template molecule.
* To whom correspondence should be addressed. Tel: +49 341 9952 501; Fax: +49 341 9952 555; Email: paabo{at}eva.mpg.de
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. Brotherton, J. J. Sanchez, A. Cooper, and P. Endicott Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX Nucleic Acids Res., October 27, 2009; (2009) gkp897v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Stiller, M. Knapp, U. Stenzel, M. Hofreiter, and M. Meyer Direct multiplex sequencing (DMPS)--a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA Genome Res., October 1, 2009; 19(10): 1843 - 1848. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. W. Briggs, J. M. Good, R. E. Green, J. Krause, T. Maricic, U. Stenzel, C. Lalueza-Fox, P. Rudan, D. Brajkovic, Z. Kucan, et al. Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes Science, July 17, 2009; 325(5938): 318 - 321. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Schwarz, R. Debruyne, M. Kuch, E. McNally, H. Schwarcz, A. D. Aubrey, J. Bada, and H. Poinar New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains Nucleic Acids Res., June 1, 2009; 37(10): 3215 - 3229. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Geist, H. Wunderlich, and R. Kuehn Use of mollusc shells for DNA-based molecular analyses J. Mollus. Stud., November 1, 2008; 74(4): 337 - 343. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 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]
|
|
|
|
 |
|
 M. P. Richards, M. Pacher, M. Stiller, J. Quiles, M. Hofreiter, S. Constantin, J. Zilhao, and E. Trinkaus Isotopic evidence for omnivory among European cave bears: Late Pleistocene Ursus spelaeus from the Pestera cu Oase, Romania PNAS, January 15, 2008; 105(2): 600 - 604. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Lalueza-Fox, H. Rompler, D. Caramelli, C. Staubert, G. Catalano, D. Hughes, N. Rohland, E. Pilli, L. Longo, S. Condemi, et al. A Melanocortin 1 Receptor Allele Suggests Varying Pigmentation Among Neanderthals Science, November 30, 2007; 318(5855): 1453 - 1455. [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]
|
|
|
|
|
|
A. W. Briggs, U. Stenzel, P. L. F. Johnson, R. E. Green, J. Kelso, K. Prufer, M. Meyer, J. Krause, M. T. Ronan, M. Lachmann, et al. Patterns of damage in genomic DNA sequences from a Neandertal PNAS, September 11, 2007; 104(37): 14616 - 14621. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M.L Sampietro, O Lao, D Caramelli, M Lari, R Pou, M Marti, J Bertranpetit, and C Lalueza-Fox Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe Proc R Soc B, September 7, 2007; 274(1622): 2161 - 2167. [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]
|
|
|
|
 |
|
 L. Orlando, M. Pages, S. Calvignac, S. Hughes, and C. Hanni Does the 43 bp sequence from an 800 000 year old Cretan dwarf elephantid really rewrite the textbook on mammoths? Biol Lett, February 22, 2007; 3(1): 58 - 60. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. V Lia, V. A Confalonieri, N. Ratto, J. A. C. Hernandez, A. M. M. Alzogaray, L. Poggio, and T. A Brown Microsatellite typing of ancient maize: insights into the history of agriculture in southern South America Proc R Soc B, February 22, 2007; 274(1609): 545 - 554. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. P. Noonan, G. Coop, S. Kudaravalli, D. Smith, J. Krause, J. Alessi, F. Chen, D. Platt, S. Paabo, J. K. Pritchard, et al. Sequencing and Analysis of Neanderthal Genomic DNA. Science, November 17, 2006; 314(5802): 1113 - 1118. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Fernandez, S. Hughes, J.-D. Vigne, D. Helmer, G. Hodgins, C. Miquel, C. Hanni, G. Luikart, and P. Taberlet Divergent mtDNA lineages of goats in an Early Neolithic site, far from the initial domestication areas PNAS, October 17, 2006; 103(42): 15375 - 15379. [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]
|
|
|
|
|
|
H. Rompler, N. Rohland, C. Lalueza-Fox, E. Willerslev, T. Kuznetsova, G. Rabeder, J. Bertranpetit, T. Schoneberg, and M. Hofreiter Nuclear gene indicates coat-color polymorphism in mammoths. Science, July 7, 2006; 313(5783): 62 - 62. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R Bollongino, C.J Edwards, K.W Alt, J Burger, and D.G Bradley Early history of European domestic cattle as revealed by ancient DNA Biol Lett, March 22, 2006; 2(1): 155 - 159. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Barnes and M. G Thomas Evaluating bacterial pathogen DNA preservation in museum osteological collections Proc R Soc B, March 22, 2006; 273(1587): 645 - 653. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Marchetti, L. Felicioni, F. Buttitta, M.-S. Tsao, S. Kamel-Reid, and F. A. Shepherd Assessing EGFR Mutations N. Engl. J. Med., February 2, 2006; 354(5): 526 - 528. [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]
|
|
|
|
|
|
H. N. Poinar, C. Schwarz, J. Qi, B. Shapiro, R. D. E. MacPhee, B. Buigues, A. Tikhonov, D. H. Huson, L. P. Tomsho, A. Auch, et al. Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA Science, January 20, 2006; 311(5759): 392 - 394. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. L. Topf, M. T. P. Gilbert, J. P. Dumbacher, and A. R. Hoelzel Tracing the Phylogeography of Human Populations in Britain Based on 4th-11th Century mtDNA Genotypes Mol. Biol. Evol., January 1, 2006; 23(1): 152 - 161. [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]
|
|
|
|
|
|
F. Verginelli, C. Capelli, V. Coia, M. Musiani, M. Falchetti, L. Ottini, R. Palmirotta, A. Tagliacozzo, I. De Grossi Mazzorin, and R. Mariani-Costantini Mitochondrial DNA from Prehistoric Canids Highlights Relationships Between Dogs and South-East European Wolves Mol. Biol. Evol., December 1, 2005; 22(12): 2541 - 2551. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. Haak, P. Forster, B. Bramanti, S. Matsumura, G. Brandt, M. Tanzer, R. Villems, C. Renfrew, D. Gronenborn, K. W. Alt, et al. Ancient DNA from the First European Farmers in 7500-Year-Old Neolithic Sites Science, November 11, 2005; 310(5750): 1016 - 1018. [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]
|
|
|
|
|
|
J. P. Noonan, M. Hofreiter, D. Smith, J. R. Priest, N. Rohland, G. Rabeder, J. Krause, J. C. Detter, S. Paabo, and E. M. Rubin Genomic Sequencing of Pleistocene Cave Bears Science, July 22, 2005; 309(5734): 597 - 599. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. E. Deagle, S. N. Jarman, D. Pemberton, and N. J. Gales Genetic Screening for Prey in the Gut Contents from a Giant Squid (Architeuthis sp.) J. Hered., July 1, 2005; 96(4): 417 - 423. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Bower, M. Spencer, S. Matsumura, R. E. R. Nisbet, and C. J. Howe 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., May 3, 2005; 33(8): 2549 - 2556. [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]
|
|
|
|
|
|
M. Hofreiter, D. Serre, N. Rohland, G. Rabeder, D. Nagel, N. Conard, S. Munzel, and S. Paabo Lack of phylogeography in European mammals before the last glaciation PNAS, August 31, 2004; 101(35): 12963 - 12968. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Serre, M. Hofreiter, and S. Paabo Mutations Induced by Ancient DNA Extracts? Mol. Biol. Evol., August 1, 2004; 21(8): 1463 - 1467. [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]
|
|
|
|
|
|
E. Wienholds, F. van Eeden, M. Kosters, J. Mudde, R. H.A. Plasterk, and E. Cuppen Efficient Target-Selected Mutagenesis in Zebrafish Genome Res., December 1, 2003; 13(12): 2700 - 2707. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Orlando, D. Bonjean, H. Bocherens, A. Thenot, A. Argant, M. Otte, and C. Hanni Ancient DNA and the Population Genetics of Cave Bears (Ursus spelaeus) Through Space and Time Mol. Biol. Evol., November 1, 2002; 19(11): 1920 - 1933. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. W. Schmitz, D. Serre, G. Bonani, S. Feine, F. Hillgruber, H. Krainitzki, S. Paabo, and F. H. Smith The Neandertal type site revisited: Interdisciplinary investigations of skeletal remains from the Neander Valley, Germany PNAS, October 1, 2002; 99(20): 13342 - 13347. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Hofreiter, C. Capelli, M. Krings, L. Waits, N. Conard, S. Munzel, G. Rabeder, D. Nagel, M. Paunovic, G. Jambresic, et al. Ancient DNA Analyses Reveal High Mitochondrial DNA Sequence Diversity and Parallel Morphological Evolution of Late Pleistocene Cave Bears Mol. Biol. Evol., August 1, 2002; 19(8): 1244 - 1250. [Abstract] [Full Text] [PDF]
|
|