Extensive human DNA contamination in extracts from ancient dog bones and teeth

Molecular Biology and Evolution

Volumn 22, Issue 10, 2005, Pages 2040-2047

  Malmström, Helena ^a   Storå, Jan ^b   Dalén, Love ^b   Holmlund, Gunilla ^c   Götherström, Anders ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b STOCKHOLM UNIVERSITY   (Sweden)

^c LINKÖPING UNIVERSITY   (Sweden)

Author keywords

Ancient DNA; Authentication; Mitochondrial DNA; Quantitative PCR

Indexed keywords

DNA;

AMPLICON; ANIMAL TISSUE; ARTICLE; BONE; CONTROLLED STUDY; DNA DETERMINATION; DNA EXTRACTION; DNA SEQUENCE; DNA TEMPLATE; DOG; HAPLOTYPE; HUMAN; HUMAN TISSUE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; REAL TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; TISSUE SECTION; TOOTH;

ANIMALS; BASE SEQUENCE; BONE AND BONES; DNA; DNA PRIMERS; DNA PROBES; DNA, MITOCHONDRIAL; DOGS; DRUG CONTAMINATION; HUMANS; POLYMERASE CHAIN REACTION; SPECIES SPECIFICITY; TEMPLATES, GENETIC; TOOTH;

CANIS FAMILIARIS;

EID: 24744437359     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi195     Document Type: Article

References (46)

1. Abbot, A. 2003. Anthropologists cast doubt on human DNA evidence. Nature 423:468.
2. Alonso, A., P. Martín, C. Albarrán, P. García, O. García, L. Fernández de Simón, J. García-Hirschfeld, M. Sancho, C. de la Rúa, and J. Fernández-Piqueras. 2004. Real-time PCR designs to estimate nuclear and mitochondrial DNA copy number in forensic and ancient DNA studies. Forensic Sci. Int. 139:141-149.
3. Anderson, S., A. T. Bankier, B. G. Barrell et al. (14 co-authors). 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.
4. Anderung, C., A. Bouwman, P. Persson et al. (10 co-authors). 2005. Prehistoric contacts over the Straits of Gibraltar indicated by genetic analysis of Iberian Bronze Age cattle. Proc. Natl. Acad. Sci. USA 102:8431-8435.
5. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl. 1999. Short protocols in molecular biology. 4th edition. Wiley John and Sons Inc., New York, p. A2-1.
6. Bandelt, H.-J. 2004. Etruscan artifacts. Am. J. Hum. Genet. 75:919-920.
7. Barbujani, G., and G. Bertorelle. 2003. Were Cro-Magnons too like us for DNA to tell? Nature 424:127.
8. Barbujani, G., C. Vernesi, D. Caramelli, L. Castrí, C. Lalueza-Fox, and G. Bertorelle. 2004. Etruscan artifacts: much ado about nothing. Am. J. Hum. Genet. 75:923-927.
9. Cappellini, E., B. Chiarelli, L. Sineo, A. Casoli, A. Di Gioia, C. Vernesi, M. C. Biella, and D. Caramelli. 2004. Biomolecular study of the human remains from tomb 5859 in the Etruscan necropolis of Monterozzi, Tarquinia (Viterbo, Italy). J. Archaeol. Sci. 31:603-612.
10. Caramelli, D., C. Lalueza-Fox, C. Vernesi et al. (11 co-authors). 2003. Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans. Proc. Natl. Acad. Sci. USA 100:6593-6597.
11. Cooper, A. 1992. Removal of colourings, inhibitors of PCR, and the carrier effect of PCR contamination from ancient DNA samples. Anc. DNA Newslett. 1:31-32.
12. Cooper, A., and H. N. Poinar. 2000. Ancient DNA: do it right or not at all. Science 289:1139.
13. Di Benedetto, G., I. S. Nasidze, M. Stenico, L. Nigro, M. Krings, M. Lanzinger, L. Vigilant, M. Stoneking, S. Pääbo, and G. Barbujani. 2000. Mitochondrial DNA sequences in prehistoric human remains from the Alps. Eur. J. Hum. Genet. 8:669-677.
14. Gilbert, M. T. P., J. Cuccui, W. White, N. Lynnerup, R. W. Titball, A. Cooper, and M. B. Prentice. 2004a. Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims. Microbiology 150:341-354.
15. Gilbert, M. T. P., L. Rudbeck, E. Willerslev et al. (15 co-authors). 2005. Biochemical and physical correlates of DNA contamination in archaeological bones and teeth excavated at Matera, Italy. J. Archaeol. Sci. 32:785-793.
16. Gilbert, M. T. P., E. Willerslev, A. J. Hansen, I. Barnes, L. Rudbeck, N. Lynnerup, and A. Cooper. 2003. Distribution patterns of post mortem damage in human mitochondrial DNA. Am. J. Hum. Genet. 72:32-47.
17. Gilbert, M. T. P., A. S. Wilson, M. Bunce et al. (12 co-authors). 2004b. Ancient mitochondrial DNA from hair. Curr. Biol. 14:R463-R464.
18. Handt, O., M. Höss, M. Krings, and S. Pääbo. 1994. Ancient DNA: methodological challenges. Experientia 50:524-529.
19. Handt, O., M. Krings, R. H. Ward, and S. Pääbo. 1996. The retrieval of ancient human DNA sequences. Am. J. Hum. Genet. 59:368-376.
20. Hansen, A. J., E. Willerslev, C. Wiuf, T. Mourier, and P. Arctander. 2001. Statistical evidence for miscoding lesions in ancient DNA templates. Mol. Biol. Evol. 18:262-265.
21. Hofreiter, M., V. Jaenicke, D. Serre, A. von Haeseler, and S. Pääbo. 2001a. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 29:4793-4799.
22. Hofreiter, M., D. Serre, H. N. Poinar, M. Kuch, and S. Pääbo. 2001b. Ancient DNA. Nat. Rev. Genet. 2:353-359.
23. Izagirre, N., and C. de la Rúa. 1999. An mtDNA analysis in ancient Basque populations: implications for haplogroup V as a marker for a major paleolithic expansion from south-western Europe. Am. J. Hum. Genet. 65:199-207.
24. Kim, K. S., S. E. Lee, H. W. Jeong, and J. H. Ha. 1998. The complete nucleotide sequence of the domestic dog (Canis familiaris) mitochondrial genome. Mol. Phylogenet. Evol. 10:210-220.
25. Kolman, C. J., and N. Tuross. 2000. Ancient DNA analysis of human populations. Am. J. Phys. Anthropol. 111:5-23.
26. Krings, M., A. Stone, R. W. Schmitz, H. Krainitzki, M. Stoneking, and S. Pääbo. 1997. Neandertal DNA sequences and the origin of modern humans. Cell 90:19-30.
27. Kwok, S., and R. Higuchi. 1989. Avoiding false positives with PCR. Nature 339:237-238.
28. Lalueza-Fox, C., M. T. P. Gilbert, A. J. Martínez-Fuentes, F. Calafell, and J. Bertranpetit. 2003. Mitochondrial DNA from pre-Columbian Ciboneys from Cuba and the prehistoric colonization of the Carribean. Am. J. Phys. Anthropol. 121:97-108.
29. Lindblom, B., and G. Holmlund. 1988. Purification for restriction fragment length polymorphism analysis. Gene Anal. Tech. 5:97-101.
30. Malyarchuk, B. A., and I. B. Rogozin. 2004. On the Etruscan mitochondrial DNA contribution to modern humans. Am. J. Hum. Genet. 75:920-923.
31. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
32. Pääbo, S., J. A. Gilford, and A. C. Wilson. 1988. Mitochondrial DNA sequences from a 7000-year old brain. Nucleic Acids Res. 16:9775-9787.
33. Pääbo, S., H. Poinar, D. Serre, V. Jaenicke-Després, J. Hebler, N. Rohland, M. Kuch, J. Krause, L. Vigilant, and M. Hofreiter. 2004. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38:645-679.
34. Pruvost, M., and E. M. Geigl. 2004. Real-time quantitative PCR to assess the authenticity of ancient DNA amplification. J. Archaeol. Sci. 31:1191-1197.
35. Pusch, C. M., and L. Bachmann. 2004. Spiking of contemporary human template DNA with ancient DNA extracts induces mutations under PCR and generates nonauthentic mitochondrial sequences. Mol. Biol. Evol. 21:957-964.
36. Pusch, C. M., M. Broghammer, G. J. Nicholson, A. G. Nerlich, A. Zink, I. Kennerknecht, L. Bachmann, and N. Blin. 2004. PCR-induced sequence alterations hamper the typing of prehistoric bone samples for diagnostic achondroplasia mutations. Mol. Biol. Evol. 21:2005-2011.
37. Richards, M. B., B. C. Sykes, and R. E. M. Hedges. 1995. Authenticating DNA extracted from ancient skeletal remains. J. Archaeol. Sci. 22:291-299.
38. Sambrock, E., F. Fritsch, and T. Maniatis. 1989. Molecular cloning. Cold Spring Harbor Press, New York.
39. Schmitz, R. W., D. Serre, G. Bonani, S. Feine, F. Hillgruber, H. Krainitzki, S. Pääbo, and F. H. Smith. 2002. The Neandertal type site revisited: interdisciplinary investigations of skeletal remains from the Neander Valley, Germany. Proc. Natl. Acad. Sci. USA 99:13342-13347.
40. Serre, D., M. Hofreiter, and S. Pääbo. 2004. Mutations induced by ancient DNA extracts.? Mol. Biol. Evol. 21:1463-1467.
41. Serre, D., A. Langaney, M. Chech, M. Teschler-Nicola, M. Paunovic, P. Mennecier, M. Hofreiter, G. Possnert, and S. Pääbo. 2004. No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol. 2:0313-0317.
42. Smith, C. I., A. T. Chamberlain, M. S. Riley, C. Stringer, and M. J. Collins. 2003. The thermal history of human fossils and the likelihood of successful DNA amplification. J. Hum. Evol. 45:203-217.
43. Stone, A. C., and M. Stoneking. 1998. mtDNA analysis of a prehistoric Oneota population: implications for the peopling of the New World. Am. J. Hum. Genet. 62:1153-1170.
44. Vernesi, C., D. Caramelli, I. Dupanloup et al. (13 co-authors). 2004. The Etruscans: a population-genetic study. Am. J. Hum. Genet. 74:694-704.
45. Yang, D. Y., B. Eng, and S. R. Saunders. 2003. Hypersensitive PCR, ancient human mtDNA, and contamination. Hum. Biol. 75:355-364.
46. Yang, D. Y., B. Eng, J. S. Waye, J. C. Dudar, and S. R. Saunders. 1998. Technical note: improved DNA extraction from ancient bones using silica-based spin columns. Am. J. Phys. Anthropol. 105:539-543.