Preservation of ancient DNA in thermally damaged archaeological bone

Naturwissenschaften

Volumn 96, Issue 2, 2009, Pages 267-278

  Ottoni, Claudio ^a   Koon, Hannah E C ^b   Collins, Matthew J ^b   Penkman, Kirsty E H ^b   Rickards, Olga ^a   Craig, Oliver E ^a,b  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b UNIVERSITY OF YORK   (United Kingdom)

Author keywords

Ancient DNA; Bone diagenesis; Collagen; Cooking

Indexed keywords

ARCHAEOLOGICAL EVIDENCE; BONE; CATTLE; COLLAGEN; DIAGENESIS; DISPERSAL; DNA; DOMESTICATION; PRESERVATION;

ANIMALS; ARCHAEOLOGY; BONE AND BONES; CATTLE; DNA; DNA, MITOCHONDRIAL; FOSSILS; HISTORY, MEDIEVAL; POLYMERASE CHAIN REACTION; PRESERVATION, BIOLOGICAL;

ANIMALIA; BOS;

EID: 58249124358     PISSN: 00281042     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00114-008-0478-5     Document Type: Article

References (47)

1. I Barnes JPW Young KM Dobney 2000 DNA-based identification of goose species from two archaeological sites in Lincolnshire J Archaeol Sci 27 91 100
2. LS Bell MF Skinner SJ Jones 1996 The speed of post mortem change to the human skeleton and its taphonomic significance Forensic Sci Int 82 129 140
3. R Bollongino CJ Edwards KW Alt J Burger DG Bradley 2006 Early history of European domestic cattle as revealed by ancient DNA Biol Lett 2 155 159
4. AW Briggs U Stenzel PL Johnson RE Green J Kelso K Prüfer M Meyer J Krause MT Ronan M Lachmann S Pääbo 2007 Patterns of damage in genomic DNA sequences from a Neanderthal Proc Natl Acad Sci U.S.A. 104 14616 14621
5. P Brotherton P Endicott JJ Sanchez M Beaumont R Barnett J Austin A Cooper 2007 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 35 5717 57128
6. M Buckley A Walker SY Ho Y Yang C Smith P Ashton JT Oates E Cappellini H Koon K Penkman B Elsworth D Ashford C Solazzo P Andrews J Strahler B Shapiro P Ostrom H Gandhi W Miller B Raney MI Zylber MT Gilbert RV Prigodich M Ryan KF Rijsdijk A Janoo MJ Collins 2008 Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry" Science 319 33
7. Budowle B, Moretti T, Smith J, Dizinno J (2000) DNA typing protocols: molecular biology and forensic analysis. Eaton, Natick
8. S Colgan L O'Brien M Maher N Shilton K McDonnell S Ward 2001 Development of a DNA-based assay for species identification in meat and bone meal Food Res Int 34 409 414
9. IB Colson JB Bailey M Vercauteren B Sykes R Hedges 1997 The preservation of Ancient DNA and bone diagenesis Ancient Biomol 1 109 117
10. A Cooper 1992 Removal of colourings, inhibitors of PCR, and the carrier effect of PCR contamination from ancient DNA samples Anc DNA Newslett 1 31 32
11. A Cooper HN Poinar 2000 Ancient DNA: do it right or not at all Science 289 1139
12. B Deagle JP Eveson S Jarman 2006 Quantification of damage in DNA recovered from highly degraded samples-a case study on DNA in faeces Front Zool 3 11
13. CJ Edwards DE MacHugh M Keith KM Dobney L Martin N Russell KL Horwitz SK McIntosh KC MacDonald D Helmer A Tresset JD Vigne DG Bradley 2004 Ancient DNA analysis of 101 cattle remains: limits and prospects J Archaeol Sci 31 695 710
14. CJ Edwards R Bollongino A Scheu A Chamberlain A Tresset JD Vigne JF Baird G Larson SY Ho TH Heupink B Shapiro AR Freeman MG Thomas RM Arbogast B Arndt L Bartosiewicz N Benecke M Budja L Chaix AM Choyke E Coqueugniot HJ Döhle H Göldner S Hartz D Helmer B Herzig H Hongo M Mashkour M Ozdogan E Pucher G Roth S Schade-Lindig U Schmölcke RJ Schulting E Stephan HP Uerpmann I Vörös B Voytek DG Bradley J Burger 2007 Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs Proc Biol Sci 274 1377 1385
15. MTP Gilbert L Rudbeck E Willerslev AJ Hansen C Smith KE Penkman K Prangenberg CM Nielsen-Marsh ME Jans P Arthur N Lynnerup G Turner-Walker M Biddle B Kjølbye-Biddle MJ Collins 2005 Biochemical and physical correlates of DNA contamination in archaeological human bones and teeth excavated at Matera, Italy J Archaeol Sci 32 785 793
16. MT Gilbert J Binladen W Miller C Wiuf E Willerslev HN Poinar JE Carlson JH Leebens-Mack SC Schuster 2006 Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis Nucleic Acids Res 35 1 10
17. A Götherström C Anderung L Hellborg R Elburg C Smith DG Bradley H Ellegren 2005 Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe Proc Biol Sci 272 2345 2350
18. S Haynes JB Searl A Bretman KM Dobney 2002 Bone preservation and ancient DNA: the application of screening methods for predicting DNA survival J Archaeol Sci. 29 585 592
19. RL Hill 1965 Hydrolysis of proteins Adv Protein Chem 20 37 107
20. M Hofreiter V Jaenicke D Serre A Haeseler Av S Pääbo 2001 DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA Nucleic Acids Res. 29 4793 4799
21. MME Jans CM Nielsen-Marsh CI Smith MJ Collins H Kars 2004 Characterisation of microbial attack on archaeological bone J Archaeol Sci 31 87 95
22. DS Kaufman WF Manley 1998 A new procedure for determining DL amino acid ratios in fossils using reverse phase liquid chromatography Quat Sci Rev 17 987 1000
23. BM Kemp DG Smith 2005 Use of bleach to eliminate contaminating DNA from the surface of bones and teeth Forensic Sci Int 154 53 61
24. Koon, HEC (2006) Detecting cooked bone in the archaeological record: a study of the thermal stability and deterioration of bone collagen. PhD thesis, University of York
25. HEC Koon RA Nicholson MJ Collins 2003 A practical approach to the identification of low temperature heated bone using TEM J Archaeol Sci 30 1393 1399
26. PL Kronick P Cooke 1996 Thermal stabilization of collagen fibers by calcification Connect Tissue Res 33 275 282
27. G Larson U Albarella K Dobney P Rowley-Conwy J Schibler A Tresset JD Vigne CJ Edwards A Schlumbaum A Dinu A Balaçsescu G Dolman A Tagliacozzo N Manaseryan P Miracle L Van Wijngaarden-Bakker M Masseti DG Bradley A Cooper 2007 Ancient DNA, pig domestication, and the spread of the Neolithic into Europe Proc Natl Acad Sci USA 104 15276 15281
28. JA Leonard O Shanks M Hofreiter E Kreuz L Hodges W Ream RC Wayne RK Fleischer 2007 Animal DNA in PCR reagents plagues ancient DNA research J Arch Sci 34 1361 1366
29. T Lindahl B Nyberg 1972 Rate of depurination of native deoxyribonucleic acid Biochem 11 3610
30. H Malmström J Stora L Dalen G Holmlund A Götherström 2005 Extensive human DNA contamination in extracts from ancient dog bones and teeth Mol Biol Evol 22 2040 2047
31. H Malmström EM Svensson MT Gilbert E Willerslev A Götherström G Holmlund 2007 More on contamination: the use of asymmetric molecular behaviour to identify authentic ancient human DNA Mol Biol Evol 24 998 1004
32. Newman ME, Parboosingh SE, Bridgeb PJ, Howard C (2002) Identification of Archaeological Animal Bone by PCR/DNA Analysis. J Archaeol Sci. doi: 10.1006/jasc.2001.0688
33. RA Nicholson 1993 A morphological investigation of burnt animal bone and an evaluation of it utility in archaeology J Archaeol Sci 20 411 428
34. JP Noonan M Hofreiter D Smith JR Priest N Rohland G Rabeder J Krause JC Detter S Pääbo EM Rubin 2005 Genomic sequencing of Pleistocene cave bears Science 309 597 600
35. O'Connor TP (1989) Bones from Anglo-Scandinavian Levels at 16-22 Coppergate. The Archaeology of York 15 (3). Council for British Archaeology, London
36. S Pääbo H Poinar D Serre V Jaenicke-Despres J Hebler N Rohland M Kuch J Krause L Vigilant M Hofreiter 2004 Genetic analyses from ancient DNA Annu Rev Genet 38 645 679
37. HN Poinar AB Stankiewicz 1999 Protein preservation and DNA retrieval from ancient tissues Proc Natl Acad Sci USA 96 8426 8431
38. HN Poinar M Hoss JL Bada S Pääbo 1996 Amino acid racemization and the preservation of ancient DNA Science 272 864 866
39. S Roberts C Smith R Millard MJ Collins 2002 The taphonomy of cooked bone: characterizing boiling and its physico-chemical effects Archaeometry 44 485 494
40. N Rohland M Hofreiter 2007 Comparison and optimization of ancient DNA extraction Biotechniques 42 343 352
41. M Salamon N Tuross B Arensburg S Weiner 2005 Relatively well preserved DNA is present in the crystal aggregates of fossil bones Proc Natl Acad Sci USA 102 13783 13788
42. P Shipman GF Foster M Schoeniger 1984 Burnt bones and teeth: an experimental study of colour, morphology, crystal structure and shrinkage J Archaeol Sci 11 307 325
43. CI Smith AT Chamberlain MS Riley C Stringer MJ Collins 2003 The thermal history of human fossils and the likelihood of successful DNA amplification J Hum Evol 45 203 217
44. EM Svensson A Götherström M Vretemark 2008 A DNA test for sex identification in cattle confirms osteometric results J Arch Sci 35 942 946
45. CS Troy DE MacHugh JF Bailey DA Magee RT Loftus P Cunningham AT Chamberlain BC Sykes DG Bradley 2001 Genetic evidence for Near-Eastern origins of European cattle Nature 410 6832 1088 1091
46. G Turner-Walker CM Nielsen-Marsh U Syversen H Kars MJ Collins 2002 Sub-micron spongiform porosity is the major ultra-structural alteration occurring in archaeological bone Int J Osteoarchaeol 12 407 414
47. M Zoledziewska S Gronkiewicz T Dobosz 2002 Comparison of various decalcificators in preparation of DNA from human rib bones Anthropol Rev 65 75 80