Methodological strategies to assess the degree of bone preservation for ancient DNA studies

References

• Alessio M, Bella F, Cortesi C. 1966. University of Rome Carbon-14 Dates, IV. Radiocarbon 8:404–405
   Google Scholar
• Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147
   PubMed Web of Science ®Google Scholar
• Bada JL, Wang XS, Poinar HN, Pääbo S, Poinar GO. 1994. Amino acid racemization in amber-entombed insects: implications for DNA preservation. Geochimi Cosmochim Ac 58:3131–3135
   PubMed Web of Science ®Google Scholar
• Barrett EP, Joyner LG, Halenda PH. 1951. The determination of pore volume and area distributions in porous substances. I. Computations from nitrogen isotherms. J Am Chem Soc 73:373–380
   Web of Science ®Google Scholar
• Bollongino R, Tresset A, Vigne J-D. 2008. Environment and excavation: Pre-lab impacts on ancient DNA analyses. CR Paleovol 7:91–98
   Web of Science ®Google Scholar
• Brown TA, Nelson DE, Vogel JS, Southon JR. 1988. Improved collagen extraction by modified Longin method. Radiocarbon 30:171–177
   Web of Science ®Google Scholar
• Brunauer S, Emmett PH, Teller E. 1938. Adsorption of gases in multimolecular layers. J Am Chem Soc 60:309–319
   Web of Science ®Google Scholar
• Cai DW, Han L, Zhang XL, Zhou H, Zhu H. 2007. DNA analysis of archaeological sheep remains from China. J Archaeol Sci 34:1347–1355
   Web of Science ®Google Scholar
• Collins MJ, Penkman KE, Rohland N, Shapiro B, Dobberstein RC, Ritz-Timme S, Hofreiter M. 2009. Is amino acid racemization a useful tool for screening for ancient DNA in bone? Proc R Soc Biol Sci 276:2971–2977
   PubMed Web of Science ®Google Scholar
• Colonese AC, Zanchetta G, Fallick AE, Martini F, Manganelli G, Lo Vetro D. 2007. Stable isotope composition of late glacial land snail shells from Grotta del Romito (Southern Italy): Palaeoclimatic implications. Palaeogeogr Palaeocl 254:550–560
   Web of Science ®Google Scholar
• Cooper A, Poinar HN. 2000. Ancient DNA: do it right or not at all. Science 289:1139
   PubMed Web of Science ®Google Scholar
• De Angelis F, Scorrano G, Rickards O. 2013. DNA antico: principi e metodologie. Med Secoli 25:51–83
   PubMedGoogle Scholar
• Deagle BE, Eveson JP, Jarman S. 2006. Quantification of damage in DNA recovered from highly degraded samples-a case study on DNA in faeces. Front Zool 3:11
   Google Scholar
• Fabbri PF, Graziosi P, Guerri M, Mallegni F. 1989. Les hommes des sépoltures de la grotte du Romito à Papsidero (Cosenza, Italie). In: Giacobini G, editor. Hominidae: Proceedings of the 2nd International Congress of Human Paleontology. Milano: Jaca book. p 487–494
   Google Scholar
• Featherstone JD, Pearson S, LeGeros RZ. 1984. An infrared method for quantification of carbonate in carbonated apatites. Caries Res 8:63–66
   Google Scholar
• Fiammenghi CA. 2003. La Necropoli di Elea-Velia: qualche osservazione preliminare. Pozzuoli: Naus
   Google Scholar
• Graziosi P. 1971. Derniéres découvertes de gravures paléolithiques dans la grotte du Romito en Calabre. In: École Pratique des Hautes Études, Vie Section, Centre de Recherches Historiques, editor. Mélanges offerts à André Varagnac. Paris: Sevpen. p 355–357
   Google Scholar
• Hammer M. 2001. The superefficient company. Harvard Busi Rev 79:82–91
   PubMed Web of Science ®Google Scholar
• Hedges REM, Millard AR. 1995. Bones and groundwater—towards the modeling of diagenetic processes. J Archaeol Sci 22:155–164
   Web of Science ®Google Scholar
• Hofreiter M, Jenicke V, Serre D, von Haeseler A, Pääbo S. 2001. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res 23:4793–4799
   Web of Science ®Google Scholar
• Lee-Thorp JA, van der Merwe NJ. 1991. Aspects of the chemistry of modern and fossil biological apatites. J Archaeol Sci 18:343–354
   Web of Science ®Google Scholar
• Loreille O, Vigne JD, Hardy C, Callou C, Treinen-Claustre F, Dennebouy N, Monnerot M. 1997. First distinction of sheep and goat archaeological bones by the means of their fossil mtDNA. J Archaeol Sci 24:33–37
   Web of Science ®Google Scholar
• Lowell S, Shields JE, Thomas MA, Thommes M. 2004. Characterization of porous solids and powders: surface area, pore size and density, vol. 16. New York: Springer
   Google Scholar
• Martini F, Bisconti M, Casciarri S, Fabbri PF, Leonini V, Lo Vetro D, Mallegni F, et al. 2004. La nuova sepoltura epigravettiana ‘Romito 7’ a Papasidero. In: I.I.P.P., editor. Atti della XXXVII Riunione Scientifica I.I.P.P., ‘Preistoria e Protostoria della Calabria’. Firenze: Istituto Italiano di Preistoria e Protostoria. p 101–111
   Google Scholar
• Martini F. 2002. Grotta del Romito. Firenze: Museo e Istituto Fiorentino di Preistoria
   Google Scholar
• Nielsen-Marsh CM, Gernaey A, Turner-Walker G, Hedges REM, Pike A, Collins MJ. 2000b. The chemical degradation of bone. In: Cox M, Mays S, editors. Human osteology in Archaeology and Forensic Science. Cambridge: Cambridge University Press. p 439–455
   Google Scholar
• Nielsen-Marsh CM, Hedges REM, Mann T, Collins MJ. 2000a. A preliminary investigation of the application of differential scanning calorimetry to the study of collagen degradation in archaeological bone. Thermochim Acta 365:129–139
   Web of Science ®Google Scholar
• Nielsen-Marsh CM, Hedges REM. 1999. Bone porosity and the use of mercury intrusion porosimetry in bone diagenesis studies. Archaeometry 41:165–174
   Web of Science ®Google Scholar
• Nielsen-Marsh CM, Hedges REM. 2000. Patterns of diagenesis in bone I: The effects of site environments. J Archaeol Sci 27:1139–1150
   Web of Science ®Google Scholar
• Nielsen-Marsh CM. 1997. Studies in archaeological bone diagenesis. Oxford: University of Oxford
   Google Scholar
• Ohtani S, Yamada Y, Yamamoto T, Arany S, Gonmori K, Yoshioka N. 2004. Comparison of age estimated from degree of racemization of aspartic acid, glutamic acid and alanine in the femur. J Forensic Sci 49:441–445
   PubMed Web of Science ®Google Scholar
• Okazaki M, Yoshida Y, Yamaguchi S, Kaneno M, Elliott JC. 2001. Affinity binding phenomena of DNA onto apatite crystals. Biomaterials 22:2459–2464
   PubMed Web of Science ®Google Scholar
• Pääbo S, Irwin D, Wilson A. 1990. DNA damage promotes jumping between templates during enzymatic amplification. J Biol Chem 265:4718–4721
   PubMed Web of Science ®Google Scholar
• Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, et al. 2004. Genetic analyses from ancient DNA. Annu Rev Genet 38:645–679
   PubMed Web of Science ®Google Scholar
• Paget E, Monrozier LJ, Simonet P. 1992. Adsorption of DNA on clay-minerals—Protection against Dnasei and influence on gene-transfer. FEMS Microbiol Lett 97:31–39
   Web of Science ®Google Scholar
• Poinar HN, Hoss M, Bada JL, Pääbo S. 1996. Amino acid racemization and the preservation of ancient DNA. Science 272:864–866
   PubMed Web of Science ®Google Scholar
• Reiche I, Favre-Quattropani L, Vignaud C, Bocherens H, Charlet L, Menu M. 2003. A multi-analytical study of bone diagenesis: the Neolithic site of Bercy (Paris, France). Measurement Sci Technol 14:1608–1619
   Web of Science ®Google Scholar
• Rolfo MF, Lelli R, Martínez-Labarga C, Passacantando D, Scorrano G, Salari L, Rickards O. 2012. La comunità neolitica di grotta Mora Cavorso a Jenne (Rm): osservazioni deposizionali, paleobiologiche e faunistiche. In: Negroni Catacchio, N, editor. Preistoria e Protostoria in Etruria. Decimo incontro di studi. L’Etruria dal Paleolitico al Primo Ferro: lo stato delle ricerche. Milano: Centro Studi di Preistoria e Archeologia. p 131–145
   Google Scholar
• Rolfo MF, Mancini D, Salari L, Zarattini A. 2010. La grotta di ‘Mora Cavorso’ a Jenne (Roma). Nuove ricerche. In: Ghini G, editor. Atti del VI incontro di studi ‘Lazio e Sabina’. Roma: Quasar. p 11–17
   Google Scholar
• Shemesh A. 1990. Crystallinity and diagenesis of sedimentary apatites. Geochimi Cosmochim Ac 54:2433–2438
   Web of Science ®Google Scholar
• Smith CI, Nielsen-Marsh CM, Jans MME, Collins MJ. 2007. Bone diagenesis in the European Holocene I: patterns and mechanisms. J Archaeol Sci 34:1485–1493
   Web of Science ®Google Scholar
• Sosa C, Vispe E, Nunez C, Baeta M, Casalod Y, Bolea M, Hedges RE, Martinez-Jarreta B. 2013. Association between ancient bone preservation and dna yield: a multidisciplinary approach. Am J Phys Anthropol 151:102–109
   PubMed Web of Science ®Google Scholar
• Surovell TA, Sitner MC. 2001. Standardizing infra-red measures of bone mineral crystallinity: An experimental approach. J Archaeol Sci 28:633–642
   Web of Science ®Google Scholar
• Turner-Walker G, Nielsen-Marsh CM, Syversen U, Kars H, Collins MJ. 2002. Sub-micron spongiform porosity is the major ultra-structural alteration occurring in archaeological bone. Int J Osteoarchaeol 12:407–414
   Web of Science ®Google Scholar
• Verzijl N, DeGroot J, Thorpe SR, Bank RA, Shaw JN, Lyons TJ, et al. 2000. Effect of collagen turnover on the accumulation of advanced glycation end products. J Biol Chem 275:39027–39031
   PubMed Web of Science ®Google Scholar
• Yang DY, Eng B, Waye JS, Dudar JC, Saunders SR. 1998. Technical Note: Improved DNA extraction from ancient bones using silica-based spin columns. Am J Phys Antrhopol 105:539–543
   PubMed Web of Science ®Google Scholar