title: New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains.
abstract: Despite being plagued by heavily degraded DNA in palaeontological remains, most studies addressing the state of DNA degradation have been limited to types of damage which do not pose a hindrance to Taq polymerase during PCR. Application of serial qPCR to the two fractions obtained during extraction (demineralization and protein digest) from six permafrost mammoth bones and one partially degraded modern elephant bone has enabled further insight into the changes which endogenous DNA is subjected to during diagenesis. We show here that both fractions exhibit individual qualities in terms of the prevailing type of DNA (i.e. mitochondrial versus nuclear DNA) as well as the extent of damage, and in addition observed a highly variable ratio of mitochondrial to nuclear DNA among the six mammoth samples. While there is evidence suggesting that mitochondrial DNA is better preserved than nuclear DNA in ancient permafrost samples, we find the initial DNA concentration in the bone tissue to be as relevant for the total accessible mitochondrial DNA as the extent of DNA degradation post-mortem. We also evaluate the general applicability of indirect measures of preservation such as amino-acid racemization, bone crystallinity index and thermal age to these exceptionally well-preserved samples.
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University Hamilton, 1280 Main Street West, Hamilton, ON, Canada.
authors.forename: Carsten
authors.initials: C
authors.lastname: Schwarz
authors.forename: Regis
authors.initials: R
authors.lastname: Debruyne
authors.forename: Melanie
authors.initials: M
authors.lastname: Kuch
authors.forename: Elizabeth
authors.initials: E
authors.lastname: McNally
authors.forename: Henry
authors.initials: H
authors.lastname: Schwarcz
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Aubrey
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Bada
authors.forename: Hendrik
authors.initials: H
authors.lastname: Poinar