title: Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA.
abstract: DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 5'-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments.
authors.affiliation: Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. susanna_sawyer@eva.mpg.de
authors.forename: Susanna
authors.initials: S
authors.lastname: Sawyer
authors.forename: Johannes
authors.initials: J
authors.lastname: Krause
authors.forename: Katerina
authors.initials: K
authors.lastname: Guschanski
authors.forename: Vincent
authors.initials: V
authors.lastname: Savolainen
authors.forename: Svante
authors.initials: S
authors.lastname: Pääbo
mesh_terms: D000818:Animals; D001482:Base Composition; D004247:DNA / Q000235:genetics*; D004249:DNA Damage; D053938:DNA Fragmentation; D004272:DNA, Mitochondrial / Q000235:genetics*; D015723:Gene Library; D006071:Gorilla gorilla; D006801:Humans; D010163:Paleontology / Q000379:methods; D016133:Polymerase Chain Reaction / Q000379:methods; D017422:Sequence Analysis, DNA; D013997:Time Factors
chemical_list: D004272:DNA, Mitochondrial; D004247:DNA