Cited by 489Forensic and Genetic ResearchArchaeology and ancient environmental studiesPleistocene-Era Hominins and Archaeology

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Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

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Sawyer, Susanna, Krause, Johannes, Guschanski, Katerina, Savolainen, Vincent, Pääbo, Svante·2012·PLoS ONE

DOI 10.1371/journal.pone.0034131PMC PMC3316601

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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.

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Authors: Sawyer, S., Krause, J., Guschanski, K., Savolainen, V., & Pääbo, S.
Affiliations: Max Planck Society (DE)
University of Tübingen (DE)
University of Lausanne (CH)
Imperial College London (GB)
Corresponding author: Sawyer, Susanna
ORCID: Sawyer, Susanna
Krause, Johannes
Guschanski, Katerina
Savolainen, Vincent
Pääbo, Svante
Venue: PLoS ONE
Publisher: Public Library of Science (PLoS)
Published: 2012-03-30
Volume: 7
Issue: 3
Pages: e34131
ISSN: 1932-6203 (ISSN-L)
DOI: 10.1371/journal.pone.0034131
PMC: PMC3316601
OpenAlex: W2022327489
Cited by: 489
References: 26
Citations by year: 2026: 26 · 2025: 31 · 2024: 22 · 2023: 29 · 2022: 33 · 2021: 56 · 2020: 54 · 2019: 27 · 2018: 52 · 2017: 46 · 2016: 31 · 2015: 33 · 2014: 25 · 2013: 19 · 2012: 4
FWCI: 15.36
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: PLoS ONE (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
IRIS (submittedVersion)
Uppsala University Publications (Uppsala University) (submittedVersion, other-oa)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Figshare (submittedVersion, cc-by)
Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
SERVAL (Université de Lausanne) (submittedVersion, other-oa)
Funders: Max-Planck-Gesellschaft
Natural Environment Research Council
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Social Sciences › Archeology › Archaeology and ancient environmental studies
Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
Keywords: ancient DNA, DNA fragmentation, nucleotide misincorporation, strand breaks, mitochondrial DNA, DNA damage, DNA contamination, temporal patterns, museum specimens, endogenous DNA
MeSH terms: Animals, Base Composition, DNA, DNA Damage, DNA, Mitochondrial, Gorilla gorilla, Humans, Paleontology, Time Factors, Gene Library, Polymerase Chain Reaction, Sequence Analysis, DNA, DNA Fragmentation

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Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

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