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

The DOI matches its Crossref record; 26 of the 26 references it cites were found in a registry or an index.

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

Open access
Sawyer, Susanna, Krause, Johannes, Guschanski, Katerina, Savolainen, Vincent, Pääbo, Svante·2012·PLoS ONE
DOI 10.1371/journal.pone.0034131PMC PMC3316601
Open this paper in CoChat — free accountOpen PDF

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.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1371/journal.pone.0034131

Cites

26 of 26 references verified0 citation errors · 0 not checkable

Statistics

Figures

Figure 1 Amounts of endogenous mtDNA sequences (bp) determined per milligram (mg) of tissue as a function of age. Note that since the Neandertal specimens were all ascertained for containing endogenous DNA they are excluded from this analysis. Nine samples known to have been “roasted” over fire and treated with ponal glue are indicated by crosses and four samples treated by the “Leipzig cocktail” are indicated by circles.
Figure 1 Amounts of endogenous mtDNA sequences (bp) determined per milligram (mg) of tissue as a function of age. Note that since the Neandertal specimens were all ascertained for containing endogenous DNA they are excluded from this analysis. Nine samples known to have been “roasted” over fire and treated with ponal glue are indicated by crosses and four samples treated by the “Leipzig cocktail” are indicated by circles.CC BY · PubMed Central
Figure 2 Median length of endogenous mtDNA fragment as a function of age. Nine samples known to have been “roasted” over fire and treated with ponal glue are indicated by crosses and four samples treated by the “Leipzig cocktail” are indicated by circles.
Figure 2 Median length of endogenous mtDNA fragment as a function of age. Nine samples known to have been “roasted” over fire and treated with ponal glue are indicated by crosses and four samples treated by the “Leipzig cocktail” are indicated by circles.CC BY · PubMed Central
Figure 3 Characteristics of purine frequency prior to strand breaks. A: Base frequencies 5′ and 3′ of 5′-ends of endogenous mtDNA fragments of a horse (sample 54). B: Increase in purine frequency at position immediately 5′ (position −1) of mtDNA fragment ends relative to positions −5 to −10 as a function of age. Nine samples known to have been “roasted” over fire and treated with ponal glue are indicated by crosses and four samples treated by the “Leipzig cocktail” are indicated by circles. C: Increase in A (blue) and G (red) frequencies at position −1 of mtDNA fragment. Nine samples known to have been “roasted” over fire and treated with ponal glue are indicated by crosses and four samples treated by the “Leipzig cocktail” are indicated by circles.
Figure 3 Characteristics of purine frequency prior to strand breaks. A: Base frequencies 5′ and 3′ of 5′-ends of endogenous mtDNA fragments of a horse (sample 54). B: Increase in purine frequency at position immediately 5′ (position −1) of mtDNA fragment ends relative to positions −5 to −10 as a function of age. Nine samples known to have been “roasted” over fire and treated with ponal glue are indicated by crosses and four samples treated by the “Leipzig cocktail” are indicated by circles. C: Increase in A (blue) and G (red) frequencies at position −1 of mtDNA fragment. Nine samples known to have been “roasted” over fire and treated with ponal glue are indicated by crosses and four samples treated by the “Leipzig cocktail” are indicated by circles.CC BY · PubMed Central
Figure 4 Characteristics of C to T misincorporations. A: C to T misincorporations at the first 15 bases of endogenous mtDNA fragments from of a 500–600 year old horse sample (sample 54). B: C to T misincorporations at the first position of mtDNA fragments as a function of age. Nine samples known to have been “roasted” over fire and treated with ponal glue are indicated by crosses and four samples treated by the “Leipzig cocktail” are indicated by circles.
Figure 4 Characteristics of C to T misincorporations. A: C to T misincorporations at the first 15 bases of endogenous mtDNA fragments from of a 500–600 year old horse sample (sample 54). B: C to T misincorporations at the first position of mtDNA fragments as a function of age. Nine samples known to have been “roasted” over fire and treated with ponal glue are indicated by crosses and four samples treated by the “Leipzig cocktail” are indicated by circles.CC BY · PubMed Central

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 26 references

Cited by

Sorted by citations

Items 401–489 of 489

Related

See all

Metadata

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
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
Licence
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review