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Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA - PubMed

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Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA

Susanna Sawyer et al. PLoS One. 2012.

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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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
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 2
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 3
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 4
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.

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