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Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA.

Sawyer S, Krause J, Guschanski K, Savolainen V, Pääbo S - PLoS ONE (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. susanna_sawyer@eva.mpg.de

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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Related in: MedlinePlus

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.
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pone-0034131-g001: 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.

Mentions: We first estimated the amount of endogenous mtDNA preserved in the specimens by calculating the number of base pairs (bp) sequenced per milligram (mg) of tissue for all 80 animal samples analyzed. The amount of DNA varied from 12 bp/mg (a 600–700-year-old horse) to 1,941,450 bp/mg (50-year-old monkey). Despite a very large variation in DNA amounts, there is a significant negative correlation between amounts of endogenous DNA and age (rho = −0.625, p-value = 5.90e-10) (Fig. 1). The removal of three young samples which contain almost an order of magnitude more DNA than the others only slightly reduces the correlation (rho = −0.623, p-value = 1.44e-09) (Fig. 1).


Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA.

Sawyer S, Krause J, Guschanski K, Savolainen V, Pääbo S - PLoS ONE (2012)

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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3316601&req=5

pone-0034131-g001: 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.
Mentions: We first estimated the amount of endogenous mtDNA preserved in the specimens by calculating the number of base pairs (bp) sequenced per milligram (mg) of tissue for all 80 animal samples analyzed. The amount of DNA varied from 12 bp/mg (a 600–700-year-old horse) to 1,941,450 bp/mg (50-year-old monkey). Despite a very large variation in DNA amounts, there is a significant negative correlation between amounts of endogenous DNA and age (rho = −0.625, p-value = 5.90e-10) (Fig. 1). The removal of three young samples which contain almost an order of magnitude more DNA than the others only slightly reduces the correlation (rho = −0.623, p-value = 1.44e-09) (Fig. 1).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany. susanna_sawyer@eva.mpg.de

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.

Show MeSH
Related in: MedlinePlus