Fragmentation of Contaminant and Endogenous DNA in Ancient Samples
Author Information
Author(s): García-Garcerà Marc, Gigli Elena, Sanchez-Quinto Federico, Ramirez Oscar, Calafell Francesc, Civit Sergi, Lalueza-Fox Carles
Primary Institution: Institut de Biologia Evolutiva, CSIC-UPF, Barcelona, Spain
Hypothesis
Can the fragmentation patterns of contaminant and endogenous DNA in ancient samples be distinguished?
Conclusion
The study suggests that endogenous and contaminant DNA sequences cannot be easily distinguished based on fragmentation patterns alone.
Supporting Evidence
- The efficiency of retrieval of endogenous sequences is below 1% in all cases.
- Contaminant sequences show a fragmentation pattern similar to that of endogenous sequences.
- Bleach treatment may convey ancient characteristics on contaminant DNA.
- Entropy decreases at the breaking point in both contaminant and endogenous sequences.
Takeaway
This study looked at old DNA from ancient samples and found that it's really hard to tell if the DNA is from the original organism or from modern contamination.
Methodology
The study used 454-FLX pyrosequencing to analyze ancient DNA samples from different species and ages.
Potential Biases
There is a risk of misidentifying contaminant DNA as endogenous due to the difficulty in distinguishing between the two.
Limitations
The efficiency of DNA retrieval was low in all samples, and the study relied on samples with known contamination histories.
Statistical Information
P-Value
p<0.05
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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