Journal of Molecular Evolution

, Volume 73, Issue 3, pp 244–255

Evaluating the Impact of Post-Mortem Damage in Ancient DNA: A Theoretical Approach

Article

DOI: 10.1007/s00239-011-9474-z

Cite this article as:
Molak, M. & Ho, S.Y.W. J Mol Evol (2011) 73: 244. doi:10.1007/s00239-011-9474-z

Abstract

The growth of ancient DNA research has offered exceptional opportunities and raised great expectations, but has also presented some considerable challenges. One of the ongoing issues is the impact of post-mortem damage in DNA molecules. Nucleotide alterations and DNA strand breakages lead to a significant decrease in the quantity of DNA molecules of useful length in a sample and to errors in the final DNA sequences obtained. We present a model of age-dependent DNA damage and quantify the influence of that damage on subsequent steps in the sequencing process, including the polymerase chain reaction and cloning. Calculations using our model show that deposition conditions, rather than the age of a sample, have the greatest influence on the level of DNA damage. In turn, this affects the probability of interpreting an erroneous (possessing damage-derived mutations) sequence as being authentic. We also evaluated the effect of post-mortem damage on real data sets using a Bayesian phylogenetic approach. According to our study, damage-derived sequence alterations appear to have little impact on the final DNA sequences. This indicates the effectiveness of current methods for sequence authentication and validation.

Keywords

Ancient DNA Post-mortem damage Miscoding lesions Depurination Cytosine deamination Thermal age 

Supplementary material

239_2011_9474_MOESM1_ESM.pdf (2.5 mb)
Supplementary material 1 (PDF 2590 kb)

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.School of Biological SciencesUniversity of SydneySydneyAustralia