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MBE Advance Access originally published online on April 16, 2008
Molecular Biology and Evolution 2008 25(7):1503-1511; doi:10.1093/molbev/msn095
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Bayesian Inference of Errors in Ancient DNA Caused by Postmortem Degradation

Ligia M. Mateiu* and Bruce H. Rannala{dagger}

* Department of Forest Sciences/Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
{dagger} Genome Center and Department of Evolution and Ecology, University of California, Davis

E-mail: brannala{at}ucdavis.edu.

Accepted for publication April 11, 2008.

Methods for extracting and amplifying sequences using ancient DNA (aDNA) can be prone to errors caused by postmortem modifications of the DNA strand. A new statistical method is developed for predicting errors in aDNA sequences caused by such processes. In addition to the canonical DNA substitution model parameters, a discrete Markov chain is used to describe nucleotide substitutions occurring via postmortem degradation of the aDNA sequences. A computer program, BYPASSR-degr, was developed implementing the method and was used in subsequent analyses of simulated data sets under the new model. Simulation studies show that the new method can be powerful and accurate in identifying damaged sites. The method is applied to analyze aDNA sequences of Etruscans, Adélie penguins, and horses. No significant signals of degradation were observed at any sites of the aDNA sequences we analyzed.

Key Words: Bayesian phylogenetic inference • molecular evolution • Markov process • site-specific rates • Metropolis–Hastings algorithm • ancient DNA • DNA damage • gene amplification

Jeffery Thorne, Associate Editor


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