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MBE Advance Access published online on April 16, 2008
Molecular Biology and Evolution, 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 Article

Bayesian Inference of Errors in Ancient DNA Caused by Post Mortem Degradation

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

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

{dagger}Corresponding Author, Bruce H. Rannala, Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616 USA, Ph: (530) 754-4060, Fax: (780) 492-1354, Email: brannala{at}ucdavis.edu

Received for publication December 20, 2007. Revision received April 9, 2008. Accepted for publication April 11, 2008.

Methods for extracting and amplifying sequences using ancient DNA (aDNA) can be prone to errors caused by post mortem 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 post mortem degradation of the aDNA sequences. A computer program, BYPASSR-degr, was developed implementing the method and was used in subsequent analyses of simulated datasets 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


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