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Bioinformatics Advance Access originally published online on July 28, 2008
Bioinformatics 2008 24(19):2157-2164; doi:10.1093/bioinformatics/btn391
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Is there an acceleration of the CpG transition rate during the mammalian radiation?

M. Peifer 1,*, J. E. Karro 2,3 and H. H. von Grünberg 1

1Institute of Chemistry, Karl-Franzens University Graz, Graz, Austria, 2Department of Computer Science and Systems Analysis and 3Department of Microbiology, Miami University, OH, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: In this article we build a model of the CpG dinucleotide substitution rate and use it to challenge the claim that, that rate underwent a sudden mammalian-specific increase approximately 90 million years ago. The evidence supporting this hypothesis comes from the application of a model of neutral substitution rates able to account for elevated CpG dinucleotide substitution rates. With the initial goal of improving that model's accuracy, we introduced a modification enabling us to account for boundary effects arising by the truncation of the Markov field, as well as improving the optimization procedure required for estimating the substitution rates.

Results: When using this modified method to reproduce the supporting analysis, the evidence of the rate shift vanished. Our analysis suggests that the CpG-specific rate has been constant over the relevant time period and that the asserted acceleration of the CpG rate is likely an artifact of the original model.

Contact: peifer{at}uni-graz.at

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on April 11, 2008; revised on July 27, 2008; accepted on July 27, 2008

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