Journal Article

Is there an acceleration of the <i>CpG</i> transition rate during the mammalian radiation?

M. Peifer, J. E. Karro and H. H. von Grünberg

in Bioinformatics

Volume 24, issue 19, pages 2157-2164
Published in print October 2008 | ISSN: 1367-4803
Published online July 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn391
Is there an acceleration of the CpG transition rate during the mammalian radiation?

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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@uni-graz.at

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  6979 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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