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

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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. © The Author 2008. Published by Oxford University Press. All rights reserved.

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Peifer, M., Karro, J. E., & von Grünberg, H. H. (2008). Is there an acceleration of the CpG transition rate during the mammalian radiation? Bioinformatics, 24(19), 2157–2164. https://doi.org/10.1093/bioinformatics/btn391

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