Is there an acceleration of the CpG transition rate during the mammalian radiation?
BACKGROUND
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.
Peifer
M
M
Institute of Chemistry, Karl-Franzens University Graz, Graz, Austria. peifer@uni-graz.at
Karro
J E
JE
von Grünberg
H H
HH
D000465:Algorithms; D000818:Animals; D018899:CpG Islands; D019175:DNA Methylation; D019143:Evolution, Molecular; D016678:Genome; D015894:Genome, Human; D006801:Humans; D008322:Mammals; D008390:Markov Chains; D051379:Mice