High Apparent Rate of Simultaneous Compensatory Base-Pair Substitutions in Ribosomal RNA

Corresponding author: Richard A. Collins, Department of Molecular and Medical Genetics, Faculty of Medicine, University of Toronto, 1 King’s College Circle, Toronto, Ontario, Canada M5S 1A8, rick.collins{at}utoronto.ca (E-mail).

Communicating editor: G. BRIAN GOLDING

We present a model for the evolution of paired bases in RNA sequences. The new model allows for the instantaneous rate of substitution of both members of a base pair in a compensatory substitution (e.g., A-UG -C) and expands our previous work by allowing for unpaired bases or noncanonical pairs. We implemented the model with distance and maximum likelihood methods to estimate the rates of simultaneous substitution of both bases, _d, vs. rates of substitution of individual bases, _s in rRNA. In the rapidly evolving D2 expansion segments of Drosophila large subunit rRNA, we estimate a low ratio of _d/_s, indicating that most compensatory substitutions involve a G -U intermediate. In contrast, we find a surprisingly high ratio of _d/_s in the core small subunit rRNA, indicating that the evolution of the slowly evolving rRNA sequences is modeled much more accurately if simultaneous substitution of both members of a base pair is allowed to occur approximately as often as substitution of individual bases. Using simulations, we have ruled out several potential sources of error in the estimation of _d/_s. We conclude that in the core rRNA sequences compensatory substitutions can be fixed so rapidly as to appear to be instantaneous.

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