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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-U-->G-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, alphad, vs. rates of substitution of individual bases, alphas in rRNA. In the rapidly evolving D2 expansion segments of Drosophila large subunit rRNA, we estimate a low ratio of alphad/alphas, indicating that most compensatory substitutions involve a G-U intermediate. In contrast, we find a surprisingly high ratio of alphad/alphas 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 alphad/alphas. We conclude that in the core rRNA sequences compensatory substitutions can be fixed so rapidly as to appear to be instantaneous.
E R Tillier, and
R A Collins
September 2001,
Genetics,
E R Tillier, and
R A Collins
February 2009,
RNA (New York, N.Y.),
E R Tillier, and
R A Collins
October 1990,
Nucleic acids research,
E R Tillier, and
R A Collins
August 1977,
Cell,
E R Tillier, and
R A Collins
April 2006,
Nature structural & molecular biology,
E R Tillier, and
R A Collins
March 1971,
Journal of molecular biology,
E R Tillier, and
R A Collins
October 1995,
RNA (New York, N.Y.),
E R Tillier, and
R A Collins
April 1982,
Nucleic acids research,
E R Tillier, and
R A Collins
May 1990,
Nucleic acids research,
E R Tillier, and
R A Collins
December 2002,
DNA repair,
