Title: 
RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximumlikelihood methods.
N J Savill, D C Hoyle, and P G Higgs 
Speaker: 
Anne Condon

Abstract 
We test models for the evolution of helical regions of RNA sequences, where the base pairing constraint leads to correlated compensatory substitutions occurring on either side of the pair. These models are of three types: 6state models include only the four WatsonCrick pairs plus GU and UG; 7state models include a single mismatch state that combines all of the 10 possible mismatches; 16state models treat all mismatch states separately. We analyzed a set of eubacterial ribosomal RNA sequences with a wellestablished phylogenetic tree structure. For each model, the maximumlikelihood values of the parameters were obtained. The models were compared using the Akaike information criterion, the likelihoodratio test, and Cox's test. With a high significance level, models that permit a nonzero rate of double substitutions performed better than those that assume zero double substitution rate. Some models assume symmetry between GC and CG, between AU and UA, and between GU and UG. Models that relaxed this symmetry assumption performed slightly better, but the tests did not all agree on the significance level. The most general timereversible model significantly outperformed any of the simplifications. We consider the relative merits of all these models for molecular phylogenetics.
