ESTIMATING SUBSTITUTION RATES IN RIBOSOMAL-RNA GENES

A model is introduced describing nucleotide substitution in ribosomal RNA (rRNA) genes. In this model, substitution in the stem and loop reg ions of rRNA is modeled with 16- and four-state continuous time Markov chains, respectively. The mean substitution rates at nucleotide sites are assumed to follow gamma distributions that are different for the two types of regions. The simplest formulation of the model allows for explicit expressions for transition probabilities of the Markov proce sses to be found. These expressions were used to analyze several 16S-l ike rRNA genes from higher eukaryotes with the maximum likelihood meth od. Although the observed proportion of invariable sites was only slig htly higher in the stem regions, the estimated average substitution ra tes in the stem regions were almost two times as high as in the loop r egions. Therefore, the degree of site heterogeneity of substitution ra tes in the stem regions seems to be higher than in the loop regions of animal 16S-like rRNAs due to presence of a few rapidly evolving sites . The model appears to be helpful in understanding the regularities of nucleotide substitution in rRNAs and probably minimizing errors in re covering phylogeny for distantly related taxa from these genes.