A QUANTITATIVE MAP OF NUCLEOTIDE SUBSTITUTION RATES IN BACTERIAL RIBOSOMAL-RNA

A recently developed method for estimating the variability of nucleoti de sites in a sequence alignment [Van de Peer, Y., Van der Auwera, G, and,De Wachter, R. (1996) J. Mel. Evol. 42, 201-210] was applied to ba cterial 16S, 5S and 23S rRNAs, In this method, the variability of each nucleotide site is defined as its evolutionary rate relative to the a verage evolutionary rate of all the nucleotide sites of the molecule. Spectra of evolutionary rates were calculated for each rRNA and show t he fastest evolving sites substituting at rates more than 1000 times t hat of the slowest ones. Variability maps are presented for each rRNA, consisting of secondary structure models where the variability of eac h nucleotide site is indicated by means of a colored dot. The maps can be interpreted in terms of higher order structure, function and evolu tion of the molecules and facilitate the selection of areas suitable f or the design of PCR primers and hybridization probes. Variability mea surement is also important for the precise estimation of evolutionary distances and the inference of phylogenetic trees.