Rates and patterns of base change in the small subunit ribosomal RNA gene

The small subunit ribosomal RNA gene (srDNA) has been used extensively for phylogenetic analyses. One common assumption in these analyses is that substitution rates are biased toward transitions. We have developed a simple method for estimating relative rates of base change that does not assume rate constancy and takes into account base composition biases in different structures and taxa. We have applied this method to srDNA sequences from taxa with a noncontroversial phylogeny to measure relative rates of evolution in various structural regions of srRNA and relative rates of the different transitions and transversions. We find that: (1) the long single-stranded regions of the RNA molecule evolve slowest, (2) biases in base composition associated with structure and phylogenetic position exist, and (3) the srDNAs studied lack a consistent transition/transversion bias. We have made suggestions based on these findings for refinement of phylogenetic analyses using srDNA data.