Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis

Using sequence data from the 28S ribosomal RNA (rRNA) genes of selectedvertebrates, we investigated the effects that constraints imposed bysecondary structure have on the phylogenetic analysis of rRNA sequencedata. Our analysis indicates that characters from both base-pairing regions(stems) and non-base-pairing regions (loops) contain phylogeneticinformation, as judged by the level of support of the phylogenetic resultscompared with a well-established tree based on both morphological andmolecular data. The best results (the greatest level of support ofwell-accepted nodes) were obtained when the complete data set was used.However, some previously supported nodes were resolved using either thestem or loop bases alone. Stem bases sustain a greater number ofcompensatory mutations than would be expected at random, but the number is< 40% of that expected under a hypothesis of perfect compensation tomaintain secondary structure. Therefore, we suggest that in phylogeneticanalyses, the weighting of stem characters be reduced by no more than 20%,relative to that of loop characters. In contrast to previous suggestions,we do not recommend weighting of stem positions by one-half, compared withthat of loop positions, because this overcompensates for the constraintsthat selection imposes on the secondary structure of rRNA.