Large subunit mitochondrial rRNA secondary structures and site-specific rate variation in two lizard lineages.

A phylogenetic-comparative approach was used to assess and refine existing secondary structure models for a frequently studied region of the mitochondrial encoded large subunit (16S) rRNA in two large lizard lineages within the Scincomorpha, namely the Scincidae and the Lacertidae. Potential pairings and mutual information were analyzed to identify site interactions present within each lineage and provide consensus secondary structures. Many of the interactions proposed by previous models were supported, but several refinements were possible. The consensus structures allowed a detailed analysis of rRNA sequence evolution. Phylogenetic trees were inferred from Bayesian analyses of all sites, and the topologies used for maximum likelihood estimation of sequence evolution parameters. Assigning gamma-distributed relative rate categories to all interacting sites that were homologous between lineages revealed substantial differences between helices. In both lineages, sites within helix G2 were mostly conserved, while those within helix E18 evolved rapidly. Clear evidence of substantial site-specific rate variation (covarion-like evolution) was also detected, although this was not strongly associated with specific helices. This study, in conjunction with comparable findings on different, higher-level taxa, supports the ubiquitous nature of site-specific rate variation in this gene and justifies the incorporation of covarion models in phylogenetic inference.