Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs

The alignment of ribosomal RNA (rRNA) by computer requires assumptions about the evolutionary costs for gaps in the alignment that are undefinable when uniformly applied across the entire molecule. The conservation of rRNA secondary structures exceeds that of its nucleotides, and therefore it is recommended that secondary structures guide decisions about the assignment of homologous positions for phylogenetic studies. Suggestions for alignment, data presentation, and character description are made in the context of an example from frog large subunit nuclear rRNA. Realignment improved congruence with previously published morphological conclusions and the format used in data presentation facilitated the description of character-based conclusions at each node in the cladogram. The data presented allow a discrimination between the fully resolved shortest tree and conclusions that the data actually support with any reasonable confidence: a monophyletic Pipanura, Neobatrachia, and Ranoidea without further resolution within the Neobatrachia.