Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA

Secondary structure models are an important step for aligning sequences,understanding probabilities of nucleotide substitutions, and evaluating thereliability of phylogenetic reconstructions. A set of conserved sequencemotifs is derived from comparative sequence analysis of 184 invertebrateand vertebrate taxa (including many taxa from the same genera, families,and orders) with reference to a secondary structure model for domain III ofanimal mitochondrial small subunit (12S) ribosomal RNA. A template ispresented to assist with secondary structure drawing. Our model is similarto previous models but is more specific to mitochondrial DNA, fitting bothinvertebrate and vertebrate groups, including taxa with markedly differentnucleotide compositions. The second half of the domain III sequence can bedifficult to align precisely, even when secondary structure information isconsidered. This is especially true for comparisons of anciently divergedtaxa, but well-conserved motifs assist in determining biologicallymeaningful alignments. Patterns of conservation and variability in bothpaired and unpaired regions make differential phylogenetic weighting interms of "stems" and "loops" unsatisfactory. We emphasize looking carefullyat the sequence data before and during analyses, and advocate the use ofconserved motifs and other secondary structure information for assessingsequencing fidelity.