CONSERVED SEQUENCE MOTIFS, ALIGNMENT, AND SECONDARY STRUCTURE FOR THE3RD-DOMAIN OF ANIMAL 12S RIBOSOMAL-RNA

Secondary structure models are an important step for aligning sequence s, understanding probabilities of nucleotide substitutions, and evalua ting the reliability of phylogenetic reconstructions. A set of conserv ed sequence motifs is derived from comparative sequence analysis of 18 4 invertebrate and vertebrate taxa (including many taxa from the same genera, families, and orders) with reference to a secondary structure model for domain III of animal mitochondrial small subunit (12S) ribos omal RNA. A template is presented to assist with secondary structure d rawing. Our model is similar to previous models but is more specific t o mitochondrial DNA, fitting both invertebrate and vertebrate groups, including taxa with markedly different nucleotide compositions. The se cond half of the domain LIT sequence can be difficult to align precise ly, even when secondary structure information is considered. This is e specially true for comparsions of anciently diverged taxa, but well-co nserved motifs assist in determining biologically meaningful alignment s. Patterns of conservation and variability in both paired and unpaire d regions make differential phylogenetic weighting in terms of ''stems '' and ''loops'' unsatisfactory. We emphasize looking carefully at the sequence data before and during analyses, and advocate the use of con served motifs and other secondary structure information for assessing sequencing fidelity.