COMPENSATORY SUBSTITUTIONS AND THE EVOLUTION OF THE MITOCHONDRIAL 12SRIBOSOMAL-RNA GENE IN MAMMALS

12S ribosomal RNA (rRNA) gene sequences from a suite of mammalian taxa (13 placentals, 4 marsupials, 1 monotreme), for which phylogenetic re lationships are well established based on independent criteria, were e mployed to study the evolution of this gene. Phylogenetic analysis of 12S sequences produces a phylogeny that agrees with expectations. Base composition provides evidence for directional symmetrical substitutio n pressure in loops; in stems, base composition is much more even. Rat es of nucleotide substitution are lower in stems than loops. Patterns of nucleotide substitution show an overall preference for transitions over transversions, with this difference more profound in stems than l oops. Among different transversion pathways, there is a wide range of transformation frequencies. An analysis of compensatory substitutions shows that there is strong evidence for their occurrence and that a we ighting factor of 0.61 should be applied in phylogenetic analyses to a ccount for the dependence of mutations at stem positions relative to p ositions where changes are independent. Among stem variables (i.e., st em length, interaction distance, substitution rates, G+C content, and the percentage of bases that are paired), several significant correlat ions were discovered, but stem length and interaction distance are unc orrelated with other variables.