Secondary structure of mitochondrial 12S rRNA among fish and its phylogenetic applications

The complete 12S ribosomal RNA(rRNA) sequences from 23 gobioid species and nine diverse assortments of other fish species were employed to establish a core secondary structure model for fish 12S rRNA. Of the 43 stems recognized, 41 were supported by at least some compensatory evidence among vertebrates. The rates of nucleotide substitution were lower in stems than in loops. This may produce less phylogenetic information in stems when recently diverged taxa are compared. An analysis of compensatory substitution shows that the percentage of covariation is 68%, and the weighting factor for phylogenetic analyses to account for the dependence of mutations should be 0.66. Different stem-loop weighting schemes applied to the analyses of phylogenetic relationships of the Gobioidei indicate that down-weighting paired regions because of nonindependence could not improve the present phylogenetic analysis. A biased nucleotide composition (adenine% [A%] > thymine% [T%], cytosine% [C%] > guanine% [G%]) in the loop regions was also observed in the mammalian counterpart. The excess of A and C in the loop regions may be because of the asymmetric mechanism of mtDNA replication, which leads to the spontaneous deamination of C and A. This process may also be responsible for a transition-transversion bias and the patterns of nucleotide substitutions in both stems and loops.