PATTERNS OF NUCLEOTIDE CHANGE IN MITOCHONDRIAL RIBOSOMAL-RNA GENES AND THE PHYLOGENY OF PIRANHAS

The patterns and rates of nucleotide substitution in mitochondrial rib osomal RNA genes are described and applied in a phylogenetic analysis of fishes of the subfamily Serrasalminae (Teleostei, Characiformes, Ch aracidae). Fragments of 345 bp of the 12S and 535 bp of the 16S genes were sequenced for 37 taxa representing all but three genera in the su bfamily. Secondary-structure models based on comparative sequence anal ysis were derived to characterize the pattern of change among paired a nd unpaired nucleotides, forming stem and loop regions, respectively. Base compositional biases were in the direction of A-rich loops and G- rich stems. Ninety-five percent of substitutions in stem regions were compensatory mutations, suggesting that selection for maintenance of b ase pairing is strong and that independence among characters cannot be assumed in phylogenetic analyses of stem characters. The relative rat e of nucleotide substitution was similar in both fragments sequenced b ut higher in loop than in stem regions. In both genes, C-T transitions were the most common type of change, and overall transitions outnumbe red transversions by a factor of two in 16S and four in 12S. Phylogene tic analysis of the mitochondrial DNA sequences suggests that a clade formed by the genera Piaractus, Colossoma, and Mylossoma is the sister group to all other serrasalmins and that the genera Myleus, Serrasalm us, and Pristobrycon are paraphyletic. A previous hypothesis concernin g relationships for the serrasalmins, based on morphological evidence, is not supported by the molecular data. However, phylogenetic analysi s of host-specific helminth parasites and cytogenetic data support the phylogeny of the Serrasalminae obtained in this study and provide evi dence for coevolution between helminth parasites and their fish hosts.