Abstract. The patterns and rates of nucleotide substitution in mitochondrial ribosomal RNA genes are described and applied in a phylogenetic analysis of fishes of the subfamily Serrasalminae (Teleostei, Characiformes, Characidae). 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 subfamily. Secondary-structure models based on comparative sequence analysis were derived to characterize the pattern of change among paired and 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 base pairing is strong and that independence among characters cannot be assumed in phylogenetic analyses of stem characters. The relative rate of nucleotide substitution was similar in both fragments sequenced but higher in loop than in stem regions. In both genes, C-T transitions were the most common type of change, and overall transitions outnumbered transversions by a factor of two in 16S and four in 12S. Phylogenetic 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, Serrasalmus, and Pristobrycon are paraphyletic. A previous hypothesis concerning relationships for the serrasalmins, based on morphological evidence, is not supported by the molecular data. However, phylogenetic analysis of host-specific helminth parasites and cytogenetic data support the phylogeny of the Serrasalminae obtained in this study and provide evidence for coevolution between helminth parasites and their fish hosts.

Previous studies based on DNA sequences of mitochondrial (mt) rRNA genes showed three main groups within the subfamily Serrasalminae: (1) a "pacu" clade of herbivores (Colossoma, Mylossoma, Piaractus); (2) the "Myleus" clade (Myleus, Mylesinus, Tometes, Ossubtus); and (3) the "piranha" clade (Serrasalmus, Pygocentrus, Pygopristis, Pristobrycon, Catoprion, Metynnis). The genus Acnodon was placed as the sister taxon of clade (2+3). However, poor resolution within each clade was obtained due to low levels of variation among rRNA gene sequences. Complete sequences of the hypervariable mtDNA control region for a total of 45 taxa, and additional sequences of 12S and 16S rRNA from a total of 74 taxa representing all genera in the family are now presented to address intragroup relationships. Control region sequences of several serrasalmid species exhibit tandem repeats of short motifs (12 to 33 bp) in the 3' end of this region, accounting for substantial length variation. Bayesian inference and maximum parsimony analyses of these sequences identify the same groupings as before and provide further evidence to support the following observations: (a) Serrasalmus gouldingi and species of Pristobrycon (non-striolatus) form a monophyletic group that is the sister group to other species of Serrasalmus and Pygocentrus; (b) Catoprion, Pygopristis, and Pristobrycon striolatus form a well supported clade, sister to the group described above; (c) some taxa assigned to the genus Myloplus (M. asterias, M tiete, M ternetzi, and M rubripinnis) form a well supported group whereas other Myloplus species remain with uncertain affinities (d) Mylesinus, Tometes and Myleus setiger form a monophyletic group.

No abstract