The radiation of characiform fishes and the limits of resolution of mitochondrial ribosomal DNA sequences.

Phylogenetic relationships among fishes from ostariophysan orders, characiform families, and serrasalmin genera (e.g., "piranhas") were examined using partial mitochondrial ribosomal DNA sequences of the 12S and 16S genes. Phylogenetic information content of these sequences was assessed at three levels of taxonomic inclusiveness by analyzing the patterns of nucleotide substitution using secondary structure models. Conserved and variable regions were identified, mapped onto the structural models, and compared at increasing levels of taxonomic divergence. In general, loop regions (unpaired) exhibited a higher level of variation than did stem regions (paired). A high proportion of compensatory substitutions was observed in stem regions in three data sets, suggesting strong selection to maintain the secondary structure. Saturation due to multiple substitutions was indicated by decreasing transition/transversion ratios and strong structural constraints on variation in comparisons among orders of Ostariophysi but was not obvious among families of Characiformes and was not detected among serrasalmin genera. Reliable phylogenetic signal successfully reconstructed relationships among serrasalmin genera. However, aside from a few well-supported clades, relationships could not be reconstructed with confidence among characiform families and ostariophysan orders. The reciprocal monophyly of African and Neotropical characiform lineages was rejected (based on maximum likelihood ratio tests), and some support for previous hypotheses based on morphology was provided by the molecular data. The radiation of characiform fishes is discussed in a historical biogeographic context.