THE RADIATION OF CHARACIFORM FISHES AND THE LIMITS OF RESOLUTION OF MITOCHONDRIAL RIBOSOMAL DNA-SEQUENCES

Phylogenetic relationships among fishes from ostariophysan orders, cha raciform families, and serrasalmin genera (e.g., ''piranhas'') were ex amined 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 struct ural models, and compared at increasing levels of taxonomic divergence . In general, loop regions (unpaired) exhibited a higher level of vari ation than did stem regions (paired). A high proportion of compensator y substitutions was observed in stem regions in three data sets, sugge sting 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 fam iles of Characiformes and was not detected among serrasalmin genera. R eliable phylogenetic signal successfully reconstructed relationships a mong serrasalmin genera. However, aside from a few well-supported clad es, relationships could not be reconstructed with confidence among cha raciform families and ostariophysan orders. The reciprocal monophyly o f African and Neotropical characiform lineages was rejected (based on maximum likelihood ratio tests), and some support for previous hypothe ses based on morphology was provided by the molecular data. The radiat ion of characiform fishes is discussed in a historical biogeographic c ontext.