SEQUENCE EVOLUTION AND PHYLOGENETIC SIGNAL IN CONTROL-REGION AND CYTOCHROME-B SEQUENCES OF RAINBOW FISHES (MELANOTAENIIDAE)

The nucleotide sequences of segments of the cytochrome b gene (351 bp) , the tRNA(Pro) gene (49 bp), and the control region (similar to 313 b p) of mitochondrial DNA were obtained from 26 fish representing differ ent populations and species of Melanotaenia and one species of Glossol epis, freshwater rainbow fishes confined to Australia and New Guinea. The purpose was to investigate relative rates and patterns of sequence evolution. Overall levels of divergence were similar for the cytochro me b and tRNA control-region sequences, both ranging from <1% within s ubspecies to 15%-19% between genera. However, the patterns of sequence evolution differed. For the cytochrome b gene, transitions consistent ly exceeded transversions, the bias ranging from 4.2:1 to 2:1, dependi ng on the level of sequence divergence. However, in the control-region sequence, a bias toward transitions (2:1) was observed only in compar isons between very similar sequences, and transversions outnumbered tr ansitions in comparisons of divergent sequences. Graphic comparisons s uggested that the control region was saturated for transitions at rela tively low levels of sequence divergence but accumulated transversions at a greater rate than did the cytochrome b sequence. These distinct patterns of base substitution are associated with differences in A+T c ontent, which is 70% for the tRNA control-region segment versus 50% fo r cytochrome b. A test for skewness in the distribution of lengths of random trees indicated that both segments contained phylogenetic signa l. Parsimony analyses of the data from the two regions, with or withou t weighting schemes appropriate to the respective patterns of sequence evolution, identified the same five groupings of sequences, but the r elationships among the groups differed. However, in most cases the bra nches uniting different combinations of groups were poorly supported, and the differences among topologies were insignificant. Considering t he observed patterns of base substitution and the results of the phylo genetic analyses, we deduce that both the control region and cytochrom e b are appropriate for population genetic studies but that the contro l region is less effective than cytochrome b for resolving relationshi ps among divergent lineages of rainbow fishes.