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Phylogenetic relationships among fruit flies, Bactrocera (Diptera, Tephritidae), based on the mitochondrial rDNA sequences

Nucleotide sequences of a 1.6 kb long portion of the mitochondrial DNA containing the majority of the 16S rRNA gene, the tRNAval gene, and the 5′ half‐region of the 12S rRNA gene were determined for forty‐eight individuals of nineteen Bactrocera species and one other tephritid taxon, Anastrepha ludens. Phylogenetic analyses were performed using the consistently aligned 1.5 kb long sequences, excluding seventeen portions that could not be aligned unambiguously and were aligned inconsistently among analyses using different programs and parameters. Results of phylogenetic analyses were highly congruent among distance, unweighted parsimony, and weighted parsimony methods in terms of topology of resulting trees. Bootstrap analyses supported many of the phylogenetic relationships resolved by these analyses. Although aligned sequences showed apparent biases in nucleotide content and substitutions that differed among sites within the stem/loop structure of rRNA molecules, compensation for such factors did not greatly affect the topology. The results are discussed in relation to the taxonomic positions of species used in this study and in relation to the phylogenetic and diagnostic utility of the mitochondrial rDNA fragment.