The phylogenetic relationships of 43 species in the subtribe Carpomyina (39 Rhagoletis spp., plus Carpomya schineri (Loew), Oedicarena latifrons (Wulp), Rhagoletotrypeta pastranai Aczél, and Zonosemata electa (Say)) are examined using morphological and mitochondrial DNA (mtDNA) characters. The taxon sample includes 5 Palearctic Rhagoletis species (R. almatensis Rohdendorf, R. batava Hering, R. flavicincta (Loew), R. flavigenualis Hering, and R. magniterebra (Rohdendorf)) and 5 Neotropical Rhagoletis species (R. blanchardi Aczél, R. ferruginea Hendel, R. lycopersella Smyth, R. nova (Schiner), and R. psalida Hendel) whose mtDNA relationships have not been previously analyzed. Phylogenetic analysis of 77 morphological features using unweighted parsimony yielded 28,671 most parsimonious reconstructions (MPRs). A strict consensus of these MPRs contained 12 clades, and further analysis using successive approximations improved phylogenetic resolution. Analysis of 1027 aligned nucleotide positions in the mitochondrial COI/COII region indicated that, as previously hypothesized, the genus Rhagoletis may not be strictly monophyletic. Monophyly of Rhagoletis, in the strict holophyletic sense (sensu Hennig), was disrupted by Z. electa and C. schineri; however, these phylogenetic placements did not have bootstrap support. Analysis of mtDNA supported our previous hypothesis that R. batava and R. flavigenualis have phylogenetic affinity to five taxonomically-defined North American species groups. In addition, mtDNA data grouped R. almatensis and R. flavicincta with R. cerasi (L.), a result consistent with our present analysis of morphology. Analyses of both morphology and mtDNA place R. magniterebra as a sister taxon to R. meigenii (Loew). The Neotropical Rhagoletis species form a distinct group based on mtDNA analysis and, with the exception of the placement of Rh. pastranai, these relationships are consistent with morphology. Several clades observed in the morphological analysis were in conflict with those observed in the mtDNA analysis. Partition homogeneity tests indicated that significantly different phylogenetic signals emanate from the morphological and mtDNA data; therefore these data sets were not combined for analysis. Recent phylogenetic analyses of several Rhagoletis spp. based on DNA sequences of alleles at anonymous nuclear loci indicate that random genetic drift and/or hybridization and introgression may be playing a large role in the evolution of Rhagoletis species. We argue that these forces, combined with differential selection, can lead to fixation of alternate alleles in different lineages and result in the phylogenetic conflicts observed in the morphological and mtDNA analyses.

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