Molecular diagnostics and systematics of the genus Ceratitis (Diptera: Tephritidae)

The predominately Afrotropical fruit fly genus Ceratitis (Diptera: Tephritidae) contains many species of agricultural importance. The majority of these Ceratitis pest species are polyphagous and potentially invasive. Consequently, the development of markers useful to diagnose Ceratitis species and analyze their systematic relationships is an important goal for pest control and quarantine agencies. Although morphological markers have been useful in the development of keys to the adult stage, identification of immature stages is currently not possible. In addition, systematic studies of morphological and host use characters have not provided a single well-supported phylogenetic hypothesis for Ceratitis.; This dissertation describes the utility of molecular markers for species diagnosis and phylogenetic reconstruction of the genus Ceratitis. Diagnostic tools developed for PCR (polymerase chain reaction) and RFLP (restriction fragment length polymorphism) techniques can resolve twenty-seven species (plus an unresolved cluster of three species). PCR-RFLP analysis of three mitochondrial genes (12S ribosomal RNA, 16S ribosomal RNA, and NADH- dehydrogenase subunit 6) is sufficient to diagnose twenty-five species. Molecular systematic analysis of Ceratitis using two mitochondrial genes (cytochrome oxidase I and NADH-dehydrogenase subunit 6) and a nuclear (period) gene produced phylogenetic hypotheses that are congruent with several relationships recovered in morphological studies and suggested several alternative hypotheses that may be tested with morphological characters. Analysis of gene trees suggests that the subgenus Pardalaspis is monophyletic, subsection A of the subgenus Pterandrus is monophyletic, the subgenus Pterandrus may be either paraphyletic or polyphyletic, the subgenus Ceratalaspis is polyphyletic, and the subgenus Ceratitis sensu stricto is not monophyletic. In addition, genetic variability in NADH-dehydrogenase subunit 6 sequences is used to characterize the population structure of three Ceratitis species of economic importance. Results suggest that (1) samples of C. anonae from Ghana and Kenya are not genetically distinct, (2) samples of C. fasciventris from Mali and Kenya are genetically divergent and may represent samples from an unresolved species complex, (3) there is restricted gene flow between Kenyan and South African populations of C. rosa, and (4) the island sample from Reunion is more similar to the South African sample than it is to the Kenyan sample of C. rosa.