The apple maggot, Rhagoletis pomonella (Walsh), was introduced into the apple-growing regions of the Pacific Northwest in the U.S.A. during the past 60-100 yr. Apple maggot (larvae, puparia, and adults) is difficult to distinguish from its morphologically similar sister species, Rhagoletis zephyria Snow, which is native and abundant in the Pacific Northwest. While morphological identifications are common practice, a simple, inexpensive assay based on genetic differences would be very useful when morphological traits are unclear. Here we report nucleotide substitution and insertion-deletion mutations in the nontranscribed spacer (NTS) of the ribosomal RNA gene cistron of R. pomonella and R. zephyria that appear to be diagnostic for these two fly species. Insertion-deletion variation is substantial and results in a 49 base-pair difference in PCR amplicon size between R. zephyria and R. pomonella that can be scored using agarose gel electrophoresis. PCR amplification and DNA sequencing of 766 bp of the NTS region from 38 R. pomonella individuals and 35 R. zephyria individuals from across their geographic ranges led to the expected PCR fragments of approx. 840 bp and 790 bp, respectively, as did amplification and sequencing of a smaller set of 26 R. pomonella and 16 R. zephyria flies from a sympatric site in Washington State. Conversely, 633 bp mitochondrial COI barcode sequences from this set of flies were polyphyletic with respect to R. pomonella and R. zephyria. Thus, differences in NTS PCR products on agarose gels potentially provide a simple way to distinguish between R. pomonella and R. zephyria.

Tephritid fruit flies belonging to the Rhagoletis pomonella sibling species complex are controversial because they have been proposed to diverge in sympatry (in the absence of geographic isolation) by shifting and adapting to new host plants. Here, we report evidence suggesting a surprising source of genetic variation contributing to sympatric host shifts for these flies. From DNA sequence data for three nuclear loci and mtDNA, we infer that an ancestral, hawthorn-infesting R. pomonella population became geographically subdivided into Mexican and North American isolates ≈1.57 million years ago. Episodes of gene flow from Mexico subsequently infused the North American population with inversion polymorphism affecting key diapause traits, forming adaptive clines. Sometime later (perhaps ±1 million years), diapause variation in the latitudinal clines appears to have aided North American flies in adapting to a variety of plants with differing fruiting times, helping to spawn several new taxa. Thus, important raw genetic material facilitating the adaptive radiation of R. pomonella originated in a different time and place than the proximate ecological host shifts triggering sympatric divergence.

In this study, we addressed the question of whether or not native stands of blueberry (Vaccinium spp.) and/or huckleberry (Gaylussacia spp.) support populations of blueberry maggot, Rhagoletis mendax Curran, in the Great Lakes region. Infestation of commercial blueberries by the blueberry maggot, R. mendax, is a serious problem in many areas where blueberries are grown. In the past 10-20 yr, commercial bighbush blueberry, Vaccinium corymbosum L., production has expanded into places such as southern Ontario and southern Quebec where blueberry maggot had not previously been reported. In the mid-1990s, isolated infestations of commercial highbush blueberry were reported in southern Ontario. Because R. mendax was not considered endemic to that area, it was widely assumed that the pests had come into the fields via movement from exotic localities. Here we present an alternative hypothesis, that the blueberry maggots infesting newly established highbush plantations are derived from native blueberries growing in the vicinity. To test this hypothesis, in 1997-1999, we sampled potential native hosts for R. mendax (Vaccinium spp. and Gaylussacia spp.) from 31 localities in the Great Lakes region, primarily in Michigan and Ontario. R. mendax was reared from fruits of native hosts collected at four sites in Michigan and one site each in Ontario, Indiana, and Ohio. V. corymbosum was the predominant host infested, with infestation of this host observed at five of the seven sites. However, two huckleberry species [Gaylussacia baccata (Wangenheim) K. Koch, and Gaylussacia dumosa (Andersson) Torrey & Gray] had the highest rates of infestation that we observed (25.4 and 17.6%, respectively). These data represent the first published reports of R. mendax infesting native host plants in the Great Lakes region, and support the hypothesis that infestations observed in commercial fields may have originated from infested native host plants.

Genetic divergence among 57 isolates of Colletotrichum lindemuthianum collected in north, central and south America and The Netherlands was assessed on the basis of PCR-RFLP analysis and sequencing of the nuclear rDNA region of the two internal transcribed spacers (ITS 1 and ITS 2) and the 5.8S rRNA gene. A reproducible 0.58 kb fragment was amplified in all 57 isolates. Races of C. lindemuthianum formed two groups based on the restriction of the PCR-amplified ITS regions. Group I consisted mainly of Middle American races (65%), whereas 85% of Andean races belonged in group II. Genetic distances calculated from the sequence polymorphism in the rDNA region ranged from 0.2 to 1.8% among 14 isolates of C. lindemuthianum. The neighbour-joining and parsimony analyses of the sequence data showed no association of any particular ITS genotype with host gene pool, virulence or geographic origin of races. These data suggest that virulence can arise in different geographic areas at different times, independent of genetic background. Molecular polymorphism among isolates of races 7, 17, 31 and 73 collected in different countries was demonstrated by RFLP analysis of the ITS regions. A similar lack of agreement was observed in the sequence data between isolates of race 73 from Mexico and the United States and the Jukes—Cantor genetic distance between the isolates was large (0.9%). These findings support a level of molecular variability within C. lindemuthianum greater than the variability previously characterized by virulence analysis and suggest independent evolution of specific virulence patterns.

Despite a considerable literature describing the biology of flies in the tephritid genus Rhagoletis, the phylogenetic relationships of the more than 60 species classified within the genus are not well resolved. Knowledge of these relationships is important, not only in terms of obtaining information that will be useful for the control of Rhagoletis where it is an agricultural pest, but also in determining what role host plant shifts have played in the generation of Rhagoletis species diversity, a focal point in debate over the role of sympatric speciation in the evolutionary process. In this paper, the phylogenetic history of 28 Rhagoletis species and 6 species in related tephritid genera is inferred from nucleotide sequences of subunit II of the mitochondrial cytochrome oxidase (COII) gene and the adjacent tRNALeu/COII intergenic region. Analyses of the data using distance and character-state approaches suggest the following: (i) the genus Rhagoletis as currently defined is not monophyletic; (ii) the 5 predominantly North American Rhagoletis species groups do constitute a monophyletic assemblage; (iii) the North American species groups form 2 clades, 1 consisting of taxa in the R. pomonella and R. tabellaria species groups (plus R. fausta), and the other consisting of taxa in the R. ribicola, R. cingulata, and R. suavis species groups; and (iv) the origin(s) of the North American species groups is obscure, as evidenced by the recovery of clades containing both Palearctic and Neotropical taxa. Areas of congruence and conflict with published phylogenies of Rhagoletis are examined and, while many areas of conflict may be due to an insufficient number of characters or incomplete taxon sampling, we cannot discount the possibility that real differences exist between the Rhagoletis mitochondrial DNA gene tree and the Rhagoletis species tree.