rearrangements to introgress implies that these regions of the genome have accumulated additional genetic changes, causing reproductive isolation between Mexican and U.S. flies after their initial establishment in secondary inversion clines in the North. Not all of these changes necessarily reflect host-associated or ecological adaptations. There is no reason that non-host-related differences resulting in prezygotic isolation and hybrid inviability and sterility should not also have accumulated between Mexican and Northern demes during periods of allopatry. Given secondary contact and differential gene flow, the chromosomal speciation models predict that these differences should be concentrated in inversions (Arnold, 1992; Noor et al., 2001b). Therefore, the extent to which intrinsic genomic incompatibilities map to inversion differences between Mexican and U.S. flies needs to be examined. If true, then the inversions would be simultaneously affecting speciation across both allopatric and sympatric scales in R. pomonella. It would be particularly intriguing if any derived differences in the inversions in the U.S. related to latitudinal variation in hawthorn fruiting phenology or interactions between sympatric R. pomonella taxa using different hosts feed back to restrict gene flow between U.S. and Mexican flies, closing the speciation mode braid.
Also, we stress that not all of the host-related changes contributing to sympatric host shifts are diapause-related. Differences in host discrimination (habitat-specific mating) also played a key role in generating the R. pomonella complex. Recently, we demonstrated that host fruit-odor discrimination is an important element of habitat choice for R. pomonella (Linn et al., 2003, 2004). Host choice is important in Rhagoletis because the fly mates only on or near the fruit of its respective host plants (Prokopy et al., 1971, 1972). Thus, variation in host choice translates directly into differences in mate choice and prezygotic isolation. The genetics of fruit-odor discrimination appear to involve loci affecting both preference and avoidance for volatile compounds emitted from the surface of natal and nonnatal fruit (H.D. and J.L.F., unpublished data). Also, F1 hybrids appear to have a reduced ability to orient to host fruit odor in flight-tunnel tests, signifying potentially reduced fitness in the field (Linn et al., 2004). Therefore, the genetics and evolutionary history of host discrimination may prove to be different from diapause traits and not associated with periods of geographic isolation. Because hawthorns are fundamentally similar in Mexico and the United States, there is no reason to expect hawthorn discrimination to be under differential selection or to display a cline.
In conclusion, our study highlights the reticulate nature of speciation at both the population and genomic levels. Students of plant speciation have long embraced this perspective (Anderson, 1949; Arnold, 1992; Grant, 1971; Stebbins, 1959), whereas workers in animal systems are gaining an increased appreciation for the importance of hybridization in meta-