lished data). Consequently, the positions of the inversion clines represent a balance between diapause selection and migration. In contrast to the inversions, loci mapping to other chromosomal regions generally do not differ in allele frequency between the host races, vary clinally, correlate with the timing of eclosion, nor display high levels of linkage disequilibrium in nature (Berlocher, 2000; Berlocher and McPheron, 1996; Feder et al., 1990, 1993, 2003b). Therefore, these apparently collinear regions of the genome may have introgressed more readily at times in the past between Mexico and the North, homogenizing in frequency because of a lack of differential selection combined with recombination.

The contrasting pattern of genetic differentiation seen for chromosomes 1–3 vs. other genomic regions is consistent with new models of chromosomal speciation (Navarro and Barton, 2003; Noor et al., 2001b; Rieseberg, 2001). In these models, reduced recombination associated with rearrangements facilitates the retention of linked genes conferring adaptation or reproductive isolation between hybridizing taxa. However, collinear portions of the genome tend to introgress because recombination results in weak or no linkage of most genes in these regions to loci causing reproductive isolation. Studies in sunflowers (Rieseberg et al., 1999), the Drosophila pseudoobscura subgroup (Brown et al., 2004; Machado et al., 2002; Noor et al., 2001a), and Anopheles mosquitoes (Besansky et al., 2003; dellaTorre et al., 1997) have found evidence for greater introgression in collinear segments of the genome than inverted segments. If differential introgression is true also for Rhagoletis, then the prediction is that loci mapping outside the inversion carrying chromosomes 1–3 should generally show less genetic divergence between Altiplano and U.S. flies compared with genes within the rearranged chromosomes. Coalescence times for noninverted regions should primarily date to the most recent period of contact and gene flow; rearrangements should display deeper divergence times congruent with the initial separation of Mexican and Northern populations. Thus, the chromosome model is predicated on Rhagoletis inversions having partially introgressed at a distant time in the past. During subsequent periods of geographic isolation between Mexican and Northern populations, these inverted regions accumulated additional host-related, as well as possibly non-host-related, genetic changes. Some of the changes, because of their linkage in rearrangements differing between the populations, reduced the potential for the inversions to introgress between Mexican and U.S. flies.

Here, we examine the applicability of the “rearrangement” model to R. pomonella by means of an expanded DNA sequence analysis of loci encompassing both inverted and likely collinear regions of the genome of the fly. We report a pattern of genetic differentiation that is consistent with the rearrangement hypothesis for differential gene flow; gene trees