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variation. In contrast, quantitative genetic models of speciation assume that response to selection, at least in the early stages of divergence, is based on standing genetic variation (Dieckmann and Doebeli, 1999; Burger and Schneider, 2006). There is little direct evidence for either assumption (Noor and Coyne, 2006). The topic is interesting because speciation from standing variation is potentially more rapid than that from new mutations, because the waiting time for new mutations is skipped and alleles present as standing variation begin at higher frequency (Hermisson and Pennings, 2005; Barrett and Schluter, 2008). Standing genetic variation can result in the same alleles being used repeatedly in separate speciation events, enhancing the probability of parallel evolution of reproductive isolation.

The apple maggot, a recently evolved race of the haw fly, Rhagoletis pomonella, provides a possible example of standing genetic variation contributing to speciation. The haw fly exploits haw fruits, but in the 1880s it expanded its host range to domestic apple. Haw and apple differ in their peak fruiting times, and accordingly the 2 races have diverged in pupal diapause traits (affecting overwinter dormancy) that also affect their timing of emergence as adults. This seasonal difference contributes to strong (although still incomplete) reproductive isolation. Significantly, racial differences in pupal diapause traits map to genomic regions that are polymorphic for chromosomal inversions. Each inverted version of a specific chromosomal region is at higher frequency in the apple race than in the ancestral haw race (Feder et al., 2003b). Remarkably, phylogenies based on gene sequences within the inverted regions reveal that the inversions themselves are old and that they occur as standing variation within R. pomonella across its geographic range. The frequency of the inversions declines from the southern to northeastern United States (Feder et al., 2003a). The pattern suggests that formation and divergence of the apple race involved selection of preexisting genetic variation for pupal diapause traits located on inversions, although the presence of these traits in southern populations needs to be confirmed.

A second possible example occurs in the Lake Victoria cichlids, Pundamilia pundamilia and Pundamilia neyereri, which have different alleles at the long-wave sensitive opsin gene. These alleles affect sensitivity to wavelengths of ambient light at the different depths in the lake where the 2 species reside (Seehausen et al., 2008), and they may also influence the color (red vs. blue) of males chosen by breeding females, contributing to assortative mating. However, whereas the red and blue Pundamilia are sister species, each being the other’s closest relative, the 2 long-wave-sensitive alleles are not sister lineages on the phylogenetic tree of opsin gene sequences (Seehausen et al., 2008). Rather, the 2 opsin alleles share a common ancestral opsin sequence at a time well before the divergence of the 2 Pundamilia species, perhaps even before the appearance of Lake Victoria itself. This implies that speciation in Pundamilia used preexisting genetic variation.

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