have accumulated that the new species and their diverse adaptations will persist even if the pattern of natural selection changes.
This 2-stage model reverses the roles that are sometimes assumed for different forms of reproductive isolation during speciation (Coyne and Orr, 1989, 1997). In allopatric speciation, postzygotic genetic incompatibilities accumulate while populations are geographically isolated. These cause reproductive isolation when populations come back into contact. It is then that ecologically based prezygotic isolation plays its secondary role, evolving under selection to “reinforce” the existing postzygotic isolation and prevent the production of sterile or inviable hybrids. In contrast, in ecological speciation with gene flow, various ecologically based barriers to gene flow evolve first, as a result of adaptation under divergent selection. Once migration between the incipient species is essentially eliminated, they become ecologically allopatric, and postzygotic incompatibilities can accumulate. These DMIs then play the secondary reinforcing role by rendering the earlier evolution of ecologically based reproductive isolation difficult to reverse.
One hazard of the retrospective spyglass approach to speciation is that patterns of genetic divergence early in the process of speciation can become obscured or even invisible over time as additional divergence between the new species accumulates. This is likely to be the fate of divergence hitchhiking during the process of ecological speciation.
Early in ecological speciation with gene flow, populations diverge under selection at genomic regions that affect key ecologically important traits, while gene flow continues across the rest of the genome (Fig. 1.3). Fst outliers found during this period (stage 1) will tend to map to these selected regions, as suggested by our analyses (Via and West, 2008). However, by the time most of the genome is phylogenetically concordant and retrospective analyses begin, the genomic signature of the original divergent selection will have faded. Outliers might be found, but they should not be expected to mark the genomic regions under early divergent selection.
During stage 2 of ecological speciation with gene flow, genetic divergence occurs mostly in genomic areas that were not originally affected by divergent selection. As overall genomic divergence between the new species increases through drift or independent responses to selection, the distinctive genetic signature of divergence hitchhiking (excessive divergence in regions near divergently selected QTL) becomes assimilated into a more widespread pattern of genetic divergence between the new species. So, it is perhaps not surprising that decades of retrospective analyses