sequences within regions of divergence hitchhiking can begin to diverge by genetic drift or independent responses to directional and stabilizing selection within each race. The free recombination enjoyed within races can accelerate divergence at these loci by allowing beneficial mutations to spread within races, while divergence hitchhiking blocks their export to the other race. Some allelic substitutions within regions of divergence hitchhiking may produce genetic incompatibilities between the new species. Thus, an additional prediction of this model is that genes for hybrid sterility or inviability that are found close to “branch-defining” QTL will have, on average, a greater time to most recent common ancestor than will those found in other genomic regions.

By the end of stage 1, most gene exchange is likely to have already been blocked by the ecologically based reproductive isolation that reduces effective migration. The incipient species are now essentially “ecologically allopatric.” Thus begins stage 2, in which the parts of the genome outside regions of divergence hitchhiking begin to differentiate by genetic drift or independent responses to selection within the new lineages. This secondary divergence will eventually bring all of the variation in polymorphic gene trees into widespread phylogenetic concordance with the branching pattern determined earlier by divergent selection on QTL affecting the key ecologically important traits.

Given that only a small fraction of the genome may be affected by divergent selection during stage 1, most of the eventual genetic divergence between new ecological species is likely to occur during stage 2. Genetic analyses of hybrid sterility and inviability reveal that genetic incompatibilities are numerous and scattered throughout the genome (Masly and Presgraves, 2007). It is thus probable that by the end of stage 2, the number of genetic incompatibilities that have accumulated could far outnumber, and potentially obscure, the adaptive genetic changes that were actually involved in the initial evolution of reproductive isolation under divergent selection during stage 1. This is one of the major drawbacks of the exclusive use of the spyglass in the study of speciation genetics.

In many cases of speciation by divergent selection, enough ecologically based reproductive isolation will evolve to isolate a pair of new species before many DMIs can accumulate. Even so, the genetic incompatibilities that lead to hybrid sterility and inviability play a very important role in ecological speciation because they make the ecologically based reproductive isolation that evolved earlier permanent and irreversible. By the end of stage 2, it is likely that enough genetic incompatibilities will