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have not seen these important, but transient, regions of interrace linkage disequilibrium around divergent QTL.

Fst outliers may still be found late in stage 2 or in hybrid zones between “good species” [e.g., Yatabe et al. (2007)], but interpreting their cause becomes increasingly difficult as the overall level of genetic divergence between the new species grows. A high Fst marker seen late in speciation or in a hybrid zone is more likely to be the result of genetic drift or a recent selective sweep within 1 species than it is to be a signature of the divergent selection that caused speciation. Therefore, outliers found between new species or in hybrid zones, or between incipient species in secondary contact after a period of allopatric divergence, should not necessarily be expected to mark genomic regions affected by divergent phenotypic selection during the initial phases of ecological speciation.

Outlier analyses of races or morphs that have become partially reproductively isolated under divergent selection thus offer a privileged, but transient, view of the genetic mechanisms involved in early ecological speciation. It is in regions of divergence hitchhiking that ecological speciation with gene flow begins, and the divergence of the ecologically important QTL at their center determines the eventual pattern of branching seen later in the species tree. However, by the time that good species are recognized, the distinctive pattern of divergence hitchhiking around key QTL is gone, and the opportunity to analyze the genomic regions pivotal to ecological speciation with gene flow has been lost.


In allopatric populations, where there is no possibility for gene exchange, virtually any type or strength of selection will eventually lead to reproductive isolation, and barriers to gene flow may be of virtually any kind. In their classic survey of reproductive isolation between Drosophila species, Coyne and Orr (1989, 1997) found that in allopatry, prezygotic (ecologically based) and postzygotic reproductive isolation (from DMIs) appeared to evolve at about the same rate.

In contrast, for speciation to occur without physical barriers to gene flow, divergent selection must be strong and “multifarious,” i.e., affecting several different traits, which causes ecologically based isolation to evolve relatively rapidly (Rice and Hostert, 1993; Schluter, 2001; Via, 2001; Hendry et al., 2007). Consistent with this, Coyne and Orr’s comparative analyses (Coyne and Orr, 1989, 1997) suggest that in sympatric populations, prezygotic isolation precedes the evolution of postzygotic isolation. The primacy of ecologically based isolation in speciation with gene flow is supported by empirical analyses of taxa in which divergent selection is

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