of genetic incompatibilities under the term by-product does not do much to advance our mechanistic understanding of speciation. To fully connect the views through the magnifying glass and the spyglass, we must understand how different ecological situations lead to particular types of barriers to gene flow and on what timetable these different forms of reproductive isolation evolve. It is particularly important to ask under what circumstances and how often ecologically based reproductive isolation produce virtually complete reproductive isolation before appreciable genetic incompatibility has evolved (Ramsey et al., 2003; Coyne and Orr, 2004, pp. 57–59).

Ecological speciation can occur in either geographically isolated populations (allopatry) or in settings with no physical barriers to gene flow (sympatry or parapatry). When gene exchange is physically impossible, the conditions under which reproductive isolation can evolve are nonrestrictive: allopatric speciation can be driven by strong or weak divergent selection, sexual selection, uniform selection, or even stabilizing selection. It may occur quickly under divergent selection or extremely slowly under uniform or balancing selection.

In contrast, the conditions under which sympatric or parapatric speciation with gene flow can occur are not so forgiving: genetically based phenotypic divergence requires much stronger selection to occur and be maintained when gene flow is possible than when geography makes it an impossibility [e.g., Rice and Hostert (1993); Via (2001)]. In the presence of migration, the establishment of genomic regions that resist gene flow sufficiently to maintain phenotypic differentiation is only likely if divergent (or possibly sexual) selection is strong, and so the initial barriers to gene flow in sympatry are likely to evolve quickly (Rice and Hostert, 1993; Via, 2001; Hendry et al., 2007). Speciation with gene flow (Rice and Hostert, 1993) is thus unlikely to occur under weak divergent selection, and it is certainly not expected under uniform or balancing selection (except perhaps by polyploidy). One fortuitous effect of the strong selection required for speciation with gene flow is that the genomic regions that cause reproductive isolation become particularly distinctive relative to the rest of the genome. This facilitates their discovery in empirical analyses.

Until recently, genetic models of speciation with gene flow have been extremely simplified, and they have suggested quite a restrictive set of conditions for sympatric speciation. In particular, critics cite the difficulty of evolving assortative mating in the face of free recombination (Coyne and Orr, 2004, pp. 127–141). Although Felsenstein (1981) showed that this constraint is significantly reduced under linkage between genes affecting performance and mating, that result has been largely ignored (Via, 2001).