A variety of conditions that facilitate ecological speciation with gene flow are now well described (Rice and Hostert, 1993; Via, 2001). They include strong divergent selection on multiple traits associated with resource or habitat use and ecologically based selection against migrants and/or hybrids. Recent work suggests that assortative mating can evolve rather easily if habitat choice determines the choice of mates (Rice and Hostert, 1993; Via, 2001), if mate choice is a correlate of the traits under divergent selection (Schluter, 2001), or if recombination is reduced by physical linkage or pleiotropy (Felsenstein, 1981; Hawthorne and Via, 2001). Some of the best-studied divergent races in the wild, including the ecologically specialized host races of the pea aphid [Acyrthosiphon pisum (Harris)] satisfy these conditions (Via, 2001), providing strong empirical support for the argument that reproductive isolation can evolve, or at least persist, in the face of gene flow.

The first step in using the magnifying glass to study speciation involves estimating the magnitude of gene flow between a pair of partially reproductively isolated taxa. That process is not as straightforward as it may seem.

Empirical estimates of gene flow assume neutrality of markers and a balance between migration and random drift [e.g., Hartl and Clark (1997)]. This emphasis on gene flow under neutrality implies that there is just 1 “true” estimate of gene exchange between 2 taxa. Moreover, the minimal gene flow required to counter drift under Wright’s island model (Hartl and Clark, 1997, pp. 194 and 195) conjures up a picture of gene flow as a force that will easily homogenize adjacent populations (Fig. 1.2A). Yet, one can easily find phenotypically divergent and ecologically specialized populations living in close adjacency with no physical barrier to gene flow. Is this a contradiction? Not necessarily, because the degree to which a genomic region affecting a given trait is homogenized by migration depends not on the estimated gene flow under neutrality, but on the realized gene flow at that region after selection.

It is a maxim of population genetics that migration and genetic drift affect the entire genome, whereas the effects of natural selection are limited to genomic regions harboring loci that affect the selected phenotypic traits. In ecologically specialized populations, divergent selection on traits associated with the use of resources or habitats is strong enough to maintain divergence in the parts of the genome that affect those traits, while gene flow continues in other genomic regions (Figs. 1.2B and 1.3). Between such populations, the estimated gene flow under neutrality may