under mutation-order speciation (Mani and Clarke, 1990; Schluter, 2009), populations diverge as they accumulate a different series of mutations under similar selection pressures (Fig. 3.1). Natural selection drives alleles to fixation in both speciation mechanisms, but selection favors divergence only under ecological speciation. Divergence occurs by chance under the mutation-order process.

There is growing evidence in support of both ecological and mutation-order speciation in nature (Price, 2008; Schluter, 2009), yet numerous aspects of these mechanisms remain obscure. One of the most glaring deficiencies is the almost complete absence of information on the genetics of ecological speciation. Here, we review several aspects of the problem. We address characteristics of genes underlying premating isolation; the evolution and genetics of postzygotic isolation; and the role of standing genetic variation as a source of alleles for the evolution of reproductive isolation. Although data are not plentiful, it is possible to reach some conclusions about how the genetic process of ecological speciation should work and how it might differ from that mutation-order speciation. We end with a summary of evidence for ecological speciation in a threespine stickleback system and address the possible role of standing genetic variation in their adaptation to freshwater environments. We present a hypothesis for the repetitive origin of freshwater stickleback species involving natural selection of standing genetic variation.

Premating isolation is the reduced probability of mating between individuals from different populations as a result of behavioral, ecological, or other phenotypic differences. In ecological speciation, premating isolation is of 2 general types. The first is selection against migrants or “immigrant inviability” between locally adapted populations (Via et al., 2000; Nosil et al., 2005). Interbreeding is reduced when spatial proximity of individuals is required for mating, and when the survival, growth, or reproductive success of immigrant individuals is diminished because their phenotype is less well adapted than the resident population to local conditions. This form of premating isolation is unique to ecological speciation, although it is not always present (e.g., when populations or gametes move between environments during mating). Immigrant inviability can account for a high fraction of total reproductive isolation (Nosil et al., 2005; Lowry et al., 2008).

Because it arises from direct selection on the phenotypes of individuals, the genetics of immigrant inviability is identical to the genetics of local adaptation. Any locus under divergent natural selection between parental environments contributes to immigrant inviability and therefore