Species originate frequently by natural selection. A general mechanism by which this occurs is ecological speciation, defined as the evolution of reproductive isolation between populations as a result of ecologically-based divergent natural selection. The alternative mechanism is mutation-order speciation in which populations fix different mutations as they adapt to similar selection pressures. Although numerous cases now indicate the importance of ecological speciation in nature, very little is known about the genetics of the process. Here, we summarize the genetics of premating and postzygotic isolation and the role of standing genetic variation in ecological speciation. We discuss the role of selection from standing genetic variation in threespine stickleback (Gasterosteus aculeatus), a complex of species whose ancestral marine form repeatedly colonized and adapted to freshwater environments. We propose that ecological speciation has occurred multiple times in parallel in this group via a ''transporter'' process in which selection in freshwater environments repeatedly acts on standing genetic variation that is maintained in marine populations by export of freshwater-adapted alleles from elsewhere in the range. Selection from standing genetic variation is likely to play a large role in ecological speciation, which may partly account for its rapidity.reproductive isolation ͉ stickleback ͉ standing genetic variation ͉ transporter hypothesis O ne of Darwin's greatest ideas was that new species originate by natural selection (1). It has taken evolutionary biologists almost until now to realize that he was probably correct. Darwin looked at species mainly as sets of individuals closely resembling each other (1), in which case adaptive divergence in phenotype eventually leads to speciation almost by definition. Later, Dobzhansky (2) and Mayr (3) defined species and speciation by the criterion of reproductive isolation instead. Recent evidence indicates that reproductive isolation also evolves frequently by natural selection (4-7).Speciation by natural selection occurs by 2 general mechanisms (4, 7). The first of these is ecological speciation, defined as the evolution of reproductive isolation between populations, or subsets of a single population, as a result of ecologically-based divergent natural selection (6,(8)(9)(10). Under this process natural selection acts in contrasting directions between environments, which drives the fixation of different alleles each advantageous in one environment but not in the other (Fig. 1). In contrast, under mutation-order speciation (7, 11), populations diverge as they accumulate a different series of mutations under similar selection pressures (Fig. 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 (4, 7), yet numerous aspects of ...