One of Darwin’s greatest ideas was that new species originate by natural selection (Darwin, 1859). 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 (Darwin, 1859), in which case adaptive divergence in phenotype eventually leads to speciation almost by definition. Later, Dobzhansky (1937) and Mayr (1942) defined species and speciation by the criterion of reproductive isolation instead. Recent evidence indicates that reproductive isolation also evolves frequently by natural selection (Schluter, 2000, 2009; Coyne and Orr, 2004; Price, 2008).
Speciation by natural selection occurs by 2 general mechanisms (Price, 2008; Schluter, 2009). 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 (Schluter, 2000, 2001; Rundle and Nosil, 2005; Funk, 2009). 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. 3.1). In contrast,