has been to test whether the evolution of particular traits is associated with species diversity. For example, clades of flowering plants that have independently evolved floral nectar spurs show a statistically significant trend for increased species diversity compared with nonspurred clades (Hodges and Arnold, 1995; Hodges, 1997; Kay et al., 2006). This finding has led to the nectar spurs being considered a “key innovation” with the implication that they mechanistically increase the likelihood of speciation.
Another way to test for trends during evolutionary history is to test explicitly for directionality of trait evolution on a phylogeny. Critical to such analyses is the reconstruction of ancestral states (Schluter et al., 1997; Mooers and Schluter, 1999). Here, maximum-likelihood methods have been used to statistically distinguish between a 1-rate model (in which both directions of evolution have the same rate) and a 2-rate model (Pagel et al., 2004). However, the ability to test between such models depends on the number of shifts observed (Mooers and Schluter, 1999). Because adaptive radiations often are composed of a large number of species and have entailed multiple shifts in characters, they are prime foci for tests of directional trends [e.g., Mooers and Schluter (1999)].
As the development, use, and availability of genomic tools for non-model organisms has increased (Abzhanov et al., 2008), the ability to determine the genetic basis of adaptations and speciation is becoming possible for an increasing number of taxa. Long-standing questions about whether particular kinds of genes [e.g., regulatory versus structural; see Britten and Davidson (1969), King and Wilson (1975), Barrier et al. (2001), Hoekstra and Coyne (2007)] and/or particular types of mutations such as substitutions, duplications, or transposable elements are responsible for adaptation and speciation can now be addressed. Adaptive radiations are especially amenable to such studies for a number of reasons. First, because adaptive radiations have been studied for some time, particular trait values have often been substantiated as adaptations. Second, recent adaptive radiations often consist of taxa that can be hybridized, thus making possible the genetic dissection of traits. Third, adaptive radiations may entail a diversity of adaptive traits or the repeated evolution of the same traits in different lineages providing multiple comparisons within and between traits in a single system. Finally, because recent and rapid adaptive radiations necessarily consist of closely related taxa, the development of genomic tools for 1 species will likely provide tools for analysis across the entire group (Abzhanov et al., 2008). Thus, adaptive radiations offer the possibility of determining general molecular trends across traits and whether convergence at the phenotypic level involves convergence at the molecular level.
Here, we illustrate the use of adaptive radiations to understand the processes of adaptation and speciation by reviewing studies of the col-