Since its discovery in 1907, polyploidy has been recognized as an important phenomenon in vascular plants, and several lines of evidence indicate that most, if not all, plant species ultimately have a polyploid ancestry. However, previous estimates of the frequency of polyploid speciation suggest that the formation and establishment of neopolyploid species is rare. By combining information from the botanical community's vast cytogenetic and phylogenetic databases, we establish that 15% of angiosperm and 31% of fern speciation events are accompanied by ploidy increase. These frequency estimates are higher by a factor of four than earlier estimates and lead to a standing incidence of polyploid species within genera of 35% ( n = 1,506). Despite this high incidence, we find no direct evidence that polyploid lines, once established, enjoy greater net species diversification. Thus, the widespread occurrence of polyploid taxa appears to result from the substantial contribution of polyploidy to cladogenesis, but not from subsequent increases in diversification rates of polyploid lines.

The origin of new homoploid species via hybridization is theoretically difficult because it requires the development of reproductive isolation in sympatry. Nonetheless, this mode is often and carelessly used by botanists to account for the formation of species that are morphologically intermediate with respect to related congeners. Here, I review experimental, theoretical, and empirical studies of homoploid hybrid speciation to evaluate the feasibility, tempo, and frequency of this mode. Theoretical models, simulation studies, and experimental syntheses of stabilized hybrid neospecies indicate that it is feasible, although evolutionary conditions are stringent. Hybrid speciation appears to be promoted by rapid chromosomal evolution and the availability of a suitable hybrid habitat. A selfing breeding system may enhance establishment of hybrid species, but this advantage appears to be counterbalanced by lower rates of natural hybridization among selfing taxa. Simulation studies and crossing experiments also suggest that hybrid speciation can be rapid—a prediction confirmed by the congruence observed between the genomes of early generation hybrids and ancient hybrid species. The frequency of this mode is less clear. Only eight natural examples in plants have been rigorously documented, suggesting that it may be rare. However, hybridization rates are highest in small or peripheral populations, and hybridization may be important as a stimulus for the genetic or chromosomal reorganization envisioned in founder effect and saltational models of speciation.

Hybridization is frequent in many organismal groups, but its role in adaptation is poorly understood. In sunflowers, species found in the most extreme habitats are ancient hybrids, and new gene combinations generated by hybridization are speculated to have contributed to ecological divergence. This possibility was tested through phenotypic and genomic comparisons of ancient and synthetic hybrids. Most trait differences in ancient hybrids could be recreated by complementary gene action in synthetic hybrids and were favored by selection. The same combinations of parental chromosomal segments required to generate extreme phenotypes in synthetic hybrids also occurred in ancient hybrids. Thus, hybridization facilitated ecological divergence in sunflowers.

The production of extreme or ‘transgressive’ phenotypes in segregating hybrid populations has been speculated to contribute to niche divergence of hybrid lineages. Here, we assess the frequency of transgressive segregation in hybrid populations, describe its genetic basis and discuss the factors that best predict its occurrence. From a survey of 171 studies that report phenotypic variation in segregating hybrid populations, we show that transgression is the rule rather than the exception. In fact, 155 of the 171 studies (91%) report at least one transgressive trait, and 44% of 1229 traits examined were transgressive. Transgression occurred most frequently in intraspecific crosses involving inbred, domesticated plant populations, and least frequently in interspecific crosses between outbred, wild animal species. Quantitative genetic studies of plant hybrids consistently point to the action of complementary genes as the primary cause of transgression, although overdominance and epistasis also contribute. Complementary genes appear to be common for most traits, with the possible exception of those with a history of disruptive selection. These results lend credence to the view that hybridization may provide the raw material for rapid adaptation and provide a simple explanation for niche divergence and phenotypic novelty often associated with hybrid lineages.