The importance of hybridization in plant speciation and evolution has been debated for decades, with opposing views of hybridization as either a creative evolutionary force or evolutionary noise. Hybrid speciation may occur at either the homoploid (i.e., between two species of the same ploidy) or the polyploid level, each with its attendant genetic and evolutionary consequences. Whereas allopolyploidy (i.e., resulting from hybridization and genome doubling) has long been recognized as an important mode of plant speciation, the implications of genome duplication have typically not been taken into account in most fields of plant biology. Recent developments in genomics are revolutionizing our views of angiosperm genomes, demonstrating that perhaps all angiosperms have likely undergone at least one round of polyploidization and that hybridization has been an important force in generating angiosperm species diversity. Hybridization and polyploid formation continue to generate species diversity, with several new allopolyploids having originated just within the past century or so. The origins of polyploid species—whether via hybridization between species or between genetically differentiated populations of a single species—and the immediate genetic consequences of polyploid formation are therefore receiving enthusiastic attention. The time is therefore right for a review of the role of hybridization in plant speciation.

Homoploid hybrid speciation (HHS) is the establishment of a novel species through introgressive hybridization without a change in chromosome number. We discuss different routes by which this might occur and propose a novel term, 'hybrid trait speciation', which combines the idea that hybridization can generate adaptive novelty with the 'magic trait' model of ecological speciation. Heliconius butterflies contain many putative examples of hybrid colour patterns, but only recently has the HHS hypothesis been tested explicitly in this group. Molecular data has shown evidence for gene flow between many distinct species. Furthermore, the colour pattern of Heliconius heurippa can be recreated in laboratory crosses between Heliconius melpomene and Heliconius cydno and, crucially, plays a role in assortative mating between the three species. Nonetheless, although the genome of H. heurippa shows evidence for hybridization, it is not a mosaic of the two parental species. Instead, ongoing hybridization has likely blurred any signal of the original speciation event. We argue that where hybridization leads to novel adaptive traits that also cause reproductive isolation, it is likely to trigger speciation.

Episodic selection encompasses any sudden environmental disturbance likely to lead to a significant alteration in a species' population structure. Such disturbances include geographical transposition, a change in substrate availability, exposure to a new host or a new vector, climate change, and pollution stress. Today, such events may often be brought about by man. Their role in the promotion of fungal microevolution is discussed. In some circumstances, episodic selection may result in the emergence of a highly fitted clone from an originally heterogeneous population, and sustained disturbance may lead to clonal speciation. Clonal speciation accompanied by loss of sexual function, whether under episodic selection or under less intensive but analagous environmental conditions, could account for the origin of many of today's imperfect taxa (Deuteromycotina). Geographical transposition, a special form of episodic selection, can lead to hybridization between previously allopatric species. This may result in modifications to existing species via the acquisition of new loci or cytoplasmic elements, in the production of new taxa via secondary speciation, or in the emergence of hybrid swarms. Episodic selection will also favour survival of novel genotypes by providing new habitats for exploitation, so encouraging novel evolutionary development. Key words: episodic selection, fungal speciation, hybridization, introgression.

Mating between different species produces hybrids that are usually asexual and stuck as diploids, but can also lead to the formation of new species. Here, we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis. We find that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B) that are 5% divergent in sequence. Isolates vary greatly in the extent of homogenization between A and B, making their genomes a mosaic of highly heterozygous regions interspersed with homozygous regions. Separate phylogenetic analyses of SNPs in the A- and B-derived portions of the genome produces almost identical trees of the isolates with four major clades. However, the presence of two mutually exclusive genotype combinations at the mating type locus, and recombinant mitochondrial genomes diagnostic of inter-clade mating, shows that the species C. orthopsilosis does not have a single evolutionary origin but was created at least four times by separate interspecies hybridizations between parents A and B. Older hybrids have lost more heterozygosity. We also identify two isolates with homozygous genomes derived exclusively from parent A, which are pure non-hybrid strains. The parallel emergence of the same hybrid species from multiple independent hybridization events is common in plant evolution, but is much less documented in pathogenic fungi.