I.II.III.IV.V.VI.References Summary Reproductive isolation in plants occurs through multiple barriers that restrict gene flow between populations, but their origins remain uncertain. Work in the past decade has shown that postpollination barriers, such as the failure to form hybrid seeds or sterility of hybrid offspring, are often less strong than prepollination barriers. Evidence implicates multiple evolutionary forces in the origins of reproductive barriers, including mutation, stochastic processes and natural selection. Although adaptation to different environments is a common element of reproductive isolation, genomic conflicts also play a role, including female meiotic drive. The genetic basis of some reproductive barriers, particularly flower colour influencing pollinator behaviour, is well understood in some species, but the genetic changes underlying many other barriers, especially pollen–stylar interactions, are largely unknown. Postpollination barriers appear to accumulate at a faster rate in annuals compared with perennials, due in part to chromosomal rearrangements. Chromosomal changes can be important isolating barriers in themselves but may also reduce the recombination of genes contributing to isolation. Important questions for the next decade include identifying the evolutionary forces responsible for chromosomal rearrangements, determining how often prezygotic barriers arise due to selection against hybrids, and establishing the relative importance of genomic conflicts in speciation.

SummaryHybridization in plants and animals is more common and has more complex outcomes than previously realized. Genome-wide analyses of introgression in organisms ranging from oaks to sunflowers to fruit flies show that a substantial fraction of their genomes are permeable to alleles from related species. Hybridization can lead to rapid genomic changes, including chromosomal rearrangements, genome expansion, differential gene expression, and gene silencing, some of which are mediated by transposable elements. These genomic changes may lead to beneficial new phenotypes, and selection for fertility and ecological traits may in turn alter genome structure. Dramatic increases in the availability of genomic tools will produce a new understanding of the genetic nature of species and will resolve a century-old debate over the basis of hybrid vigour, while the natural recombinants found in hybrid zones will permit genetic mapping of species differences and reproductive barriers in non-model organisms.In 1742, seven years after writing "nullae dantur species novae" (there are no new species) [1] Carolus Linnaeus was brought a fertile floral mutant of Linaria that he called "Peloria". The unusual floral structure convinced Linnaeus that the plant was of hybrid origin, and the fertility of Peloria and other hybrids led Linnaeus to abandon his earlier certainty in the fixed nature of species. Instead, he proposed the radical evolutionary hypothesis that new species could arise via hybridization [2]. Despite this illustrious pedigree, hybrid speciation had little scientific support until early in 20 th century when cytogenetic studies showed that hybridization may lead to speciation, especially if accompanied by chromosomal doubling (allopolyploidy). While these studies persuaded many 20 th century botanists that hybridization was a common and significant force in evolution, this view was often disputed by zoologists. Now, three centuries after the birth of Linneaus, hybridization is seen as an important phenomenon in many taxa, contributing to adaptation and speciation in plants, fish, and insects.The resurgent interest in hybridization is closely linked to the shift from genetic to genomic approaches. In this review, we take a genomic perspective on introgression and hybrid speciation. We limit ourselves to hybridization between sexually reproducing organisms, and so do not consider horizontal gene transfer in prokaryotes, between organelles and the nucleus, or interspecific transfers between organelles [reviewed in 3]. We focus on detecting hybrids and on the genomic and evolutionary consequences of introgression and hybrid speciation, while ignoring the effects of genome duplication. †

Many botanists doubt the existence of plant species, viewing them as arbitrary constructs of the human mind, as opposed to discrete, objective entities that represent reproductively independent lineages or 'units of evolution'. However, the discreteness of plant species and their correspondence with reproductive communities have not been tested quantitatively, allowing zoologists to argue that botanists have been overly influenced by a few 'botanical horror stories', such as dandelions, blackberries and oaks. Here we analyse phenetic and/or crossing relationships in over 400 genera of plants and animals. We show that although discrete phenotypic clusters exist in most genera (> 80%), the correspondence of taxonomic species to these clusters is poor (< 60%) and no different between plants and animals. Lack of congruence is caused by polyploidy, asexual reproduction and over-differentiation by taxonomists, but not by contemporary hybridization. Nonetheless, crossability data indicate that 70% of taxonomic species and 75% of phenotypic clusters in plants correspond to reproductively independent lineages (as measured by postmating isolation), and thus represent biologically real entities. Contrary to conventional wisdom, plant species are more likely than animal species to represent reproductively independent lineages.

Apomixis, the asexual production of seed, is a trait estimated to occur in fewer than 1% of flowering plant species, with an uneven distribution among lineages. In the past decade, targeted research efforts have aimed at clarifying the genetic basis of apomixis, with the goal of engineering or breeding apomictic crops. Recent work suggests a simple genetic basis for apomixis, but it also indicates that natural populations of apomicts are much more complex than is often assumed. For example, in nature, nearly all apomicts that go through a megagametophyte stage (gametophytic apomicts) are polyploid, while their sexual relatives are typically diploid. Although populations have been characterized as obligately sexual or apomictic, it is increasingly clear that many plant populations exhibit some variation in reproductive mode. Many apomicts retain residual sexual function as pollen donors and thus have the potential to spread apomixis via male gametes, thereby increasing the genetic diversity observed within apomictic populations. Here, we summarize our current understanding of the genetic basis and transmission of apomixis. We use insights from previous case studies and models for the spread of asexuality to explore the potential for establishment and spread of apomixis in nature.

The strength and extent of gene flow from crops into wild populations depends, in part, on the fitness of the crop alleles, as well as that of alleles at linked loci. Interest in crop-wild gene flow has increased with the advent of transgenic plants, but nontransgenic crop-wild hybrids can provide case studies to understand the factors influencing introgression, provided that the genetic architecture and the fitness effects of loci are known. This study used recombinant inbred lines (RILs) generated from a cross between crop and wild sunflowers to assess selection on domestication traits and quantitative trait loci (QTL) in two contrasting environments, in Indiana and Nebraska, USA. Only a small fraction of plants (9%) produced seed in Nebraska, due to adverse weather conditions, while the majority of plants (79%) in Indiana reproduced. Phenotypic selection analysis found that a mixture of crop and wild traits were favoured in Indiana (i.e. had significant selection gradients), including larger leaves, increased floral longevity, larger disk diameter, reduced ray flower size and smaller achene (seed) mass. Selection favouring early flowering was detected in Nebraska. QTLs for fitness were found at the end of linkage groups six (LG6) and nine (LG9) in both field sites, each explaining 11-12% of the total variation. Crop alleles were favoured on LG9, but wild alleles were favoured on LG6. QTLs for numerous domestication traits overlapped with the fitness QTLs, including flowering date, achene mass, head number, and disk diameter. It remains to be seen if these QTL clusters are the product of multiple linked genes, or individual genes with pleiotropic effects. These results indicate that crop trait values and alleles may sometimes be favoured in a noncrop environment and across broad geographical regions.