Summary: Enormous strides have been made in the study of polyploidy over the last 20 yr. Here, we highlight some of these discoveries and note where our understanding of polyploid evolution has changed. Genetic and genomic studies have dramatically altered the polyploidy paradigm. The estimated frequency of polyploidy has increased, and it is now recognized that multiple origins are the rule for most polyploids. Likewise, autopolyploidy is much more common than traditionally maintained. Rapid genomic rearrangements, genomic downsizing, movement of genetic elements across genomes, and the movement of foreign genetic materials into the polyploid genome illustrate the complex dynamics of polyploid genomes. Following polyploidization, both genetic and epigenetic mechanisms may play an important role in altering gene expression. Ecological studies reveal that plant polyploidy can have profound effects on interactions with animal herbivores and pollinators and that polyploidy may trigger changes in the reproductive biology of a species. Despite the recent advances in our understanding of polyploid evolution, many exciting aspects remain under‐investigated. Some of these include the consequences of genetic and genomic changes in natural polyploid populations, the physiological and ecological effects of polyploidy, and whether recurrent polyploidy prompts evolution to repeat itself.

Tragopogon mirus Ownbey and T. miscellus Ownbey are allopolyploids that formed repeatedly during the past 80 years following the introduction of three

For the last 150 years, the taxonomy of Hoffmannseggia has been variously entangled with Caesalpinia and Pomaria. Traditionally, Hoffmannseggia consisted of herbaceous or sub-shrubby perennials (rather than trees or vines) that lack spines and usually bear glandular trichomes on portions of the vegetative surfaces. However, the lack of correspondence of other characters such as flower shape, fruit type, and sepal persistence with habit and armament led to the repeated realignment of various species. Recent molecular work has shown that Hoffmannseggia forms a monophyletic group supported with several morphological synapomorphies and that it is not closely related to either Caesalpinia or Pomaria. Here we use molecular data from the nuclear ITS spacer regions, the trnL spacer and trnF intron chloroplast regions, and the rbcL gene to examine the relationships of Hoffmannseggia species. We show that there are two major clades in the genus that do not correspond to any previous infrageneric taxonomy. These clades are supported by morphological differences, the most striking of which is habit with one clade consisting of sub-shrubby species and the other of herbaceous species. We point out other characters that support subgroups within these clades, document one case of hybridization, and identify other suspected cases of hybridization. We also make the new combination Hoffmannseggia pumilio .

Polyploidy, frequently termed “whole genome duplication”, is a major force in the evolution of many eukaryotes. Indeed, most angiosperm species have undergone at least one round of polyploidy in their evolutionary history. Despite enormous progress in our understanding of many aspects of polyploidy, we essentially have no information about the role of chromosome divergence in the establishment of young polyploid populations. Here we investigate synthetic lines and natural populations of two recently and recurrently formed allotetraploids Tragopogon mirus and T. miscellus (formed within the past 80 years) to assess the role of aberrant meiosis in generating chromosomal/genomic diversity. That diversity is likely important in the formation, establishment and survival of polyploid populations and species. Applications of fluorescence in situ hybridisation (FISH) to natural populations of T. mirus and T. miscellus suggest that chromosomal rearrangements and other chromosomal changes are common in both allotetraploids. We detected extensive chromosomal polymorphism between individuals and populations, including (i) plants monosomic and trisomic for particular chromosomes (perhaps indicating compensatory trisomy), (ii) intergenomic translocations and (iii) variable sizes and expression patterns of individual ribosomal DNA (rDNA) loci. We even observed karyotypic variation among sibling plants. Significantly, translocations, chromosome loss, and meiotic irregularities, including quadrivalent formation, were observed in synthetic (S₀ and S₁ generations) polyploid lines. Our results not only provide a mechanism for chromosomal variation in natural populations, but also indicate that chromosomal changes occur rapidly following polyploidisation. These data shed new light on previous analyses of genome and transcriptome structures in de novo and establishing polyploid species. Crucially our results highlight the necessity of studying karyotypes in young (<150 years old) polyploid species and synthetic polyploids that resemble natural species. The data also provide insight into the mechanisms that perturb inheritance patterns of genetic markers in synthetic polyploids and populations of young natural polyploid species.