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Premise Plant genome size ranges widely, providing many opportunities to examine how genome size variation affects plant form and function. We analyzed trends in chromosome number, genome size, and leaf traits for the woody angiosperm clade Viburnum to examine the evolutionary associations, functional implications, and possible drivers of genome size. Methods Chromosome counts and genome size estimates were mapped onto a Viburnum phylogeny to infer the location and frequency of polyploidization events and trends in genome size evolution. Genome size was analyzed with leaf anatomical and physiological data to evaluate the influence of genome size on plant function. Results We discovered nine independent polyploidization events, two reductions in base chromosome number, and substantial variation in genome size with a slight trend toward genome size reduction in polyploids. We did not find strong relationships between genome size and the functional and morphological traits that have been highlighted at broader phylogenetic scales. Conclusions Polyploidization events were sometimes associated with rapid radiations, demonstrating that polyploid lineages can be highly successful. Relationships between genome size and plant physiological function observed at broad phylogenetic scales may be largely irrelevant to the evolutionary dynamics of genome size at smaller scales. The view that plants readily tolerate changes in ploidy and genome size, and often do so, appears to apply to Viburnum.

Premise Newly formed polyploids face significant obstacles to persistence and population establishment because of fitness costs of intercytotype mating. Selfing provides the opportunity to escape mate limitation, enabling production of new individuals and increasing the likelihood of fixation of new polyploid lineages. Still, association between self-compatibility and polyploidy is not always clear. We compared self-incompatibility and inbreeding depression in neotetraploids and their diploid progenitor to explore the direct effects of whole genome duplications on self-incompatibility and the implications of ploidy-driven changes for polyploid establishment. Methods Outcross and self-pollinations were performed in diploids and synthetic neotetraploids of Jasione maritima var. maritima, and reproductive success was measured through fruit and seed production and seed germination. Self- and outcross offspring were grown under controlled conditions, and plant performance was measured through several fitness parameters. Results Neotetraploids showed an overall lower performance than diploids. Reproductive success was negatively affected by selfing in both cytotypes. However, greater variation in the expression of self-incompatibility was observed in neotetraploids; additionally, developmental and physiological parameters were not affected by selfing on neotetraploids, with an overall similar fitness of outcrossed and selfed individuals, resulting in lower inbreeding depression indexes. Conclusions Neotetraploids might have benefited from selfing at initial stages after their formation. Genome duplications resulted in leaky self-incompatibility, enabling the production of offspring under minority cytotype disadvantage with similar fitness as outcrossed offspring. Our results support theoretical assumptions that selfing might be important for neopolyploid establishment, although changes in self-incompatibility might not be abrupt.

Premise Different cytotypes of a species may differ in their morphology, phenology, physiology, and their tolerance of extreme environments. We studied the ecological niches of two subspecies of Saxifraga rosacea with different ploidy levels: the hexaploid Central European endemic subspecies sponhemica and the more widely distributed octoploid subspecies rosacea. Methods For both cytotypes, we recorded local environmental conditions and mean plant trait values in populations across their areas of distribution, analyzed their distributions by niche modeling, studied their performance at two transplant sites with contrasting conditions, and experimentally tested their cold resistance. Results Mean annual temperature was higher in hexaploid than in octoploid populations and experiments indicated that frost tolerance of the hexaploid is lower than that of the octoploid. Reproduction of octoploids from Central Europe was higher than that of hexaploids at a transplant site in subarctic Iceland, whereas the opposite was true in temperate Luxembourg, indicating adaptation of the octoploids to colder conditions. Temperature variables were also most important in niche models predicting the distribution of the two cytotypes. Genetic differences in survival among populations were larger for the octoploids than for the hexaploids in both field gardens, suggesting that greater genetic variability may contribute to the octoploid's larger distributional range. Conclusions Our results support the hypotheses that different cytotypes may have different niches leading to spatial segregation, and that higher ploidy levels can result in a broader ecological niche and greater tolerance of more extreme conditions.

PREMISE The origin of allopolyploids is believed to shape their evolutionary potential, ecology, and geographical ranges. Morphologically distinct apomictic types sharing the same parental species belong to the most challenging groups of polyploids. We evaluated the origins and variation of two triploid taxa (Hieracium pallidiflorum, H. picroides) presumably derived from the same diploid parental pair (H. intybaceum, H. prenanthoides). METHODS We used a suite of approaches ranging from morphological, phylogenetic (three unlinked molecular markers), and cytogenetic analyses (in situ hybridization) to genome size screening and genome skimming. RESULTS Genotyping proved the expected parentage of all analyzed accessions of H. pallidiflorum and H. picroides and revealed that nearly all of them originated independently. Genome sizes and genome dosage largely corresponded to morphology, whereas the maternal origin of the allopolyploids had no discernable effect. Polyploid accessions of both parental species usually contained genetic material from other species. Given the phylogenetic distance of the parents, their chromosomes appeared only weakly differentiated in genomic in situ hybridization (GISH), as well as in overall comparisons of the repetitive fraction of their genomes. Furthermore, the repeatome of a phylogenetically more closely related species (H. umbellatum) differed significantly more. CONCLUSIONS We proved (1) multiple origins of hybridogeneous apomicts from the same diploid parental taxa, and (2) allopolyploid origins of polyploid accessions of the parental species. We also showed that the evolutionary dynamics of very fast evolving markers such as satellite DNA or transposable elements does not necessarily follow patterns of speciation.

Premise Divergence in functional traits and adaptive responses to environmental change underlies the ecological advantage of polyploid plants in the wild. While established polyploids may benefit from combined outcomes of genome doubling, hybridization, and polyploidy-enabled adaptive evolution, whether genome doubling alone can drive ecological divergence or whether the outcome is genetically variable remains less clear. Methods Using synthetic, colchicine-induced, autotetraploid (4x) plants derived from self-pollinated diploid (2x) seeds, and their colchicine-treated but unconverted diploid (2x.nc) full sibs from two diploid wild strawberry taxa (Fragaria vesca subsp. vesca and F. vesca subsp. bracteata), we examined the effects of genome doubling on functional traits, heat stress tolerance, and fitness components across taxa and maternal families (i.e., genetic families) within taxa. Results Comparisons between 2x and 2x.nc plants indicated a negligible effect of colchicine treatment on functional traits. Genome doubling increased stomatal length and decreased stomatal density, specific leaf area, and leaf vein density, recapitulating patterns observed in wild polyploid Fragaria. Trichome density, heat stress tolerance, and relative growth rate were not significantly affected by genome doubling. Although clonal reproduction was reduced in response to genome doubling, this effect was strongly genetic-family dependent. Conclusions The results suggest that genome doubling during incipient speciation alone can generate ecological divergence and variation among genetic lineages. This response potentially allows for rapid short-term evolutionary adaptation and fuels genomic diversity and independent origins of polyploidy.

Premise Polyploidy is a major genetic driver of ecological and evolutionary processes in plants, yet its effects on plant interactions with mutualistic microbes remain unresolved. The legume-rhizobium symbiosis regulates global nutrient cycles and plays a role in the diversification of legume species. In this mutualism, rhizobia bacteria fix nitrogen in exchange for carbon provided by legume hosts. This exchange occurs inside root nodules, which house bacterial cells and represent the interface of legume-rhizobium interactions. Although polyploidy may directly impact the legume-rhizobium mutualism, no studies have explored how it alters the internal structure of nodules. Methods We created synthetic autotetraploids using Medicago sativa subsp. caerulea. Neotetraploid plants and their diploid progenitors were singly inoculated with two strains of rhizobia, Sinorhizobium meliloti and S. medicae. Confocal microscopy was used to quantify internal traits of nodules produced by diploid and neotetraploid plants. Results Autotetraploid plants produced larger nodules with larger nitrogen fixation zones than diploids for both strains of rhizobia, although the significance of these differences was limited by power. Neotetraploid M. sativa subsp. caerulea plants also produced symbiosomes that were significantly larger, nearly twice the size, than those present in diploids. Conclusions This study sheds light on how polyploidy directly affects a plant-bacterium mutualism and uncovers novel mechanisms. Changes in plant-microbe interactions that directly result from polyploidy likely contribute to the increased ability of polyploid legumes to establish in diverse environments.

PREMISE Disjunct distributions have been commonly observed in mountain plant species and have stimulated phylogeographic and phylogenetic research. Here we studied Alyssum repens, a member of the polyploid species complex A. montanum-A. repens, which exhibits SE Alpine-Carpathian disjunctions with a large elevational span and consists of diploid and tetraploid populations. We aimed to investigate the species' genetic and cytotype structure in the context of its distribution patterns, to elucidate the polyploid origins and to propose an appropriate taxonomic treatment. METHODS We combined AFLP fingerprinting markers, sequence variation of the highly repetitive ITS region of rDNA and the low-copy DET1 nuclear gene, genome size, and morphometric data. RESULTS We identified four geographically structured genetic lineages. One consisted of diploid populations from the foothills of the Southeastern Alps and neighboring regions, and the three others were allopatric montane to alpine groups comprising diploids and tetraploids growing in the Southeastern Carpathians and the Apuseni Mts. in Romania. CONCLUSIONS We inferred a vicariance scenario associated with Quaternary climatic oscillations, accompanied by one auto- and two allopolyploidization events most likely involving a northern Balkan relative. Whereas genetic differentiation and allopatric distribution would favor the taxonomic splitting of this species, the genetic lineages largely lack morphological distinguishability, and their ecological, cytotype and genome size divergence is only partial. Even though we probably face here a case of incipient speciation, we propose to maintain the current taxonomic treatment of Alyssum repens as a single, albeit variable, species.

Plants with separate sexes often show "inconstant" or "leaky" sex expression, with females or males producing a few flowers of the opposite sex. The frequency and degree of such inconstancy may reflect residual hermaphroditic sex allocation after an evolutionary transition from combined to separate sexes. Sex inconstancy also represents a possible first step in the breakdown of dioecy back to hermaphroditism. In the Mercurialis annua (Euphorbiaceae) species complex, monoecy and androdioecy have evolved from dioecy in polyploid populations. Here, we characterize patterns of sex inconstancy in dioecious M. annua and discuss how sex inconstancy may have contributed to the breakdown of separate sexes in the genus. We measured sex inconstancy in three common gardens of M. annua over 2 years using a modification of Lloyd's phenotypic gender in terms of frequency and degree, with the degree calibrating inconstancy against the sex allocation of constant males and constant females, yielding a measure of gender that does not depend on the distribution of gender in the population. Unusually for dioecious plants, the frequency of sex inconstancy in M. annua was greater in females, but its degree was greater for males in the 2 years of study. We suggest that this pattern is consistent with the maintenance of inconstancy in dioecious M. annua by selection for reproductive assurance under mate limitation. Our study illustrates the utility of decomposing measures of sex inconstancy into its frequency and its degree and throws new light on the origin of variation in sexual systems in Mercurialis.

Premise of the study Polyploidy, or whole genome duplication (WGD), is common in plants despite theory suggesting that polyploid establishment is challenging and polyploids should be evolutionarily transitory. There is renewed interest in understanding the mechanisms that could facilitate polyploid establishment and explain their pervasiveness in nature. In particular, premating isolation from their diploid progenitors is suggested to be a crucial factor. To evaluate how changes in assortative mating occur, we need to understand the phenotypic effects of WGD on reproductive traits. Methods We used literature surveys and a meta-analysis to assess how WGD affects floral morphology, flowering phenology, and reproductive output in plants. We focused specifically on comparisons of newly generated polyploids (neopolyploids) and their parents to mitigate potential confounding effects of adaptation and drift that may be present in ancient polyploids. Key results The results indicated that across a broad representation of angiosperms, floral morphology traits increased in size, reproductive output decreased, and flowering phenology was unaffected by WGD. Additionally, we found that increased trait variation after WGD was uncommon for the phenotypic traits examined. Conclusions Our results suggest that the phenotypic effects on traits important to premating isolation of neopolyploids are small, in general. Changes in flowering phenology, reproductive output, and phenotypic variation resulting from WGD may be less critical in facilitating premating isolation and neopolyploid establishment. However, floral traits for which size is an important component of function (e.g., pollen transfer) could be strongly influenced by WGD.

Premise of the study Clonal reproduction is often associated with polyploidy and is expected to influence polyploid establishment success, but the immediate effects of whole-genome duplication (WGD) on clonal reproduction in autopolyploids are unknown. Methods We used synthesized neopolyploids to assess the direct effects of WGD on stolon and plantlet production in the wild strawberry Fragaria vesca by (1) comparing absolute clonal investment between diploids and neotetraploids under high and low resource conditions in the greenhouse and (2) determining realized clonal plantlet establishment and genet spatial structure using artificial field populations comprising both cytotypes. Key results Neotetraploids produced fewer stolons and plantlets than diploids at slower weekly rates in the greenhouse when resources were high, resulting in lower total investment in clonal reproduction. Low resources led to smaller reductions in clonal biomass for neotetraploids and less pronounced differences between cytotypes. Comparisons between neotetraploids representing 13 independent WGD events and close diploid relatives revealed considerable variation in the response to polyploidization for some clonal traits. Field populations corroborated greenhouse results; neotetraploid genets were smaller than diploid genets, containing 28% fewer stolons and 46% fewer rooted plantlets. Conclusions WGD significantly decreases the clonal output of neotetraploid F. vesca, which is likely attributable to slower whole-plant growth of the neotetraploids than the diploids. In natural populations, smaller neotetraploid genets could decrease the probability of polyploid establishment in this species. However, variation between separate neopolyploid lines emphasizes that the response of clonal investment to WGD may not be uniform across polyploid origins.

Premise Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear. Methods Phylo-transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny. Results Well-supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae-specific WGD event Th-ɑ are presented. This work also provides evidence for previously hypothesized WGDs, including a well-supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae. Conclusions Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods.

PREMISE OF THE STUDY Unrecognized variation in ploidy level can lead to an underestimation of species richness and a misleading delineation of geographic range. Caltha leptosepala (Ranunculaceae) comprises a complex of hexaploids (6x), rare nonaploids (9x), and dodecaploids (12x), all with unknown distributions. We delineate the geographic distribution and contact zones of the cytotypes, investigate morphologies of cytotypes and subspecies, and discuss the biogeography and evolutionary history of the polyploid complex. METHODS Using cytologically determined specimens as reference, propidium iodide flow cytometry was performed on silica-dried samples and herbarium specimens from across the range of C. leptosepala s.l. Genome size estimates from flow cytometry were used to infer cytotypes. A key morphological character, leaf length-to-width ratio, was measured to evaluate whether these dimensions are informative for taxon and/or cytotype delimitation. KEY RESULTS Dodecaploids were more northerly in distribution than hexaploids, and a single midlatitude population in the Northern Rockies yielded nonaploids. Genome size estimates were significantly different between all cytotypes and between hexaploid subspecies. Leaf length-to-width ratios were significantly different between subspecies and some cytotypes. CONCLUSIONS Caltha leptosepala presents clear patterns of cytotype distribution at the large scale. Marked differences in morphology, range, and genome size were detected between the hexaploid subspecies, C. leptosepala subsp. howellii in the Cascade-Sierra axis and C. leptosepala subsp. leptosepala in the Rockies. Sympatry between cytotypes in the Cascades and a parapatric distribution in the Northern Rockies suggest unique origins and separate lineages in the respective contact zones.

Premise Polyploidy is known to cause physiological changes in plants which, in turn, can affect species interactions. One major physiological change predicted in polyploid plants is a heightened demand for growth-limiting nutrients. Consequently, we expect polyploidy to cause an increased reliance on the belowground mutualists that supply these growth-limiting nutrients. An important first step in investigating how polyploidy affects nutritional mutualisms in plants, then, is to characterize differences in the rate at which diploids and polyploids interact with belowground mutualists. Methods We used Heuchera cylindrica (Saxifragaceae) to test how polyploidy influences interactions with arbuscular mycorrhizal fungi (AMF). Here we first confirmed the presence of AMF in H. cylindrica, and then we used field-collected specimens to quantify and compare the presence of AMF structures while controlling for site-specific variation. Results Tetraploids had higher colonization rates as measured by total, hyphal, and nutritional-exchange structures; however, we found that diploids and tetraploids did not differ in vesicle colonization rates. Conclusions The results suggest that polyploidy may alter belowground nutritional mutualisms with plants. Because colonization by nutritional-exchange structures was higher in polyploids but vesicle colonization was not, polyploids might form stronger associations with their AMF partners. Controlled experiments are necessary to test whether this pattern is driven by the direct effect of polyploidy on AMF colonization.

PREMISE: When two populations of related cytotypes grow in sympatry, the rarer cytotype tends to be excluded due to a frequency‐dependent mating disadvantage. Evolutionary models predict that polyploids, which are typically the rarer cytotype upon first formation, should have higher relative fitness and/or higher selfing rates to establish and then coexist with diploid parents. METHODS: Performance during early recruitment was compared among three co‐occurring rupicolous fern species: the allotetraploid Cheilanthes tinaei and its diploid ancestors, C. hispanica and C. maderensis. In culture experiments, fresh spores and samples of soil spore banks were tested for variation among cytotypes in germination, survival, fecundity, and mating system of gametophytes. RESULTS: Compared with its diploid parents, C. tinaei fresh spores had higher abortion percentages, lower dispersal ability as a result of its larger spores, and similar vigor at germination. For gametophytes from soil spore banks, C. tinaei had high survival similar to C. maderensis, but its sex expression resembled that of C. hispanica, with a high proportion of males. Patterns of sporophyte formation by females and bisexuals indicate that the polyploid does not have an increased gametophytic selfing rate. Gametophytes were larger in C. tinaei, but its reproductive success (sporophyte formation) was intermediate relative to diploids. CONCLUSIONS: Our results show no evidence of higher selfing or fitness advantage of the allopolyploid over both diploid parents at any stage of early recruitment. These two unexpected findings suggest that further factors, such as niche differentiation, play a more important role in cytotype coexistence.

PREMISE OF THE STUDY Studies of natural populations of polyploids increasingly highlight complex patterns of variation in ploidy and geographic distribution of cytotypes. As our understanding of the complexity of polyploidy grows, our understanding of the morphological correlates of polyploidy should expand as well. Here we examine in what ways, and to what degree, polyploidy affects the overall phenotype of a species across its distribution when there are three ploidies and geographic complexity in cytotype distribution. METHODS We measured 31 morphological traits from stems, leaves, and flowers from up to 25 individuals from 11 sites across the distribution of Phlox amabilis. Chromosome counts and flow cytometry confirmed and expanded upon earlier research documenting diploid, tetraploid, and hexaploid populations, and also identified a site with two ploidies. Univariate and multivariate statistics were used to characterize the morphological effects of polyploidy. KEY RESULTS We detected significant associations between morphology and ploidy in 11 traits spread across vegetative and reproductive structures. Generally, diploid individuals differed from polyploid individuals to a greater extent, and in different ways, than tetraploid and hexaploid plants differed from each other. Multivariate morphometrics demonstrated that the two primary axes of overall variation are driven by morphological traits associated with polyploidy, and individuals of different ploidies can be discriminated with 95% success. CONCLUSIONS Polyploidy plays a major role in shaping overall morphological diversity in natural populations of P. amabilis.

PREMISE OF THE STUDY The depiction of polyploid speciation as instantaneous implies that strong prezygotic and postzygotic isolation form as a direct result of whole-genome duplication. However, the direct vs. indirect contributions of genome duplication to phenotypic divergence and prezygotic isolation are rarely quantified across multiple reproductive barriers. METHODS We compared the phenotypic differences between diploid and both naturally occurring and synthesized tetraploids (neotetraploids) of the plant Chamerion angustifolium. Using this information and additional published values for this species, we compared the magnitude of isolation (ecological, flowering, pollinator, and gametic) between diploids and natural-occurring tetraploids to that between diploids and neotetraploids. KEY RESULTS Differences among ploidy cytotypes were observed for eight of 12 vegetative and reproductive traits measured. Neotetraploids resembled diploids but differed from natural tetraploids with respect to four traits, including flowering time and plant height. Diploid-neotetraploid (2x-4xneo) experimental arrays exhibited lower pollinator fidelity to cytotype and seed set compared with 2x-4xnat arrays. Based on these results and published evidence, reproductive isolation between diploids and neotetraploids across all four life stages averaged 0.48 and deviated significantly from that between diploids and natural tetraploids (RI = 0.96). CONCLUSIONS Genome duplication causes phenotypic shifts and contributes directly to prezygotic isolation for some barriers (gametic isolation) but cannot account for the cumulative isolation from diploids observed in natural tetraploids. Therefore, conditions for species formation through genome duplication are not necessarily instantaneous and selection to strengthen prezygotic barriers in young polyploids is critical for the establishment of polyploid species in sympatry.

Premise of the study Polyploidy is widely recognized as a mechanism of diversification. Contributions of polyploidy to specific pre- and postzygotic barriers-and classifications of polyploid speciation as "ecological" vs. "non-ecological"-are more contentious. Evaluation of these issues requires comprehensive studies that test ecological characteristics of cytotypes as well as the coincidence of genetic structure with cytotype distributions. Methods We investigated a classical example of autopolyploid speciation, Larrea tridentata, at multiple areas of cytotype co-occurrence. Habitat and phenological differences were compared between diploid, tetraploid, and hexaploid populations on the basis of edaphic, community composition, and flowering time surveys. Frequency of hybridization between diploids and tetraploids was investigated using a diploid-specific chloroplast DNA (cpDNA) marker; genetic structure for all cytotypes was assessed using amplified fragment length polymorphisms (AFLPs). Key results Across contact zones, we found cytotypes in habitats distinguished by soil and vegetation. We observed modest differences in timing and production of flowers, indicating a degree of assortative mating that was asymmetric between cytotypes. Nonetheless, cpDNA analyses in diploid-tetraploid contact zones suggested that ∼5% of tetraploid plants had hybrid origins involving unilateral sexual polyploidization. Genetic structure of AFLPs largely coincided with cytotype distributions in diploid-tetraploid contact zones. In contrast, there was little structure in areas of contact between tetraploids and hexaploids, suggesting intercytotype gene flow or recurrent hexaploid formation. Conclusions Diploid, tetraploid, and hexaploid cytotypes of L. tridentata are segregated by environmental distributions and flowering phenology in contact zones, with diploid and tetraploid populations having corresponding differences in genetic structure.

Premise of the study Whole-genome duplication (WGD) in angiosperms has been hypothesized to be advantageous in unstable environments and/or to increase diversification rates, leading to radiations. Under the first hypothesis, floras in stable environments are predicted to have lower proportions of polyploids than highly, recently disturbed floras, whereas species-rich floras would be expected to have higher than expected proportions of polyploids under the second. The South African Cape flora is used to discriminate between these two hypotheses because it features a hyperdiverse flora predominantly generated by a limited number of radiations (Cape clades), against a backdrop of climatic and geological stability. Methods We compiled all known chromosome counts for species in 21 clades present in the Cape (1653 species, including 24 Cape clades), inferred ploidy levels for these species by inspection or derived from the primary literature, and compared Cape to non-Cape ploidy levels in these clades (17,520 species) using G tests. Key results The Cape flora has anomalously low proportions of polyploids compared with global levels. This pattern is consistently observed across nearly half the clades and across global latitudinal gradients, although individual lineages seem to be following different paths to low levels of WGD and to differing degrees. Conclusions This pattern shows that the diversity of the Cape flora is the outcome of primarily diploid radiations and supports the hypothesis that WGD may be rare in stable environments.

Investigators have long searched for a polyploidy paradigm-rules or principles that might be common following polyploidization (whole-genome duplication, WGD). Here we attempt to integrate what is known across the more thoroughly investigated polyploid systems on topics ranging from genetics to ecology. We found that while certain rules may govern gene retention and loss, systems vary in the prevalence of gene silencing vs. homeolog loss, chromosomal change, the presence of a dominant genome (in allopolyploids), and the relative importance of hybridization vs. genome doubling per se. In some lineages, aspects of polyploidization are repeated across multiple origins, but in other species multiple origins behave more stochastically in terms of genetic and phenotypic change. Our investigation also reveals that the path to synthesis is hindered by numerous gaps in our knowledge of even the best-known systems. Particularly concerning is the absence of linkage between genotype and phenotype. Moreover, most recent studies have focused on the genetic and genomic attributes of polyploidy, but rarely is there an ecological or physiological context. To promote a path to a polyploidy paradigm (or paradigms), we propose a major community goal over the next 10-20 yr to fill the gaps in our knowledge of well-studied polyploids. Before a meaningful synthesis is possible, more complete data sets are needed for comparison-systems that include comparable genetic, genomic, chromosomal, proteomic, as well as morphological, physiological, and ecological data. Also needed are more natural evolutionary model systems, as most of what we know about polyploidy continues to come from a few crop and genetic models, systems that often lack the ecological context inherent in natural systems and necessary for understanding the drivers of biodiversity.

Premise of the study Introgression is widely acknowledged as a potential source of valuable genetic variation, and growing effort is being invested in analysis of interspecific crosses conferring transgressive variation. Experimental backcross populations provide an opportunity to study transmission genetics following interspecific hybridization, identifying opportunities and constraints to introgressive crop improvement. The evolutionary consequences of introgression have been addressed at the theoretical level, however, issues related to levels and patterns of introgression among (plant) species remain inadequately explored, including such factors as polyploidization, subgenome interaction inhabiting a common nucleus, and the genomic distribution and linkage relationships of introgressant alleles. Methods We analyze introgression into the polyploid Gossypium hirsutum (upland cotton) from its sister G. tomentosum and compare the level and pattern with that of G. barbadense representing a different clade tracing to the same polyploidization. Key results Across the genome, recurrent backcrossing to Gossypium hirsutum yielded only one-third of the expected average frequency of the G. tomentosum allele, although one unusual region showed preferential introgression. Although a similar rate of introgression is found in the two subgenomes of polyploid (AtDt) G. hirsutum, a preponderance of multilocus interactions were largely within the Dt subgenome. Conclusions Skewed G. tomentosum chromatin transmission is polymorphic among two elite G. hirsutum genotypes, which suggests that genetic background may profoundly affect introgression of particular chromosomal regions. Only limited correspondence is found between G. hirsutum chromosomal regions that are intolerant to introgression from the two species, G. barbadense and G. tomentosum, concentrated near possible inversion polymorphisms. Complex transmission of introgressed chromatin highlights the challenges to utilization of exotic germplasm in crop improvement.

PREMISE OF THE STUDY Deleterious recessive mutations are an important determinant of fitness (mutational load) in the sporophytic phase of plants and a major cause of inbreeding depression; however, their role in gametophyte function is less well documented but may account for variation in pollen tube growth and siring ability, especially between diploid and polyploid plants, which can mask the load. METHODS We investigated the role of mutational load in pollen performance using the perennial polyploid Chamerion angustifolium by comparing tube growth of pollen, in styles and in growth medium, from inbred (selfed) and outbred diploids to that of inbred and outbred tetraploids. Pollen from tetraploids is expected to mask deleterious mutations more effectively in the outbred condition but reveal them after inbreeding. In contrast, gametophytes from diploids should express the same genetic load in inbred or outbred plants. KEY RESULTS Pollen tube growth measured in growth medium was highest in outbred tetraploids and generally lower in inbred than outbred plants. The effect of selfing was significant in pollen from tetraploids but not diploids. The differential effect of selfing was also evident in the proportion of pollen reaching the base of styles, but the ploidy × pollination interaction was not significant. Selfing also had a negative effect on sporophyte fitness but was greater in diploids than tetraploids. CONCLUSIONS Pollen performance is influenced by the expression of mutational load, which is masked in polyploids. This effect may partly explain strong siring success of tetraploids in this species.

PREMISE OF THE STUDY Delimitation of Amelanchier species is difficult because of polyploidy and gametophytic apomixis. A first step in unraveling this species problem is understanding the diversity of the diploids that contributed genomes to polyploid apomicts. This research helps clarify challenging species-delimitation problems attending polyploid, apomictic complexity. METHODS We sampled 431 diploid accessions from 13 species, of which 10 are North American and three are Old World. Quantitative morphological analyses tested the null hypothesis of no discrete groups. Using three to nine diploid accessions per species, we constructed phylogenies with DNA sequences from ETS, ITS, the second intron of LEAFY, and chloroplast regions rpoB-trnC, rpl16, trnD-trnT, and ycf6-psbM. KEY RESULTS Most Amelanchier diploid taxa are morphologically and ecogeographically distinct and genetically exclusive lineages. They rarely hybridize with one another. Nuclear and chloroplast DNA sequences almost completely resolve the Amelanchier phylogeny. The backbone is the mostly western North American clade A, eastern North American clade B, and Old World clade O. DNA sequences and morphology support clades A and O as sister taxa. Despite extensive paralogy, our LEAFY data are phylogenetically informative and identify a clade (T) of three arborescent taxa within clade B. CONCLUSIONS Amelanchier diploids differ strikingly from polyploid apomicts, in that hybridization among them is rare, and they form taxa that would qualify as species by most species concepts. Knowledge of diploid morphology, phylogeny, and ecogeography provides a foundation for understanding the evolutionary history of polyploid apomicts, their patterns of diversification, and their species status.

PREMISE OF THE STUDY Successful establishment of neopolyploids, and therefore polyploid speciation, is thought to be contingent on environmental niche shifts from their progenitors. We explore this niche shift hypothesis in the obligate outcrosser Arabidopsis arenosa complex, which includes diploid and recently formed autotetraploid populations. METHODS To characterize the climatic niches for both cytotypes in Arabidopsis arenosa, we first gathered climatic data from localities with known ploidy types. We then estimated the climatic niches for diploids and autotetraploids and calculated niche overlap. Using this niche overlap statistic, we tested for niche equivalency and similarity. We explored differences in niches by estimating and comparing niche optimum and breadth and then calculated indices of niche expansion and unfilling. KEY RESULTS Climatic niche overlap between diploids and autotetraploids is substantial. Although the two niche models are not significantly divergent, they are not identical as they differ in both optimum and breadth along two environmental gradients. Autotetraploids fill nearly the entire niche space of diploids and have expanded into novel environments. CONCLUSIONS We find climatic niche expansion but not divergence, together with a moderate change in the niche optimum, in the autotetraploid lineage of Arabidopsis arenosa. These results indicate that the climatic niche shift hypothesis alone cannot explain the coexistence of tetraploid and diploid cytotypes.

Premise of the study Whereas population genetic studies have examined allopolyploids, comparable studies of naturally occurring autopolyploids remain rare. To address fundamental questions regarding autopolyploidy, we undertook a detailed population genetic study of one of the classic examples of autopolyploidy, Galax urceolata (Diapensiaceae), which comprises diploid, triploid, and autotetraploid cytotypes. Galax is endemic to the Appalachian Mountains, the adjacent piedmont, sandhills, and coastal plain and represents perhaps the most widely known example of autopolyploidy in nature. Methods Flow cytometry was used to diagnose ploidal level of ∼1000 individuals across 71 populations. We used 10 microsatellite markers to examine genetic variation across the geographic range of Galax and assessed multiple origins though comparisons of diploid, triploid, and tetraploid accessions using multiple analytical approaches. Key results Tetraploids had higher levels of heterozygosity than diploids did. Genetic variation in diploid and tetraploid Galax is geographically structured among the ecoregions of the southeastern United States. Autotetraploidy in Galax urceolata has occurred independently at least 46 times, with triploidy having occurred a minimum of 31 times. Conclusions Genetic differentiation among ecoregions suggests historical patterns of local adaptation. The numerous independent origins of tetraploid Galax reported here are among the highest frequencies of independent polyploidizations ever reported for any polyploid (auto- or allopolyploid).

 Premise of the study: Single-copy nuclear loci can provide powerful insights into polyploid evolution. Chenopodium (Amaranthaceae) is a globally distributed genus composed of approximately 50–75 species. The genus includes several polyploid species, some of which are considered noxious agricultural weeds, and a few are domesticated crops. Very little research has addressed their evolutionary origin to date. We construct a phylogeny for Chenopodium based on two introns of the single-copy nuclear locus Salt Overly Sensitive 1 ( SOS1 ) to clarify the relationships among the genomes of the allotetraploid and allohexaploid species, and to help identify their genome donors.  Methods: Diploid species were sequenced directly, whereas homeologous sequences of polyploid genomes were fi rst separated by plasmid-mediated cloning. Data were evaluated in maximum likelihood and Bayesian phylogenetic analyses.  Key results: Homeologous sequences of polyploid species were found in four clades, which we designate as A–D. Two distinct polyploid lineages were identifi ed: one composed of American tetraploid species with A and B class homeologs and a second composed of Eastern Hemisphere hexaploid species with B, C, and D class homeologs.  Conclusions: We infer that the two polyploid lineages arose independently and that each lineage may have originated only once. The American diploid, C. standleyanum , was identifi ed as the closest living diploid relative of the A genome donor for American tetraploids, including domesticated C. quinoa , and is of potential importance for quinoa breeding. The east Asian diploid species, C. bryoniifolium , groups with American diploid species, which suggests a transoceanic dispersal.

UNLABELLED • PREMISE OF THE STUDY Polyploidization frequently results in the creation of new plant species, the establishment of which is thought to often be facilitated by ecological niche differentiation from the diploid species. We tested this hypothesis using the cosmopolitan grass genus Phalaris (Poaceae), consisting of 19 species that range from diploid to tetraploid to hexaploid. Specifically, we tested whether (1) polyploids occupy more extreme environments and/or (2) have broader niche breadths and/or (3) whether the polyploid species' distributions indicate a niche shift from diploid species.• METHODS We employed a bootstrapping approach using distribution data for each species and eight environmental variables to investigate differences between species in the means, extremes, and breadths of each environmental variable. We used a kernel smoothing technique to quantify niche overlap between species.• KEY RESULTS Although we found some support for the three hypotheses for a few diploid-polyploid pairs and for specific environmental variables, none of these hypotheses were generally supported.• CONCLUSIONS Our results suggest that these commonly held hypotheses about the effects of polyploidization on ecological distributions are not universally applicable. Correlative biogeographic studies like ours provide a necessary first step for suggesting specific hypotheses that require experimental verification. A combination of genetic, physiological, and ecological studies will be required to achieve a better understanding of the role of polyploidization in niche evolution.

UNLABELLED • PREMISE OF THE STUDY Information about geographic distribution of cytotypes can provide insight into the origin and maintenance of autopolyploid complexes and builds a foundation for understanding cytotype differentiation and the dynamics of mixed-ploidy populations. Here, we investigate environmental correlates of the geographic distributions of 6x and 9x individuals in the ecologically dominant grass Andropogon gerardii to examine the role of climate in shaping patterns of cytotype distribution in this species.• METHODS Flow cytometry was used to estimate ploidy level in 352 individuals from 32 populations across North America. Ecological differentiation of cytotypes was tested by relating BIOCLIM variables to cytotype distribution using principal components analysis and partial linear regression.• KEY RESULTS Broad geographic sampling confirmed two primary cytotypes-6x (hexaploid) and 9x (enneaploid)-and revealed that 9x plants are more common than previously thought. Enneaploids occur frequently in the southern portions of the range, with hexaploids dominating in northern regions. Mixed-ploidy populations were common (46.9%). Principal components analysis and partial linear regression indicated that reduced summer precipitation and increased variation in diurnal and seasonal temperature range were significant predictors of the frequency of 9x plants in a population.• CONCLUSIONS Results indicate that (1) geographic distribution of 6x and 9x individuals is nonrandom; (2) environmental variables are associated with cytotype distribution in A. gerardii; and (3) nearly half of populations surveyed include both 6x and 9x individuals. The persistence of mixed-ploidy populations may reflect a combination of recurrent polyploid formation and the prevalence of clonal reproduction.

 Premise of the study: Polyploidy—the possession of more than two copies of each chromosome in the nucleus—is common in fl owering plants. Polyploid plants can occupy different geographic ranges than their diploid progenitors, but the factors responsible for maintaining these range differences are poorly understood. Polyploidy can have signifi cant physiological consequences, and the present study aims to determine whether previously described physiological differences between cytotypes are correlated with climatic niches and geographic distributions.  Methods: Prior research indicates that tetraploid plants of Chamerion angustifolium (Onagraceae) are more tolerant of drought and less tolerant of freezing than diploids, which suggests that they should occupy a niche that is warmer and drier than that of diploids. We extracted climate data for 134 populations of C. angustifolium classifi ed as pure diploid, pure tetraploid, or mixedploidy. We compared climatic conditions between these population categories and generated ecological niche models to compare their geographic distribution with prior qualitative estimates.  Key results: Pure tetraploid populations occupy habitats that are warmer and drier than those of pure diploid populations. Mixed-ploidy populations occur in habitats that are not strictly intermediate between pure diploid and pure tetraploid populations, but are as cold as pure diploid populations and have intermediate soil moisture defi cits. Our niche models were similar to previous qualitative estimates of cytotype geographic distribution.  Conclusions: The correspondence between the physiological tolerances of cytotypes, their climatic niches, and their geographic distributions suggests that physiological traits are at least partially responsible for differences in the realized climatic niches of diploid and tetraploid C. angustifolium .

PREMISE OF THE STUDY Interpreting relationships within groups containing polyploids, which are frequent in angiosperms, can be greatly assisted by genomic techniques. In this study, we used a genome-skimming approach to investigate the evolutionary relationships and origins of polyploids in the monophyletic group, Ludwigia section Macrocarpon (Onagraceae), which includes diploid, tetraploid, and hexaploid taxa. METHODS We sampled all known taxa and ploidy levels in the section and conducted shotgun sequencing. We assembled plastomes, mitochondrial sequences, and completed nuclear ribosomal regions, reconstructed phylogenies, and conducted comparative genomic analyses for plastomes to gain insights into the relationships among studied taxa. KEY RESULTS Within the section, results showed that the South American diploid taxa L. bonariensis and L. lagunae were closely related. We reported the first chromosome count (2n = 4× = 32) for L. neograndiflora, which is closely related to the two South American diploid taxa, although its exact origin remains unclear. The samples of the widespread, polyploid taxon L. octovalvis do not form a monophyletic group. Both tetraploid and hexaploid L. octovalvis lineages have originated more than once. At least one tetraploid in the L. octovalvis lineage may have been involved in the origins of hexaploids. One or more extinct/unsampled intermediate tetraploids in the L. octovalvis lineages had also likely been involved in the origins of hexaploids. CONCLUSIONS Genome skimming provided important insights into the complex evolutionary relationships within sect. Macrocarpon, but additional sampling and data from single-copy nuclear regions are necessary to further elucidate the origins of the polyploids in this section.

Premise of the studyDiatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and contributions to primary production motivate comparisons to flowering plants, whose genomes have been inordinately shaped by whole genome duplication (WGD). These events that have been linked to speciation and increased rates of lineage diversification, identifying WGDs as a principal driver of angiosperm evolution. We synthesized a relatively large but scattered body of evidence that, taken together, suggests that polyploidy may be common in diatoms.MethodsWe used data from gene counts, gene trees, and patterns of synonymous divergence to carry out the first large-scale phylogenomic analysis of genome-scale duplication histories for a phylogenetically diverse set of 37 diatom taxa.Key resultsSeveral methods identified WGD events of varying age across diatoms, though determining the exact number and placement of events and, more broadly, inferences of WGD at all, were greatly impacted by gene-tree uncertainty. Gene-tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with particularly strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.ConclusionsWhole genome duplication appears to have been an important driver of genome evolution in diatoms. Denser taxon sampling will better pinpoint the timing of WGDs and likely reveal many more of them. We outline potential challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the evolutionary roles of genome duplication in a group that likely harbors substantial genomic diversity.

UNLABELLED • PREMISE OF THE STUDY Amelanchier polyploid apomicts differ from sexual diploids in their more complex diversification, greater species problems, and geographic distribution. To understand these differences, we investigated the occurrence of polyploidy and frequency of apomixis. This research helps clarify species delimitation in an evolutionarily complex genus.• METHODS We used flow cytometry to estimate genome size of 1355 plants. We estimated the frequency of apomixis from flow-cytometrically determined ploidy levels of embryo and endosperm and from a progeny study using RAPD markers. We explored relationships of triploids to other ploidy levels and of ploidy levels to latitude plus elevation.• KEY RESULTS Diploids (32% of sample) and tetraploids (62%) were widespread. Triploids (6%) mostly occurred in small numbers with diploids from two or more species or with diploids and tetraploids. Seeds from diploids were 2% apomictic, the first report of apomixis in Amelanchier diploids. Seeds from triploids were 75% apomictic. We documented potential triploid bridge and triploid block from unbalanced endosperm and low pollen viability. Seeds from tetraploids were 97% apomictic, and tetraploids often formed microspecies. We did not find strong evidence for geographical parthenogenesis in North American Amelanchier. Most currently recognized species contained multiple ploidy levels that were morphologically semicryptic.• CONCLUSIONS Documentation of numerous transitions from diploidy to polyploidy helps clarify diversification, geographic distribution, and the species problem in Amelanchier. Despite the infrequent occurrence of triploids, their retention of 25% sexuality and capacity for triploid bridge may be important steps between sexual diploids and predominantly apomictic tetraploids.

• Premise of the study: Tropical regions have high species diversity, and polyploidization is a major mechanism of speciation in plants. However, few cases of natural polyploidy have been reported in tropical regions. Lippia alba, is a tropical, aromatic shrub with a wide distribution, extensive morphological plasticity, and several chemotypes. The species has long been recognized as a diploid with 2n = 30 chromosomes. Recently, two variations in chromosome number (2n = 60; 2n = 12-60) have been reported, suggesting the occurrence of polyploidy within the species.• Methods: Flow cytometry was used to investigate the genome size in 106 accessions from 14 Brazilian States. Conventional and molecular cytogenetic techniques and pollen viability analysis were employed to characterize each chromosome number observed.• Key results: The DNA 1C-value varied from 1.17 to 3.45 pg, showing a large variation in genome size. Five distinct chromosome numbers were observed (2n = 30, 38, 45, 60, 90); three are cytogenetically described here for the first time. The 5S rDNA signals varied proportionally according to each chromosome number, but 45S rDNA sites did not. High rates of meiotic irregularity were observed, mainly in cytotypes with higher chromosome numbers.• Conclusions: The data provide new support for the occurrence of a polyploid series in Lippia alba. We provide a hypothesis for how this complex may have arisen. Other cryptic polyploid complexes may remain undiscovered in tropical regions.

 Premise of the study: Dihaploids result when tetraploids produce reduced eggs that develop without fertilization into diploid progeny. This process is useful for reducing genome complexity and studying trait expression at different ploidal levels. In this study we evaluated genetic inheritance and expression of diplospory ( D ) and parthenogenesis ( P ) in a population of dihaploids produced by tetraploid apomictic Erigeron .  Methods: From 400 mostly maternal (tetraploid) progeny, we identifi ed 64 (16%) dihaploids with 2n = 18 (53 plants) or 2n = 19 (11 plants). Differential interference contrast (DIC) imaging of ovules was used to evaluate megasporogenesis (meiosis vs. diplospory) and capacity for parthenogenetic embryo development. Seed production was estimated as the proportion of fi seeds.  Key results: For 60 analyzed dihaploids, diplospory vs. meiosis segregated approximately 1: 1 ( P = 0.44) while all exhibited parthenogenetic embryo development. Parthenogenesis for meiotic progeny ( n = 27) was observed in approximately 50% of ovules. Apomictic dihaploids (combining D and P ; n = 33) produced seeds with mean 24.8% (range 1.3–74.4%) of total fl owers.  Conclusions: The dihaploid population consisted of half apomicts ( D + P ) and half parthenogens ( P only). We infer that formation of dihaploid seeds requires the parthenogenesis locus. The highest seed values obtained for diploid apomicts are comparable to those recorded for wild type polyploid apomicts. This is one of the fi rst reports of diploid apomixis in the Asteraceae and it demonstrates that both diplospory and parthenogenesis can be transmitted and expressed at a high level in the diploid condition.

• Premise of study: Polyploid plants, when compared with diploids, show similar molecular, morphological, physiological, and ecological tendencies across unrelated groups, but the degree to which these form “rules” of polyploid evolution are unclear. The Glycine (Leguminosae) allopolyploid complex affords the opportunity to test whether polyploidy in similar genetic backgrounds produces similar effects on geographical range or climatic space.• Methods: We used information on locality presence of four closely related Glycine allopolyploid species and their diploid progenitors to build models of the potentially available Australian ranges based on climate using Maxent3.3.3k. Principal coordinate analysis was used to characterize the multidimensional climate space occupied by each species.• Key results: Each of the four Glycine allopolyploids showed intermediacy in potential geographical space and in ecological space, relative to its diploid progenitors. The four allopolyploids did not have consistently larger ranges than their progenitors, though all four occupied a portion of climate niche space not available to its progenitors. The polyploids also differed in their exploitation of potentially available geographical range. Australian ranges and environmental space did not correlate with greater colonizing ability in these polyploids.• Conclusions: The four Glycine allopolyploids do not show many common range- or climate-related features, other than intermediacy. Thus, despite their similar genetic and evolutionary backgrounds, polyploidy has not produced convergent ecological effects.

Premise of the study Because seeds have essential functions in the life cycle of plants, even subtle changes in their characteristics may have important demographic consequences. In this study, we examined whether potential changes in seed characteristics as a result of polyploidy or postintroduction evolution may have contributed to the invasion of Centaurea stoebe (Asteraceae). This plant occurs as diploid and tetraploid cytotypes in its native range in Europe, whereas only tetraploids have been found and become invasive in North America. Specific comparisons among these three "geo-cytotypes" allow us to explore hypotheses of preadaptation resulting from polyploidy (European diploids vs. European tetraploids) and postintroduction evolution (European tetraploids vs. North American tetraploids). Methods Using seeds collected from plants of each geo-cytotype grown in a common maternal environment, we compared seed mass, morphology (achene and pappus size), dispersal potential (falling velocity, seed roughness), survival, germination, and seedling emergence in a combination of laboratory, greenhouse and field experiments. Key results We found increased seed mass in North American tetraploids compared with European tetraploids. Seed morphology and dispersal potential were largely similar in all geo-cytotypes. Seed survival under field conditions was higher in native and invasive tetraploids compared with diploids. Germination in the laboratory was similar among all geo-cytotypes, but seedling emergence under field conditions was higher in invasive tetraploids than in the other geo-cytotypes. Conclusions Our findings suggest that a combination of preadaptation due to polyploidy (increased seed survival) and further postintroduction evolution in North American tetraploids (increased seed mass and seedling emergence) may have contributed to their invasion.

 Premise of the study: Hybridization has played an important role in the evolution and ecological adaptation of diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identifi ed as A. tridentata subsp. wyomingensis or as autotetraploids of diploid subspecies tridentata and vaseyana . Few details are available as to how these tetraploids are formed or how they are related to diploid subspecies.  Methods: We used amplicon sequencing to assess phylogenetic relationships among three recognized subspecies: tridentata , vaseyana , and wyomingensis . DNA sequence data from putative genes were pyrosequenced and assembled from 329 samples. Nucleotide diversity and putative haplotypes were estimated from the high-read coverage. Phylogenies were constructed from Bayesian coalescence and neighbor-net network analyses.  Key results: Analyses support distinct diploid subspecies of tridentata and vaseyana in spite of known hybridization in ecotones. Nucleotide diversity estimates of populations compared to the total diversity indicate the relationships are predominately driven by a small proportion of the amplicons. Tetraploids, including subspecies wyomingensis , are polyphyletic occurring within and between diploid subspecies groups.  Conclusions: Artemisia tridentata is a species comprising phylogenetically distinct diploid progenitors and a tetraploid complex with varying degrees of phylogenetic and morphological affi nities to the diploid subspecies. These analyses suggest tetraploids are formed locally or regionally from diploid tridentata and vaseyana populations via autotetraploidy, followed by introgression between tetraploid groups. Understanding the phylogenetic vs. ecological relationships of A. tridentata subspecies will have bearing on how to restore these desert ecosystems.

 Premise of the study: Molecular studies have shown that multiple origins of polyploid taxa are the rule rather than the exception. To understand the distribution and ecology of polyploid species and the evolutionary signifi cance of polyploidy in general, it is important to delineate these independently derived lineages as accurately as possible. Although gene fl ow among polyploid lineages and backcrossing to their diploid parents often confound this process, such post origin gene fl ow is very infrequent in asexual polyploids. In this study, we estimate the number of independent origins of the apomictic allopolyploid fern Astrolepis integerrima , a morphologically heterogeneous species most common in the southwestern United States and Mexico, with outlying populations in the southeastern United States and the Caribbean.  Methods: Plastid DNA sequence and AFLP data were obtained from 33 A. integerrima individuals. Phylogenetic analysis of the sequence data and multidimensional clustering of the AFLP data were used to identify independently derived lineages.  Key results: Analysis of the two datasets identifi ed 10 genetic groups within the 33 analyzed samples. These groups suggest a minimum of 10 origins of A. integerrima in the northern portion of its range, with both putative parents functioning as maternal donors, both supplying unreduced gametes, and both contributing a signifi cant portion of their genetic diversity to the hybrids.  Conclusions: Our results highlight the extreme cryptic genetic diversity and systematic complexity that can underlie a single polyploid taxon.

Polyploidy is one of the major processes shaping angiosperm evolution (Wendel, 2000; Hegarty and Hiscock, 2007, 2008; Leitch and Leitch, 2008; Hufton and Panopoulou, 2009). This is evident from early whole-genome duplications in the ancestor of essentially all extant angiosperms (Wendel, 2000; Wolfe, 2001; Adams and Wendel, 2005a, b; De Bodt et al., 2005; Jiao et al., 2011) as well as from more recent poly ploidization events affecting most angiosperms (Masterson, 1994; Leitch and Bennett, 1997; Leitch and Leitch, 2008). Whereas autopolyploids originate from multiplication of the usually identical chromosome sets within a single (sub)species, allopolyploids derive from hybridization and multiplication of the usually differentiated chromosome sets coming from two or more progenitor (sub)species (Comai, 2005; Chen et al., 2007; Otto, 2007). Although the distinction between auto- and allopolyploids is difficult in polyploids exhibiting intermediate chromosome pairing behavior (expected polysomic inheritance in autopolyploids vs. disomic inheritance in allopolyploids; Ramsey and Schemske, 2002; Otto, 2007), both types are unambiguously known to occur frequently in nature (Tate et al., 2005; Soltis et al., 2007), where they often originate recurrently (Soltis et al., 2007; Dixon et al., 2009). Polyploidy plays an important role in race differentiation and eventually speciation. Polyploidization leads to an instantaneous increase in the amount of genetic material upon which evolution can work, potentially leading to the evolution of new functions in duplicated genes (neofunctionalization; Ohno, 1970; Wolfe, 2001; Liu and Wendel, 2002). Furthermore, polyploids often show accelerated genomic evolution expressed as a higher rate of chromosome structural rearrangements and associated pairing behavior in meiosis (Weiss and Maluszynska, 2000; Ramsey and Schemske, 2002; Otto, 2007; Schubert and Lysak, 2011), or genome size changes (Bennetzen and Kellogg, 1997; Bennetzen et al., 2005; Leitch and Leitch, 2008; Hawkins et al., 2008), contributing to the isolation of a polyploid from its lower-ploid ancestor(s). Finally, polyploidization contributes to stabilization of genomes after hybridization, a phenomenon common in plants (Anderson and Stebbins, 1954; Grant, 1981; Mallet, 2005, 2007; Rieseberg and Willis, 2007), by restoring regular meiotic pairing and fertility, thus creating crossing barriers with the parental taxa (allopolyploid speciation: Tate et al., 2005; Hegarty and Hiscock, 2007, 2008; Paun et al., 2009). A prerequisite for studying processes associated with the evolution of polyploid genomes is a sound knowledge of their origin. Molecular sequence data have proven particularly useful for identifying the parental lineages of allopolyploids. Although incongruence between gene trees obtained from plastid DNA (cpDNA; inherited maternally in Asteraceae; Corriveau and Coleman, 1988; Harris and Ingram, 1991), and nuclear DNA (inherited from both parents; Sang et al., 1997; Hughes et al., 2002; Kim et al., 2008) provides evidence for allopolyploidy, this approach is hampered by the often low variation in cpDNA sequences and by concerted evolution of the commonly used nuclear ribosomal internal transcribed spacer (nrITS) region (alvarez and Wendel, 2003). In low-copy nuclear genes, analyses of individual gene copies stemming from the maternal and paternal lineages can be recovered, rendering these genes a powerful and successful tool for inferring the origin of allo polyploids (Ferguson and Sang, 2001; Sang, 2002; Small et al., 2004; Lihova et al., 2006; Fortune et al., 2007; Kim et al., 2008; Shimizu-Inatsugi et al., 2009; Weiss-Schneeweiss et al., 2012). A well-suited group for studying polyploid evolution is the white-rayed complex of Melampodium sect Melampodium ser. Leucantha (Asteraceae; Stuessy, 1972). Characterized by white instead of yellow or orange ray florets, it is a phylogenetically distinct group (Bloch et al., 2009) comprising three xerophytic subshrub species (M. argophyllum, M. cinereum, M. leucanthum) distributed in the arid regions of northern Mexico and the southwestern United States (Fig. 1; Stuessy, 1972; Stuessy et al., 2004). Like the entire sect. Melampodium, species of ser. Leucantha have a basic chromosome number of x = 10 (Weiss-Schneeweiss et al., 2009). The widespread M. cinereum and M. leucanthum comprise both diploid and tetraploid cytotypes (Fig. 1). These originated recurrently via autopolyploidy, as suggested by chromosomal studies and genetic data (Turner and King, 1964; Stuessy et al., 2004; Rebernig et al., 2010a, b). The third species of the complex is the hexaploid M. argophyllum (Stuessy, 1972; Stuessy et al., 2004), restricted to northeastern Mexico (Fig. 1). It shares morphological features with the two other species and has thus been hypothesized to be of allopolyploid origin involving M. cinereum and M. leucanthum (Stuessy et al., 2004). Thus, ser. Leucantha provides an excellent system to compare the type and extent of genomic changes in closely related polyploids with contrasting evolutionary histories. Fig. 1 Distribution map of the analyzed populations of the white-rayed complex of Melampodium. Here, we used molecular sequence (plastid and nuclear DNA, including a low-copy gene), fingerprint (AFLPs), and restriction data in conjunction with karyological, and genome size data to investigate the origin and evolution of ser. Leucantha with special emphasis on M. argophyllum. Specifically, we wanted to (1) infer phylogenetic relationships among M. argophyllum, M. cinereum, and M. leucanthum, in particular to test the hypothesis of an allopolyploid origin for M. argophyllum; and (2) compare karyotype structure, genome size, and rDNA loci number and localization in polyploids of presumably different ages and modes of origin (recent auto- vs. ancient allopolyploidy).

Polyploidy is a common mode of speciation that can have far-reaching consequences for plant ecology and evolution. Because polyploidy can induce an array of phenotypic changes, there can be cascading effects on interactions with other species. These interactions, in turn, can have reciprocal effects on polyploid plants, potentially impacting their establishment and persistence. Although there is a wealth of information on the genetic and phenotypic effects of polyploidy, the study of species interactions in polyploid plants remains a comparatively young field. Here we reviewed the available evidence for how polyploidy may impact many types of species interactions that range from mutualism to antagonism. Specifically, we focused on three main questions: (1) Does polyploidy directly cause the formation of novel interactions not experienced by diploids, or does it create an opportunity for natural selection to then form novel interactions? (2) Does polyploidy cause consistent, predictable changes in species interactions vs. the evolution of idiosyncratic differences? (3) Does polyploidy lead to greater evolvability in species interactions? From the scarce evidence available, we found that novel interactions are rare but that polyploidy can induce changes in pollinator, herbivore, and pathogen interactions. Although further tests are needed, it is likely that selection following whole-genome duplication is important in all types of species interaction and that there are circumstances in which polyploidy can enhance the evolvability of interactions with other species.