Plant polyploidy and non-uniform effects on insect herbivores

Neopolyploidy-induced changes in giant duckweed (Spirodela polyrhiza) alter herbivore preference and performance and plant population performance

PREMISE

Polyploidy is a widespread mutational process in angiosperms that may alter population performance of not only plants but also their interacting species. Yet, knowledge of whether polyploidy affects plant-herbivore dynamics is scarce. Here, we tested whether aphid herbivores exhibit preference for diploid or neopolyploid plants, whether polyploidy impacts plant and herbivore performance, and whether these interactions depend on the plant genetic background.

METHODS

Using independently synthesized neotetraploid strains paired with their diploid progenitors of greater duckweed (Spirodela polyrhiza), we evaluated the effect of neopolyploidy on duckweed's interaction with the water-lily aphid (Rhopalosiphum nymphaeae). Using paired-choice experiments, we evaluated feeding preference of the herbivore. We then evaluated the consequences of polyploidy on aphid and plant performance by measuring population growth over multiple generations.

RESULTS

Aphids preferred neopolyploids when plants were provided at equal abundances but not at equal surface areas, suggesting the role of plant population surface area in driving this preference. Additionally, neopolyploidy increased aphid population performance, but this result was dependent on the plant's genetic lineage. Lastly, the impact of herbivory on neopolyploid vs. diploid duckweed varied greatly with genetic lineage, where neopolyploids appeared to be variably tolerant compared to diploids, sometimes mirroring the effect on herbivore performance.

CONCLUSIONS

By experimentally testing the impacts of polyploidy on trophic species interactions, we showed that polyploidization can impact the preference and performance of herbivores on their plant hosts. These results have significant implications for the establishment and persistence of plants and herbivores in the face of plant polyploidy.

Evaluating global Vaccinium germplasm for resistance against invasive Drosophila suzukii (Diptera: Drosophilidae)

Control of spotted-wing Drosophila, Drosophila suzukii, in small fruits emphasizes biological, cultural, and chemical approaches, whereas studies of host plant resistance as a form of genetic control are just getting underway. The identification of resistance patterns among genotypes of host plants whose fruit, leaves, roots, stems, or seeds are specifically targeted by an invasive pest is the first step in the development of an effective genetic control. Therefore, a detached fruit bioassay was developed to screen for D. suzukii oviposition and larval infestation within berries from 25 representative species and hybrids of wild and cultivated Vaccinium. Ten Vaccinium species showed strong resistance; among them, two wild diploids originating from within the fly's native range: V. myrtoides and V. bracteatum. Other resistant species came from the sections Pyxothamnus and Conchophyllum. They included New World V. consanguineum and V. floribundum. Large-cluster blueberry, V. amoenum, and three Floridian genotypes of related rabbiteye blueberry, V. virgatum, were the only hexaploids expressing strong resistance against D. suzukii. Most screened blueberry genotypes from managed lowbush and cultivated highbush types were susceptible to the flies' attacks (i.e., oviposition). Tetraploid blueberries tended to host the most eggs, whereas diploids and hexaploids harbored 50%-60% fewer eggs, on average. D. suzukii cannot lay eggs or complete development in the smallest, sweetest, and firmest diploid fruits. Likewise, certain genotypes of large-fruited tetraploid and hexaploid blueberry strongly curbed D. suzukii egg-laying and larval growth, indicating the possibility of heritable resistance operating against this invasive fly species.

Cytogenetics and Consequences of Polyploidization on Different Biotic-Abiotic Stress Tolerance and the Potential Mechanisms Involved

The application of polyploidy in sustainable agriculture has already brought much appreciation among researchers. Polyploidy may occur naturally or can be induced in the laboratory using chemical or gaseous agents and results in complete chromosome nondisjunction. This comprehensive review described the potential of polyploidization on plants, especially its role in crop improvement for enhanced production and host-plant resistance development against pests and diseases. An in-depth investigation on techniques used in the induction of polyploidy, cytogenetic evaluation methods of different ploidy levels, application, and current research trends is also presented. Ongoing research has mainly aimed to bring the recurrence in polyploidy, which is usually detected by flow cytometry, chromosome counting, and cytogenetic techniques such as fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH). Polyploidy can bring about positive consequences in the growth and yield attributes of crops, making them more tolerant to abiotic and biotic stresses. However, the unexpected change in chromosome set and lack of knowledge on the mechanism of stress alleviation is hindering the application of polyploidy on a large scale. Moreover, a lack of cost-benefit analysis and knowledge gaps on the socio-economic implication are predominant. Further research on polyploidy coupling with modern genomic technologies will help to bring real-world market prospects in the era of changing climate. This review on polyploidy provides a solid foundation to do next-generation research on crop improvement.

Impact of polyploidy on plant tolerance to abiotic and biotic stresses

Polyploidy, defined as the coexistence of three or more complete sets of chromosomes in an organism's cells, is considered as a pivotal moving force in the evolutionary history of vascular plants and has played a major role in the domestication of several crops. In the last decades, improved cultivars of economically important species have been developed artificially by inducing autopolyploidy with chemical agents. Studies on diverse species have shown that the anatomical and physiological changes generated by either natural or artificial polyploidization can increase tolerance to abiotic and biotic stresses as well as disease resistance, which may positively impact on plant growth and net production. The aim of this work is to review the current literature regarding the link between plant ploidy level and tolerance to abiotic and biotic stressors, with an emphasis on the physiological and molecular mechanisms responsible for these effects, as well as their impact on the growth and development of both natural and artificially generated polyploids, during exposure to adverse environmental conditions. We focused on the analysis of those types of stressors in which more progress has been made in the knowledge of the putative morpho-physiological and/or molecular mechanisms involved, revealing both the factors in common, as well as those that need to be addressed in future research.

Pollinator assemblage and pollen load differences on sympatric diploid and tetraploid cytotypes of the desert-dominant Larrea tridentata

PREMISE

Whole-genome duplication (polyploidy) is an important force shaping flowering-plant evolution. Ploidy-specific plant-pollinator interactions represent important community-level biotic interactions that can lead to nonrandom mating and the persistence of mixed-ploidy populations.

METHODS

At a naturally occurring diploid-tetraploid contact zone of the autopolyploid desert shrub Larrea tridentata, we combined flower phenology analyses, collections of bees on plants of known cytotype, and flow cytometry analyses of bee-collected pollen loads to investigate whether (1) diploid and tetraploid plants have unique bee pollinator assemblages, (2) bee taxa exhibit ploidy-specific visitation and pollen collection biases, and (3) specialist and generalist bee taxa have ploidy-specific visitation and pollen collection biases.

RESULTS

Although bee assemblages overlapped, we found significant differences in bee visitation to co-occurring diploids and tetraploids, with the introduced honeybee (Apis mellifera) and one native species (Andrena species 12) more frequently visiting tetraploids. Consistent with bee assemblage differences, we found that diploid pollen was overrepresented among pollen loads on native bees, while pollen loads on A. mellifera did not deviate from the random expectation. However, mismatches between the ploidy of pollen loads and plants were common, consistent with ongoing intercytotype gene flow.

CONCLUSIONS

Our data are consistent with cytotype-specific bee visitation and suggest that pollinator behavior contributes to reduced diploid-tetraploid mating. Differences in bee visitation and pollen movement potentially contribute to an easing of minority cytotype exclusion and the facilitation of cytotype co-occurrence.

Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.

Impact of genome duplication on secondary metabolite composition in non-cultivated species: a systematic meta-analysis

BACKGROUND AND AIMS

Whole-genome duplication is known to influence ecological interactions and plant physiology; however, despite abundant case studies, much is still unknown about the typical impact of genome duplication on plant secondary metabolites (PSMs). In this study, we assessed the impact of polyploidy events on PSM characteristics in non-cultivated plants.

METHODS

We conducted a systematic review and meta-analysis to compare composition and concentration of PSMs among closely related plant species or species complexes differing in ploidy level.

KEY RESULTS

We assessed 53 studies that focus on PSMs among multiple cytotypes, of which only 14 studies compared concentration quantitatively among cytotypes. We found that whole-genome duplication can have a significant effect on PSM concentration; however, these effects are highly inconsistent.

CONCLUSION

Overall, there was no consistent effect of whole-genome duplication on PSM concentrations or profiles.

Analysis of small RNA changes in different Brassica napus synthetic allopolyploids

Allopolyploidy is an evolutionary and mechanisticaly intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the small RNA changes of eight F2 synthetic B. napus using small RNA sequencing. We found that a part of miRNAs and siRNAs were non-additively expressed in the synthesized B. napus allotetraploid. Differentially expressed miRNAs and siRNAs differed among eight F2 individuals, and the differential expression of miR159 and miR172 was consistent with that of flowering time trait. The GO enrichment analysis of differential expression miRNA target genes found that most of them were concentrated in ATP-related pathways, which might be a potential regulatory process contributing to heterosis. In addition, the number of siRNAs present in the offspring was significantly higher than that of the parent, and the number of high parents was significantly higher than the number of low parents. The results have shown that the differential expression of miRNA lays the foundation for explaining the trait separation phenomenon, and the significant increase of siRNA alleviates the shock of the newly synthesized allopolyploidy. It provides a new perspective between small RNA changes and trait separation in the early stages of allopolyploid polyploid formation.

Impacts of soil nitrogen and phosphorus levels on cytotype performance of the circumboreal herb Chamerion angustifolium: implications for polyploid establishment

PREMISE

Although polyploidy commonly occurs in angiosperms, not all polyploidization events lead to successful lineages, and environmental conditions could influence cytotype dynamics and polyploid success. Low soil nitrogen and/or phosphorus concentrations often limit ecosystem primary productivity, and changes in these nutrients might differentially favor some cytotypes over others, thereby influencing polyploid establishment.

METHODS

We grew diploid, established tetraploid, and neotetraploid Chamerion angustifolium (fireweed) in a greenhouse under low and high soil nitrogen and phosphorus conditions and different competition treatments and measured plant performance (height, biomass, flower production, and root bud production) and insect damage responses. By comparing neotetraploids to established tetraploids, we were able to examine traits and responses that might directly arise from polyploidization before they are modified by natural selection and/or genetic drift.

RESULTS

We found that (1) neopolyploids were the least likely to survive and flower and experienced the most herbivore damage, regardless of nutrient conditions; (2) both neo- and established tetraploids had greater biomass and root bud production under nutrient-enriched conditions, whereas diploid biomass and root bud production was not significantly affected by nutrients; and (3) intra-cytotype competition more negatively affected diploids and established tetraploids than it did neotetraploids.

CONCLUSIONS

Following polyploidization, biomass and clonal growth might be more immediately affected by environmental nutrient availabilities than plant survival, flowering, and/or responses to herbivory, which could influence competitive dynamics. Specifically, polyploids might have competitive and colonizing advantages over diploids under nutrient-enriched conditions favoring their establishment, although establishment may also depend upon the density and occurrences of other related cytotypes in a population.

Polyploidy in creosote bush (Larrea tridentata) shapes the biogeography of specialist herbivores

AIM

Whole-genome duplication (polyploidy) can influence the biogeography and ecology of plants that differ in ploidy level (cytotype). Here, we address how two consequences of plant polyploidy (parapatry of cytotypes and altered species interactions) shape the biogeography of herbivorous insects.

LOCATION

Warm deserts of North America.

TAXA

Gall midges (Asphondylia auripila group, Diptera: Cecidomyiidae) that attack three parapatric cytotypes of creosote bush (Larrea tridentata, Zygophyllaceae).

METHODS

We surveyed Asphondylia species diversity at 177 sites across a 2300-km extent. After noting a correspondence between the distributions of eight Asphondylia species and L. tridentata cytotypes, we fine-mapped Asphondylia species range limits with transects spanning cytotype contact zones. We then tested whether plant-insect interactions and/or abiotic factors explain this coincidence by (1) comparing attack rates and gall midge communities on alternative cytotypes in a narrow zone of sympatry and (2) using species distribution models (SDMs) to determine if climatically suitable habitat for each midge species extended beyond cytotype contact zones.

RESULTS

The range limits of 6/17 Asphondylia species (including two novel putative species confirmed with COI sequencing) perfectly coincided with the contact zone of diploid and tetraploid L. tridentata. One midge species was restricted to diploid host plants while five were restricted to tetraploid and hexaploid host plants. Where diploid and tetraploid L. tridentata are sympatric, cytotype-restricted midge species more frequently attacked their typical host and Asphondylia community structure differed markedly between cytotypes. SDMs predicted that distributions of cytotype-restricted midge species were not constrained by climatic conditions near cytotype contact zones.

MAIN CONCLUSIONS

Contact zones between plant cytotypes are dispersal barriers for many Asphondylia species due to plant-insect interactions. The distribution of L. tridentata cytotypes therefore shapes herbivore species ranges and herbivore community structure across North American deserts. Our results demonstrate that polyploidy in plants can affect the biogeography of ecological communities.

Effects of soil nitrogen on diploid advantage in fireweed, Chamerion angustifolium (Onagraceae)

In many ecosystems, plant growth and reproduction are nitrogen limited. Current and predicted increases of global reactive nitrogen could alter the ecological and evolutionary trajectories of plant populations. Nitrogen is a major component of nucleic acids and cell structures, and it has been predicted that organisms with larger genomes should require more nitrogen for growth and reproduction and be more negatively affected by nitrogen scarcities than organisms with smaller genomes. In a greenhouse experiment, we tested this hypothesis by examining whether the amount of soil nitrogen supplied differentially influenced the performance (fitness, growth, and resource allocation strategies) of diploid and autotetraploid fireweed (Chamerion angustifolium). We found that soil nitrogen levels differentially impacted cytotype performance, and in general, diploids were favored under low nitrogen conditions, but this diploid advantage disappeared under nitrogen enrichment. Specifically, when nitrogen was scarce, diploids produced more seeds and allocated more biomass toward seed production relative to investment in plant biomass or total plant nitrogen than did tetraploids. As nitrogen supplied increased, such discrepancies between cytotypes disappeared. We also found that cytotype resource allocation strategies were differentially dependent on soil nitrogen, and that whereas diploids adopted resource allocation strategies that favored current season reproduction when nitrogen was limiting and future reproduction when nitrogen was more plentiful, tetraploids adopted resource allocation strategies that favored current season reproduction under nitrogen enrichment. Together these results suggest nitrogen enrichment could differentially affect cytotype performance, which could have implications for cytotypes' ecological and evolutionary dynamics under a globally changing climate.

Evolutionary dynamics of mixed-ploidy populations in an annual herb: dispersal, local persistence and recurrent origins of polyploids

Background and Aims

Despite the recent wealth of studies targeted at contact zones of cytotypes in various species, some aspects of polyploid evolution are still poorly understood. This is especially the case for the frequency and success rate of spontaneous neopolyploidization or the temporal dynamics of ploidy coexistence, requiring massive ploidy screening and repeated observations, respectively. To fill this gap, an extensive study of spatio-temporal patterns of ploidy coexistence was initiated in the widespread annual weed Tripleurospermum inodorum (Asteraceae).

Methods

DNA flow cytometry along with confirmatory chromosome counts was employed to assess ploidy levels of 11 018 adult individuals and 1263 ex situ germinated seedlings from 1209 Central European populations. The ploidy screening was conducted across three spatial scales and supplemented with observations of temporal development of 37 mixed-ploidy populations.

Key Results

The contact zone between the diploid and tetraploid cytotypes has a diffuse, mosaic-like structure enabling common cytotype coexistence from the within-population to the landscape level. A marked difference in monoploid genome size between the two cytotypes enabled the easy distinction of neotetraploid mutants from long-established tetraploids. Neotetraploids were extremely rare (0·03 %) and occurred solitarily. Altogether five ploidy levels (2 x -6 x ) and several aneuploids were discovered; the diversity in nuclear DNA content was highest in early ontogenetic stages (seedlings) and among individuals from mixed-ploidy populations. In spite of profound temporal oscillations in cytotype frequencies in mixed-ploidy populations, both diploids and tetraploids usually persisted up to the last census.

Conclusions

Diploids and tetraploids commonly coexist at all spatial scales and exhibit considerable temporal stability in local ploidy mixtures. Mixed-ploidy populations containing fertile triploid hybrids probaby act as effective generators of cytogenetic novelty and may facilitate inter-ploidy gene flow. Neopolyploid mutants were incapable of local establishment.

The effects of genome duplications in a community context

Contents 57 I. 57 II. 59 III. 59 IV. 63 V. 64 VI. 64 VII. 66 66 References 66 SUMMARY: Whole-genome duplication (WGD), or polyploidy, has important effects on the genotype and phenotype of plants, potentially altering ecological interactions with other organisms. Even though the connections between polyploidy and species interactions have been recognized for some time, we are only just beginning to test whether WGD affects community context. Here I review the sparse information on polyploidy and community context and then present a set of hypotheses for future work. Thus far, community-level studies of polyploids suggest an array of outcomes, from no changes in community context to shifts in the abundance and composition of interacting species. I propose a number of mechanisms for how WGD could alter community context and how the emergence of polyploids in populations could also alter the community context of parental diploids and other plant species. Resolving how and when these changes are expected to occur will require a deeper understanding of the connections among WGD, phenotypic changes, and the direct and indirect effects of species interactions.

Differential transcript profiling alters regulatory gene expression during the development of Gossypium arboreum, G.stocksii and somatic hybrids

Polyploidy or genome doubling (i.e., the presence of two or more diploid parental genome sets within an organism) are very important in higher plants. Of particular interest are the mechanisms in the new microenvironment of the common nucleus, where doubled regulatory networks interact to generate a viable genetic system capable of regulating growth, development and responses to the environment. To determine the effects of whole genome merging and doubling on the global gene expression architecture of a new polyploid, derived from protoplast fusion of the A₁A₁ genome of Gossypium arboreum and the E₁E₁ genome of Gossypium stocksii, we monitored gene expression through cDNA-AFLP in the somatic hybrids (G. arboreum + G. stocksii). The genomic expression patterns of the somatic hybrids revealed that changes in expression levels mainly involved regulatory genes (31.8% of the gene expression profiles), and the AA and EE genomes contributed equally to genome-wide expression in the newly formed AAEE genome from additivity and dominance effects. These results provide a novel perspective on polyploid gene regulation and hint at the underlying genetic basis of allopolyploid adaption in the new microenvironmental nucleus.

Diversification of Trait Combinations in Coevolving Plant and Insect Lineages

Closely related species often have similar traits and sometimes interact with the same species. A crucial problem in evolutionary ecology is therefore to understand how coevolving species diverge when they interact with a set of closely related species from another lineage rather than with a single species. We evaluated geographic differences in the floral morphology of all woodland star plant species (Lithophragma, Saxifragaceae) that are pollinated by Greya (Prodoxidae) moths. Flowers of each woodland star species differed depending on whether plants interact locally with one, two, or no pollinating moth species. Plants of one species grown in six different environments showed few differences in floral traits, suggesting that the geographic differences are not due significantly to trait plasticity. Greya moth populations also showed significant geographic divergence in morphology, depending on the local host and on whether the moth species co-occurred locally. Divergence in the plants and the moths involved shifts in combinations of partially correlated traits, rather than any one trait. The results indicate that the geographic mosaic of coevolution can be amplified as coevolving lineages diversify into separate species and come together in different combinations in different ecosystems.

Contrasting effects of ploidy level on seed production in a diploid tetraploid system

Previous studies demonstrated the effects of polyploidy on various aspects of plant life. It is, however, difficult to determine which plant characteristics are responsible for fitness differences between cytotypes. We assessed the relationship between polyploidy and seed production. To separate the effects of flowering phenology, flower head size and herbivores from other possible causes, we collected data on these characteristics in single flower heads of diploid and tetraploid Centaurea phrygia in an experimental garden. We used structural equation modelling to identify the main pathways determining seed production. The results showed that the relationship between polyploidy and seed production is mediated by most of the studied factors. The different factors acted in opposing directions. Wider flower heads displayed higher above the ground suggested higher seed production in diploids. In contrast, earlier flowering and a lower abundance of herbivores suggested higher seed production in tetraploids. However, because phenology was the strongest driver of seed production in this system, the sum of all the pathways suggested greater seed production in tetraploids than in diploids. The pathway linking ploidy level directly to seed production, representing unstudied factors, was not significant. This suggests that the factors studied likely are drivers of the between-cytotype differences. Overall, this study demonstrated that tetraploids possess overall higher fitness estimated as seed production. Regardless of the patterns observed here, strong between year fluctuations in the composition and diversity of insect communities have been observed. The direction of the selection may thus vary between years. Consequently, understanding the structure of the interactions is more important for understanding the system than the overall effects of cytotype on a fitness trait in a specific year. Such knowledge can be used to model the evolution of species traits and plant-herbivore and plant-pollinator interactions in diploid-polyploid systems.

Enhanced rhizobial symbiotic capacity in an allopolyploid species of Glycine (Leguminosae)

PREMISE OF THE STUDY

Previous studies have shown that polyploidy can alter biotic interactions, and it has been suggested that these effects may contribute to the increased ability for colonization of new habitats shown by many allopolyploids. Little is known, however, about the effects of allopolyploidy, which combines hybridity and genome doubling, on symbiotic interactions with rhizobial bacteria.

METHODS

We examined interactions of the allopolyploid Glycine dolichocarpa (designated T2) with novel rhizobial partners, such as might occur in a context of colonization, and compared these with the responses of its diploid progenitors, G. tomentella (D3) and G. syndetika (D4). We assessed root hair response, nodule formation, nodule mass, nodule number, and plant biomass.

KEY RESULTS

The allopolyploid (T2) showed a greater root hair deformation response when exposed to rhizobia, compared with either diploid. T2 had a greater probability of forming nodules with NGR234 compared with diploid D4, and greater total nodule mass per nodulated plant compared with diploid D3. T2 also had greater plant biomass responses to nitrogen and when exposed to NGR234.

CONCLUSIONS

The allopolyploid is characterized by transgressive responses to rhizobia for some variables, while also combining certain parental diploid responses such that its capacity for interactions with rhizobia appears to be greater than for either diploid progenitor. This overall enhanced nodulation capacity and the ability to make greater gains from exposure to both rhizobia and additional nitrogen indicate a greater potential of the allopolyploid to benefit from these factors both generally and in a context of colonization.

Species interactions and plant polyploidy

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.

Polyploidy: Pitfalls and paths to a paradigm

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.

Can enemy release explain the invasion success of the diploid Leucanthemum vulgare in North America?

Enemy release is a commonly accepted mechanism to explain plant invasions. Both the diploid Leucanthemum vulgare and the morphologically very similar tetraploid Leucanthemum ircutianum have been introduced into North America. To verify which species is more prevalent in North America we sampled 98 Leucanthemum populations and determined their ploidy level. Although polyploidy has repeatedly been proposed to be associated with increased invasiveness in plants, only two of the populations surveyed in North America were the tetraploid L. ircutianum. We tested the enemy release hypothesis by first comparing 20 populations of L. vulgare and 27 populations of L. ircutianum in their native range in Europe, and then comparing the European L. vulgare populations with 31 L. vulgare populations sampled in North America. Characteristics of the site and associated vegetation, plant performance and invertebrate herbivory were recorded. In Europe, plant height and density of the two species were similar but L. vulgare produced more flower heads than L. ircutianum. Leucanthemum vulgare in North America was 17 % taller, produced twice as many flower heads and grew much denser compared to L. vulgare in Europe. Attack rates by root- and leaf-feeding herbivores on L. vulgare in Europe (34 and 75 %) was comparable to that on L. ircutianum (26 and 71 %) but higher than that on L. vulgare in North America (10 and 3 %). However, herbivore load and leaf damage were low in Europe. Cover and height of the co-occurring vegetation was higher in L. vulgare populations in the native than in the introduced range, suggesting that a shift in plant competition may more easily explain the invasion success of L. vulgare than escape from herbivory.

Butterfly oviposition preference is not related to larval performance on a polyploid herb

The preference–performance hypothesis predicts that female insects maximize their fitness by utilizing host plants which are associated with high larval performance. Still, studies with several insect species have failed to find a positive correlation between oviposition preference and larval performance. In the present study, we experimentally investigated the relationship between oviposition preferences and larval performance in the butterfly Anthocharis cardamines. Preferences were assessed using both cage experiments and field data on the proportion of host plant individuals utilized in natural populations. Larval performance was experimentally investigated using larvae descending from 419 oviposition events by 21 females on plants from 51 populations of two ploidy types of the perennial herb Cardamine pratensis. Neither ploidy type nor population identity influenced egg survival or larval development, but increased plant inflorescence size resulted in a larger final larval size. There was no correlation between female oviposition preference and egg survival or larval development under controlled conditions. Moreover, variation in larval performance among populations under controlled conditions was not correlated with the proportion of host plants utilized in the field. Lastly, first instar larvae added to plants rejected for oviposition by butterfly females during the preference experiment performed equally well as larvae growing on plants chosen for oviposition. The lack of a correlation between larval performance and oviposition preference for A. cardamines under both experimental and natural settings suggests that female host choice does not maximize the fitness of the individual offspring.

Copy number variation and genetic diversity of MHC Class IIb alleles in an alien population of Xenopus laevis

Xenopus laevis (the African clawed frog), which originated through hybridisation and whole genome duplication, has been used as a model for genetics and development for many years, but surprisingly little is known about immune gene variation in natural populations. The purpose of this study was to use an isolated population of X. laevis that was introduced to Wales, UK in the past 50 years to investigate how variation at the MHC compares to that at other loci, following a severe population bottleneck. Among 18 individuals, we found nine alleles based on exon 2 sequences of the Class IIb region (which includes the peptide binding region). Individuals carried from one to three of the loci identified from previous laboratory studies. Genetic variation was an order of magnitude higher at the MHC compared with three single-copy nuclear genes, but all loci showed high levels of heterozygosity and nucleotide diversity and there was not an excess of homozygosity or decrease in diversity over time that would suggest extensive inbreeding in the introduced population. Tajima’s D was positive for all loci, which is consistent with a bottleneck. Moreover, comparison with published sequences identified the source of the introduced population as the Western Cape region of South Africa, where most commercial suppliers have obtained their stocks. These factors suggest that despite founding by potentially already inbred individuals, the alien population in Wales has maintained substantial genetic variation at both adaptively important and neutral genes.

Are tetraploids more successful? Floral signals, reproductive success and floral isolation in mixed-ploidy populations of a terrestrial orchid

BACKGROUND AND AIMS

Polyploidization, the doubling of chromosome sets, is common in angiosperms and has a range of evolutionary consequences. Newly formed polyploid lineages are reproductively isolated from their diploid progenitors due to triploid sterility, but also prone to extinction because compatible mating partners are rare. Models have suggested that assortative mating and increased reproductive fitness play a key role in the successful establishment and persistence of polyploids. However, little is known about these factors in natural mixed-ploidy populations. This study investigated floral traits that can affect pollinator attraction and efficiency, as well as reproductive success in diploid and tetraploid Gymnadenia conopsea (Orchidaceae) plants in two natural, mixed-ploidy populations.

METHODS

Ploidy levels were determined using flow cytometry, and flowering phenology and herbivory were also assessed. Reproductive success was determined by counting fruits and viable seeds of marked plants. Pollinator-mediated floral isolation was measured using experimental arrays, with pollen flow tracked by means of staining pollinia with histological dye.

KEY RESULTS

Tetraploids had larger floral displays and different floral scent bouquets than diploids, but cytotypes differed only slightly in floral colour. Significant floral isolation was found between the two cytotypes. Flowering phenology of the two cytotypes greatly overlapped, and herbivory did not differ between cytotypes or was lower in tetraploids. In addition, tetraploids had higher reproductive success compared with diploids.

CONCLUSIONS

The results suggest that floral isolation and increased reproductive success of polyploids may help to explain their successful persistence in mixed-ploidy populations. These factors might even initiate transformation of populations from pure diploid to pure tetraploid.

Ecological studies of polyploidy in the 100 years following its discovery

Polyploidy is a mutation with profound phenotypic consequences and thus hypothesized to have transformative effects in plant ecology. This is most often considered in the context of geographical and environmental distributions-as achieved from divergence of physiological and life-history traits-but may also include species interactions and biological invasion. This paper presents a historical overview of hypotheses and empirical data regarding the ecology of polyploids. Early researchers of polyploidy (1910 s-1930 s) were geneticists by training but nonetheless savvy to its phenotypic effects, and speculated on the importance of genome duplication to adaptation and crop improvement. Cytogenetic studies in the 1930 s-1950 s indicated that polyploids are larger (sturdier foliage, thicker stems and taller stature) than diploids while cytogeographic surveys suggested that polyploids and diploids have allopatric or parapatric distributions. Although autopolyploidy was initially regarded as common, influential writings by North American botanists in the 1940 s and 1950 s argued for the principle role of allopolyploidy; according to this view, genome duplication was significant for providing a broader canvas for hybridization rather than for its phenotypic effects per se. The emphasis on allopolyploidy had a chilling effect on nascent ecological work, in part due to taxonomic challenges posed by interspecific hybridization. Nonetheless, biosystematic efforts over the next few decades (1950s-1970s) laid the foundation for ecological research by documenting cytotype distributions and identifying phenotypic correlates of polyploidy. Rigorous investigation of polyploid ecology was achieved in the 1980s and 1990 s by population biologists who leveraged flow cytometry for comparative work in autopolyploid complexes. These efforts revealed multi-faceted ecological and phenotypic differences, some of which may be direct consequences of genome duplication. Several classical hypotheses about the ecology of polyploids remain untested, however, and allopolyploidy--regarded by most botanists as the primary mode of genome duplication--is largely unstudied in an ecological context.

The causes and molecular consequences of polyploidy in flowering plants

Polyploidy is an important force shaping plant genomes. All flowering plants are descendants of an ancestral polyploid species, and up to 70% of extant vascular plant species are believed to be recent polyploids. Over the past century, a significant body of knowledge has accumulated regarding the prevalence and ecology of polyploid plants. In this review, we summarize our current understanding of the causes and molecular consequences of polyploidization in angiosperms. We also provide a discussion on the relationships between polyploidy and adaptation and suggest areas where further research may provide a better understanding of polyploidy.

Is more better? Polyploidy and parasite resistance

Ploidy-level variation is common and can drastically affect organismal fitness. We focus on the potential consequences of this variation for parasite resistance. First, we elucidate connections between ploidy variation and key factors determining resistance, including allelic diversity, gene expression and physiological condition. We then argue that systems featuring both natural and artificially manipulated ploidy variation should be used to evaluate whether ploidy level influences host-parasite interactions.

The more the better? The role of polyploidy in facilitating plant invasions

BACKGROUND

Biological invasions are a major ecological and socio-economic problem in many parts of the world. Despite an explosion of research in recent decades, much remains to be understood about why some species become invasive whereas others do not. Recently, polyploidy (whole genome duplication) has been proposed as an important determinant of invasiveness in plants. Genome duplication has played a major role in plant evolution and can drastically alter a plant's genetic make-up, morphology, physiology and ecology within only one or a few generations. This may allow some polyploids to succeed in strongly fluctuating environments and/or effectively colonize new habitats and, thus, increase their potential to be invasive.

SCOPE

We synthesize current knowledge on the importance of polyploidy for the invasion (i.e. spread) of introduced plants. We first aim to elucidate general mechanisms that are involved in the success of polyploid plants and translate this to that of plant invaders. Secondly, we provide an overview of ploidal levels in selected invasive alien plants and explain how ploidy might have contributed to their success.

CONCLUSIONS

Polyploidy can be an important factor in species invasion success through a combination of (1) 'pre-adaptation', whereby polyploid lineages are predisposed to conditions in the new range and, therefore, have higher survival rates and fitness in the earliest establishment phase; and (2) the possibility for subsequent adaptation due to a larger genetic diversity that may assist the 'evolution of invasiveness'. Alternatively, polyploidization may play an important role by (3) restoring sexual reproduction following hybridization or, conversely, (4) asexual reproduction in the absence of suitable mates. We, therefore, encourage invasion biologists to incorporate assessments of ploidy in their studies of invasive alien species.

Differences in spatial distribution, morphology, and communities of herbivorous insects among three cytotypes of Solidago altissima (Asteraceae)

PREMISE OF THE STUDY

Polyploidy in plants can result in genetic isolation, ecological differences among cytotypes, and, ultimately, speciation. Cytotypes should be sympatric only if they are segregated in an ecological niche or through prezygotic isolation. We tested whether sympatric diploid, tetraploid, and hexaploid ramets of Solidago altissima L. (Asteraceae) differ in their ecological niche.

METHODS

We measured how cytotypes were distributed within habitats, their morphology, and the composition of their communities of herbivorous insects at 10 natural field sites. We also conducted a common garden experiment to confirm whether observed differences in morphology or communities of herbivores were due to cytotype or environmental effects.

KEY RESULTS

Diploid ramets often grew in open areas, relatively far from woody plants, and were associated with a high species richness of herbaceous plants, especially grasses. Hexaploids often grew in heavy shading under woody plants where grasses were scarce. Finally, tetraploids usually grew in transition areas between diploids and hexaploids. Hexaploid ramets also were taller than ramets of the other cytotypes and had larger leaves. Two species of insects, the leaf-galling fly Asteromyia carbonifera and the phloem-tapping aphid Uroleucon nigrotuberculatum, were more abundant on hexaploid ramets than on ramets of other cytotypes in the field. When grown in a common garden, however, cytotypes were similar in morphology and communities of herbivores.

CONCLUSIONS

We conclude that cytotypes of S. altissima differ in their spatial distribution within habitats and that spatial variation in environmental factors influence plant morphology and communities of herbivorous insects.

Entangling ancient allotetraploidization in Asian Mitella: an integrated approach for multilocus combinations

The reconstruction of an ancient polyploidization history is often challenging, although it is a crucial step in clarifying the mechanisms underlying the contemporary success and diversity of polyploids. Phylogenetic relationships of duplicated gene pairs of polyploids, with respect to their orthologs in related diploids, have been used to address this problem, but they often result in conflicting topologies among different genes. Asimitellaria is an East Asian endemic tetraploid lineage of perennials (genus Mitella; Saxifragaceae) that has diversified in riparian habitats. Phylogenetic analyses of four nuclear-encoded, single-copy (per haploid) genes GBSSI-A, GBSSI-B, GS-II, and PepCK all supported a single allopolyploid origin of Asimitellaria, but they did not lead to a consensus about which diploid lineage gave rise to each of the Asimitellaria subgenomes. To address this issue, we used an integrated approach, whereby the four gene data sets and an additional nuclear ribosomal external transcribed spacer and internal transcribed spacer (including a 5.8S ribosomal DNA) data set were concatenated in all possible combinations, and the most probable data combination was determined together with the phylogenetic inference. This resulted in relatively robust support for the two closely related North American diploid species as the ancestral lineages of the Asimitellaria subgenomes, suggesting ancient intercontinental migration of the diploid or tetraploid lineages and subsequent tetraploid diversification in the Japanese Archipelago. The present approach enabled sorting out the duplicated genes into their original combinations in their preduplication ancestors under a maximum-likelihood framework, and its extension toward genome sequencing data may help in the reconstruction of ancestral, preduplicated, whole-genome structures.

Neopolyploidy and diversification in Heuchera grossulariifolia

Newly formed polyploid lineages must contend with several obstacles to avoid extinction, including minority cytotype exclusion, competition, and inbreeding depression. If polyploidization results in immediate divergence of phenotypic characters these hurdles may be reduced and establishment made more likely. In addition, if polyploidization alters the phenotypic and genotypic associations between traits, that is, the P and G matrices, polyploids may be able to explore novel evolutionary paths, facilitating their divergence and successful establishment. Here, we report results from a study of the perennial plant Heuchera grossulariifolia in which the phenotypic divergence and changes in phenotypic and genotypic covariance matrices caused by neopolyploidization have been estimated. Our results reveal that polyploidization causes immediate divergence for traits relevant to establishment and results in significant changes in the structure of the phenotypic covariance matrix. In contrast, our results do not provide evidence that polyploidization results in immediate and substantial shifts in the genetic covariance matrix.

The coevolving web of life

Coevolution--reciprocal evolutionary change in interacting species--is one of the central biological processes organizing the web of life, and most species are involved in one or more coevolved interactions. We have learned in recent years that coevolution is a highly dynamic process that continually reshapes interactions among species across ecosystems, creating geographic mosaics over timescales sometimes as short as thousands or even hundreds of years. If we take that as our starting point, what should we now be asking about the coevolutionary process? Here I suggest five major questions that we need to answer if we are to understand how coevolution shapes the web of life. How evolutionarily dynamic is specialization to other species, and what is the role of coevolutionary alternation in driving those dynamics? Does the geographic mosaic of coevolution shape adaptation in fundamentally different ways in different forms of interaction? How does the geographic mosaic of coevolution shape speciation? How does the structure of reciprocal selection change during the assembly of large webs of interacting species? How important are genomic events such as whole-genome duplication (i.e., polyploidy) and whole-genome capture (i.e., hybridization) in generating novel webs of interacting species? I end by suggesting four points about coevolution that we should tell every new student or researcher in biology.

Retention of mutualism in a geographically diverging interaction

A current challenge in coevolutionary biology is to understand how interactions between pairs of species change as they diversify into multispecific interactions. We tested whether the previously demonstrated pairwise mutualism between the widespread pollinating floral parasite Greya politella and its Lithophragma hostplants is ecologically enhanced or diminished in a region in which another Greya species, Greya obscura, uses the same host, Lithophragma cymbalaria. Field surveys and experimental trials showed that pollination efficacy by G. politella was more than an order of magnitude higher than by G. obscura, but G. politella abundance varied greatly between years. Greya obscura had a strongly positive effect on seed set in a year when G. politella densities were exceptionally low. Our results suggest that the coevolving mutualism between Greya and Lithophragma has potentially been enhanced rather than diminished as this interaction has diversified in the number of pollinating Greya species.

Evolutionary consequences of autopolyploidy

Autopolyploidy is more common in plants than traditionally assumed, but has received little attention compared with allopolyploidy. Hence, the advantages and disadvantages of genome doubling per se compared with genome doubling coupled with hybridizations in allopolyploids remain unclear. Autopolyploids are characterized by genomic redundancy and polysomic inheritance, increasing effective population size. To shed light on the evolutionary consequences of autopolyploidy, we review a broad range of studies focusing on both synthetic and natural autopolyploids encompassing levels of biological organization from genes to evolutionary lineages. The limited evidence currently available suggests that autopolyploids neither experience strong genome restructuring nor wide reorganization of gene expression during the first generations following genome doubling, but that these processes may become more important in the longer term. Biogeographic and ecological surveys point to an association between the formation of autopolyploid lineages and environmental change. We thus hypothesize that polysomic inheritance may provide a short-term evolutionary advantage for autopolyploids compared to diploid relatives when environmental change enforces range shifts. In addition, autopolyploids should possess increased genome flexibility, allowing them to adapt and persist across heterogeneous landscapes in the long run.

A combinational theory for maintenance of sex

Sexual reproduction implies high costs, but it is difficult to give evidence for evolutionary advantages that would explain the predominance of meiotic sex in eukaryotes. A combinational theory discussing evolution, maintenance and loss of sex may resolve the problem. The main function of sex is the restoration of DNA and consequently a higher quality of offspring. Recombination at meiosis evolved, perhaps, as a repair mechanism of DNA strand damages. This mechanism is most efficient for DNA restoration in multicellular eukaryotes, because the initial cell starts with a re-optimized genome, which is passed to all the daughter cells. Meiosis acts also as creator of variation in haploid stages, in which selection can purge most efficiently deleterious mutations. A prolonged diploid phase buffers the effects of deleterious recessive alleles as well as epigenetic defects and is thus optimal for prolonged growth periods. For complex multicellular organisms, the main advantage of sexuality is thus the alternation of diploid and haploid stages, combining advantages of both. A loss of sex is constrained by several, partly group-specific, developmental features. Hybridization may trigger shifts from sexual to asexual reproduction, but crossing barriers of the parental sexual species limit this process. For the concerted break-up of meiosis-outcrossing cycles plus silencing of secondary features, various group-specific changes in the regulatory system may be required. An establishment of asexuals requires special functional modifications and environmental opportunities. Costs for maintenance of meiotic sex are consequently lower than a shift to asexual reproduction.

Genomic expression dominance in allopolyploids

BACKGROUND

Allopolyploid speciation requires rapid evolutionary reconciliation of two diverged genomes and gene regulatory networks. Here we describe global patterns of gene expression accompanying genomic merger and doubling in inter-specific crosses in the cotton genus (Gossypium L.).

RESULTS

Employing a micro-array platform designed against 40,430 unigenes, we assayed gene expression in two sets of parental diploids and their colchicine-doubled allopolyploid derivatives. Up to half of all genes were differentially expressed among diploids, a striking level of expression evolution among congeners. In the allopolyploids, most genes were expressed at mid-parent levels, but this was achieved via a phenomenon of genome-wide expression dominance, whereby gene expression was either up- or down-regulated to the level of one of the two parents, independent of the magnitude of gene expression. This massive expression dominance was approximately equal with respect to direction (up- or down-regulation), and the same diploid parent could be either the dominant or the recessive genome depending on the specific genomic combination. Transgressive up- and down-regulation were also common in the allopolyploids, both for genes equivalently or differentially expressed between the parents.

CONCLUSION

Our data provide novel insights into the architecture of gene expression in the allopolyploid nucleus, raise questions regarding the responsible underlying mechanisms of genome dominance, and provide clues into the enigma of the evolutionary prevalence of allopolyploids.

Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio

Interspecific hybridization is an important mechanism of speciation in higher plants. In flowering plants, hybrid speciation is usually associated with polyploidy (allopolyploidy), but hybrid speciation without genome duplication (homoploid hybrid speciation) is also possible, although it is more difficult to detect. The combination of divergent genomes within a hybrid can result in profound changes to both genome and transcriptome. Recent transcriptomic studies of wild and resynthesized homoploid and allopolyploid hybrids have revealed widespread changes to gene expression in hybrids relative to expression levels in their parents. Many of these changes to gene expression are 'non-additive', i.e. not simply the sum of the combined expression levels of parental genes. Some gene expression changes are far outside the range of gene expression in either parent, and can therefore be viewed as 'transgressive'. Such profound changes to gene expression may enable new hybrids to survive in novel habitats not accessible to their parent species. Here, we give a brief overview of hybrid speciation in plants, with an emphasis on genomic change, before focusing discussion on findings from recent transcriptomic studies. We then discuss our current work on gene expression change associated with hybrid speciation in the genus Senecio (ragworts and groundsels) focusing on the findings from a reanalysis of gene expression data obtained from recent microarray studies of wild and resynthesized allopolyploid Senecio cambrensis. These data, showing extensive non-additive and transgressive gene expression changes in Senecio hybrids, are discussed in the light of findings from other model systems, and in the context of the potential importance of gene expression change to hybrid speciation in plants.

Reciprocal Pleistocene origin and postglacial range formation of an allopolyploid and its sympatric ancestors (Androsace adfinis group, Primulaceae)

The biogeographic history of polyploids and their lower-ploid ancestors is an important feature to achieve a better understanding of polyploid evolution. This is exemplified here using the ecologically congruent members of the Androsace adfinis group (Primulaceae) endemic to the southwestern European Alps. Employing relative genome size, AFLP fingerprint and chloroplast sequence haplotype data, we show that Androsace brigantiaca is a recent (probably no more than 0.2 million years) allopolyploid derivative of the geographically close A. adfinis and A. puberula, which formed reciprocally in a comparatively restricted area in the southern Southwestern Alps. Bayesian admixture analysis--also of artificial additive AFLP profiles--shows that the nuclear genome of A. brigantiaca is significantly biased towards the puberula-genome irrespective of maternal parentage. Nevertheless, there is no evidence for genetic interaction (hybridization, introgression) of A. brigantiaca with either of its ancestors, including the widely sympatric A. puberula. Sympatry might be facilitated by ecological displacement on a local scale or might be a transitory phase on the way to competitive replacement via, for instance, polyploid superiority.