Molecular constraints on tolerance-resistance trade-offs: Is there a cost?

Plants possess myriad defenses against their herbivores, including constitutive and inducible chemical compounds and regrowth strategies known as tolerance. Recent studies have shown that plant tolerance and resistance are positively associated given they are co-localized in the same molecular pathway, the oxidative pentose phosphate pathway. However, given that both defensive strategies utilize carbon skeletons from a shared resource pool in the oxidative pentose phosphate pathway there are likely costs in maintaining both resistance-tolerance strategies. Here we investigate fitness costs in maintaining both strategies by utilizing a double knockout of cyp79B2 and cyp79B3, key enzymes in the biosynthetic process of indole glucosinolates, which convert tryptophan to indole-3-acetaldoxime (IAOx) and is further used to produce indole glucosinolates. These mutant plants are devoid of any indole glucosinolates thus reducing plant resistance. Results show that knocking out indole glucosinolate production and thus one of the resistance pathways leads to an approximate 94% increase in fitness compensation shifting the undercompensating wild-type Columbia-0 to an overcompensating genotype following damage. We discuss the potential mechanistic basis for the observed patterns.

Herbivory and Soil Water Availability Induce Changes in Arbuscular Mycorrhizal Fungal Abundance and Composition.

We tested the prediction that abundance and composition of arbuscular mycorrhizal fungi (AMF) in Ipomopsis aggregata roots and soils are influenced by ungulate herbivory and drought conditions by examining the effects in a field setting over two years. We used a multi-metric approach to quantify AMF root colonization, AMF reproduction, and AMF community composition in roots and soils. We incorporated complimentary community characterization assays by morphologically identifying spores from trap cultures and the use of terminal restriction fragment length polymorphism (T-RFLP) fingerprinting. Herbivory caused a twofold increase in spore production, an increase in AMF taxa diversity in roots, and a shift in AMF species composition in rhizosphere soils. The impact of herbivory was dependent on water availability, which differed in the two contrasting years. This study demonstrates that both soil water availability and herbivory shape arbuscular mycorrhizal fungi communities. The changes to mycorrhizal communities may help in understanding mycorrhizal function in changing climates.

Dietary antioxidant vitamin C influences the evolutionary path of insecticide resistance in Drosophila melanogaster.

Herbivorous insects encounter a variety of toxic environmental substances ranging from ingested plant defensive compounds to human-introduced insecticidal agents. Dietary antioxidants are known to reduce the negative physiological impacts of toxins in mammalian systems through amelioration of reactive oxygen-related cellular damage. The analogous impacts to insects caused by multigenerational exposure to pesticides and the effects on adaptive responses within insect populations, however, are currently unknown. To address these research gaps, we used Drosophila as a model system to explore adaptive phenotypic responses to acute dichlorodiphenyltrichloroethane (DDT) exposure in the presence of the dietary antioxidant vitamin C and to examine the structural genomic consequences of this exposure. DDT resistance increased significantly among four replicates exposed to a low concentration of DDT for 10 generations. In contrast, dietary intake of vitamin C significantly reduced DDT resistance after mutigenerational exposure to the same concentration of DDT. As to the genomic consequences, no significant differences were predicted in overall nucleotide substitution rates across the genome between any of the treatments. Despite this, replicates exposed to a low concentration of DDT without vitamin C showed the highest number of synonymous and non-synonymous variants (3196 in total), followed by the DDT plus vitamin C (1174 in total), and vitamin C alone (728 in total) treatments. This study demonstrates the potential role of diet (specifically, antioxidant intake) on adaptive genome responses, and thus on the evolution of pesticide resistance within insect populations.

Individual and interactive effects of herbivory on plant fitness: endopolyploidy as a driver of genetic variation in tolerance and resistance.

Previous studies have shown a causal link between mammalian herbivory, tolerance, and chemical defense in Arabidopsis thaliana, driven by the process of endoreduplication (replication of the genome without mitosis). Removal of the apical meristem by mammalian herbivores lowers auxin, which triggers entry into the endocycle. Increasing chromosome number through endoreduplication, and therefore gene copy number, provides a means of increasing gene expression promoting rapid regrowth rates, higher defensive chemistry and enhanced fitness. Here, we assess whether insect leaf-feeding elicits the same compensatory response as the removal of apical dominance. Insect feeding has been shown to downregulate auxin production, which should trigger endoreduplication. Results here support this contention; insect leaf-feeding by Trichoplusia ni elicited a compensatory response similar to that of mammalian herbivores-an ecotype-specific response consistent with the level of endoreduplication. The interactive effects of mammalian and insect herbivory were also assessed to determine whether interactions were additive (pairwise) or non-additive (diffuse) on tolerance (fitness). Specifically, results indicate that herbivory is either diffuse (a significant clipping × T. ni interaction) or pairwise (no significant interaction between clipping and T. ni herbivory), dependent upon plant genotype and compensatory ability. In general, herbivore-induced changes in plant quality appear to be responsible for the observed differences in herbivory and fitness compensation. We discuss the importance of evaluating endoreduplication among plants within a population to avoid masking the association between tolerance and resistance and the fitness consequences of multi-herbivore interactions.

Overcompensation: a 30-year perspective.

Biomass removal by herbivores usually incurs a fitness cost for the attacked plants, with the total cost per unit lost tissue depending on the value of the removed tissue (i.e., how costly it is to be replaced by regrowth). Optimal defense theory, first outlined in the 1960s and 1970s, predicted that these fitness costs result in an arms race between plants and herbivores, in which selection favors resistance strategies that either repel herbivores through morphological and chemical resistance traits in order to reduce their consumption, or result in enemy escape through rapid growth or by timing the growth or flowering to the periods when herbivores are absent. Such resistance against herbivores would most likely evolve when herbivores are abundant, cause extensive damage, and consume valuable plant tissues. The purpose of this Special Feature is to celebrate the 30th anniversary of the phenomenon of overcompensation, specifically, where the finding has brought us and where it is leading us 30 yr later. We first provide a short overview of how the phenomenon of overcompensation has led to broader studies on plant tolerance to herbivory, summarize key findings, and then discuss some promising new directions in light of six featured research papers.

Molecular constraints on resistance-tolerance trade-offs.

Plants have numerous mechanisms to cope with the negative effects of herbivory, including plant resistance, structural and chemical traits that reduce damage, and plant tolerance, the ability to compensate for tissues lost. It has been argued that resistance and tolerance represent alternate strategies and thus there should be a trade-off between resistance and tolerance. However, resistance and tolerance are controlled via the same molecular pathway, the oxidative pentose phosphate pathway and the process of endoreduplication. Endoreduplication is the replication of the genome without mitosis, which leads to an increase in cellular chromosome number. Increasing chromosome number and therefore gene copy number provides a means of increasing gene expression that has been shown to enhance compensation following herbivory. By measuring glucosinolate levels and seed production following the removal of apical dominance in genotypes of Arabidopsis thaliana we show that there is a positive association between tolerance and induced chemical defense. Similarly, the direct association between tolerance and resistance is demonstrated by genetically manipulating the endoreduplication pathway. By overexpressing ILP1, a positive regulator of endoreduplication, and thus compensation, we experimentally increased glucosinolate production and tolerance in the Col-0 genotype. We suggest that many herbaceous plants that endoreduplicate (~90%) would show a positive relationship between compensation and chemical defense, given that the molecular pathways are shared in common. We discuss these findings in light of contrasting results on measures of tolerance and resistance, given that the true relationship can be masked by ignoring genetic variation in endoreduplication and the timing of chemical measurement.

Characterization of Arabidopsis thaliana regrowth patterns suggests a trade-off between undamaged fitness and damage tolerance.

Herbivory is a fundamental type of plant-animal interaction that presents substantial selection pressure on plants to replace lost tissues and to prevent subsequent losses in fitness. Apical herbivory, which entails removal or damage to the apical meristem, causes a change in plant architecture by disrupting the balance of hormones produced in part by the apical meristem. Therefore, for an annual semelparous plant, the ability to preserve reproductive success following damage (i.e., to tolerate damage) is largely dependent on the plant's pre-damage investment into fitness and its regrowth pattern following damage. Using multiple regression analyses, we assessed the relationship of developmental and architectural traits of experimentally damaged plants relative to undamaged plants of 33 Arabidopsis thaliana genotypes that display a wide range of undamaged fitness and damage tolerance. Our analyses revealed evidence for an evolutionary bet-hedging strategy within a subset of genotypes to presumably maximize fitness under natural herbivory-genotypes with the greatest seed production when undamaged exhibited a significant reduction in seed yield when damaged, while genotypes with low undamaged seed production were the only genotypes whose seed yield increased when damaged. Patterns of endopolyploidy paralleled those of seed production, such that the increase in whole-plant ploidy by genome re-replication during growth/regrowth contributes to undamaged fitness, damage tolerance, and their trade-off. Overall, this study provides the first large-scale characterization of A. thaliana regrowth patterns and suggests that investment into fitness and endopolyploidy when undamaged may come at a cost to tolerance ability once damaged.

Belowground fungal associations and water interact to influence the compensatory response of Ipomopsis aggregata.

Although the concept that some plants benefit from being eaten is counterintuitive, there is now considerable evidence demonstrating enhanced fitness following herbivory. It has been assumed that plants growing in high resource conditions are the ones best able to compensate for herbivory. However, just the opposite has been found for dicotyledonous plants exhibiting patterns of overcompensation, with most occurring in resource-poor conditions. Long-term studies of the monocarpic biennial, scarlet gilia, Ipomopsis aggregata growing in resource-poor conditions have shown that ungulate herbivory by mule deer and elk can result in a threefold increase in plant fitness over uneaten controls. These observations led us to hypothesize that fungal associations would facilitate the compensatory response most commonly observed in this Arizona population of scarlet gilia; perhaps mutualistic associations with fungi, such as arbuscular mycorrhizal fungi, would explain the phenomenon of overcompensation altogether. Fungal removal experiments, using Captan®, a commercially available fungicide, showed that a reduction in fungal abundance altered the compensatory response following ungulate herbivory, particularly in years in which water was limited, increasing fitness compensation from equal compensation to overcompensation. A multifactorial experiment revealed that the interactive effects of water and fungicide maximized fruit production following herbivory. Our results are counter to the "modification of tolerance hypothesis" in which plants associating with mycorrhizal fungi will have higher tolerance to herbivory. It is likely that arbuscular mycorrhizal fungi and dark septate endophytes compete with plants for photosynthates following herbivory, thereby limiting the magnitude of compensation. Thus, fungi appear to be parasitic on scarlet gilia following ungulate herbivory.

The role of invertases in plant compensatory responses to simulated herbivory.

BACKGROUND: The ability of a plant to overcome animal-induced damage is referred to as compensation or tolerance and ranges from undercompensation (decreased fitness when damaged) to overcompensation (increased fitness when damaged). Although it is clear that genetic variation for compensation exists among plants, little is known about the specific genetic underpinnings leading to enhanced fitness. Our previous study identified the enzyme GLUCOSE-6-PHOSPHATE DEHYDROGENASE 1 (G6PD1) as a key regulator contributing to the phenomenon of overcompensation via its role in the oxidative pentose phosphate pathway (OPPP). Apart from G6PD1 we also identified an invertase gene which was up-regulated following damage and that potentially integrates with the OPPP. The invertase family of enzymes hydrolyze sucrose to glucose and fructose, whereby the glucose produced is shunted into the OPPP and presumably supports plant regrowth, development, and ultimately compensation. In the current study, we measured the relative expression of 12 invertase genes over the course of plant development in the Arabidopsis thaliana genotypes Columbia-4 and Landsberg erecta, which typically overcompensate and undercompensate, respectively, when damaged. We also compared the compensatory performances of a set of invertase knockout mutants to the Columbia-4 wild type. RESULTS: We report that Columbia-4 significantly up-regulated 9 of 12 invertase genes when damaged relative to when undamaged, and ultimately overcompensated for fruit production. Landsberg erecta, in contrast, down-regulated two invertase genes following damage and suffered reduced fitness. Knockout mutants of two invertase genes both exhibited significant undercompensation for fruit production, exhibiting a complete reversal of the wild type Col-4's overcompensation. CONCLUSION: Collectively, these results confirm that invertases are essential for not only normal plant growth and development, but also plants' abilities to regrow and ultimately compensate for fitness following apical damage.

Plasticity in ploidy: a generalized response to stress.

Endoreduplication, the replication of the genome without mitosis, leads to an increase in the cellular ploidy of an organism over its lifetime, a condition termed 'endopolyploidy'. Endopolyploidy is thought to play significant roles in physiology and development through cellular, metabolic, and genetic effects. While the occurrence of endopolyploidy has been observed widely across taxa, studies have only recently begun to characterize and manipulate endopolyploidy with a focus on its ecological and evolutionary importance. No compilation of these examples implicating endoreduplication as a generalized response to stress has thus far been made, despite the growing evidence supporting this notion. We review here the recent literature of stress-induced endopolyploidy and suggest that plants employ endoreduplication as an adaptive, plastic response to mitigate the effects of stress.

Plasticity in ploidy underlies plant fitness compensation to herbivore damage.

How plants mitigate damage by animal herbivores is a fundamental ecological and evolutionary question of plant-animal interactions. Some plants can increase their fitness when damaged in a phenomenon termed 'overcompensation'. Despite overcompensation being observed in a variety of plant species, its mechanistic basis remains elusive. Recent research has shown that the Arabidopsis thaliana genotype Columbia-4 employs endoreduplication, the replication of the genome without mitosis, following damage and that it overcompensates for seed yield. The related genotype Landsberg erecta, in contrast, does not increase its endoreduplication following damage and suffers reduced seed yield. While these results suggest that a plant's ability to plastically increase its ploidy during regrowth may promote its mitigation of damage, no studies have explicitly linked the endoreduplication genetic pathway to the regrowth and fitness of damaged plants. By comparing fitness and ploidy between undamaged and damaged plants of Columbia-4, Landsberg erecta and their offspring, we provide evidence that endoreduplication is directly involved in compensatory performance. We then overexpressed an endoreduplication regulator and compared this mutant's endoreduplication and compensation with its background genotype Columbia-0, an undercompensator. Enhancing Columbia-0's ability to endoreduplicate during regrowth led to the complete mitigation of the otherwise detrimental effects of damage on its fitness. These results suggest that the ability of these plants to increase their ploidy via endoreduplication directly impacts their abilities to compensate for damage, providing a novel mechanism by which some plants can mitigate or even benefit from apical damage with potential across the wide range of plant taxa that endoreduplicate.

Rates of genomic divergence in humans, chimpanzees and their lice.

The rate of DNA mutation and divergence is highly variable across the tree of life. However, the reasons underlying this variation are not well understood. Comparing the rates of genetic changes between hosts and parasite lineages that diverged at the same time is one way to begin to understand differences in genetic mutation and substitution rates. Such studies have indicated that the rate of genetic divergence in parasites is often faster than that of their hosts when comparing single genes. However, the variation in this relative rate of molecular evolution across different genes in the genome is unknown. We compared the rate of DNA sequence divergence between humans, chimpanzees and their ectoparasitic lice for 1534 protein-coding genes across their genomes. The rate of DNA substitution in these orthologous genes was on average 14 times faster for lice than for humans and chimpanzees. In addition, these rates were positively correlated across genes. Because this correlation only occurred for substitutions that changed the amino acid, this pattern is probably produced by similar functional constraints across the same genes in humans, chimpanzees and their ectoparasites.

Can endopolyploidy explain body size variation within and between castes in ants?

Endoreduplication is the process by which the nuclear genome is repeatedly replicated without mitotic cell division, resulting in nuclei that contain numerous additional genome copies. Endoreduplication occurs widely throughout Eucarya and is particularly common in angiosperms and insects. Although endoreduplication is an important process in the terminal differentiation of some specialized cell types, and often increases cell size and metabolism, the direct effects of increasing nuclear ploidy on cell function are not well resolved. Here, we examine if endoreduplication may play a role in body size and/or caste differentiation in ants. Nuclear ploidy was measured by flow cytometry of whole individuals (providing the basis for overall body size patterns) and individual body segments for multiple polymorphic ant species. We used cell cycle values, interpreted as the mean number of endocycles performed by each cell in the sample, as our measure of overall endoreduplication. Among females of four polymorphic ant species, endoreduplication was positively related with size within the worker caste, but was not related to caste generally in two species where we also examined queens. Additionally, abdomens had the greatest endoreduplication of all body parts regardless of caste or size. We also found that males, having derived from haploid unfertilized eggs, had the highest rates of endoreduplication and may compensate for their haploid origin by performing an additional endocycle relative to females. These results suggest that endoreduplication may play a role in body size variation in eusocial insects and the development of some segment-specific tissues.

Overcompensation in response to herbivory in Arabidopsis thaliana: the role of glucose-6-phosphate dehydrogenase and the oxidative pentose-phosphate pathway.

That some plants benefit from being eaten is counterintuitive, yet there is now considerable evidence demonstrating enhanced fitness following herbivory (i.e., plants can overcompensate). Although there is evidence that genetic variation for compensation exists, little is known about the genetic mechanisms leading to enhanced growth and reproduction following herbivory. We took advantage of the compensatory variation in recombinant inbred lines of Arabidopsis thaliana, combined with microarray and QTL analyses to assess the molecular basis of overcompensation. We found three QTL explaining 11.4, 10.1, and 26.7% of the variation in fitness compensation, respectively, and 109 differentially expressed genes between clipped and unclipped plants of the overcompensating ecotype Columbia. From the QTL/microarray screen we uncovered one gene that plays a significant role in overcompensation: glucose-6-phosphate-1-dehydrogenase (G6PDH1). Knockout studies of Transfer-DNA (T-DNA) insertion lines and complementation studies of G6PDH1 verify its role in compensation. G6PDH1 is a key enzyme in the oxidative pentose-phosphate pathway that plays a central role in plant metabolism. We propose that plants capable of overcompensating reprogram their transcriptional activity by up-regulating defensive genes and genes involved in energy metabolism and by increasing DNA content (via endoreduplication) with the increase in DNA content feeding back on pathways involved in defense and metabolism through increased gene expression.

Chromosomal plasticity: mitigating the impacts of herbivory.

Endoreduplication, the replication of the genome without mitosis, leads to endopolyploidy, an increase in cellular chromosome number. Although endoreduplication is widespread among angiosperms and other groups of eukaryotes, the degree to which this process is plastic under varying environmental conditions and its potential adaptive significance are not known. Here, using flow cytometry, we measured plasticity in chromosome number following the removal of apical dominance (simulating natural herbivory) in two ecotypes of Arabidopsis thaliana: Columbia and Landsberg erecta. We report that endopolyploidy of clipped Columbia plants was significantly different than unclipped controls following the removal of apical dominance and regrowth, and that cellular ploidy is positively associated with attributes of fitness (biomass, flower, fruit, and seed production). In contrast, clipped Landsberg erecta showed no significant differences in endopolyploidy and a decrease in seed production compared to unclipped controls; representing a significant genotype x environment interaction between ecotypes. Altering ploidy via endoreduplication adds a previously unknown way in which plants may be able to cope with environmental stress: enhancing regrowth rates and fitness following plant damage.

Candidate genes detected in transcriptome studies are strongly dependent on genetic background.

Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds.

Phylogeographic history of white spruce during the last glacial maximum: uncovering cryptic refugia.

Although a recent study of white spruce using chloroplast DNA uncovered the presence of a glacial refuge in Alaska, chloroplast failed to provide information on the number or specific localities of refugia. Recent studies have demonstrated the utility of nuclear microsatellites to refine insights into postglacial histories. The greater relative rate of mutation may allow finer scale resolution of historic dynamics, including the number, location, and sizes of refugia. Genetic data were acquired from screening 6 microsatellite loci on approximately 14 trees from each of 22 populations located across the central and western boreal forests of Canada and Alaska. Our studies combining microsatellites with Bayesian analyses of population structure in white spruce support the phylogeographic patterns uncovered using chloroplast, separating Alaskan from non-Alaskan regions. Results also support the idea that north-central Alaska served as a glacial refugium during the last glacial maximum. Additionally, the relationship between the degree of genetic differentiation and geographic distance indicated that gene flow played a more important role in structuring non-Alaskan populations, whereas drift played a more important role in structuring Alaskan populations (R(ST)'s for non-Alaskan populations 0.029 ± 0.007 and 0.083 ± 0.012 for Alaskan populations). Microsatellites also substantiate the bidirectional patterns of gene flow previously uncovered using chloroplast DNA but indicate much greater movement and mixing. Results from our Bayesian analyses also suggest the existence of additional cryptic refugia. However, the locations have been obscured by high gene flow (R(ST) averaging 0.057 ± 0.004).

Heritable variation in the inflorescence replacement program of Arabidopsis thaliana.

Owing to their sessile habits and trophic position within global ecosystems, higher plants display a sundry assortment of adaptations to the threat of predation. Unlike animals, nearly all higher plants can replace reproductive structures lost to predators by activating reserved growing points called axillary meristems. As the first step in a program aimed at defining the genetic architecture of the inflorescence replacement program (IRP) of Arabidopsis thaliana, we describe the results of a quantitative germplasm survey of developmental responses to loss of the primary reproductive axis. Eighty-five diverse accessions were grown in a replicated common garden and assessed for six life history traits and four IRP traits, including the number and lengths of axillary inflorescences present on the day that the first among them re-flowered after basal clipping of the primary inflorescence. Significant natural variation and high heritabilities were observed for all measured characters. Pairwise correlations among the 10 focal traits revealed a multi-dimensional phenotypic space sculpted by ontogenic and plastic allometries as well as apparent constraints and outliers of genetic interest. Cluster analysis of the IRP traits sorted the 85 accessions into 5 associations, a topology that establishes the boundaries within which the evolving Arabidopsis genome extends and restricts the species' IRP repertoire to that observable worldwide.

A genomewide assessment of inbreeding depression: gene number, function, and mode of action.

Although the genetic basis of inbreeding depression is still being debated, most fitness effects are thought to be the result of increased homozygosity for recessive or partially recessive deleterious alleles rather than the loss of overdominant genes. It is unknown how many loci are associated with inbreeding depression, the genes or gene pathways involved, or their mode of action. To uncover genes associated with variation in fitness following inbreeding, we generated a set of inbred lines of Drosophila melanogaster for which only the third chromosome varied among lines and measured male competitive reproductive success among these lines to estimate inbreeding depression. Male competitive reproductive success for different lines validated our prediction that equally inbred lines show variation in inbreeding depression. To begin to assess the molecular basis of inbreeding depression for male competitive reproductive success, we detected variation in whole-genome gene expression across these inbred lines with commercially available high-density oligonucleotide microarrays. A total of 567 genes were differentially expressed among these inbred lines, indicating that inbreeding directly or indirectly affects a large number of genes: genes that are disproportionately involved in metabolism, stress and defense responses. Subsequently, we generated a set of outbred lines by crossing the highest inbreeding depression lines to each other and contrasted gene expression between parental inbred lines and F(1) hybrids with transcript abundance as a quantitative phenotype to determine the mode of action of the genes associated with inbreeding depression. Although our results indicated that approximately 75% of all genes involved in inbreeding depression were additive, partially additive, or dominant, about 25% of all genes expressed patterns of overdominance. These results should be viewed with caution given that they may be confounded by issues of statistical inference or associative overdominance.