Antagonistic selection and pleiotropy constrain the evolution of plant chemical defenses

Uncoupling FRUITFULL's functions through modification of a protein motif identified by co-ortholog analysis

Many plant transcription factors (TFs) are multifunctional and regulate growth and development in more than one tissue. These TFs can generally associate with different protein partners depending on the tissue type, thereby regulating tissue-specific target gene sets. However, how interaction specificity is ensured is still largely unclear. Here, we examine protein-protein interaction specificity using subfunctionalized co-orthologs of the FRUITFULL (FUL) subfamily of MADS-domain TFs. In Arabidopsis, FUL is multifunctional, playing important roles in flowering and fruiting, whereas these functions have partially been divided in the tomato co-orthologs FUL1 and FUL2. By linking protein sequence and function, we discovered a key amino acid motif that determines interaction specificity of MADS-domain TFs, which in Arabidopsis FUL determines the interaction with AGAMOUS and SEPALLATA proteins, linked to the regulation of a subset of targets. This insight offers great opportunities to dissect the biological functions of multifunctional MADS TFs.

The evolution and ecology of multiple antipredator defences

Prey seldom rely on a single type of antipredator defence, often using multiple defences to avoid predation. In many cases, selection in different contexts may favour the evolution of multiple defences in a prey. However, a prey may use multiple defences to protect itself during a single predator encounter. Such "defence portfolios" that defend prey against a single instance of predation are distributed across and within successive stages of the predation sequence (encounter, detection, identification, approach (attack), subjugation and consumption). We contend that at present, our understanding of defence portfolio evolution is incomplete, and seen from the fragmentary perspective of specific sensory systems (e.g., visual) or specific types of defences (especially aposematism). In this review, we aim to build a comprehensive framework for conceptualizing the evolution of multiple prey defences, beginning with hypotheses for the evolution of multiple defences in general, and defence portfolios in particular. We then examine idealized models of resource trade-offs and functional interactions between traits, along with evidence supporting them. We find that defence portfolios are constrained by resource allocation to other aspects of life history, as well as functional incompatibilities between different defences. We also find that selection is likely to favour combinations of defences that have synergistic effects on predator behaviour and prey survival. Next, we examine specific aspects of prey ecology, genetics and development, and predator cognition that modify the predictions of current hypotheses or introduce competing hypotheses. We outline schema for gathering data on the distribution of prey defences across species and geography, determining how multiple defences are produced, and testing the proximate mechanisms by which multiple prey defences impact predator behaviour. Adopting these approaches will strengthen our understanding of multiple defensive strategies.

Genetic architecture of multiple mutualisms and mating system in Turnera ulmifolia

Plants often associate with multiple arthropod mutualists. These partners provide important services to their hosts, but multiple interactions can constrain a plant's ability to respond to complex, multivariate selection. Here, we quantified patterns of genetic variance and covariance among rewards for pollination, biotic defence and seed dispersal mutualisms in multiple populations of Turnera ulmifolia to better understand how the genetic architecture of multiple mutualisms might influence their evolution. We phenotyped plants cultivated from 17 Jamaican populations for several mutualism and mating system-related traits. We then fit genetic variance-covariance (G) matrices for the island metapopulation and the five largest individual populations. At the metapopulation level, we observed significant positive genetic correlations among stigma-anther separation, floral nectar production and extrafloral nectar production. These correlations have the potential to significantly constrain or facilitate the evolution of multiple mutualisms in T. ulmifolia and suggest that pollination, seed dispersal and defence mutualisms do not evolve independently. In particular, we found that positive genetic correlations between floral and extrafloral nectar production may help explain their stable coexistence in the face of physiological trade-offs and negative interactions between pollinators and ant bodyguards. Locally, we found only small differences in G among our T. ulmifolia populations, suggesting that geographic variation in G may not shape the evolution of multiple mutualisms.

The Boechera model system for evolutionary ecology

Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.

Herbivore-Mediated Selection on Floral Display Covaries Nonlinearly With Plant-Antagonistic Interaction Intensity Among Primrose Populations

Quantifying the relations between plant-antagonistic interactions and natural selection among populations is important for predicting how spatial variation in ecological interactions drive adaptive differentiation. Here, we investigate the relations between the opportunity for selection, herbivore-mediated selection, and the intensity of plant-herbivore interaction among 11 populations of the insect-pollinated plant Primula florindae over 2 years. We experimentally quantified herbivore-mediated directional selection on three floral traits (two display and one phenological) within populations and found evidence for herbivore-mediated selection for a later flowering start date and a greater number of flowers per plant. The opportunity for selection and strength of herbivore-mediated selection on number of flowers varied nonlinearly with the intensity of herbivory among populations. These parameters increased and then decreased with increasing intensity of plant-herbivore interactions, defined as an increase in the ratio of herbivore-damaged flowers per individual. Our results provide novel insights into how plant-antagonistic interactions can shape spatial variation in selection on floral traits and contribute toward understanding the mechanistic basis of geographic variation in angiosperm flowers.

Dual-species origin of an adaptive chemical defense polymorphism

Allopolyploid speciation and chemical defense diversification are two of the most characteristic features of plant evolution; although the former has likely shaped the latter, this has rarely been documented. Here we document allopolyploidy-mediated chemical defense evolution in the origin of cyanogenesis (HCN release upon tissue damage) in white clover (Trifolium repens). We combined linkage mapping of the loci that control cyanogenesis (Ac, controlling production of cyanogenic glucosides; and Li, controlling production of their hydrolyzing enzyme linamarase) with genome sequence comparisons between white clover, a recently evolved allotetraploid, and its diploid progenitors (Trifolium pallescens, Trifolium occidentale). The Ac locus (a three-gene cluster comprising the cyanogenic glucoside pathway) is derived from T. occidentale; it maps to linkage group 2O (occidentale subgenome) and is orthologous to a highly similar cluster in the T. occidentale reference genome. By contrast, Li maps to linkage group 4P (pallescens subgenome), indicating an origin in the other progenitor species. These results indicate that cyanogenesis evolved in white clover as a product of the interspecific hybridization that created the species. This allopolyploidization-derived chemical defense, together with subsequent selection on intraspecific cyanogenesis variation, appears to have contributed to white clover's ecological success as a globally distributed weed species.

Depicting the phenotypic space of the annual plant Diplotaxis acris in hyperarid deserts

The phenotypic space encompasses the assemblage of trait combinations yielding well-suited integrated phenotypes. At the population level, understanding the phenotypic space structure requires the quantification of among- and within-population variations in traits and the correlation pattern among them. Here, we studied the phenotypic space of the annual plant Diplotaxis acris occurring in hyperarid deserts. Given the advance of warming and aridity in vast regions occupied by drylands, D. acris can indicate the successful evolutionary trajectory that many other annual plant species may follow in expanding drylands. To this end, we conducted a greenhouse experiment with 176 D. acris individuals from five Saudi populations to quantify the genetic component of variation in architectural and life history traits. We found low among-population divergence but high among-individual variation in all traits. In addition, all traits showed a high degree of genetic determination in our study experimental conditions. We did not find significant effects of recruitment and fecundity on fitness. Finally, all architectural traits exhibited a strong correlation pattern among them, whereas for life history traits, only higher seed germination implied earlier flowering. Seed weight appeared to be an important trait in D. acris as individuals with heavier seeds tended to advance flowering and have a more vigorous branching pattern, which led to higher fecundity. Population divergence in D. acris might be constrained by the severity of the hyperarid environment, but populations maintain high among-individual genetic variation in all traits. Furthermore, D. acris showed phenotypic integration for architectural traits and, to a lesser extent, for life history traits. Overall, we hypothesize that D. acris may be fine-tuned to its demanding extreme environments. Evolutionary speaking, annual plants facing increasing warming, aridity, and environmental seasonality might modify their phenotypic spaces toward new phenotypic configurations strongly dominated by correlated architectural traits enhancing fecundity and seed-related traits advancing flowering time.

Character displacement in the presence of multiple trait differences: Evolution of the storage effect in germination and growth

Ecological character displacement is a prominent hypothesis for the maintenance of ecological differences between species that are critical to stable coexistence. Models of character displacement often ascribe interspecific competitive interactions to a single character, but multiple characters contribute to competition, and their effects on selection can be nonadditive. Focusing on one character, we ask if other characters that affect competition alter evolutionary outcomes for the focal character. We address this question using the variable environment seed bank model for two species with two traits. The focal trait is the temporal pattern of germination, which is evolutionary labile. The other trait is the temporal pattern of plant growth, which is assumed fixed. We ask whether evolutionary divergence of germination patterns between species depends on species differences in plant growth. Patterns of growth can affect selection on germination patterns in two ways. First, cues present at germination can provide information about future growth. Second, germination and growth jointly determine the biomass of plants, which determines demand for resources. Germination and growth contribute to the selection gradient in distinct components, one density-independent and the other density-dependent. Importantly, the relative strengths of the components are key. When the density-dependent component is stronger, displacement in germination patterns between species is larger. Stronger cues at germination strengthen the density-independent component by increasing the benefits of germinating in years of favorable growth. But cues also affect the density-dependent component by boosting a species' biomass, and hence its competitive effect, in good years. Consequently, cues weaken character displacement when growth patterns are similar for two competitors, but favor displacement when growth patterns are species-specific. Understanding how these selection components change between contexts can help understand the origin and maintenance of species differences in germination patterns in temporally fluctuating environments.

Herbivore-induced defenses are not under phylogenetic constraints in the genus Quercus (oak): Phylogenetic patterns of growth, defense, and storage

The evolution of plant defenses is often constrained by phylogeny. Many of the differences between competing plant defense theories hinge upon the differences in the location of meristem damage (apical versus auxiliary) and the amount of tissue removed. We analyzed the growth and defense responses of 12 Quercus (oak) species from a well-resolved molecular phylogeny using phylogenetically independent contrasts. Access to light is paramount for forest-dwelling tree species, such as many members of the genus Quercus. We therefore predicted a greater investment in defense when apical meristem tissue was removed. We also predicted a greater investment in defense when large amounts of tissue were removed and a greater investment in growth when less tissues were removed. We conducted five simulated herbivory treatments including a control with no damage and alterations of the location of meristem damage (apical versus auxiliary shoots) and intensity (25% versus 75% tissue removal). We measured growth, defense, and nutrient re-allocation traits in response to simulated herbivory. Phylomorphospace models were used to demonstrate the phylogenetic nature of trade-offs between characteristics of growth, chemical defenses, and nutrient re-allocation. We found that growth-defense trade-offs in control treatments were under phylogenetic constraints, but phylogenetic constraints and growth-defense trade-offs were not common in the simulated herbivory treatments. Growth-defense constraints exist within the Quercus genus, although there are adaptations to herbivory that vary among species.

The ecological, genetic and genomic architecture of local adaptation and population differentiation in Boechera stricta

Differential local adaptation restricts gene flow between populations inhabiting distinct environments, resulting in isolation by adaptation. In addition to the statistical inferences of genotype-environment associations, an integrative approach is needed to investigate the effect of local adaptation on population divergence at the ecological, genetic and genomic scale. Here, we combine reciprocal transplant, genome-environment association and QTL mapping to investigate local adaptation in Boechera stricta (Drummond's rockcress). With reciprocal transplant experiment, we found local genetic groups exhibit phenotypic characteristics corresponding to the distinct selection forces from different water availability. At the genetic level, the local allele of a major fitness QTL confers higher and sturdier flowering stalks, maximizing the fecundity fitness component under sufficient water supply, and its genetic variation is associated with precipitation across the landscape. At the genomewide scale, we further showed that multiple loci associated with precipitation are highly differentiated between genetic groups, suggesting that local adaptation has a widespread effect on reducing gene flow. This study provides one of the few comprehensive examples demonstrating how local adaptation facilitates population divergence at the trait, gene and genome level.

Comparative Metabolomics of Fruits and Leaves in a Hyperdiverse Lineage Suggests Fruits Are a Key Incubator of Phytochemical Diversification

Interactions between plants and leaf herbivores have long been implicated as the major driver of plant secondary metabolite diversity. However, other plant-animal interactions, such as those between fruits and frugivores, may also be involved in phytochemical diversification. Using 12 species of Piper, we conducted untargeted metabolomics and molecular networking with extracts of fruits and leaves. We evaluated organ-specific secondary metabolite composition and compared multiple dimensions of phytochemical diversity across organs, including richness, structural complexity, and variability across samples at multiple scales within and across species. Plant organ identity, species identity, and the interaction between the two all significantly influenced secondary metabolite composition. Leaves and fruit shared a majority of compounds, but fruits contained more unique compounds and had higher total estimated chemical richness. While the relative levels of chemical richness and structural complexity across organs varied substantially across species, fruit diversity exceeded leaf diversity in more species than the reverse. Furthermore, the variance in chemical composition across samples was higher for fruits than leaves. By documenting a broad pattern of high phytochemical diversity in fruits relative to leaves, this study lays groundwork for incorporating fruit into a comprehensive and integrative understanding of the ecological and evolutionary factors shaping secondary metabolite composition at the whole-plant level.

Evolutionary Genomics of Plant Gametophytic Selection

It has long been recognized that natural selection during the haploid gametophytic phase of the plant life cycle may have widespread importance for rates of evolution and the maintenance of genetic variation. Recent theoretical advances have further highlighted the significance of gametophytic selection for diverse evolutionary processes. Genomic approaches offer exciting opportunities to address key questions about the extent and effects of gametophytic selection on plant evolution and adaptation. Here, we review the progress and prospects for integrating functional and evolutionary genomics to test theoretical predictions, and to examine the importance of gametophytic selection on genetic diversity and rates of evolution. There is growing evidence that selection during the gametophyte phase of the plant life cycle has important effects on both gene and genome evolution and is likely to have important pleiotropic effects on the sporophyte. We discuss the opportunities to integrate comparative population genomics, genome-wide association studies, and experimental approaches to further distinguish how differential selection in the two phases of the plant life cycle contributes to genetic diversity and adaptive evolution.

Allelic differences of clustered terpene synthases contribute to correlated intraspecific variation of floral and herbivory-induced volatiles in a wild tobacco

Plant volatile emissions can recruit predators of herbivores for indirect defense and attract pollinators to aid in pollination. Although volatiles involved in defense and pollinator attraction are primarily emitted from leaves and flowers, respectively, they will co-evolve if their underlying genetic basis is intrinsically linked, due either to pleiotropy or to genetic linkage. However, direct evidence of co-evolving defense and floral traits is scarce. We characterized intraspecific variation of herbivory-induced plant volatiles (HIPVs), the key components of indirect defense against herbivores, and floral volatiles in wild tobacco Nicotiana attenuata. We found that variation of (E)-β-ocimene and (E)-α-bergamotene contributed to the correlated changes in HIPVs and floral volatiles among N. attenuata natural accessions. Intraspecific variations of (E)-β-ocimene and (E)-α-bergamotene emissions resulted from allelic variation of two genetically co-localized terpene synthase genes, NaTPS25 and NaTPS38, respectively. Analyzing haplotypes of NaTPS25 and NaTPS38 revealed that allelic variations of NaTPS25 and NaTPS38 resulted in correlated changes of (E)-β-ocimene and (E)-α-bergamotene emission in HIPVs and floral volatiles in N. attenuata. Together, these results provide evidence that pleiotropy and genetic linkage result in correlated changes in defenses and floral signals in natural populations, and the evolution of plant volatiles is probably under diffuse selection.