Christina L. Richards

Plant phenotypic plasticity in a changing climate

Climate change is altering the availability of resources and the conditions that are crucial to plant performance. One way plants will respond to these changes is through environmentally induced shifts in phenotype (phenotypic plasticity). Understanding plastic responses is crucial for predicting and managing the effects of climate change on native species as well as crop plants. Here, we provide a toolbox with definitions of key theoretical elements and a synthesis of the current understanding of the molecular and genetic mechanisms underlying plasticity relevant to climate change. By bringing ecological, evolutionary, physiological and molecular perspectives together, we hope to provide clear directives for future research and stimulate cross-disciplinary dialogue on the relevance of phenotypic plasticity under climate change.

PHENOTYPIC PLASTICITY AND INTERACTIONS AMONG PLANTS

We know a great deal about the plastic responses of plant phenotypes to the abiotic and biotic environment, but very little about the consequences of phenotypic plas- ticity for plant communities. In other words, we know that plant traits can vary widely for a given genotype, but we know little about the importance of trait-mediated interactions (TMI) among plants. Here, we discuss three major factors that affect the expression of phenotypic plasticity: variation in the abiotic environment, variation in the presence or identity of neighbors, and variation in herbivory. We consider how plastic responses to these factors might affect interactions among plants. Plastic responses to the abiotic en- vironment have important consequences for conditionality in competitive effects, to the point of causing shifts from competitive to facilitative interactions. Because plants show a high degree of plasticity in response to neighbors, and even to the specific identify of neighbors, phenotypic plasticity may allow species to adjust to the composition of their communities, promoting coexistence and community diversity. Likewise, plastic responses to consumers may have various and counterintuitive consequences: induction of plant re- sistance, compensatory growth, and increased resource uptake may affect interactions among plants in ways that cannot be predicted simply by considering biomass lost to consumers. What little we know about TMI among plants suggests that they should not be ignored in plant community theory. Although work to date on the community consequences of phenotypic plasticity has been hampered by experimental constraints, new approaches such as manipulating phenotypes by using signals instead of actual environmental conditions and the use of transgenic plants should allow us to rapidly expand our understanding of the community consequences of plant plasticity.

Invasion of diverse habitats by few Japanese knotweed genotypes is correlated with epigenetic differentiation

The expansion of invasive species challenges our understanding of the process of adaptation. Given that the invasion process often entails population bottlenecks, it is surprising that many invasives appear to thrive even with low levels of sequence-based genetic variation. Using Amplified Fragment Length Polymorphism (AFLP) and methylation sensitive-AFLP (MS-AFLP) markers, we tested the hypothesis that differentiation of invasive Japanese knotweed in response to new habitats is more correlated with epigenetic variation than DNA sequence variation. We found that the relatively little genetic variation present was differentiated among species, with less differentiation among sites within species. In contrast, we found a great deal of epigenetic differentiation among sites within each species and evidence that some epigenetic loci may respond to local microhabitat conditions. Our findings indicate that epigenetic effects could contribute to phenotypic variation in genetically depauperate invasive populations. Deciphering whether differences in methylation patterns are the cause or effect of habitat differentiation will require manipulative studies.

What Role Does Heritable Epigenetic Variation Play in Phenotypic Evolution

To explore the potential evolutionary relevance of heritable epigenetic variation, the National Evolutionary Synthesis Center recently hosted a catalysis meeting that brought together molecular epigeneticists, experimental evolutionary ecologists, and theoretical population and quantitative geneticists working across a wide variety of systems. The group discussed the methods available to investigate epigenetic variation and epigenetic inheritance, and how to evaluate their importance for phenotypic evolution. We found that understanding the relevance of epigenetic effects in phenotypic evolution will require clearly delineating epigenetics within existing terminology and expanding research efforts into ecologically relevant circumstances across model and nonmodel organisms. In addition, a critical component of understanding epigenetics will be the development of new and current statistical approaches and expansion of quantitative and population genetic theory. Although the importance of heritable epigenetic effects on evolution is still under discussion, investigating them in the context of a multidisciplinary approach could transform the field.

Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis thaliana.

Heritable phenotypic variation in plants can be caused not only by underlying genetic differences, but also by variation in epigenetic modifications such as DNA methylation. However, we still know very little about how relevant such epigenetic variation is to the ecology and evolution of natural populations. We conducted a greenhouse experiment in which we treated a set of natural genotypes of Arabidopsis thaliana with the demethylating agent 5-azacytidine and examined the consequences of this treatment for plant traits and their phenotypic plasticity. Experimental demethylation strongly reduced the growth and fitness of plants and delayed their flowering, but the degree of this response varied significantly among genotypes. Differences in genotypes’ responses to demethylation were only weakly related to their genetic relatedness, which is consistent with the idea that natural epigenetic variation is independent of genetic variation. Demethylation also altered patterns of phenotypic plasticity, as well as the amount of phenotypic variation observed among plant individuals and genotype means. We have demonstrated that epigenetic variation can have a dramatic impact on ecologically important plant traits and their variability, as well as on the fitness of plants and their ecological interactions. Epigenetic variation may thus be an overlooked factor in the evolutionary ecology of plant populations.

Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

Molecular ecology has moved beyond the use of a relatively small number of markers, often noncoding, and it is now possible to use whole‐genome measures of gene expression with microarrays and RNAseq (i.e. transcriptomics) to capture molecular response to environmental challenges. While transcriptome studies are shedding light on the mechanistic basis of traits as complex as personality or physiological response to catastrophic events, these approaches are still challenging because of the required technical expertise, difficulties with analysis and cost. Still, we found that in the last 10 years, 575 studies used microarrays or RNAseq in ecology. These studies broadly address three questions that reflect the progression of the field: (i) How much variation in gene expression is there and how is it structured? (ii) How do environmental stimuli affect gene expression? (iii) How does gene expression affect phenotype? We discuss technical aspects of RNAseq and microarray technology, and a framework that leverages the advantages of both. Further, we highlight future directions of research, particularly related to moving beyond correlation and the development of additional annotation resources. Measuring gene expression across an array of taxa in ecological settings promises to enrich our understanding of ecology and genome function.

Plasticity in salt tolerance traits allows for invasion of novel habitat by Japanese knotweed s. l. (Fallopia japonica and F.×bohemica, Polygonaceae)

Japanese knotweeds are among the most invasive organisms in the world. Their recent expansion into salt marsh habitat provides a unique opportunity to investigate how invasives establish in new environments. We used morphology, cytology, and AFLP genotyping to identify taxa and clonal diversity in roadside and salt marsh populations. We conducted a greenhouse study to determine the ability to tolerate salt and whether salt marsh populations are more salt tolerant than roadside populations as measured by the efficiency of PSII, leaf area, succulence, height, root-to-shoot ratio, and total biomass. Clonal diversity was extremely low with one F. japonica clone and five F. ×bohemica genotypes. The two taxa were significantly different in several traits, but did not vary in biomass or plasticity of any trait. All traits were highly plastic in response to salinity, but differed significantly among genets. Despite this variation, plants from the salt marsh habitats did not perform better in the salt treatment, suggesting that they are not better adapted to tolerate salt. Instead, our data support the hypothesis that plasticity in salt tolerance traits may allow these taxa to live in saline habitats without specific adaptation to tolerate salt.

Understanding natural epigenetic variation

Recently, there has been increased interest in understanding the role of epigenetic processes in ecology and evolution (e.g. Richards, 2006; Bossdorf et al., 2008; Johannes et al., 2008; Richards et al., 2010). We now know that some epigenetic marks are not reset each generation, but are faithfully transmitted across generations (Jablonka & Raz, 2009), that natural variation can exist not only in the DNA sequence but also at the epigenetic level (e.g. Vaughn et al., 2007) and that epigenetic variation can cause significant heritable variation in phenotypic traits (e.g. Johannes et al., 2009). Moreover, heritable epigenetic modifications can be triggered by exposure to different environmental conditions (e.g. Verhoeven et al., 2010). If we put these different pieces of evidence together, then this clearly suggests that epigenetic mechanisms could add an additional layer of complexity to heritable phenotypic variation, and thus to the diversity and evolutionary potential of natural populations. However, in spite of abundant speculation about the potential ecological and evolutionary implications of epigenetic processes, most previous work has been carried out on only a few types of agricultural crops and on model species such as Arabidopsis thaliana, frequently under artificial conditions, and we therefore still have no idea of the true importance of epigenetic processes in natural populations. Because of this, several authors have argued for expanding research efforts into ecologically relevant circumstances across model and nonmodel organisms and have outlined experimental and statistical approaches that would facilitate the merging of molecular-based insight with sound evolutionary ecology (Bossdorf et al., 2008; Johannes et al., 2008; Richards, 2008). In this issue of New Phytologist (pp. 867–876), Herrera & Bazaga provide an intriguing example of how researchers are now beginning to respond to this call.

Ecological Epigenetics: Beyond MS-AFLP

Ecological Epigenetics studies the relationship between epigenetic variation and ecologically relevant phenotypic variation. As molecular epigenetic mechanisms often control gene expression, even across generations, they may impact many evolutionary processes. Multiple molecular epigenetic mechanisms exist, but methylation of DNA so far has dominated the Ecological Epigenetic literature. There are several molecular techniques used to screen methylation of DNA; here, we focus on the most common technique, methylation-sensitive-AFLP (MS-AFLP), which is used to identify genome-wide methylation patterns. We review studies that used MS-AFLP to address ecological questions, that describe which taxa have been investigated, and that identify general trends in the field. We then discuss, noting the general themes, four studies across taxa that demonstrate characteristics that increase the inferences that can be made from MS-AFLP data; we suggest that future MS-AFLP studies should incorporate these methods and techniques. We then review the short-comings of MS-AFLP and suggest alternative techniques that might address some of these limitations. Finally, we make specific suggestions for future research on MS-AFLP and identify questions that are most compelling and tractable in the short term.

Habitat Range and Phenotypic Variation in Salt Marsh Plants

Ecologists have long speculated that species with wider environmental ranges would have broader ranges in phenotype; however, most tests of this hypothesis have involved small numbers of species and/or closely related taxa. We related phenotypic variation in twelve salt marsh plant species from six families to variation in four environmental variables using multiple regression. Within species, plant phenotype was predictably related to environmental variation. Salinity was the most common predictor of plant traits, followed by organic content, water content and elevation. Across species, regressions of single plant trait CVs on range (2 × SD) of single environmental variables were not significant and did not support the hypothesis that species occupying broad environmental ranges would have broad ranges in phenotypes. However, regression of a composite phenotypic PCA1 on a composite environmental PCA1 showed a marginally significant (P = 0.054). linear relationship for 10 species. Considering the different patterns of response across species, the lack of a relationship between variation in single phenotypic traits and single environmental variables is likely because the distantly-related taxa employed fundamentally different morphological and physiological strategies to respond to environmental stress gradients. The significant relationship between composite environmental and phenotypic variables reflects the complex nature of species phenotypic response to multivariate environmental gradients. Specifically, in this system, species increase variation in the number of leaves, but decrease variation in leaf size in response to an increase in range of salinity and decrease in range of water and organic content.