CHARACTERIZING SELECTION ON PHENOTYPIC PLASTICITY IN RESPONSE TO NATURAL ENVIRONMENTAL HETEROGENEITY

Phenotypic plasticity and genetic diversity shed light on endemism of rare Boechera perstellata and its potential vulnerability to climate warming

The rapid pace of contemporary environmental change puts many species at risk, especially rare species constrained by limited capacity to adapt or migrate due to low genetic diversity and/or fitness. But the ability to acclimate can provide another way to persist through change. We compared the capacity of rare Boechera perstellata (Braun's rockcress) and widespread B. laevigata to acclimate to change. We investigated the phenotypic plasticity of growth, biomass allocation, and leaf morphology of individuals of B. perstellata and B. laevigata propagated from seed collected from several populations throughout their ranges in a growth chamber experiment to assess their capacity to acclimate. Concurrently, we assessed the genetic diversity of sampled populations using 17 microsatellite loci to assess evolutionary potential. Plasticity was limited in both rare B. perstellata and widespread B. laevigata, but differences in the plasticity of root traits between species suggest that B. perstellata may have less capacity to acclimate to change. In contrast to its widespread congener, B. perstellata exhibited no plasticity in response to temperature and weaker plastic responses to water availability. As expected, B. perstellata also had lower levels of observed heterozygosity than B. laevigata at the species level, but population-level trends in diversity measures were inconsistent due to high heterogeneity among B. laevigata populations. Overall, the ability of phenotypic plasticity to broadly explain the rarity of B. perstellata versus commonness of B. laevigata is limited. However, some contextual aspects of our plasticity findings compared with its relatively low genetic variability may shed light on the narrow range and habitat associations of B. perstellata and suggest its vulnerability to climate warming due to acclimatory and evolutionary constraints.

Adaptive divergence generates distinct plastic responses in two closely related Senecio species

The evolution of plastic responses to external cues allows species to maintain fitness in response to the environmental variations they regularly experience. However, it remains unclear how plasticity evolves during adaptation. To test whether distinct patterns of plasticity are associated with adaptive divergence, we quantified plasticity for two closely related but ecologically divergent Sicilian daisy species (Senecio, Asteraceae). We sampled 40 representative genotypes of each species from their native range on Mt. Etna and then reciprocally transplanted multiple clones of each genotype into four field sites along an elevational gradient that included the native elevational range of each species, and two intermediate elevations. At each elevation, we quantified survival and measured leaf traits that included investment (specific leaf area), morphology, chlorophyll fluorescence, pigment content, and gene expression. Traits and differentially expressed genes that changed with elevation in one species often showed little changes in the other species, or changed in the opposite direction. As evidence of adaptive divergence, both species performed better at their native site and better than the species from the other habitat. Adaptive divergence is, therefore, associated with the evolution of distinct plastic responses to environmental variation, despite these two species sharing a recent common ancestor.

Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed

Plastic phenotypic responses to environmental change are common, yet we lack a clear understanding of the fitness consequences of these plastic responses. Here, we use the evolution of herbicide resistance in the common morning glory (Ipomoea purpurea) as a model for understanding the relative importance of adaptive and maladaptive gene expression responses to herbicide. Specifically, we compare leaf gene expression changes caused by herbicide to the expression changes that evolve in response to artificial selection for herbicide resistance. We identify a number of genes that show plastic and evolved responses to herbicide and find that for the majority of genes with both plastic and evolved responses, plastic responses appear to be adaptive. We also find that selection for herbicide response increases gene expression plasticity. Overall, these results show the importance of adaptive plasticity for herbicide resistance in a common weed and that expression changes in response to strong environmental change can be adaptive.

Selection favors adaptive plasticity in a long-term reciprocal transplant experiment

Spatial and temporal environmental variation can favor the evolution of adaptive phenotypic plasticity, such that genotypes alter their phenotypes in response to local conditions to maintain fitness across heterogeneous landscapes. When individuals show greater fitness in one habitat than another, asymmetric migration can restrict adaptation to the lower quality environment. In these cases, selection is predicted to favor traits that enhance fitness in the higher-quality (source) habitat at the expense of fitness in the marginal (sink) habitat. Here, we test whether plasticity is adaptive in a system regulated by demographic source-sink dynamics. Vaccinium elliottii (Ericaceae) occurs in dry upland and flood-prone bottomland forests throughout the southeastern United States, but has larger populations and higher average individual fitness in upland sites. We conducted a multi-year field experiment to evaluate whether plasticity in foliar morphology increases survival and lifespan. Both across and within habitats, selection favored plasticity in specific leaf area, stomatal density, and leaf size. Stabilizing selection acted on plasticity in stomatal density within habitats, suggesting that extreme levels of plasticity are disadvantageous. Thus, even in systems driven by source-sink dynamics, temporal and spatial variation in conditions across the landscape and within habitat types can favor the evolution of plasticity.

Multiple modes of selection can influence the role of phenotypic plasticity in species' invasions: Evidence from a manipulative field experiment

In exploring the roles of phenotypic plasticity in the establishment and early evolution of invading species, little empirical attention has been given to the importance of correlational selection acting upon suites of functionally related plastic traits in nature. We illustrate how this lack of attention has limited our ability to evaluate plasticity's role during invasion and also, the costs and benefits of plasticity. We addressed these issues by transplanting clones of European-derived Plantago lanceolata L. genotypes into two temporally variable habitats in the species' introduced range in North America. Phenotypic selection analyses were performed for each habitat to estimate linear, quadratic, and correlational selection on phenotypic trait values and plasticities in the reproductive traits: flowering onset and spike and scape lengths. Also, we measured pairwise genetic correlations for our "colonists." Results showed that (a) correlational selection acted on trait plasticity after transplantation, (b) selection favored certain combinations of genetically correlated and uncorrelated trait values and plasticities, and (c) using signed, instead of absolute, values of plasticity in analyses facilitated the detection of correlational selection on trait value-plasticity combinations and their adaptive value. Based on our results, we urge future studies on species invasions to (a) measure correlational selection and (b) retain signed values of plasticity in order to better discriminate between adaptive and maladaptive plasticity.

Climate explains population divergence in drought-induced plasticity of functional traits and gene expression in a South African Protea

Long-term environmental variation often drives local adaptation and leads to trait differentiation across populations. Additionally, when traits change in an environment-dependent way through phenotypic plasticity, the genetic variation underlying plasticity will also be under selection. These processes could create a landscape of differentiation across populations in traits and their plasticity. Here, we performed a dry-down experiment under controlled conditions to measure responses in seedlings of a shrub species from the Cape Floristic Region, the common sugarbush (Protea repens). We measured morphological and physiological traits, and sequenced whole transcriptomes of leaf tissues from eight populations that represent both the climatic and the geographical distribution of this species. We found that there is substantial variation in how populations respond to drought, but we also observed common patterns such as reduced leaf size and leaf thickness, and up-regulation of stress-related and down-regulation of growth-related gene groups. Both high environmental heterogeneity and milder source site climates were associated with higher plasticity in various traits and co-expression gene networks. Associations between traits, trait plasticity, gene networks and the source site climate suggest that temperature may play a greater role in shaping these patterns when compared to precipitation, in line with recent changes in the region due to climate change. We also found that traits respond to climatic variation in an environment-dependent manner: some associations between traits and climate were apparent only under certain growing conditions. Together, our results uncover common responses of P. repens populations to drought, and climatic drivers of population differentiation in functional traits, gene expression and their plasticity.

Enhanced leaky sex expression in response to pollen limitation in the dioecious plant Mercurialis annua

In dioecious plants, males and females frequently show ‘leaky’ sex expression, with individuals occasionally producing flowers of the opposite sex. This leaky sex expression may have enabled the colonization of oceanic islands by dioecious plant species, and it is likely to represent the sort of variation upon which selection acts to bring about evolutionary transitions from dioecy to hermaphroditism. Although leakiness is commonly reported for dioecious species, it is not known whether it has plastic component. The question is interesting because males or females with an ability to enhance their leakiness plastically in the absence of mates would have an advantage of being able to produce progeny by self‐fertilization. Here, we demonstrate that leaky sex expression in the wind‐pollinated dioecious herb Mercurialis annua is plastically responsive to its mating context. We compared experimental populations of females growing either with or without males. Females growing in the absence of males were leakier in their sex expression than controls growing with males, producing more than twice as many male flowers. Our results thus provide a striking instance of plasticity in the reproductive behaviour of plants that is likely adaptive. We consider how females might sense their mating environment as a function of pollen availability, and we discuss possible constraints on the evolution of plasticity in sex expression when the environmental signals that individuals receive are unreliable.

Plant adaptation to climate change - Where are we?

Climate change poses critical challenges for population persistence in natural communities, agriculture and environmental sustainability, and food security. In this review, we discuss recent progress in climatic adaptation in plants. We evaluate whether climate change exerts novel selection and disrupts local adaptation, whether gene flow can facilitate adaptive responses to climate change, and if adaptive phenotypic plasticity could sustain populations in the short term. Furthermore, we discuss how climate change influences species interactions. Through a more in-depth understanding of these eco-evolutionary dynamics, we will increase our capacity to predict the adaptive potential of plants under climate change. In addition, we review studies that dissect the genetic basis of plant adaptation to climate change. Finally, we highlight key research gaps, ranging from validating gene function, to elucidating molecular mechanisms, expanding research systems from model species to other natural species, testing the fitness consequences of alleles in natural environments, and designing multifactorial studies that more closely reflect the complex and interactive effects of multiple climate change factors. By leveraging interdisciplinary tools (e.g., cutting-edge omics toolkits, novel ecological strategies, newly-developed genome editing technology), researchers can more accurately predict the probability that species can persist through this rapid and intense period of environmental change, as well as cultivate crops to withstand climate change, and conserve biodiversity in natural systems.

Adaptation and divergence in edaphic specialists and generalists: serpentine soil endemics in the California flora occur in barer serpentine habitats with lower soil calcium levels than serpentine tolerators

PREMISE

Adaptation to harsh edaphic substrates has repeatedly led to the evolution of edaphic specialists and generalists. Yet, it is unclear what factors promote specialization versus generalization. Here, we search for habitat use patterns associated with serpentine endemics (specialists) and serpentine tolerators (generalists) to indirectly test the hypothesis that trade-offs associated with serpentine adaptation promote specialization. We predict that (1) endemics have adapted to chemically harsher and more bare serpentine habitats than tolerators, and (2) edaphic endemics show more habitat divergence from their sister species than tolerators do among on- and off-serpentine populations.

METHODS

We selected 8 serpentine endemic and 9 serpentine tolerator species representing independent adaptation to serpentine. We characterized soil chemistry and microhabitat bareness from one serpentine taxon of each species and from a paired nonserpentine sister taxon, resulting in 8 endemic and 9 tolerator sister-taxa pairs.

RESULTS

We find endemic serpentine taxa occur in serpentine habitats averaging twice as much bare ground as tolerator serpentine taxa and 25% less soil calcium, a limiting macronutrient in serpentine soils. We do not find strong evidence that habitat divergence between sister taxa of endemic pairs is greater than between sister taxa of tolerator pairs.

CONCLUSIONS

These results suggest serpentine endemism is associated with adaptation to chemically harsher and more bare serpentine habitats. It may be that this adaptation trades off with competitive ability, which would support the longstanding, but rarely tested, competitive trade-off hypothesis.

Determining the evolutionary forces shaping G × E

Contents Summary 31 I. Introduction 31 II. The maintenance of genetic variation for plasticity 32 III. Why is there environmental variation for genetic effects? 33 IV. Conclusions 35 Acknowledgements 35 References 35 SUMMARY: Phenotypic plasticity is common in nature, yet we lack a comprehensive understanding of the evolutionary forces that shape genetic variation for plasticity. This endeavor is especially important because variation for plasticity will result in genotype-by-environment interactions (G × E), a crucial component of variation in quantitative traits. Here, I review our understanding of the evolutionary forces shaping G × E, focusing specifically on: what evolutionary forces maintain variation for plasticity; and what forces maintain different genetic architectures across environments. My specific goal is to show that genomic data can be leveraged to explain the maintenance of G × E by contrasting patterns of genetic variation for plasticity with neutral expectations.

Environmentally induced development costs underlie fitness tradeoffs

Local adaptation can lead to genotype-by-environment interactions, which can create fitness tradeoffs in alternative environments, and govern the distribution of biodiversity across geographic landscapes. Exploring the ecological circumstances that promote the evolution of fitness tradeoffs requires identifying how natural selection operates and during which ontogenetic stages natural selection is strongest. When organisms disperse to areas outside their natural range, tradeoffs might emerge when organisms struggle to reach key life history stages, or alternatively, die shortly after reaching life history stages if there are greater risks of mortality associated with costs to developing in novel environments. We used multiple populations from four ecotypes of an Australian native wildflower (Senecio pinnatifolius) in reciprocal transplants to explore how fitness tradeoffs arise across ontogeny. We then assessed whether the survival probability for plants from native and foreign populations was contingent on reaching key developmental stages. We found that fitness tradeoffs emerged as ontogeny progressed when native plants were more successful than foreign plants at reaching seedling establishment and maturity. Native and foreign plants that failed to reach seedling establishment died at the same rate, but plants from foreign populations died quicker than native plants after reaching seedling establishment, and died quicker regardless of whether they reached sexual maturity or not. Development rates were similar for native and foreign populations, but changed depending on the environment. Together, our results suggest that natural selection for environment-specific traits early in life history created tradeoffs between contrasting environments. Plants from foreign populations were either unable to develop to seedling establishment, or they suffered increased mortality as a consequence of reaching seedling establishment. The observation of tradeoffs together with environmentally dependent changes in development rate suggest that foreign environments induce organisms to develop at a rate different from their native habitat, incurring consequences for lifetime fitness and population divergence.

Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta

Phenotypic plasticity is thought to impact evolutionary trajectories by shifting trait values in a direction that is either favored by natural selection ("adaptive" plasticity) or disfavored ("nonadaptive" plasticity). However, it is unclear how commonly each of these types of plasticity occurs in natural populations. To answer this question, we measured glucosinolate defensive chemistry and reproductive fitness in over 1500 individuals of the wild perennial mustard Boechera stricta, planted in four common gardens across central Idaho, United States. Glucosinolate profiles-including total glucosinolate concentration as well as the relative abundances and overall diversity of different compounds-were strongly plastic both among habitats and within habitats. Patterns of glucosinolate plasticity varied greatly among genotypes. Plasticity among sites was predicted to affect fitness in 27.1% of cases; more often than expected by chance, glucosinolate plasticity increased rather than decreased relative fitness. In contrast, we found no evidence for within-habitat selection on glucosinolate reaction norm slopes (i.e., plasticity along a continuous environmental gradient). Together, our results indicate that glucosinolate plasticity may improve the ability of B. stricta populations to persist after migration to new habitats.

Flowering phenology shifts in response to biodiversity loss

Observational studies and experimental evidence agree that rising global temperatures have altered plant phenology-the timing of life events, such as flowering, germination, and leaf-out. Other large-scale global environmental changes, such as nitrogen deposition and altered precipitation regimes, have also been linked to changes in flowering times. Despite our increased understanding of how abiotic factors influence plant phenology, we know very little about how biotic interactions can affect flowering times, a significant knowledge gap given ongoing human-caused alteration of biodiversity and plant community structure at the global scale. We experimentally manipulated plant diversity in a California serpentine grassland and found that many plant species flowered earlier in response to reductions in diversity, with peak flowering date advancing an average of 0.6 days per species lost. These changes in phenology were mediated by the effects of plant diversity on soil surface temperature, available soil N, and soil moisture. Peak flowering dates were also more dispersed among species in high-diversity plots than expected based on monocultures. Our findings illustrate that shifts in plant species composition and diversity can alter the timing and distribution of flowering events, and that these changes to phenology are similar in magnitude to effects induced by climate change. Declining diversity could thus contribute to or exacerbate phenological changes attributed to rising global temperatures.

Population-dependent effects of ocean acidification

Elevated carbon dioxide levels and the resultant ocean acidification (OA) are changing the abiotic conditions of the oceans at a greater rate than ever before and placing pressure on marine species. Understanding the response of marine fauna to this change is critical for understanding the effects of OA. Population-level variation in OA tolerance is highly relevant and important in the determination of ecosystem resilience and persistence, but has received little focus to date. In this study, whether OA has the same biological consequences in high-salinity-acclimated population versus a low-salinity-acclimated population of the same species was investigated in the marine isopod Idotea balthica.The populations were found to have physiologically different responses to OA. While survival rate was similar between the two study populations at a future CO2 level of 1000 ppm, and both populations showed increased oxidative stress, the metabolic rate and osmoregulatory activity differed significantly between the two populations. The results of this study demonstrate that the physiological response to OA of populations from different salinities can vary. Population-level variation and the environment provenance of individuals used in OA experiments should be taken into account for the evaluation and prediction of climate change effects.

Climate and habitat interact to shape the thermal reaction norms of breeding phenology across lizard populations

Substantial plastic variation in phenology in response to environmental heterogeneity through time in the same population has been uncovered in many species. However, our understanding of differences in reaction norms of phenology among populations from a given species remains limited. As the plasticity of phenological traits is often influenced by local thermal conditions, we expect local temperature to generate variation in the reaction norms between populations. Here, we explored temporal variation in parturition date across 11 populations of the common lizard (Zootoca vivipara) from four mountain chains as a function of air temperatures during mid-gestation. We characterized among-population variation to assess how local weather conditions (mean and variance of ambient temperatures during mid-gestation) and habitat openness (an index of anthropogenic disturbance) influence the thermal reaction norms of the parturition date. Our results provide evidence of interactive effects of anthropogenic disturbance and thermal conditions, with earlier parturition dates in warmer years on average especially in closed habitats. Variation in the reaction norms for parturition date was correlated with mean local thermal conditions at a broad geographical scale. However, populations exposed to variable thermal conditions had flatter thermal reaction norms. Assessing whether environmental heterogeneity drives differentiation among reaction norms is crucial to estimate the capacity of different populations to contend with projected climatic and anthropogenic challenges.

Potential for adaptive evolution at species range margins: contrasting interactions between red coral populations and their environment in a changing ocean

Studying population-by-environment interactions (PEIs) at species range margins offers the opportunity to characterize the responses of populations facing an extreme regime of selection, as expected due to global change. Nevertheless, the importance of these marginal populations as putative reservoirs of adaptive genetic variation has scarcely been considered in conservation biology. This is particularly true in marine ecosystems for which the deep refugia hypothesis proposes that disturbed shallow and marginal populations of a given species can be replenished by mesophotic ones. This hypothesis therefore assumes that identical PEIs exist between populations, neglecting the potential for adaptation at species range margins. Here, we combine reciprocal transplant and common garden experiments with population genetics analyses to decipher the PEIs in the red coral, Corallium rubrum. Our analyses reveal partially contrasting PEIs between shallow and mesophotic populations separated by approximately one hundred meters, suggesting that red coral populations may potentially be locally adapted to their environment. Based on the effective population size and connectivity analyses, we posit that genetic drift may be more important than gene flow in the adaptation of the red coral. We further investigate how adaptive divergence could impact population viability in the context of warming and demonstrate differential phenotypic buffering capacities against thermal stress. Our study questions the relevance of the deep refugia hypothesis and highlights the conservation value of marginal populations as a putative reservoir of adaptive genetic polymorphism.

Testing local host adaptation and phenotypic plasticity in a herbivore when alternative related host plants occur sympatrically

Host race formation in phytophagous insects can be an early stage of adaptive speciation. However, the evolution of phenotypic plasticity in host use is another possible outcome. Using a reciprocal transplant experiment we tested the hypothesis of local adaptation in the aphid Brevicoryne brassicae. Aphid genotypes derived from two sympatric host plants, Brassica oleracea and B. campestris, were assessed in order to measure the extent of phenotypic plasticity in morphological and life history traits in relation to the host plants. We obtained an index of phenotypic plasticity for each genotype. Morphological variation of aphids was summarized by principal components analysis. Significant effects of recipient host on morphological variation and life history traits (establishment, age at first reproduction, number of nymphs, and intrinsic growth rate) were detected. We did not detected genotype × host plant interaction; in general the genotypes developed better on B. campestris, independent of the host plant species from which they were collected. Therefore, there was no evidence to suggest local adaptation. Regarding plasticity, significant differences among genotypes in the index of plasticity were detected. Furthermore, significant selection on PC1 (general aphid body size) on B. campestris, and on PC1 and PC2 (body length relative to body size) on B. oleracea was detected. The elevation of the reaction norm of PC1 and the slope of the reaction norm for PC2 (i.e., plasticity) were under directional selection. Thus, host plant species constitute distinct selective environments for B. brassicae. Aphid genotypes expressed different phenotypes in response to the host plant with low or nil fitness costs. Phenotypic plasticity and gene flow limits natural selection for host specialization promoting the maintenance of genetic variation in host exploitation.

The evolution of quantitative traits in complex environments

Species inhabit complex environments and respond to selection imposed by numerous abiotic and biotic conditions that vary in both space and time. Environmental heterogeneity strongly influences trait evolution and patterns of adaptive population differentiation. For example, heterogeneity can favor local adaptation, or can promote the evolution of plastic genotypes that alter their phenotypes based on the conditions they encounter. Different abiotic and biotic agents of selection can act synergistically to either accelerate or constrain trait evolution. The environmental context has profound effects on quantitative genetic parameters. For instance, heritabilities measured in controlled conditions often exceed those measured in the field; thus, laboratory experiments could overestimate the potential for a population to respond to selection. Nevertheless, most studies of the genetic basis of ecologically relevant traits are conducted in simplified laboratory environments, which do not reflect the complexity of nature. Here, we advocate for manipulative field experiments in the native ranges of plant species that differ in mating system, life-history strategy and growth form. Field studies are vital to evaluate the roles of disparate agents of selection, to elucidate the targets of selection and to develop a nuanced perspective on the evolution of quantitative traits. Quantitative genetics field studies will also shed light on the potential for natural populations to adapt to novel climates in highly fragmented landscapes. Drawing from our experience with the ecological model system Boechera (Brassicaceae), we discuss advancements possible through dedicated field studies, highlight future research directions and examine the challenges associated with field studies.

Early developmental responses to seedling environment modulate later plasticity to light spectral quality

Correlations between developmentally plastic traits may constrain the joint evolution of traits. In plants, both seedling de-etiolation and shade avoidance elongation responses to crowding and foliage shade are mediated by partially overlapping developmental pathways, suggesting the possibility of pleiotropic constraints. To test for such constraints, we exposed inbred lines of Impatiens capensis to factorial combinations of leaf litter (which affects de-etiolation) and simulated foliage shade (which affects phytochrome-mediated shade avoidance). Increased elongation of hypocotyls caused by leaf litter phenotypically enhanced subsequent elongation of the first internode in response to low red∶far red (R∶FR). Trait expression was correlated across litter and shade conditions, suggesting that phenotypic effects of early plasticity on later plasticity may affect variation in elongation traits available to selection in different light environments.

Evolutionary genetics of plant adaptation

Plants provide unique opportunities to study the mechanistic basis and evolutionary processes of adaptation to diverse environmental conditions. Complementary laboratory and field experiments are important for testing hypotheses reflecting long-term ecological and evolutionary history. For example, these approaches can infer whether local adaptation results from genetic tradeoffs (antagonistic pleiotropy), where native alleles are best adapted to local conditions, or if local adaptation is caused by conditional neutrality at many loci, where alleles show fitness differences in one environment, but not in a contrasting environment. Ecological genetics in natural populations of perennial or outcrossing plants can also differ substantially from model systems. In this review of the evolutionary genetics of plant adaptation, we emphasize the importance of field studies for understanding the evolutionary dynamics of model and nonmodel systems, highlight a key life history trait (flowering time) and discuss emerging conservation issues.