WHEN DO ADAPTIVE PLASTICITY AND GENETIC EVOLUTION PREVENT EXTINCTION OF A DENSITY-REGULATED POPULATION?

Plasticity as a Sign of Developmental Bias in the Evolution of Gene Regulatory Networks

Phenotypic plasticity is an organism's ability to produce a different phenotype in response to nongenetic perturbations such as environmental disturbances. Beneficial phenotypic plasticity can be important in evolution. After an environmental disturbance, it can delay extinction giving opportunity to the appearance of beneficial mutations. In addition, plasticity may also be one of the factors that define the course that evolution takes, for example, through genetic assimilation. This is a process in which a phenotype that initially appears as a plastic response becomes under genetic control. In the end, development of such a phenotype does not require the factor that originally induced it. Here, I use a model of the evolution of gene regulatory networks to study the range of conditions that allow the association between plasticity and the course of evolution. I assayed conditions like the difference between ancestral and optimum phenotypes, the difficulty to build the optimum phenotype, the complexity of the developmental system, mutation rate, strength of plasticity limitations, fitness advantage of the optima, and the similarity between the initially induced phenotype and the optimum. I found that populations that yield a beneficial phenotype through plasticity most often evolve a similar genetically determined phenotype under all the conditions that I assayed. I also identified conditions that facilitate evolution through genetic assimilation. Notwithstanding, even under less favorable circumstances, this form of evolution still confers easier access to a new genetically determined optimum.

Accelerated Phenology Fails to Buffer Fitness Loss from Delayed Rain Onset in a Clade of Wildflowers

AbstractThe timing of early life cycle events has cascading effects on phenology and fitness. These effects may be critical for climate resilience of plant populations, especially in Mediterranean environments, where delayed rainfall onset causes delayed germination. To examine impacts of germination timing on 10 species of the Streptanthus/Caulanthus clade, we induced germination across a range of dates in ambient seasonal conditions and recorded phenological and fitness traits. Later-germinating cohorts accelerated flowering, partially stabilizing flowering date, but the degree of this compensatory plasticity differed across species. Fitness declined with later germination; the magnitude of this decline depended on the balance between direct negative effects of later germination and compensatory positive effects of accelerated flowering. The resulting species' differences in fitness responses suggest differential vulnerability to climate change. Species from wetter, cooler, less variable habitats exhibited greater phenological plasticity, accelerating flowering more and declining less in seed set with later germination than desert species. However, other fitness responses to germination timing, such as first-year fitness, were evolutionarily labile across the clade and unrelated to climate. Although compensatory phenological plasticity may buffer the impacts of delayed germination, it cannot prevent long-term declines in population fitness as fall rains come later with climate change.

Impacts of limits to adaptation on population and community persistence in a changing environment

A key issue in predicting how ecosystems will respond to environmental change is understanding why populations and communities are able to live and reproduce in some parts of ecological and geographical space, but not in others. The limits to adaptation that cause ecological niches to vary in position and width across taxa and environmental contexts determine how communities and ecosystems emerge from selection on phenotypes and genomes. Ecological trade-offs mean that phenotypes can only be optimal in some environments unless these trade-offs can be reshaped through evolution. However, the amount and rate of evolution are limited by genetic architectures, developmental systems (including phenotypic plasticity) and the legacies of recent evolutionary history. Here, we summarize adaptive limits and their ecological consequences in time (evolutionary rescue) and space (species' range limits), relating theoretical predictions to empirical tests. We then highlight key avenues for future research in this area, from better connections between evolution and demography to analysing the genomic architecture of adaptation, the dynamics of plasticity and interactions between the biotic and abiotic environment. Progress on these questions will help us understand when and where evolution and phenotypic plasticity will allow species and communities to persist in the face of rapid environmental change.This article is part of the discussion meeting issue 'Bending the curve towards nature recovery: building on Georgina Mace's legacy for a biodiverse future'.

The genetics of phenotypic plasticity. XVIII. Developmental limits restrict adaptive plasticity

After environmental change, the trait evolution needed to rescue a population depends on the functional form of the plastic change (reaction norm) of that trait. Nearly all previous models of plasticity evolution for continuous traits have assumed that the functional form is linear, that is, no limits on the range of plasticity. This paper examines the effect of developmental limits, modeled as a sigmoidal reaction norm, on evolutionary rescue after an abrupt environmental change and the subsequent evolution of plasticity, including genetic assimilation. We examined four different scenarios: (1) developmental limits only, (2) developmental limits plus a cost of plasticity, (3) developmental limits with developmental noise, and (4) developmental limits plus environmental variation. The probability of evolutionary rescue increased with an increase in phenotypic variation allowed by plastic development. With a smaller limit to the range of the plastic phenotype, the evolution of adaptive plasticity was limited, meaning the evolution of non-plastic genes was necessary. The addition of developmental constraints to the model did not speed up genetic assimilation, suggesting a new theory is needed to understand empirical observations. The modeling framework presented here could be extended to different ecological and evolutionary conditions, alternative reaction norm shapes, the evolution of additional reaction norm parameters such as the range or the location of the inflection point on the environmental axis, or other function-valued traits.

On the evolutionary origin of discrete phenotypic plasticity

Phenotypic plasticity provides an attractive strategy for adapting to various environments, but the evolutionary mechanism of the underlying genetic system is poorly understood. We use a simple gene regulatory network model to explore how a species acquires phenotypic plasticity, particularly focusing on discrete phenotypic plasticity, which has been difficult to explain by quantitative genetic models. Our approach employs a population genetic framework that integrates the developmental process, where each individual undergoes growth to develop its phenotype, which subsequently becomes subject to selection pressures. Our model considers two alternative types of environments, with the gene regulatory network including a sensor gene that turns on and off depending on the type of environment. With this assumption, we demonstrate that the system gradually adapts by acquiring the ability to produce two distinct optimum phenotypes under two types of environments without changing genotype, resulting in phenotypic plasticity. We find that the resulting plasticity is often discrete after a lengthy period of evolution. Our results suggest that gene regulatory networks have a notable capacity to flexibly produce various phenotypes in response to environmental changes. This study also shows that the evolutionary dynamics of phenotype may differ significantly between mechanistic-based developmental models and quantitative genetics models, suggesting the utility of incorporating gene regulatory networks into evolutionary models.

Understanding evolutionary rescue and parallelism in response to environmental stress

Evolutionary rescue, the process by which populations facing environmental stress avoid extinction through genetic adaptation, is a critical area of study in evolutionary biology. The order in which mutations arise and get established will be relevant to the population's rescue. This study investigates the degree of parallel evolution at the genotypic level between independent populations facing environmental stress and subject to different demographic regimes. Under density regulation, 2 regimes exist: In the first, the population can restore positive growth rates by adjusting its population size or through adaptive mutations, whereas in the second regime, the population is doomed to extinction unless a rescue mutation occurs. Analytical approximations for the likelihood of evolutionary rescue are obtained and contrasted with simulation results. We show that the initial level of maladaptation and the demographic regime significantly affect the level of parallelism. There is an evident transition between these 2 regimes. Whereas in the first regime, parallelism decreases with the level of maladaptation, it displays the opposite behavior in the rescue/extinction regime. These findings have important implications for understanding population persistence and the degree of parallelism in evolutionary responses as they integrate demographic effects and evolutionary processes.

Evolution of ion transporter Na+/K+-ATPase expression in the osmoregulatory maxillary glands of an invasive copepod

While many freshwater invaders originate from saline habitats, the physiological mechanisms involved are poorly understood. We investigated the evolution of ion transporter Na+/K+-ATPase (NKA) protein expression between ancestral saline and freshwater invading populations of the copepod Eurytemora carolleae (Atlantic clade of the E. affinis complex). We compared in situ NKA expression between populations under common-garden conditions at three salinities in the maxillary glands. We found the evolution of reduced NKA expression in the freshwater population under freshwater conditions and reduced plasticity (canalization) across salinities, relative to the saline population. Our results support the hypothesis that maxillary glands are involved in ion reabsorption from excretory fluids at low-salinity conditions in the saline population. However, mechanisms of freshwater adaptation, such as increased ion uptake from the environment, might reduce the need for ion reabsorption in the freshwater population. These patterns of ion transporter expression contribute insights into the evolution of ionic regulation during habitat change.

Weak evidence of provenance effects in spring phenology across Europe and North America

Forecasting the biological impacts of climate change requires understanding how species respond to warmer temperatures through interannual flexible variation vs through adaptation to local conditions. Yet, we often lack this information entirely or find conflicting evidence across studies, which is the case for spring phenology. We synthesized common garden studies across Europe and North America that reported spring event dates for a mix of angiosperm and gymnosperm tree species in the northern hemisphere, capturing data from 384 North American and 101 European provenances (i.e. populations) with observations from 1962 to 2019, alongside autumn event data when provided. Across continents, we found no evidence of provenance effects in spring phenology, but strong clines with latitude and mean annual temperature in autumn. These effects, however, appeared to diverge by continent and species type (gymnosperm vs angiosperm), with particularly pronounced clines in North America in autumn events. Our results suggest flexible, likely plastic responses, in spring phenology with warming, and potential limits - at least in the short term - due to provenance effects for autumn phenology. They also highlight that, after over 250 yr of common garden studies on tree phenology, we still lack a holistic predictive model of clines across species and phenological events.

Rapid and Repeated Climate Adaptation Involving Chromosome Inversions following Invasion of an Insect

Following invasion, insects can become adapted to conditions experienced in their invasive range, but there are few studies on the speed of adaptation and its genomic basis. Here, we examine a small insect pest, Thrips palmi, following its contemporary range expansion across a sharp climate gradient from the subtropics to temperate areas. We first found a geographically associated population genetic structure and inferred a stepping-stone dispersal pattern in this pest from the open fields of southern China to greenhouse environments of northern regions, with limited gene flow after colonization. In common garden experiments, both the field and greenhouse groups exhibited clinal patterns in thermal tolerance as measured by critical thermal maximum (CTmax) closely linked with latitude and temperature variables. A selection experiment reinforced the evolutionary potential of CTmax with an estimated h2 of 6.8% for the trait. We identified 3 inversions in the genome that were closely associated with CTmax, accounting for 49.9%, 19.6%, and 8.6% of the variance in CTmax among populations. Other genomic variations in CTmax outside the inversion region were specific to certain populations but functionally conserved. These findings highlight rapid adaptation to CTmax in both open field and greenhouse populations and reiterate the importance of inversions behaving as large-effect alleles in climate adaptation.

Demographic feedbacks during evolutionary rescue can slow or speed adaptive evolution

Populations declining toward extinction can persist via genetic adaptation in a process called evolutionary rescue. Predicting evolutionary rescue has applications ranging from conservation biology to medicine, but requires understanding and integrating the multiple effects of a stressful environmental change on population processes. Here we derive a simple expression for how generation time, a key determinant of the rate of evolution, varies with population size during evolutionary rescue. Change in generation time is quantitatively predicted by comparing how intraspecific competition and the source of maladaptation each affect the rates of births and deaths in the population. Depending on the difference between two parameters quantifying these effects, the model predicts that populations may experience substantial changes in their rate of adaptation in both positive and negative directions, or adapt consistently despite severe stress. These predictions were then tested by comparison to the results of individual-based simulations of evolutionary rescue, which validated that the tolerable rate of environmental change varied considerably as described by analytical results. We discuss how these results inform efforts to understand wildlife disease and adaptation to climate change, evolution in managed populations and treatment resistance in pathogens.

Latitudinal variation in survival and immature development of Ceratitis capitata populations reared in two key overwintering hosts

Ceratitis capitata, a major agricultural pest, is currently expanding its geographic distribution to northern, temperate areas of Europe. Its seasonal biology and invasion success depend on temperature, humidity and host availability. In coastal warmer Mediterranean regions and cooler temperature areas, bitter oranges and apples serve as overwintering hosts during the larval stage. We assessed the overwintering capacity of C. capitata populations obtained from different areas of the northern hemisphere by studying the survival and development rates of immature stages in both fruits under laboratory conditions. Eggs from each population were artificially inserted in the flesh of the two hosts and kept at 15, 20, or 25 °C until pupation and adult emergence. Climatic analysis of the area of the population origin showed combined effects of latitude, host and macroclimatic variables on immature survival and development rates. Egg to adult survival rates and developmental duration were longer in apples than in bitter oranges. For populations originated from southern-warmer areas, egg to adult developmental duration was prolonged and adult emergence reduced at 15 °C compared to those populations obtained from northern regions. Our findings reveal varying plastic responses of medfly populations to different overwintering hosts and temperatures highlighting the differential overwintering potential as larvae within fruits. This study contributes towards better understanding the medfly invasion dynamics in temperate areas of Northern Europe and other parts of the globe with similar climates.

Pre-fertilization gamete thermal environment influences reproductive success, unmasking opposing sex-specific responses in Atlantic salmon (Salmo salar)

The environment gametes perform in just before fertilization is increasingly recognized to affect offspring fitness, yet the contributions of male and female gametes and their adaptive significance remain largely unexplored. Here, we investigated gametic thermal plasticity and its effects on hatching success and embryo performance in Atlantic salmon (Salmo salar). Eggs and sperm were incubated overnight at 2°C or 8°C, temperatures within the optimal thermal range of this species. Crosses between warm- and cold-incubated gametes were compared using a full-factorial design, with half of each clutch reared in cold temperatures and the other in warm temperatures. This allowed disentangling single-sex interaction effects when pre-fertilization temperature of gametes mismatched embryonic conditions. Pre-fertilization temperature influenced hatch timing and synchrony, and matching sperm and embryo temperatures resulted in earlier hatching. Warm incubation benefited eggs but harmed sperm, reducing the hatching success and, overall, gametic thermal plasticity did not enhance offspring fitness, indicating vulnerability to thermal changes. We highlight the sensitivity of male gametes to higher temperatures, and that gamete acclimation may not effectively buffer against deleterious effects of thermal fluctuations. From an applied angle, we propose the differential storage of male and female gametes as a tool to enhance sustainability within the hatcheries.

How density dependence, genetic erosion and the extinction vortex impact evolutionary rescue

Following severe environmental change that reduces mean population fitness below replacement, populations must adapt to avoid eventual extinction, a process called evolutionary rescue. Models of evolutionary rescue demonstrate that initial size, genetic variation and degree of maladaptation influence population fates. However, many models feature populations that grow without negative density dependence or with constant genetic diversity despite precipitous population decline, assumptions likely to be violated in conservation settings. We examined the simultaneous influences of density-dependent growth and erosion of genetic diversity on populations adapting to novel environmental change using stochastic, individual-based simulations. Density dependence decreased the probability of rescue and increased the probability of extinction, especially in large and initially well-adapted populations that previously have been predicted to be at low risk. Increased extinction occurred shortly following environmental change, as populations under density dependence experienced more rapid decline and reached smaller sizes. Populations that experienced evolutionary rescue lost genetic diversity through drift and adaptation, particularly under density dependence. Populations that declined to extinction entered an extinction vortex, where small size increased drift, loss of genetic diversity and the fixation of maladaptive alleles, hindered adaptation and kept populations at small densities where they were vulnerable to extinction via demographic stochasticity.

Developing the genotype-to-phenotype relationship in evolutionary theory: A primer of developmental features

For decades, there have been repeated calls for more integration across evolutionary and developmental biology. However, critiques in the literature and recent funding initiatives suggest this integration remains incomplete. We suggest one way forward is to consider how we elaborate the most basic concept of development, the relationship between genotype and phenotype, in traditional models of evolutionary processes. For some questions, when more complex features of development are accounted for, predictions of evolutionary processes shift. We present a primer on concepts of development to clarify confusion in the literature and fuel new questions and approaches. The basic features of development involve expanding a base model of genotype-to-phenotype to include the genome, space, and time. A layer of complexity is added by incorporating developmental systems, including signal-response systems and networks of interactions. The developmental emergence of function, which captures developmental feedbacks and phenotypic performance, offers further model elaborations that explicitly link fitness with developmental systems. Finally, developmental features such as plasticity and developmental niche construction conceptualize the link between a developing phenotype and the external environment, allowing for a fuller inclusion of ecology in evolutionary models. Incorporating aspects of developmental complexity into evolutionary models also accommodates a more pluralistic focus on the causal importance of developmental systems, individual organisms, or agents in generating evolutionary patterns. Thus, by laying out existing concepts of development, and considering how they are used across different fields, we can gain clarity in existing debates around the extended evolutionary synthesis and pursue new directions in evolutionary developmental biology. Finally, we consider how nesting developmental features in traditional models of evolution can highlight areas of evolutionary biology that need more theoretical attention.

Patterns of Genetic And Epigenetic Diversity Across A Range Expansion in The White-Footed Mouse (Peromyscus Leucopus)

Populations at the leading front of a range expansion must rapidly adapt to novel conditions. Increased epigenetic diversity has been hypothesized to facilitate adaptation and population persistence via non-genetic phenotypic variation, especially if there is reduced genetic diversity when populations expand (i.e., epigenetic diversity compensates for low genetic diversity). In this study, we use the spatial distribution of genetic and epigenetic diversity to test this hypothesis in populations of the white-footed mouse (Peromyscus leucopus) sampled across a purported recent range expansion gradient. We found mixed support for the epigenetic compensation hypothesis and a lack of support for expectations for expansion populations of mice at the range edge, which likely reflects a complex history of expansion in white-footed mice in the Upper Peninsula of Michigan. Specifically, epigenetic diversity was not increased in the population at the purported edge of the range expansion in comparison to the other expansion populations. However, input from an additional ancestral source populations may have increased genetic diversity at this range edge population, counteracting the expected genetic consequences of expansion, as well as reducing the benefit of increased epigenetic diversity at the range edge. Future work will expand the focal populations to include expansion areas with a single founding lineage to test for the robustness of a general trend that supports the hypothesized compensation of reduced genetic diversity by epigenetic variation observed in the expansion population that was founded from a single historical source.

Evolutionary rescue under demographic and environmental stochasticity

Populations suffer two types of stochasticity: demographic stochasticity, from sampling error in offspring number, and environmental stochasticity, from temporal variation in the growth rate. By modelling evolution through phenotypic selection following an abrupt environmental change, we investigate how genetic and demographic dynamics, as well as effects on population survival of the genetic variance and of the strength of stabilizing selection, differ under the two types of stochasticity. We show that population survival probability declines sharply with stronger stabilizing selection under demographic stochasticity, but declines more continuously when environmental stochasticity is strengthened. However, the genetic variance that confers the highest population survival probability differs little under demographic and environmental stochasticity. Since the influence of demographic stochasticity is stronger when population size is smaller, a slow initial decline of genetic variance, which allows quicker evolution, is important for population persistence. In contrast, the influence of environmental stochasticity is population-size-independent, so higher initial fitness becomes important for survival under strong environmental stochasticity. The two types of stochasticity interact in a more than multiplicative way in reducing the population survival probability. Our work suggests the importance of explicitly distinguishing and measuring the forms of stochasticity during evolutionary rescue.

Behavioural responses of fishes to anthropogenic disturbances: Adaptive value and ecological consequences

Aquatic ecosystems are changing at an accelerating rate because of human activities. The changes alter the abundance and distribution of fishes, with potential consequences for ecosystem structure and function. Behavioural responses often underlie these changes in population dynamics, such as altered habitat choice or foraging activity. Here, we present a framework for understanding how and why behaviour is affected by human activities and how the behavioural responses in turn influence higher ecological levels. We further review the literature to assess the present state of the field and identify gaps in our knowledge. We begin with discussing the factors that determine how an individual responds to a change in the environment and whether the response is adaptive or not. In particular, we explain the importance of the evolutionary history of the species. We then search the literature to assess our current knowledge of the impact of human disturbances on the behaviour of fishes and the consequences for ecosystems. The search reveals that much attention has been directed to the impact of human activities on the behaviour of fishes, but that worryingly little is known about the consequences of these responses for populations, communities and ecosystems. Yet, behavioural responses can have profound ecological consequences given that behaviour underly many, if not most, species interactions. Thus, more attention should be paid to the mechanisms and pathways through which behavioural responses influence higher ecological levels. Such information is needed if we are to determine the ultimate effects of human activities on biodiversity and the function and stability of aquatic ecosystems.

Evolutionary rescue in a fluctuating environment: periodic versus quasi-periodic environmental changes

No environment is constant over time, and environmental fluctuations impact the outcome of evolutionary dynamics. Survival of a population not adapted to some environmental conditions is threatened unless, for example, a mutation rescues it, an eco-evolutionary process termed evolutionary rescue. We here investigate evolutionary rescue in an environment that fluctuates between a favourable state, in which the population grows, and a harsh state, in which the population declines. We develop a stochastic model that includes both population dynamics and genetics. We derive analytical predictions for the mean extinction time of a non-adapted population given that it is not rescued, the probability of rescue by a mutation, and the mean appearance time of a rescue mutant, which we validate using numerical simulations. We find that stochastic environmental fluctuations, resulting in quasi-periodic environmental changes, accelerate extinction and hinder evolutionary rescue compared with deterministic environmental fluctuations, resulting in periodic environmental changes. We demonstrate that high equilibrium population sizes and per capita growth rates maximize the chances of evolutionary rescue. We show that an imperfectly harsh environment, which does not fully prevent births but makes the death rate to birth rate ratio much greater than unity, has almost the same rescue probability as a perfectly harsh environment, which fully prevents births. Finally, we put our results in the context of antimicrobial resistance and conservation biology.

The ecological relevance of critical thermal maxima methodology for fishes

Critical thermal maxima methodology (CTM) has been used to infer acute upper thermal tolerance in fishes since the 1950s, yet its ecological relevance remains debated. In this study, the authors synthesize evidence to identify methodological concerns and common misconceptions that have limited the interpretation of critical thermal maximum (CT_max ; value for an individual fish during one trial) in ecological and evolutionary studies of fishes. They identified limitations of, and opportunities for, using CT_max as a metric in experiments, focusing on rates of thermal ramping, acclimation regimes, thermal safety margins, methodological endpoints, links to performance traits and repeatability. Care must be taken when interpreting CTM in ecological contexts, because the protocol was originally designed for ecotoxicological research with standardized methods to facilitate comparisons within study individuals, across species and contexts. CTM can, however, be used in ecological contexts to predict impacts of environmental warming, but only if parameters influencing thermal limits, such as acclimation temperature or rate of thermal ramping, are taken into account. Applications can include mitigating the effects of climate change, informing infrastructure planning or modelling species distribution, adaptation and/or performance in response to climate-related temperature change. The authors' synthesis points to several key directions for future research that will further aid the application and interpretation of CTM data in ecological contexts.

Insights into the molecular mechanisms of pesticide tolerance in the Aporrectodea caliginosa earthworm

Diffuse pollution of the environment by pesticides has become a major soil threat to non-target organisms, such as earthworms for which declines have been reported. However some endogeic species are still abundant and persist in intensively cultivated fields, suggesting they become tolerant to long-term anthropogenic pressure. We thus considered the working hypothesis that populations of Aporrectodea caliginosa earthworms from conventionally managed fields developed a tolerance to pesticides compared with those from organically managed fields. To investigate this hypothesis, we studied earthworm populations of the same genetic lineage from soils that were either lowly or highly contaminated by pesticides to detect any constitutive expression of differentially expressed molecular pathways between these populations. Earthworm populations were then experimentally exposed to a fungicide-epoxiconazole-in the laboratory to identify different molecular responses when newly exposed to a pesticide. State-of-the-art omics technology (RNA sequencing) and bioinformatics were used to characterize molecular mechanisms of tolerance in a non-targeted way. Additional physiological traits (respirometry, growth, bioaccumulation) were monitored to assess tolerance at higher levels of biological organization. In the present study, we generated the de novo assembly transcriptome of A. caliginosa consisting of 64,556 contigs with N50 = 2862 pb. In total, 43,569 Gene Ontology terms were identified for 21,593 annotated sequences under the three main ontologies (biological processes, cellular components and molecular functions). Overall, we revealed that two same lineage populations of A. caliginosa earthworms, inhabiting similar pedo-climatic environment, have distinct gene expression pathways after they long-lived in differently managed agricultural soils with a contrasted pesticide exposure history for more than 22 years. The main difference was observed regarding metabolism, with upregulated pathways linked to proteolytic activities and the mitochondrial respiratory chain in the highly exposed population. This study improves our understanding of the long-term impact of chronic exposure of soil engineers to pesticide residues.

Computational modelling of plasticity-led evolution

Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This mode of evolution is expected to resolve the problem of gradualism (i.e., evolution by the slow accumulation of mutations that induce phenotypic variation) implied by the Modern Evolutionary Synthesis, in the face of a large environmental change. While experimental works are essential for validating that plasticity-led evolution indeed happened, we need computational models to gain insight into its underlying mechanisms and make qualitative predictions. Such computational models should include the developmental process and gene-environment interactions in addition to genetics and natural selection. We point out that gene regulatory network models can incorporate all the above notions. In this review, we highlight results from computational modelling of gene regulatory networks that consolidate the criteria of plasticity-led evolution. Since gene regulatory networks are mathematically equivalent to artificial recurrent neural networks, we also discuss their analogies and discrepancies, which may help further understand the mechanisms underlying plasticity-led evolution.

Plastic energy allocation toward life-history functions in a consumer-resource interaction : Analyzing the temporal patterns of the consumer-resource dynamics

Various environmental alterations resulting from the current global change compromise the persistence of species in their habitual environment. To cope with the obvious risk of extinction, plastic responses provide organisms with rapid acclimatization to new environments. The premise of plastic rescue has been theoretically studied from mathematical models in both deterministic and stochastic environments, focusing on analyzing the persistence and stability of the populations. Here, we evaluate this premise in the framework of a consumer-resource interaction considering the energy investment towards reproduction vs. maintenance as a plastic trait according to positive/negative variation of the available resource. A basic consumer-resource mathematical model is formulated based on the principle of biomass conversion that incorporates the energy allocation toward vital functions of the life-cycle of consumer individuals. Our mathematical approach is based on the impulsive differential equations at fixed moments considering two impulsive effects associated with the instants at which consumers obtain environmental information and when energy allocation strategy change occurs. From a preliminary analysis of the non-plastic temporal dynamics, namely when the energy allocation is constant over time and without experiencing changes concerning the variation of resources, both the persistence and stability of the consumer-resource dynamic are dependent on the energy allocation strategies belonging to a set termed stability range. We found that the plastic energy allocation can promote a stable dynamical pattern in the consumer-resource interaction depending on both the magnitude of the energy allocation change and the time lag between environmental sensibility instants and when the expression of the plastic trait occurs.

Genetic and spatial variation in vegetative and floral traits across a hybrid zone

PREMISE

Genetic variation influences the potential for evolution to rescue populations from impacts of environmental change. Most studies of genetic variation in fitness-related traits focus on either vegetative or floral traits, with few on floral scent. How vegetative and floral traits compare in potential for adaptive evolution is poorly understood.

METHODS

We measured variation across source populations, planting sites, and genetic families for vegetative and floral traits in a hybrid zone. Seeds from families of Ipomopsis aggregata, I. tenuituba, and F₁ and F₂ hybrids of the two species were planted into three common gardens. Measured traits included specific leaf area (SLA), trichomes, water-use efficiency (WUE), floral morphology, petal color, nectar, and floral volatiles.

RESULTS

Vegetative traits SLA and WUE varied greatly among planting sites, while showing weak or no genetic variation among source populations. Specific leaf area and trichomes responded plastically to snowmelt date, and SLA exhibited within-population genetic variation. All aspects of floral morphology varied genetically among source populations, and corolla length, corolla width, and sepal width varied genetically within populations. Heritability was not detected for volatiles due to high environmental variation, although one terpene had high evolvability, and high emission of two terpenes, a class of compounds emitted more strongly from the calyx than the corolla, correlated genetically with sepal width. Environmental variation across sites was weak for floral morphology and stronger for volatiles and vegetative traits. The inheritance of three of four volatiles departed from additive.

CONCLUSIONS

Results indicate stronger genetic potential for evolutionary responses to selection in floral morphology compared with scent and vegetative traits and suggest potentially adaptive plasticity in some vegetative traits.

Environmental conditions lead to shifts in individual communication, which can cause cascading effects on soundscape composition

Climate change is increasing aridity in grassland and desert habitats across the southwestern United States, reducing available resources and drastically changing the breeding habitat of many bird species. Increases in aridity reduce sound propagation distances, potentially impacting habitat soundscapes, and could lead to a breakdown of the avian soundscapes in the form of loss of vocal culture, reduced mating opportunities, and local population extinctions. We developed an agent-based model to examine how changes in aridity will affect both sound propagation and the ability of territorial birds to audibly contact their neighbors. We simulated vocal signal attenuation under a variety of environmental scenarios for the south, central semi-arid prairies of the United States, ranging from contemporary weather conditions to predicted droughts under climate change. We also simulated how changes in physiological conditions, mainly evaporative water loss (EWL), would affect singing behavior. Under contemporary and climate change-induced drought conditions, we found that significantly fewer individuals successfully contacted all adjacent neighbors than did individuals in either the contemporary or predicted climate change conditions. We also found that at higher sound frequencies and higher EWL, fewer individuals were able to successfully contact all their neighbors, particularly in drought and climate change drought conditions. These results indicate that climate change-mediated aridification may alter the avian soundscape, such that vocal communication no longer effectively functions for mate attraction or territorial defense. As climate change progresses, increased aridity in current grasslands may favor shifts toward low-frequency songs, colonial resource use, and altered songbird community compositions.

Quantifying population and clone-specific non-linear reaction norms to food gradients in Daphnia magna

Phenotypic plasticity is normally quantified as a reaction norm which details how trait expression changes across an environmental gradient. Sometime reaction norms are linear, but often reaction norms are assumed to be linear because plasticity is typically quantified as the difference in trait expression measured in two environments. This simplification limits how plastic responses vary between genotypes and may also bias the predictions of models investigating how plasticity influences a population’s ability to adapt to a changing environment. Consequently, there is a pressing need to characterize the real shape of reaction norms and their genetic variability across ecologically relevant environmental gradients. To address this knowledge gap we measured the multi-trait plastic response of 7 Daphnia magna clones from the same population across a broad resource gradient. We used a Random Regression Mixed Model approach to characterize and quantify average and clone-specific responses to resource variation. Our results demonstrate that non-linear models outperformed a linear model for all 4 of the life-history traits we measured. The plastic reaction norms of all 4 traits were similar in shape and were often best described by a non-linear asymptotic model. Clonal variation in non-linear plastic responses was detectable for 3 out of the 4 traits that we measured although the nature and magnitude of variation across the resource gradient was trait-specific. We interpret our findings with respect to the impact that plasticity has on the evolutionary potential of a population in different resource environments.

Evolution of resource generalism via generalized stress response confers increased reproductive thermal tolerance in a pest beetle

Generalism should be favoured evolutionarily when there is no genetic constraint or loss of fitness across alternative environments. However, evolution of generalism can require substantial evolutionary change, which can confer a general stress response to other aspects of the environment. We created generalist lineages from an ancestral, resource-specialized laboratory population of seed beetles (Callosobruchus maculatus) by rearing lines over 60 generations on a mixture of both ancestral and novel host species to test for costs associated with the evolution of generalism involving evolutionary changes in gene expression and correlated phenotypic responses during a shift to generalism. Evolved lines had higher fitness on the novel resource, with no loss of fitness on the ancestral resource, indicating that they overcame initial fitness trade-offs. This involved upregulation of major stress response (heat shock protein) genes and genes coding for metabolic enzymes, suggesting an underpinning metabolic and physiological cost. Resource generalist populations also evolved greater thermal tolerance breadth, highlighting that the evolution of resource generalism might pre-adapt species to respond favourably to other environmental stressors, following selection for generalized stress response gene upregulation. The rapid gain of novel hosts during a pest invasion might also confer greater thermal resilience to ongoing climate change.

Evidence of climate-driven selection on tree traits and trait plasticity across the climatic range of a riparian foundation species

Selection on quantitative traits by heterogeneous climatic conditions can lead to substantial trait variation across a species range. In the context of rapidly changing environments, however, it is equally important to understand selection on trait plasticity. To evaluate the role of selection in driving divergences in traits and their associated plasticities within a widespread species, we compared molecular and quantitative trait variation in Populus fremontii (Fremont cottonwood), a foundation riparian distributed throughout Arizona. Using SNP data and genotypes from 16 populations reciprocally planted in three common gardens, we first performed Q_ST -F_ST analyses to detect selection on traits and trait plasticity. We then explored the environmental drivers of selection using trait-climate and plasticity-climate regressions. Three major findings emerged: 1) There was significant genetic variation in traits expressed in each of the common gardens and in the phenotypic plasticity of traits across gardens, both of which were heritable. 2) Based on Q_ST -F_ST comparisons, there was evidence of selection in all traits measured; however, this result varied from no effect in one garden to highly significant in another, indicating that detection of past selection is environmentally dependent. We also found strong evidence of divergent selection on plasticity across environments for two traits. 3) Traits and/or their plasticity were often correlated with population source climate (R² up to 0.77 and 0.66, respectively). These results suggest that steep climate gradients across the Southwest have played a major role in shaping the evolution of divergent phenotypic responses in populations and genotypes now experiencing climate change.

Gene expression studies of plastic and evolutionary responses to global warming

Phenotypic plasticity can be a rapid response for coping with global warming, yet may be insufficient to protect species from extinction. Evolutionary adaptation may reinforce adaptive or oppose maladaptive plastic responses. With advances in technology whole transcriptomes can provide us with an unprecedented overview of genes and functional processes underlying the interplay between plasticity and evolution. We advocate that insects provide ideal opportunities to study plasticity in non-adapted and thermally adapted populations to infer reaction norms across the whole transcriptome ('reactionomes'). This can advance our understanding of how the interplay between plasticity and evolution shapes responses to warming. So far, a limited number of studies suggest predominantly maladaptive plastic responses to novel environments that are reduced with time, but much more research is needed to infer general patterns.

Phenotypic plasticity and selection on leaf traits in response to snowmelt timing and summer precipitation

Vegetative traits of plants can respond directly to changes in the environment, such as those occurring under climate change. That phenotypic plasticity could be adaptive, maladaptive, or neutral. We manipulated the timing of spring snowmelt and amount of summer precipitation in factorial combination and examined responses of specific leaf area (SLA), trichome density, leaf water content (LWC), photosynthetic rate, stomatal conductance and intrinsic water-use efficiency (iWUE) in the subalpine herb Ipomopsis aggregata. The experiment was repeated in three years differing in natural timing of snowmelt. To examine natural selection, we used survival, relative growth rate, and flowering as fitness indices. A 50% reduction in summer precipitation reduced stomatal conductance and increased iWUE, and doubled precipitation increased LWC. Combining natural and experimental variation, earlier snowmelt reduced soil moisture, photosynthetic rate and stomatal conductance, and increased trichome density and iWUE. Precipitation reduction reversed the mortality selection favoring high stomatal conductance under normal and doubled precipitation, and higher LWC improved growth. Earlier snowmelt is a strong signal of climate change and can change expression of leaf morphology and gas exchange traits, just as reduced precipitation can. Stomatal conductance and SLA showed adaptive plasticity under some conditions.

Population-specific responses of floral volatiles to abiotic factors in changing environments

PREMISE

Shifts in abiotic factors can affect many plant traits, including floral volatiles. This study examined the response of floral volatiles to water availability and whether phenotypic plasticity to water availability differs among populations. It also investigated genetic differentiation in floral volatiles, determined the effect of temperature on phenotypic plasticity to water availability, and assessed temporal variation in floral scent emission between day and evening, since pollinator visitation differs at those times.

METHODS

Rocky Mountain columbine plants (Aquilegia coerulea), started from seeds collected in three wild populations in Colorado, Utah, and Arizona, were grown under two water treatments in a greenhouse in Madison, Wisconsin, United States. One population was also grown under the two water treatments, at two temperatures. Air samples were collected from enclosed flowers using dynamic headspace methods and floral volatiles were identified and quantified by gas chromatography (GC) with mass spectrometry (MS).

RESULTS

Emission of three floral volatiles increased in the wetter environment, indicating phenotypic plasticity. The response of six floral volatiles to water availability differed among populations, suggesting genetic differentiation in phenotypic plasticity. Five floral volatiles varied among populations, and emission of most floral volatiles was greater during the day.

CONCLUSIONS

Phenotypic plasticity to water availability permits a quick response of floral volatiles in changing environments. The genetic differentiation in phenotypic plasticity suggests that phenotypic plasticity can evolve but complicates predictions of the effects of environmental changes on a plant and its pollinators.

Coping With Dynamism: Phylogenetics and Phylogeographic Analyses Reveal Cryptic Diversity in Heleobia Snails of Atacama Saltpan, Chile

The species that inhabit systems highly affected by anthropic activities usually exhibit this external influence in their gene pool. In this study, we investigated the genetic patterns of populations of Heleobia atacamensis, a freshwater microgastropod endemic to the Atacama Saltpan, a system historically exposed to environmental changes, and currently subjected to conditions associated with metallic and non-metallic mining and other anthropic activities. Molecular analyses based on nuclear and mitochondrial sequences indicate that the saltpan populations are highly fragmented and that the genetic structure is mainly explained by historical geographic isolation, with little influence of contemporary factors. The microsatellite results suggest a moderate genetic diversity and sharp differentiation mediated by isolation by distance. Additionally, despite the high environmental heterogeneity detected and the marked historical dynamism of the region, our data reveal no signs of demographic instability. The patterns of contemporary gene flow suggest a change in the current genetic structure, based on the geographic proximity and specific environmental conditions for each population. Our results, highlight the role of fragmentation as a modulator of genetic diversity, but also suggest that the historical persistence of isolated populations in naturally dynamic environments could explain the apparent demographic stability detected.

Genotypic variation and plasticity in climate-adaptive traits after range expansion and fragmentation of red spruce (Picea rubens Sarg.)

Shifting range limits are predicted for many species as the climate warms. However, the rapid pace of climate change will challenge the natural dispersal capacity of long-lived, sessile organisms such as forest trees. Adaptive responses of populations will, therefore, depend on levels of genetic variation and plasticity for climate-responsive traits, which likely vary across the range due to expansion history and current patterns of selection. Here, we study levels of genetic and plastic variation for phenology and growth traits in populations of red spruce (Picea rubens), from the range core to the highly fragmented trailing edge. We measured more than 5000 offspring sampled from three genetically distinct regions (core, margin and edge) grown in three common gardens replicated along a latitudinal gradient. Genetic variation in phenology and growth showed low to moderate heritability and differentiation among regions, suggesting some potential to respond to selection. Phenology traits were highly plastic, but this plasticity was generally neutral or maladaptive in the effect on growth, revealing a potential liability under warmer climates. These results suggest future climate adaptation will depend on the regional availability of genetic variation in red spruce and provide a resource for the design and management of assisted gene flow. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.

Sexual dimorphism in phenotypic plasticity and persistence under environmental change: An extension of theory and meta-analysis of current data

Populations must adapt to environmental changes to remain viable. Both evolution and phenotypic plasticity contribute to adaptation, with plasticity possibly being more important for coping with rapid change. Adaptation is complex in species with separate sexes, as the sexes can differ in the strength or direction of natural selection, the genetic basis of trait variation, and phenotypic plasticity. Many species show sex differences in plasticity, yet how these differences influence extinction susceptibility remains unclear. We first extend theoretical models of population persistence in changing environments and show that persistence is affected by sexual dimorphism for phenotypic plasticity, trait genetic architecture, and sex-specific selection. Our models predict that female-biased adaptive plasticity-particularly in traits with modest-to-low cross-sex genetic correlations-typically promotes persistence, though we also identify conditions where sexually monomorphic or male-biased plasticity promotes persistence. We then perform a meta-analysis of sex-specific plasticity under manipulated thermal conditions. Although examples of sexually dimorphic plasticity are widely observed, systematic sex differences are rare. An exception-cold resistance-is systematically female-biased and represents a trait wherein sexually dimorphic plasticity might elevate population viability in changing environments. We discuss our results in light of debates about the roles of evolution and plasticity in extinction susceptibility.

Into the range: a latitudinal gradient or a center-margins differentiation of ecological strategies in Arabidopsis thaliana?

BACKGROUND AND AIMS

Determining within-species large-scale variation in phenotypic traits is central to elucidate the drivers of species' ranges. Intraspecific comparisons offer the opportunity to understand how trade-offs and biogeographical history constrain adaptation to contrasted environmental conditions. Here we test whether functional traits, ecological strategies from the CSR scheme and phenotypic plasticity in response to abiotic stress vary along a latitudinal or a center- margins gradient within the native range of Arabidopsis thaliana.

METHODS

We experimentally examined the phenotypic outcomes of plant adaptation at the center and margins of its geographic range using 30 accessions from southern, central and northern Europe. We characterized the variation of traits related to stress tolerance, resource use, colonization ability, CSR strategy scores, survival and fecundity in response to high temperature (34 °C) or frost (- 6 °C), combined with a water deficit treatment.

KEY RESULTS

We found evidence for both a latitudinal and a center-margins differentiation for the traits under scrutiny. Age at maturity, leaf dry matter content, specific leaf area and leaf nitrogen content varied along a latitudinal gradient. Northern accessions presented a greater survival to stress than central and southern accessions. Leaf area, C-scores, R-scores and fruit number followed a center-margins differentiation. Central accessions displayed a higher phenotypic plasticity than northern and southern accessions for most studied traits.

CONCLUSIONS

Traits related to an acquisitive/conservative resource-use trade-off followed a latitudinal gradient. Traits associated with a competition/colonization trade-off differentiated along the historic colonization of the distribution range and then followed a center-margins differentiation. Our findings pinpoint the need to consider the joint effect of evolutionary history and environmental factors when examining phenotypic variation across the distribution range of a species.

Avoiding extinction under nonlinear environmental change: models of evolutionary rescue with plasticity

Rapid environmental changes are putting numerous species at risk of extinction. For migration-limited species, persistence depends on either phenotypic plasticity or evolutionary adaptation (evolutionary rescue). Current theory on evolutionary rescue typically assumes linear environmental change. Yet accelerating environmental change may pose a bigger threat. Here, we present a model of a species encountering an environment with accelerating or decelerating change, to which it can adapt through evolution or phenotypic plasticity (within-generational or transgenerational). We show that unless either form of plasticity is sufficiently strong or adaptive genetic variation is sufficiently plentiful, accelerating or decelerating environmental change increases extinction risk compared to linear environmental change for the same mean rate of environmental change.

Gene Expression Profiles Suggest a Better Cold Acclimation of Polyploids in the Alpine Species Ranunculus kuepferi (Ranunculaceae)

Alpine habitats are shaped by harsh abiotic conditions and cold climates. Temperature stress can affect phenotypic plasticity, reproduction, and epigenetic profiles, which may affect acclimation and adaptation. Distribution patterns suggest that polyploidy seems to be advantageous under cold conditions. Nevertheless, whether temperature stress can induce gene expression changes in different cytotypes, and how the response is initialized through gene set pathways and epigenetic control remain vague for non-model plants. The perennial alpine plant Ranunculus kuepferi was used to investigate the effect of cold stress on gene expression profiles. Diploid and autotetraploid individuals were exposed to cold and warm conditions in climate growth chambers and analyzed via transcriptome sequencing and qRT-PCR. Overall, cold stress changed gene expression profiles of both cytotypes and induced cold acclimation. Diploids changed more gene set pathways than tetraploids, and suppressed pathways involved in ion/cation homeostasis. Tetraploids mostly activated gene set pathways related to cell wall and plasma membrane. An epigenetic background for gene regulation in response to temperature conditions is indicated. Results suggest that perennial alpine plants can respond to temperature extremes via altered gene expression. Tetraploids are better acclimated to cold conditions, enabling them to colonize colder climatic areas in the Alps.

The impact of individual variation on abrupt collapses in mutualistic networks

Individual variation is central to species involved in complex interactions with others in an ecological system. Such ecological systems could exhibit tipping points in response to changes in the environment, consequently leading to abrupt transitions to alternative, often less desirable states. However, little is known about how individual trait variation could influence the timing and occurrence of abrupt transitions. Using 101 empirical mutualistic networks, I model the eco‐evolutionary dynamics of such networks in response to gradual changes in strength of co‐evolutionary interactions. Results indicated that individual variation facilitates the timing of transition in such networks, albeit slightly. In addition, individual variation significantly increases the occurrence of large abrupt transitions. Furthermore, topological network features also positively influence the occurrence of such abrupt transitions. These findings argue for understanding tipping points using an eco‐evolutionary perspective to better forecast abrupt transitions in ecological systems.

Complex delayed and transgenerational effects driven by the interaction of heat and insecticide in the maternal generation of the wheat aphid, Sitobion avenae

BACKGROUND

Experience of an earlier environment plays an important role in the induction of delayed and even intergenerational phenotypes of an organism. Evidence suggests that rapid adaptation to an environmental stressor can change the performance of organisms, and even enable them to deal with other stressors. The goal of this study was to determine the effects of adult imidacloprid exposure on life-history traits within and between generations of the cereal aphid, Sitobion avenae, under three developmental conditions: constant temperature, 22°C; a low-intensity thermal condition, 22 + 34°C for 2 h per day; and a high-intensity thermal condition, 22 + 38°C for 2 h per day.

RESULTS

Early thermal experience not only changed the tolerance of S. avenae to the insecticide, imidacloprid, but also caused adults to incur fitness costs: the higher the heat intensity, the higher the costs. Negative transgenerational impacts of combined heat and insecticide stressors were limited to the developmental stage, whereas positive stimulation of heat intensity was observed during the adult stage. Overall, nymphal thermal experience exacerbated the detrimental effects of adult insecticidal exposure on the intrinsic rate of population increase in the maternal generation, but stimulated a net reproductive rate in the succeeding offspring generation.

CONCLUSION

These findings underpin the importance of considering the experience of the early developmental environment, but also enhance our understanding of the transgenerational effects of combined thermal and insecticide stressors on the population fate of S. avenae. They also help to assess the efficacy of chemical control in a warming world. © 2021 Society of Chemical Industry.

Phenotypic plasticity in courtship exposed to selection in a human-disturbed environment

When environments change rapidly, evolutionary processes may be too slow to rescue populations from decline. Persistence then hinges on plastic adjustments of critical traits to the altered conditions. However, the degree to which species harbour the necessary plasticity and the degree to which the plasticity is exposed to selection in human-disturbed environments are poorly known. We show that a population of the threespine stickleback (Gasterosteus aculeatus) harbours variation in plasticity in male courtship behaviour, which is exposed to selection when visibility deteriorates because of enhanced algal growth. Females in clear water show no preference for plastic males, while females in algal-rich, turbid water switch their mate preference towards males with adaptive plasticity. Thus, while the plasticity is not selected for in the original clear water environment, it comes under selection in turbid water. However, much maladaptive plasticity is present in the population, probably because larger turbidity fluctuations have been rare in the past. Thus, the probability that the plasticity will improve the ability of the population to cope with human-induced increases in turbidity-and possibly facilitate genetic adaptation-depends on its prevalence and genetic basis. In conclusion, our results show that rapid human-induced environmental change can expose phenotypic plasticity to selection, but that much of the plasticity can be maladaptive, also when the altered conditions represent extremes of earlier encountered conditions. Thus, whether the plasticity will improve population viability remains questionable.

Adaptive Phenotypic Plasticity Stabilizes Evolution in Fluctuating Environments

Fluctuating environmental conditions are ubiquitous in natural systems, and populations have evolved various strategies to cope with such fluctuations. The particular mechanisms that evolve profoundly influence subsequent evolutionary dynamics. One such mechanism is phenotypic plasticity, which is the ability of a single genotype to produce alternate phenotypes in an environmentally dependent context. Here, we use digital organisms (self-replicating computer programs) to investigate how adaptive phenotypic plasticity alters evolutionary dynamics and influences evolutionary outcomes in cyclically changing environments. Specifically, we examined the evolutionary histories of both plastic populations and non-plastic populations to ask: (1) Does adaptive plasticity promote or constrain evolutionary change? (2) Are plastic populations better able to evolve and then maintain novel traits? And (3), how does adaptive plasticity affect the potential for maladaptive alleles to accumulate in evolving genomes? We find that populations with adaptive phenotypic plasticity undergo less evolutionary change than non-plastic populations, which must rely on genetic variation from de novo mutations to continuously readapt to environmental fluctuations. Indeed, the non-plastic populations undergo more frequent selective sweeps and accumulate many more genetic changes. We find that the repeated selective sweeps in non-plastic populations drive the loss of beneficial traits and accumulation of maladaptive alleles, whereas phenotypic plasticity can stabilize populations against environmental fluctuations. This stabilization allows plastic populations to more easily retain novel adaptive traits than their non-plastic counterparts. In general, the evolution of adaptive phenotypic plasticity shifted evolutionary dynamics to be more similar to that of populations evolving in a static environment than to non-plastic populations evolving in an identical fluctuating environment. All natural environments subject populations to some form of change; our findings suggest that the stabilizing effect of phenotypic plasticity plays an important role in subsequent adaptive evolution.

Recombination facilitates genetic assimilation of new traits in gene regulatory networks

A new phenotypic variant may appear first in organisms through plasticity, that is, as a response to an environmental signal or other nongenetic perturbation. If such trait is beneficial, selection may increase the frequency of alleles that enable and facilitate its development. Thus, genes may take control of such traits, decreasing dependence on nongenetic disturbances, in a process called genetic assimilation. Despite an increasing amount of empirical studies supporting genetic assimilation, its significance is still controversial. Whether genetic assimilation is widespread depends, to a great extent, on how easily mutation and recombination reduce the trait's dependence on nongenetic perturbations. Previous research suggests that this is the case for mutations. Here we use simulations of gene regulatory network dynamics to address this issue with respect to recombination. We find that recombinant offspring of parents that produce a new phenotype through plasticity are more likely to produce the same phenotype without requiring any perturbation. They are also prone to preserve the ability to produce that phenotype after genetic and nongenetic perturbations. Our work also suggests that ancestral plasticity can play an important role for setting the course that evolution takes. In sum, our results indicate that the manner in which phenotypic variation maps unto genetic variation facilitates evolution through genetic assimilation in gene regulatory networks. Thus, we contend that the importance of this evolutionary mechanism should not be easily neglected.

Raised by aliens: constant exposure to an invasive predator triggers morphological but not behavioural plasticity in a threatened species tadpoles

During biotic invasions, native communities are abruptly exposed to novel and often severe selective pressures. The lack of common evolutionary history with invasive predators can hamper the expression of effective anti-predator responses in native prey, potentially accelerating population declines. Nonetheless, rapid adaptation and phenotypic plasticity may allow native species to cope with the new ecological pressures. We tested the hypothesis that phenotypic plasticity is fostered when facing invasive species and evaluated whether plasticity offers a pool of variability that might help the fixation of adaptive phenotypes. We assessed behavioural and morphological trait variation in tadpoles of the Italian agile frog (Rana latastei) in response to the invasive crayfish predator, Procambarus clarkii, by rearing tadpoles under different predation-risk regimes: non-lethal crayfish presence and crayfish absence. After two-month rearing, crayfish-exposed tadpoles showed a plastic shift in their body shape and increased tail muscle size, while behavioural tests showed no effect of crayfish exposure on tadpole behaviour. Furthermore, multivariate analyses revealed weak divergence in morphology between invaded and uninvaded populations, while plasticity levels were similar between invaded and uninvaded populations. Even if tadpoles displayed multiple plastic responses to the novel predator, none of these shifts underwent fixation after crayfish arrival (10–15 years). Overall, these findings highlight that native prey can finely tune their responses to invasive predators through plasticity, but the adaptive value of these responses in whitstanding the novel selective pressures, and the long-term consequences they can entail remain to be ascertained.

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.

Predicting population genetic change in an autocorrelated random environment: Insights from a large automated experiment

Most natural environments exhibit a substantial component of random variation, with a degree of temporal autocorrelation that defines the color of environmental noise. Such environmental fluctuations cause random fluctuations in natural selection, affecting the predictability of evolution. But despite long-standing theoretical interest in population genetics in stochastic environments, there is a dearth of empirical estimation of underlying parameters of this theory. More importantly, it is still an open question whether evolution in fluctuating environments can be predicted indirectly using simpler measures, which combine environmental time series with population estimates in constant environments. Here we address these questions by using an automated experimental evolution approach. We used a liquid-handling robot to expose over a hundred lines of the micro-alga Dunaliella salina to randomly fluctuating salinity over a continuous range, with controlled mean, variance, and autocorrelation. We then tracked the frequencies of two competing strains through amplicon sequencing of nuclear and choloroplastic barcode sequences. We show that the magnitude of environmental fluctuations (determined by their variance), but also their predictability (determined by their autocorrelation), had large impacts on the average selection coefficient. The variance in frequency change, which quantifies randomness in population genetics, was substantially higher in a fluctuating environment. The reaction norm of selection coefficients against constant salinity yielded accurate predictions for the mean selection coefficient in a fluctuating environment. This selection reaction norm was in turn well predicted by environmental tolerance curves, with population growth rate against salinity. However, both the selection reaction norm and tolerance curves underestimated the variance in selection caused by random environmental fluctuations. Overall, our results provide exceptional insights into the prospects for understanding and predicting genetic evolution in randomly fluctuating environments.

Being able to predict evolution under natural selection is important for many applied fields of biology, ranging from agriculture to medicine or conservation. However, this endeavor is complicated by factors that inherently limit our ability to predict the future, such as random fluctuations in the environment. Population genetic theory indicates that probabilistic predictions can still be made in this context, but the extent to which this holds empirically, and whether these predictions can be based on simple measurements, are still open questions. Making progress on answering these questions can be achieved by capitalizing on experiments where the environment is precisely controlled over many generations. Here, we used a pipetting robot to generate random time series of salinities with controlled patterns of fluctuations, which we imposed on a microalga, Dunaliella salina. Tracking the frequencies of two genotypes in a mixture by sequencing two short barcode sequences, we were able to show how patterns of fluctuating selection relate to the fluctuating environment. Interestingly, parts of these responses, but not all, could be predicted by simpler measurements in constant environments, allowing precise characterization the limits and prospects for predicting evolution in fluctuating environments.

Digest: On the contribution of phenotypic plasticity to adaptation in desert environments

How do organisms adapt to new environments, and what role does phenotypic plasticity play? Bittner et al. compared water consumption in laboratory-reared house mice derived from xeric and mesic populations and found evidence for adaptive phenotypic plasticity as well as genetic differences between populations.

Polygenic adaptation of rosette growth in Arabidopsis thaliana

The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its evolution in natural populations. Here, we investigate evolutionary and environmental factors shaping variation in the growth rate of Arabidopsis thaliana. We used plant diameter as a proxy to monitor plant growth over time in environments that mimicked latitudinal differences in the intensity of natural light radiation, across a set of 278 genotypes sampled within four broad regions, including an outgroup set of genotypes from China. A field experiment conducted under natural conditions confirmed the ecological relevance of the observed variation. All genotypes markedly expanded their rosette diameter when the light supply was decreased, demonstrating that environmental plasticity is a predominant source of variation to adapt plant size to prevailing light conditions. Yet, we detected significant levels of genetic variation both in growth rate and growth plasticity. Genome-wide association studies revealed that only 2 single nucleotide polymorphisms associate with genetic variation for growth above Bonferroni confidence levels. However, marginally associated variants were significantly enriched among genes with an annotated role in growth and stress reactions. Polygenic scores computed from marginally associated variants confirmed the polygenic basis of growth variation. For both light regimes, phenotypic divergence between the most distantly related population (China) and the various regions in Europe is smaller than the variation observed within Europe, indicating that the evolution of growth rate is likely to be constrained by stabilizing selection. We observed that Spanish genotypes, however, reach a significantly larger size than Northern European genotypes. Tests of adaptive divergence and analysis of the individual burden of deleterious mutations reveal that adaptive processes have played a more important role in shaping regional differences in rosette growth than maladaptive evolution.

The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its genetic variation in natural populations. Here, we investigate genetic and environmental factors shaping variation in the growth rate of Arabidopsis thaliana and ask whether genetic variation in plant growth contributes to adaptation to local environmental conditions. We grew plants under two light regimes that mimic latitudinal differences in the intensity of natural light radiation, and measured plant diameter as it grew over time. When the light supply was decreased, plant diameter grew more slowly but reached a markedly larger final size, confirming that plants can adjust their growth to prevailing light conditions. Yet, we also detected significant levels of genetic variation both in growth rate and in how the growth dynamics is adjusted to the light conditions. We show that this variation is encoded by many loci of small effect that are hard to locate in the genome but overall significantly enriched among genes associated with growth and stress reactions. We further observe that Spanish genotypes tended to reach, on average, a significantly larger rosette size than Northern European genotypes. Tests of adaptive divergence indicate that these differences may reflect adaptation to local environmental conditions.

Low potential for evolutionary rescue from climate change in a tropical fish

Climate change is increasing global temperatures and intensifying the frequency and severity of extreme heat waves. How organisms will cope with these changes depends on their inherent thermal tolerance, acclimation capacity, and ability for evolutionary adaptation. Yet, the potential for adaptation of upper thermal tolerance in vertebrates is largely unknown. We artificially selected offspring from wild-caught zebrafish (Danio rerio) to increase (Up-selected) or decrease (Down-selected) upper thermal tolerance over six generations. Selection to increase upper thermal tolerance was also performed on warm-acclimated fish to test whether plasticity in the form of inducible warm tolerance also evolved. Upper thermal tolerance responded to selection in the predicted directions. However, compared to the control lines, the response was stronger in the Down-selected than in the Up-selected lines in which evolution toward higher upper thermal tolerance was slow (0.04 ± 0.008 °C per generation). Furthermore, the scope for plasticity resulting from warm acclimation decreased in the Up-selected lines. These results suggest the existence of a hard limit in upper thermal tolerance. Considering the rate at which global temperatures are increasing, the observed rates of adaptation and the possible hard limit in upper thermal tolerance suggest a low potential for evolutionary rescue in tropical fish living at the edge of their thermal limits.