Developmental integration and evolution of labile plasticity in a complex quantitative character in a multiperiodic environment

Neglected impacts of plant protection products on invertebrate aquatic biodiversity: a focus on eco-evolutionary processes

The application of plant protection products (PPPs) may have delayed and long-term non-intentional impacts on aquatic invertebrates inhabiting agricultural landscapes. Such effects may induce population responses based on developmental and transgenerational plasticity, selection of genetic resistance, as well as increased extirpation risks associated with random genetic drift. While the current knowledge on such effects of PPPs is still scarce in non-target aquatic invertebrate species, evidences are accumulating that support the need for consideration of evolutionary components of the population response to PPPs in standard procedures of risk assessment. This mini-review, as part of a contribution to the collective scientific assessment on PPP impacts on biodiversity and ecosystem services performed in the period 2020-2022, presents a brief survey of the current results published on the subject, mainly in freshwater crustaceans, and proposes some research avenues and strategies that we feel relevant to fill this gap.

Condition dependence and the paradox of missing plasticity costs

Phenotypic plasticity plays a key role in adaptation to changing environments. However, plasticity is neither perfect nor ubiquitous, implying that fitness costs may limit the evolution of phenotypic plasticity in nature. The measurement of such costs of plasticity has proved elusive; decades of experiments show that fitness costs of plasticity are often weak or nonexistent. Here, we show that this paradox could potentially be explained by condition dependence. We develop two models differing in their assumptions about how condition dependence arises; both models show that variation in condition can readily mask costs of plasticity even when such costs are substantial. This can be shown simply in a model where plasticity itself evolves condition dependence, which would be expected if costly. Yet similar effects emerge from an alternative model where trait expression itself is condition-dependent. In this more complex model, the average condition in each environment and genetic covariance in condition across environments both determine when costs of plasticity can be revealed. Analogous to the paradox of missing trade-offs between life history traits, our models show that variation in condition can mask costs of plasticity even when costs exist, and suggest this conclusion may be robust to the details of how condition affects trait expression. Our models suggest that condition dependence can also account for the often-observed pattern of elevated plasticity costs inferred in stressful environments, the maintenance of genetic variance in plasticity, and provides insight into experimental and biological scenarios ideal for revealing a cost of phenotypic plasticity.

How development affects evolution

Natural selection acts on developmentally constructed phenotypes, but how does development affect evolution? This question prompts a simultaneous consideration of development and evolution. However, there has been a lack of general mathematical frameworks mechanistically integrating the two, which may have inhibited progress on the question. Here, we use a new mathematical framework that mechanistically integrates development into evolution to analyse how development affects evolution. We show that, while selection pushes genotypic and phenotypic evolution up the fitness landscape, development determines the admissible evolutionary pathway, such that evolutionary outcomes occur at path peaks rather than landscape peaks. Changes in development can generate path peaks, triggering genotypic or phenotypic diversification, even on constant, single-peak landscapes. Phenotypic plasticity, niche construction, extra-genetic inheritance, and developmental bias alter the evolutionary path and hence the outcome. Thus, extra-genetic inheritance can have permanent evolutionary effects by changing the developmental constraints, even if extra-genetically acquired elements are not transmitted to future generations. Selective development, whereby phenotype construction points in the adaptive direction, may induce adaptive or maladaptive evolution depending on the developmental constraints. Moreover, developmental propagation of phenotypic effects over age enables the evolution of negative senescence. Overall, we find that development plays a major evolutionary role.

Why study plasticity in multiple traits? New hypotheses for how phenotypically plastic traits interact during development and selection

Organisms can often respond adaptively to a change in their environment through phenotypic plasticity in multiple traits, a phenomenon termed as multivariate plasticity. These different plastic responses could interact and affect each other's development as well as selection on each other, but the causes and consequences of these interactions have received relatively little attention. Here, we propose a new conceptual framework for understanding how different plastic responses can affect each other's development and why organisms should have multiple plastic responses. A plastic change in one trait could alter the phenotype of a second plastic trait by changing either the cue received by the organism (cue-mediated effect) or the response to that cue (response-mediated effect). Multivariate plasticity could benefit the organism either because the plastic responses work better when expressed together (synergy) or because each response is more effective under different environmental circumstances (complementarity). We illustrate these hypotheses with case studies, focusing on interactions between behavior and morphology, plastic traits that differ in their reversibility. Future empirical and theoretical research should investigate the consequences of these interactions for additional factors important for the evolution of plasticity, such as the limits and costs of plasticity.

Properties of phenotypic plasticity in discrete threshold traits

Forms of phenotypic plasticity in key traits, and forms of selection on and genetic variation in such plasticity, fundamentally underpin phenotypic, population dynamic, and evolutionary responses to environmental variation and directional change. Accordingly, numerous theoretical and empirical studies have examined properties and consequences of plasticity, primarily considering traits that are continuously distributed on observed phenotypic scales with linear reaction norms. However, many environmentally sensitive traits are expressed as discrete alternative phenotypes and are appropriately characterized as quantitative genetic threshold traits. Here, we highlight that forms of phenotypic plasticity, genetic variation, and inheritance in plasticity, and outcomes of selection on plasticity, could differ substantially between threshold traits and continuously distributed traits (as are typically considered). We thereby highlight theoretical developments that are required to rationalize and predict phenotypic and microevolutionary dynamics involving plastic threshold traits, and outline how intrinsic properties of such traits could provide relatively straightforward explanations for apparently idiosyncratic observed patterns of phenotypic variation. We summarize how key quantitative genetic parameters underlying threshold traits can be estimated, and thereby set the scene for embedding dynamic discrete traits into theoretical and empirical understanding of the role of plasticity in driving phenotypic, population, and evolutionary responses to environmental variation and change.

An evolutionary model of sensitive periods when the reliability of cues varies across ontogeny

Sensitive periods are widespread in nature, but their evolution is not well understood. Recent mathematical modeling has illuminated the conditions favoring the evolution of sensitive periods early in ontogeny. However, sensitive periods also exist at later stages of ontogeny, such as adolescence. Here, we present a mathematical model that explores the conditions that favor sensitive periods at later developmental stages. In our model, organisms use environmental cues to incrementally construct a phenotype that matches their environment. Unlike in previous models, the reliability of cues varies across ontogeny. We use stochastic dynamic programming to compute optimal policies for a range of evolutionary ecologies and then simulate developmental trajectories to obtain mature phenotypes. We measure changes in plasticity across ontogeny using study paradigms inspired by empirical research: adoption and cross-fostering. Our results show that sensitive periods only evolve later in ontogeny if the reliability of cues increases across ontogeny. The onset, duration, and offset of sensitive periods—and the magnitude of plasticity—depend on the specific parameter settings. If the reliability of cues decreases across ontogeny, sensitive periods are favored only early in ontogeny. These results are robust across different paradigms suggesting that empirical findings might be comparable despite different experimental designs.

Morphological canalization, integration, and plasticity in response to population density in Abutilon theophrasti: Influences of soil conditions and growth stages

Phenotypic integration and developmental canalization have been hypothesized to constrain the degree of phenotypic plasticity, but little evidence exists, probably due to the lack of studies on the relationships among the three processes, especially for plants under different environments. We conducted a field experiment by subjecting plants of Abutilon theophrasti to three densities, under infertile and fertile soil conditions, and analyzing correlations among canalization, integration, and plasticity in a variety of measured morphological traits after 50 and 70 days, to investigate the relationships among the three variables in response to density and how these responses vary with soil conditions and growth stages. Results showed trait canalization decreased and phenotypic integration and the degree of plasticity (absolute plasticity) in traits increased with density. Phenotypic integration often positively correlated with absolute plasticity, whereas correlations between trait canalization and plasticity were insignificant in most cases, with a few positive ones between canalization and absolute plasticity at low and medium densities. As plants grew, these correlations intensified in infertile soil and attenuated in fertile soil. Our findings suggested the complexity of the relationship between canalization and plasticity: Decreased canalization is more likely to facilitate active plastic responses under more favorable conditions, whereas increased level of integration should mainly be an outcome of plastic responses. Soil conditions and growth stage may affect responses of these correlations to density via modifying plant size, competition strength, and plastic responses in traits. We also predicted that decreased canalization can be advantageous or disadvantageous, and the lack of response to stress may demonstrate a stronger ability of adaptation than passive response, thus should be adaptive plasticity as active response.

Ecological mechanism of climate-mediated selection in a rapidly evolving invasive species

Recurring seasonal changes can lead to the evolution of phenological cues. For example, many arthropods undergo photoperiodic diapause, a programmed developmental arrest induced by short autumnal day length. The selective mechanisms that determine the timing of autumnal diapause initiation have not been empirically identified. We quantified latitudinal clines in genetically determined diapause timing of an invasive mosquito, Aedes albopictus, on two continents. We show that variation in diapause timing within and between continents is explained by a novel application of a growing degree day (GDD) model that delineates a location-specific deadline after which it is not possible to complete an additional full life cycle. GDD models are widely used to predict spring phenology by modelling growth and development as physiological responses to ambient temperatures. Our results show that the energy accumulation dynamics represented by GDD models have also led to the evolution of an anticipatory life-history cue in autumn.

Physiological Genomics of Adaptation to High-Altitude Hypoxia

Population genomic studies of humans and other animals at high altitude have generated many hypotheses about the genes and pathways that may have contributed to hypoxia adaptation. Future advances require experimental tests of such hypotheses to identify causal mechanisms. Studies to date illustrate the challenge of moving from lists of candidate genes to the identification of phenotypic targets of selection, as it can be difficult to determine whether observed genotype-phenotype associations reflect causal effects or secondary consequences of changes in other traits that are linked via homeostatic regulation. Recent work on high-altitude models such as deer mice has revealed both plastic and evolved changes in respiratory, cardiovascular, and metabolic traits that contribute to aerobic performance capacity in hypoxia, and analyses of tissue-specific transcriptomes have identified changes in regulatory networks that mediate adaptive changes in physiological phenotype. Here we synthesize recent results and discuss lessons learned from studies of high-altitude adaptation that lie at the intersection of genomics and physiology.

Phenotypic evolution in stochastic environments: The contribution of frequency- and density-dependent selection

Understanding how environmental variation affects phenotypic evolution requires models based on ecologically realistic assumptions that include variation in population size and specific mechanisms by which environmental fluctuations affect selection. Here we generalize quantitative genetic theory for environmentally induced stochastic selection to include general forms of frequency- and density-dependent selection. We show how the relevant fitness measure under stochastic selection relates to Fisher's fundamental theorem of natural selection, and present a general class of models in which density regulation acts through total use of resources rather than just population size. In this model, there is a constant adaptive topography for expected evolution, and the function maximized in the long run is the expected factor restricting population growth. This allows us to generalize several previous results and to explain why apparently " K -selected" species with slow life histories often have low carrying capacities. Our joint analysis of density- and frequency-dependent selection reveals more clearly the relationship between population dynamics and phenotypic evolution, enabling a broader range of eco-evolutionary analyses of some of the most interesting problems in evolution in the face of environmental variation.

Temperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation System

We used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it suggests that microbial functioning, despite controlled conditions in the fermentors, fluctuates over season along with external temperature differences, which threatens a reproducible food taste. As such, we believe that our study provides a stepping-stone into novel taxonomy-functional studies that promote future work in other systems and that also is relevant in applied settings to better control surrounding conditions in food production.

We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications.

IMPORTANCE We used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it suggests that microbial functioning, despite controlled conditions in the fermentors, fluctuates over season along with external temperature differences, which threatens a reproducible food taste. As such, we believe that our study provides a stepping-stone into novel taxonomy-functional studies that promote future work in other systems and that also is relevant in applied settings to better control surrounding conditions in food production.

Coordinated changes across the O2 transport pathway underlie adaptive increases in thermogenic capacity in high-altitude deer mice

Animals native to the hypoxic and cold environment at high altitude provide an excellent opportunity to elucidate the integrative mechanisms underlying the adaptive evolution and plasticity of complex traits. The capacity for aerobic thermogenesis can be a critical determinant of survival for small mammals at high altitude, but the physiological mechanisms underlying the evolution of this performance trait remain unresolved. We examined this issue by comparing high-altitude deer mice (Peromyscus maniculatus) with low-altitude deer mice and white-footed mice (P. leucopus). Mice were bred in captivity and adults were acclimated to each of four treatments: warm (25°C) normoxia, warm hypoxia (12 kPa O2), cold (5°C) normoxia or cold hypoxia. Acclimation to hypoxia and/or cold increased thermogenic capacity in deer mice, but hypoxia acclimation led to much greater increases in thermogenic capacity in highlanders than in lowlanders. The high thermogenic capacity of highlanders was associated with increases in pulmonary O2 extraction, arterial O2 saturation, cardiac output and arterial-venous O2 difference. Mechanisms underlying the evolution of enhanced thermogenic capacity in highlanders were partially distinct from those underlying the ancestral acclimation responses of lowlanders. Environmental adaptation has thus enhanced phenotypic plasticity and expanded the physiological toolkit for coping with the challenges at high altitude.

Phenotypic Switching Resulting From Developmental Plasticity: Fixed or Reversible?

The prevalent view of developmental phenotypic switching holds that phenotype modifications occurring during critical windows of development are "irreversible" - that is, once produced by environmental perturbation, the consequent juvenile and/or adult phenotypes are indelibly modified. Certainly, many such changes appear to be non-reversible later in life. Yet, whether animals with switched phenotypes during early development are unable to return to a normal range of adult phenotypes, or whether they do not experience the specific environmental conditions necessary for them to switch back to the normal range of adult phenotypes, remains an open question. Moreover, developmental critical windows are typically brief, early periods punctuating a much longer period of overall development. This leaves open additional developmental time for reversal (correction) of a switched phenotype resulting from an adverse environment early in development. Such reversal could occur from right after the critical window "closes," all the way into adulthood. In fact, examples abound of the capacity to return to normal adult phenotypes following phenotypic changes enabled by earlier developmental plasticity. Such examples include cold tolerance in the fruit fly, developmental switching of mouth formation in a nematode, organization of the spinal cord of larval zebrafish, camouflage pigmentation formation in larval newts, respiratory chemosensitivity in frogs, temperature-metabolism relations in turtles, development of vascular smooth muscle and kidney tissue in mammals, hatching/birth weight in numerous vertebrates,. More extreme cases of actual reversal (not just correction) occur in invertebrates (e.g., hydrozoans, barnacles) that actually 'backtrack' along normal developmental trajectories from adults back to earlier developmental stages. While developmental phenotypic switching is often viewed as a permanent deviation from the normal range of developmental plans, the concept of developmental phenotypic switching should be expanded to include sufficient plasticity allowing subsequent correction resulting in the normal adult phenotype.