The ghosts of selection past reduces the probability of plastic rescue but increases the likelihood of evolutionary rescue to novel stressors in experimental populations of wild yeast

The role of spatial structure in multi-deme models of evolutionary rescue

Genetic variation and population sizes are critical factors for successful adaptation to novel environmental conditions. Gene flow between sub-populations is a potent mechanism to provide such variation and can hence facilitate adaptation, for instance by increasing genetic variation or via the introduction of beneficial variants. On the other hand, if gene flow between different habitats is too strong, locally beneficial alleles may not be able to establish permanently. In the context of evolutionary rescue, intermediate levels of gene flow are therefore often optimal for maximizing a species chance for survival in metapopulations without spatial structure. To which extent and under which conditions gene flow facilitates or hinders evolutionary rescue in spatially structured populations remains unresolved. We address this question by studying the differences between evolutionary rescue in the island model and in the stepping stone model in a gradually deteriorating habitat. We show that evolutionary rescue is modulated by the rate of gene flow between different habitats, which in turn depends strongly on the spatial structure and the pattern of environmental deterioration. We use these insights to show that in many cases spatially structured models can be translated into a simpler island model using an appropriately scaled effective migration rate.

Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions

To predict how widely distributed species will perform under future climate change, it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant Silene vulgaris across Europe. In a greenhouse experiment, we exposed the offspring of these populations to a climate change scenario for central Europe and revealed the population structure through whole-genome sequencing. Plants were grown under two temperatures (18°C and 21°C) and three precipitation regimes (65, 75, and 90 mm) to measure their response in biomass and fecundity-related traits. To reveal the population genetic structure, ddRAD sequencing was employed for a whole-genome approach. We found three major genetic clusters in S. vulgaris from Europe: one cluster comprising Southern European populations, one cluster of Western European populations, and another cluster containing central European populations. Population genetic diversity decreased with increasing latitude, and a Mantel test revealed significant correlations between F ST and geographic distances as well as between genetic and environmental distances. Our trait analysis showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate change scenario. Due to the differentiated but parallel response patterns, we assume that phenotypic plasticity plays an important role for the adaptation of the widely distributed species S. vulgaris and its intraspecific genetic lineages.

Limited plasticity in thermally tolerant ectotherm populations: evidence for a trade-off

Many species face extinction risks owing to climate change, and there is an urgent need to identify which species' populations will be most vulnerable. Plasticity in heat tolerance, which includes acclimation or hardening, occurs when prior exposure to a warmer temperature changes an organism's upper thermal limit. The capacity for thermal acclimation could provide protection against warming, but prior work has found few generalizable patterns to explain variation in this trait. Here, we report the results of, to our knowledge, the first meta-analysis to examine within-species variation in thermal plasticity, using results from 20 studies (19 species) that quantified thermal acclimation capacities across 78 populations. We used meta-regression to evaluate two leading hypotheses. The climate variability hypothesis predicts that populations from more thermally variable habitats will have greater plasticity, while the trade-off hypothesis predicts that populations with the lowest heat tolerance will have the greatest plasticity. Our analysis indicates strong support for the trade-off hypothesis because populations with greater thermal tolerance had reduced plasticity. These results advance our understanding of variation in populations' susceptibility to climate change and imply that populations with the highest thermal tolerance may have limited phenotypic plasticity to adjust to ongoing climate warming.

Ecological Memory of Historical Contamination Influences the Response of Phytoplankton Communities

Ecological memory (EM) recognizes the importance of previous stress encounters in promoting community tolerance and thereby enhances ecosystem stability, provided that gained tolerances are preserved during non-stress periods. Drawing from this concept, we hypothesized that the recruitment of tolerant species can be facilitated by imposing an initial sorting process (conditioning) during the early stages of community assembly, which should result in higher production (biomass development and photosynthetic efficiency) and stable community composition. To test this, phytoplankton resting stages were germinated from lake sediments originating from two catchments that differed in contamination history: one impacted by long-term herbicides and pesticides exposures (historically contaminated lake) from an agricultural catchment compared to a low-impacted one (near-pristine lake) from a forested catchment. Conditioning was achieved by adding an herbicide (Isoproturon, which was commonly used in the catchment of the historically contaminated lake) during germination. Afterward, the communities obtained from germination were exposed to an increasing gradient of Isoproturon. As hypothesized, upon conditioning, the phytoplankton assemblages from the historically contaminated lake were able to rapidly restore photosynthetic efficiency (p > 0.01) and became structurally (community composition) more resistant to Isoproturon. The communities of the near-pristine lake did not yield these positive effects regardless of conditioning, supporting that EM was a unique attribute of the historically stressed ecosystem. Moreover, assemblages that displayed higher structural resistance concurrently yielded lower biomass, indicating that benefits of EM in increasing structural stability may trade-off with production. Our results clearly indicate that EM can foster ecosystem stability to a recurring stressor.

Evolutionary rescue via transgenerational plasticity: Evidence and implications for conservation

When a population experiences severe stress from a changing environment, evolution by natural selection can prevent its extinction, a process dubbed "evolutionary rescue." However, evolution may be unable to track the sort of rapid environmental change being experienced by many modern-day populations. A potential solution is for organisms to respond to environmental change through phenotypic plasticity, which can buffer populations against change and thereby buy time for evolutionary rescue. In this review, we examine whether this process extends to situations in which the environmentally induced response is passed to offspring. As we describe, theoretical and empirical studies suggest that such "transgenerational plasticity" can increase population persistence. We discuss the implications of this process for conservation biology, outline potential limitations, and describe some applications. Generally, transgenerational plasticity may be effective at buying time for evolutionary rescue to occur.

Evolutionary Rescue Is Mediated by the History of Selection and Dispersal in Diversifying Metacommunities

Rapid evolution can sometimes prevent population extirpation in stressful environments, but the conditions leading to “evolutionary rescue” in metacommunities are unclear. Here we studied the eco-evolutionary response of microbial metacommunities adapting to selection by the antibiotic streptomycin. Our experiment tested how the history of antibiotic selection and contrasting modes of dispersal influenced diversification and subsequent evolutionary rescue in microbial metacommunities undergoing adaptive radiation. We first tracked the change in diversity and density of Pseudomonas fluorescens morphotypes selected on a gradient of antibiotic stress. We then examined the recovery of these metacommunities following abrupt application of a high concentration of streptomycin lethal to the ancestral organisms. We show that dispersal increases diversity within the stressed metacommunities, that exposure to stress alters diversification dynamics, and that community composition, dispersal, and past exposure to stress mediate the speed at which evolutionary rescue occurs, but not the final outcome of recovery in abundance and diversity. These findings extend recent experiments on evolutionary rescue to the case of metacommunities undergoing adaptive diversification, and should motivate new theory on this question. Our findings are also relevant to evolutionary conservation biology and research on antimicrobial resistance.

Evolutionary Rescue from a Wave of Biological Invasion

Evolution can potentially rescue populations from being driven extinct by biological invasions, but predictions for this occurrence are generally lacking. Here I derive theoretical predictions for evolutionary rescue of a resident population experiencing invasion from an introduced competitor that spreads over its introduced range as a traveling spatial wave that displaces residents. I compare the likelihood of evolutionary rescue from invasion for two modes of competition: exploitation and interference competition. I find that, all else equal, evolutionary rescue is less effective at preventing extinction caused by interference-driven invasions than by exploitation-driven invasions. Rescue from interference-driven invasions is, surprisingly, independent of invader dispersal rate or the speed of invasion and is more weakly dependent on range size than in the exploitation-driven case. In contrast, rescue from exploitation-driven invasions strongly depends on range size and is less likely during fast invasions. The results presented here have potential applications for conserving endemic species from nonnative invaders and for ensuring extinction of pests using intentionally introduced biocontrol agents.

Regenerative Adaptation to Electrochemical Perturbation in Planaria: A Molecular Analysis of Physiological Plasticity

Anatomical homeostasis results from dynamic interactions between gene expression, physiology, and the external environment. Owing to its complexity, this cellular and organism-level phenotypic plasticity is still poorly understood. We establish planarian regeneration as a model for acquired tolerance to environments that alter endogenous physiology. Exposure to barium chloride (BaCl₂) results in a rapid degeneration of anterior tissue in Dugesia japonica. Remarkably, continued exposure to fresh solution of BaCl₂ results in regeneration of heads that are insensitive to BaCl₂. RNA-seq revealed transcriptional changes in BaCl₂-adapted heads that suggests a model of adaptation to excitotoxicity. Loss-of-function experiments confirmed several predictions: blockage of chloride and calcium channels allowed heads to survive initial BaCl₂ exposure, inducing adaptation without prior exposure, whereas blockade of TRPM channels reversed adaptation. Such highly adaptive plasticity may represent an attractive target for biomedical strategies in a wide range of applications beyond its immediate relevance to excitotoxicity preconditioning.

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Exposure to BaCl₂ causes the heads of Dugesia japonica to degenerate

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Prolonged exposure to BaCl₂ results in regeneration of a BaCl₂-insensitive head

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Ion channel expression is altered in the head to compensate for excitotoxic stress

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TRPMa is upregulated in BaCl₂-treated animals; blocking TRPM prevents adaptation

Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution

In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.

The genetics of phenotypic plasticity. XV. Genetic assimilation, the Baldwin effect, and evolutionary rescue

We used an individual-based simulation model to examine the role of phenotypic plasticity on persistence and adaptation to two patterns of environmental variation, a single, abrupt step change and continual, linear change. Our model tested the assumptions and predictions of the theory of genetic assimilation, explored the evolutionary dynamics of the Baldwin effect, and provided expectations for the evolutionary response to climate change. We found that genetic assimilation as originally postulated is not likely to occur because the replacement of plasticity by fixed genetic effects takes much longer than the environment is likely to remain stable. On the other hand, trait plasticity as an enhancement to continual evolutionary change may be an important evolutionary mechanism as long as plasticity has little or no costs. Whether or not plasticity helps or hinders evolutionary rescue following a step change in the environment depends on whether plasticity is costly. For linear environmental change, noncostly plasticity always decreases extinction rates, while costly plasticity can create a fitness drag and increase the chance of extinction. Thus, with changing climates plasticity can enhance adaptation and prevent extinction under some conditions, but not others.

The effect of selection history on extinction risk during severe environmental change

Environments rarely remain the same over time, and populations are therefore frequently at risk of going extinct when changes are significant enough to reduce fitness. Although many studies have investigated what attributes of the new environments and of the populations experiencing these changes will affect their probability of going extinct, limited work has been directed towards determining the role of population history on the probability of going extinct during severe environmental change. Here, we compare the extinction risk of populations with a history of selection in a benign environment, to populations with a history of selection in one or two stressful environments. We exposed spores and lines of the green alga Chlamydomonas reinhardtii from these three different histories to a range of severe environmental changes. We found that the extinction risk was higher for populations with a history of selection in stressful environments compared to populations with a history of selection in a benign environment. This effect was not due to differences in initial population sizes. Finally, the rates of extinction were highly repeatable within histories, indicating strong historical contingency of extinction risk. Hence, information on the selection history of a population can be used to predict their probability of going extinct during environmental change.