Antagonistic coevolution limits population persistence of a virus in a thermally deteriorating environment

Evolution of thermal performance curves: A meta-analysis of selection experiments

Temperatures are increasing due to global changes, putting biodiversity at risk. Organisms are faced with a limited set of options to cope with this situation: adapt, disperse or die. We here focus on the first possibility, more specifically, on evolutionary adaptations to temperature. Ectotherms are usually characterized by a hump-shaped relationship between fitness and temperature, a non-linear reaction norm that is referred to as thermal performance curve (TPC). To understand and predict impacts of global change, we need to know whether and how such TPCs evolve. Therefore, we performed a systematic literature search and a statistical meta-analysis focusing on experimental evolution and artificial selection studies. This focus allows us to directly quantify relative fitness responses to temperature selection by calculating fitness differences between TPCs from ancestral and derived populations after thermal selection. Out of 7561 publications screened, we found 47 studies corresponding to our search criteria representing taxa across the tree of life, from bacteria, to plants and vertebrates. We show that, independently of species identity, the studies we found report a positive response to temperature selection. Considering entire TPC shapes, adaptation to higher temperatures traded off with fitness at lower temperatures, leading to niche shifts. Effects were generally stronger in unicellular organisms. By contrast, we do not find statistical support for the often discussed "Hotter is better" hypothesis. While our meta-analysis provides evidence for adaptive potential of TPCs across organisms, it also highlights that more experimental work is needed, especially for under-represented taxa, such as plants and non-model systems.

LiDAR Reveals the Process of Vision-Mediated Predator–Prey Relationships

Exploring the processes of interspecific relationships is crucial to understanding the mechanisms of biodiversity maintenance. Visually detecting interspecies relationships of large mammals is limited by the reconstruction accuracy of the environmental structure and the timely detection of animal behavior. Hence, we used backpack laser scanning (BLS) to reconstruct the high-resolution three-dimensional environmental structure to simulate the process of a predator approaching its prey, indicating that predator tigers would reduce their visibility by changing their behavior. Wild boars will nibble off about 5m of branches around the nest in order to create better visibility around the nest, adopting an anti-predation strategy to detect possible predators in advance. Our study not only points out how predator–prey relationships are affected by visibility as the environment mediates it, but also provides an operable framework for exploring interspecific relationships from a more complex dimension. Finally, this study provides a new perspective for exploring the mechanisms of biodiversity maintenance.

Bacterial Symbionts Confer Thermal Tolerance to Cereal Aphids Rhopalosiphum padi and Sitobion avenae

Simple Summary

This study assesses the putative association between the chronic and acute thermal tolerance of cereal aphids Rhopalosiphum padi (L.) and Sitobion avenae (F.) and the abundance of their bacterial symbionts. Thermal tolerance indices were determined for 5-day-old apterous aphid individuals and were associated with the aphid-specific and total bacterial symbionts’ gene abundance (copy numbers). The results show a significantly higher bacterial symbionts’ gene abundance in temperature-tolerant aphid individuals than the susceptible ones for both aphid species. Moreover, the gene abundance of total (16S rRNA) bacteria and most of the aphid-specific bacterial symbionts for both cereal aphid species were significantly and positively associated with their critical thermal maxima values. Overall, the findings of the study suggest the potential role of the bacterial symbionts of aphids in conferring thermal tolerance to their hosts.

Abstract

High-temperature events are evidenced to exert significant influence on the population performance and thermal biology of insects, such as aphids. However, it is not yet clear whether the bacterial symbionts of insects mediate the thermal tolerance traits of their hosts. This study is intended to assess the putative association among the chronic and acute thermal tolerance of two cereal aphid species, Rhopalosiphum padi (L.) and Sitobion avenae (F.), and the abundance of their bacterial symbionts. The clones of aphids were collected randomly from different fields of wheat crops and were maintained under laboratory conditions. Basal and acclimated CTmax and chronic thermal tolerance indices were measured for 5-day-old apterous aphid individuals and the abundance (gene copy numbers) of aphid-specific and total (16S rRNA) bacterial symbionts were determined using real-time RT-qPCR. The results reveal that R. padi individuals were more temperature tolerant under chronic exposure to 31 °C and also exhibited about 1.0 °C higher acclimated and basal CTmax values than those of S. avenae. Moreover, a significantly higher bacterial symbionts’ gene abundance was recorded in temperature-tolerant aphid individuals than the susceptible ones for both aphid species. Although total bacterial (16S rRNA) abundance per aphid was higher in S. avenae than R. padi, the gene abundance of aphid-specific bacterial symbionts was nearly alike for both of the aphid species. Nevertheless, basal and acclimated CTmax values were positively and significantly associated with the gene abundance of total symbiont density, Buchnera aphidicola, Serratia symbiotica, Hamilton defensa, Regiella insecticola and Spiroplasma spp. for R. padi, and with the total symbiont density, total bacteria (16S rRNA) and with all aphid-specific bacterial symbionts (except Spiroplasma spp.) for S. avenae. The overall study results corroborate the potential role of the bacterial symbionts of aphids in conferring thermal tolerance to their hosts.

Overcoming the growth-infectivity trade-off in a bacteriophage slows bacterial resistance evolution

The use of lytic bacteriophages for treating harmful bacteria (phage therapy) is faced with the challenge of bacterial resistance evolution. Phage strains with certain traits, for example, rapid growth and relatively broad infectivity ranges, may enjoy an advantage in slowing bacterial resistance evolution. Here, we show the possibility for laboratory selection programs ("evolutionary training") to yield phage genotypes with both high growth rate and broad infectivity, traits between which a trade-off has been assumed. We worked with a lytic phage that infects the bacterium Pseudomonas fluorescens and adopted three types of training strategies: evolution on susceptible bacteria, coevolution with bacteria, and rotation between evolution and coevolution phases. Overall, there was a trade-off between growth rate and infectivity range in the evolved phage isolates, including those from the rotation training programs. A small number of phages had both high growth rate and broad infectivity, and those trade-off-overcoming phages could slow or even completely prevent resistance evolution in initially susceptible bacterial populations. Our findings show the promise of well-designed evolutionary training programs, in particular an evolution/coevolution rotation selection regime, for obtaining therapeutically useful phage materials.

Intra-Population Competition during Adaptation to Increased Temperature in an RNA Bacteriophage

Evolution of RNA bacteriophages of the family Leviviridae is governed by the high error rates of their RNA-dependent RNA polymerases. This fact, together with their large population sizes, leads to the generation of highly heterogeneous populations that adapt rapidly to most changes in the environment. Throughout adaptation, the different mutants that make up a viral population compete with each other in a non-trivial process in which their selective values change over time due to the generation of new mutations. In this work we have characterised the intra-population dynamics of a well-studied levivirus, Qβ, when it is propagated at a higher-than-optimal temperature. Our results show that adapting populations experienced rapid changes that involved the ascent of particular genotypes and the loss of some beneficial mutations of early generation. Artificially reconstructed populations, containing a fraction of the diversity present in actual populations, fixed mutations more rapidly, illustrating how population bottlenecks may guide the adaptive pathways. The conclusion is that, when the availability of beneficial mutations under a particular selective condition is elevated, the final outcome of adaptation depends more on the occasional occurrence of population bottlenecks and how mutations combine in genomes than on the selective value of particular mutations.

Evolutionary rescue in host-pathogen systems

Natural populations encounter a variety of threats that can increase their risk of extinction. Populations can avoid extinction through evolutionary rescue (ER), which occurs when an adaptive, genetic response to selection allows a population to recover from an environmental change that would otherwise cause extinction. While the traditional framework for ER was developed with abiotic risk factors in mind, ER may also occur in response to a biotic source of demographic change, such as the introduction of a novel pathogen. We first describe how ER in response to a pathogen differs from the traditional ER framework; density-dependent transmission, pathogen evolution, and pathogen extinction can change the strength of selection imposed by a pathogen and make host population persistence more likely. We also discuss several variables that affect traditional ER (abundance, genetic diversity, population connectivity, and community composition) that also directly affect disease risk resulting in diverse outcomes for ER in host-pathogen systems. Thus, generalizations developed in studies of traditional ER may not be relevant for ER in response to the introduction of a pathogen. Incorporating pathogens into the framework of ER will lead to a better understanding of how and when populations can avoid extinction in response to novel pathogens.

Ecological limits to evolutionary rescue

Environments change, for both natural and anthropogenic reasons, which can threaten species persistence. Evolutionary adaptation is a potentially powerful mechanism to allow species to persist in these changing environments. To determine the conditions under which adaptation will prevent extinction (evolutionary rescue), classic quantitative genetics models have assumed a constantly changing environment. They predict that species traits will track a moving environmental optimum with a lag that approaches a constant. If fitness is negative at this lag, the species will go extinct. There have been many elaborations of these models incorporating increased genetic realism. Here, we review and explore the consequences of four ecological complications: non-quadratic fitness functions, interacting density- and trait-dependence, species interactions and fundamental limits to adaptation. We show that non-quadratic fitness functions can result in evolutionary tipping points and existential crises, as can the interaction between density- and trait-dependent mortality. We then review the literature on how interspecific interactions affect adaptation and persistence. Finally, we suggest an alternative theoretical framework that considers bounded environmental change and fundamental limits to adaptation. A research programme that combines theory and experiments and integrates across organizational scales will be needed to predict whether adaptation will prevent species extinction in changing environments. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.

Evolutionary tracking is determined by differential selection on demographic rates and density dependence

Recent ecological forecasts predict that ~25% of species worldwide will go extinct by 2050. However, these estimates are primarily based on environmental changes alone and fail to incorporate important biological mechanisms such as genetic adaptation via evolution. Thus, environmental change can affect population dynamics in ways that classical frameworks can neither describe nor predict. Furthermore, often due to a lack of data, forecasting models commonly describe changes in population demography by summarizing changes in fecundity and survival concurrently with the intrinsic growth rate (r). This has been shown to be an oversimplification as the environment may impose selective pressure on specific demographic rates (birth and death) rather than directly on r (the difference between the birth and death rates). This differential pressure may alter population response to density, in each demographic rate, further diluting the information combined to produce r. Thus, when we consider the potential for persistence via adaptive evolution, populations with the same r can have different abilities to persist amidst environmental change. Therefore, we cannot adequately forecast population response to climate change without accounting for demography and selection on density dependence. Using a continuous-time Markov chain model to describe the stochastic dynamics of the logistic model of population growth and allow for trait evolution via mutations arising during birth events, we find persistence via evolutionary tracking more likely when environmental change alters birth rather than the death rate. Furthermore, species that evolve responses to changes in the strength of density dependence due to environmental change are less vulnerable to extinction than species that undergo selection independent of population density. By incorporating these key demographic considerations into our predictive models, we can better understand how species will respond to climate change.

The evolution of host resistance and parasite infectivity is highest in seasonal resource environments that oscillate at intermediate amplitudes

Seasonal environments vary in their amplitude of oscillation but the effects of this temporal heterogeneity for host-parasite coevolution are poorly understood. Here, we combined mathematical modelling and experimental evolution of a coevolving bacteria-phage interaction to show that the intensity of host-parasite coevolution peaked in environments that oscillate in their resource supply with intermediate amplitude. Our experimentally parameterized mathematical model explains that this pattern is primarily driven by the ecological effects of resource oscillations on host growth rates. Our findings suggest that in host-parasite systems where the host's but not the parasite's population growth dynamics are subject to seasonal forcing, the intensity of coevolution will peak at intermediate amplitudes but be constrained at extreme amplitudes of environmental oscillation.

Temperature-dependent changes to host-parasite interactions alter the thermal performance of a bacterial host

Thermal performance curves (TPCs) are used to predict changes in species interactions, and hence, range shifts, disease dynamics and community composition, under forecasted climate change. Species interactions might in turn affect TPCs. Here, we investigate how temperature-dependent changes in a microbial host-parasite interaction (the bacterium Pseudomonas fluorescens, and its lytic bacteriophage, SBW[Formula: see text]) changes the host TPC and the ecological and evolutionary mechanisms underlying these changes. The bacteriophage had a narrower thermal tolerance for infection, with their critical thermal maximum ~6 °C lower than those at which the bacteria still had high growth. Consequently, in the presence of phage, the host TPC changed, resulting in a lower maximum growth rate. These changes were not just driven by differences in thermal tolerance, with temperature-dependent costs of evolved resistance also playing a major role: the largest cost of resistance occurred at the temperature at which bacteria grew best in the absence of phage. Our work highlights how ecological and evolutionary mechanisms can alter the effect of a parasite on host thermal performance, even over very short timescales.

Specific adaptation to strong competitors can offset the negative effects of population size reductions

Competition plays a crucial role in determining adaptation of species, yet we know little as to how adaptation is affected by the strength of competition. On the one hand, strong competition typically results in population size reductions, which can hamper adaptation owing to a shortage of beneficial mutations; on the other hand, specificity of adaptation to competitors may offset the negative evolutionary consequences of such population size effects. Here, we investigate how competition strength affects population fitness in the bacterium Pseudomonas fluorescens Our results demonstrate that strong competition constrains adaptation of focal populations, which can be partially explained by population size reductions. However, fitness assays also reveal specific adaptation of focal populations to particular competitors varying in competitive ability. Additionally, this specific adaptation can offset the negative effects of competitor-mediated population size reductions under strong competition. Our study, therefore, highlights the importance of opposing effects of strong competition on species adaptation, which may lead to different outcomes of colonization under intense and relaxed competitive environments in the context of population dispersal.

The paradox of tolerance: Parasite extinction due to the evolution of host defence

Host defence against parasite infection can rely on two broad strategies: resistance and tolerance. The spread of resistance traits usually lowers parasite prevalence and decreases selection for higher defence. Conversely, tolerance mechanisms increase parasite prevalence and foster selection for more tolerance. Here we examine the potential for the host to drive parasites to extinction through the evolution of one or other defence mechanism. We analysed theoretical models of resistance and tolerance evolution in both the absence and the presence of a trade-off between defence and reproduction. In the absence of costs, resistance evolves towards maximisation and, consequently, parasite extinction. Tolerance also evolves towards maximisation but the positive feedback between tolerance and disease prevents the disappearance of the parasite. On the contrary, when defence comes with costs it is impossible for the host to eliminate the infection through resistance, because costly resistance is selected against when parasites are at low prevalence. We uncover that the only path to disease clearance in the presence of costs is through tolerance. Paradoxically, however, it is by lowering tolerance -and hence increasing disease-induced mortality- that extinction can occur. We also show that such extinction can occur even in the case of parasite counter-adaptation. Our results emphasise the importance of tolerance as a defence strategy, and identify key questions for future research.

Modelling ecosystem adaptation and dangerous rates of global warming

We are in a period of relatively rapid climate change. This poses challenges for individual species and threatens the ecosystem services that humanity relies upon. Temperature is a key stressor. In a warming climate, individual organisms may be able to shift their thermal optima through phenotypic plasticity. However, such plasticity is unlikely to be sufficient over the coming centuries. Resilience to warming will also depend on how fast the distribution of traits that define a species can adapt through other methods, in particular through redistribution of the abundance of variants within the population and through genetic evolution. In this paper, we use a simple theoretical ‘trait diffusion’ model to explore how the resilience of a given species to climate change depends on the initial trait diversity (biodiversity), the trait diffusion rate (mutation rate), and the lifetime of the organism. We estimate theoretical dangerous rates of continuous global warming that would exceed the ability of a species to adapt through trait diffusion, and therefore lead to a collapse in the overall productivity of the species. As the rate of adaptation through intraspecies competition and genetic evolution decreases with species lifetime, we find critical rates of change that also depend fundamentally on lifetime. Dangerous rates of warming vary from 1°C per lifetime (at low trait diffusion rate) to 8°C per lifetime (at high trait diffusion rate). We conclude that rapid climate change is liable to favour short-lived organisms (e.g. microbes) rather than longer-lived organisms (e.g. trees).

Improvement of thermotolerance in Lachancea thermotolerans using a bacterial selection pressure

The use of thermotolerant yeast strains is an important attribute for a cost-effective high temperature biofermentation processes. However, the availability of thermotolerant yeast strains remains a major challenge. Isolation of temperature resistant strains from extreme environments or the improvements of current strains are two major strategies known to date. We hypothesised that bacteria are potential “hurdles” in the life cycle of yeasts, which could influence the evolution of extreme phenotypes, such as thermotolerance. We subjected a wild-type yeast, Lachancea thermotolerans to six species of bacteria sequentially for several generations. After coevolution, we observed that three replicate lines of yeasts grown in the presence of bacteria grew up to 37 °C whereas the controls run in parallel without bacteria could only grow poorly at 35 °C retaining the ancestral mesophilic trait. In addition to improvement of thermotolerance, our results show that the fermentative ability was also elevated, making the strains more ideal for the alcoholic fermentation process because the overall productivity and ethanol titers per unit volume of substrate consumed during the fermentation process was increased. Our unique method is attractive for the development of thermotolerant strains or to augment the available strain development approaches for high temperature industrial biofermentation.

Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria-plasmid-phage interaction

Bacteria engage in a complex network of ecological interactions, which includes mobile genetic elements (MGEs) such as phages and plasmids. These elements play a key role in microbial communities as vectors of horizontal gene transfer but can also be important sources of selection for their bacterial hosts. In natural communities, bacteria are likely to encounter multiple MGEs simultaneously and conflicting selection among MGEs could alter the bacterial evolutionary response to each MGE. Here, we test the effect of interactions with multiple MGEs on bacterial molecular evolution in the tripartite interaction between the bacterium, Pseudomonas fluorescens, the lytic bacteriophage, SBW25φ2, and conjugative plasmid, pQBR103, using genome sequencing of experimentally evolved bacteria. We show that individually, both plasmids and phages impose selection leading to bacterial evolutionary responses that are distinct from bacterial populations evolving without MGEs, but that together, plasmids and phages impose conflicting selection on bacteria, constraining the evolutionary responses observed in pairwise interactions. Our findings highlight the likely difficulties of predicting evolutionary responses to multiple selective pressures from the observed evolutionary responses to each selective pressure alone. Understanding evolution in complex microbial communities comprising many species and MGEs will require that we go beyond studies of pairwise interactions.

Stability of A Coevolving Host-parasite System Peaks at Intermediate Productivity

Habitat productivity may affect the stability of consumer-resource systems, through both ecological and evolutionary mechanisms. We hypothesize that coevolving consumer-resource systems show more stable dynamics at intermediate resource availability, while very low-level resource supply cannot support sufficiently large populations of resource and consumer species to avoid stochastic extinction, and extremely resource-rich environments may promote escalatory arms-race-like coevolution that can cause strong fluctuations in species abundance and even extinction of one or both trophic levels. We tested these ideas by carrying out an experimental evolution study with a model bacterium-phage system (Pseudomonas fluorescens SBW25 and its phage SBW25Φ2). Consistent with our hypothesis, this system was most stable at intermediate resource supply (fewer extinction events and smaller magnitude of population fluctuation). In our experiment, the rate of coevolution between bacterial resistance and phage infectivity was correlated with the magnitude of population fluctuation, which may explain the different in stability between levels of resource supply. Crucially, our results are consistent with a suggestion that, among the two major modes of antagonistic coevolution, arms race is more likely than fluctuation selection dynamics to cause extinction events in consumer-resource systems. This study suggests an important role of environment-dependent coevolutionary dynamics for the stability of consumer-resource species systems, therefore highlights the importance to consider contemporaneous evolutionary dynamics when studying the stability of ecosystems, particularly those under environmental changes.

Migration highways and migration barriers created by host-parasite interactions

Co-evolving parasites may play a key role in host migration and population structure. Using co-evolving bacteria and viruses, we test general hypotheses as to how co-evolving parasites affect the success of passive host migration between habitats that can support different intensities of host-parasite interactions. First, we show that parasites aid migration from areas of intense to weak co-evolutionary interactions and impede migration in the opposite direction, as a result of intraspecific apparent competition mediated via parasites. Second, when habitats show qualitative difference such that some environments support parasite persistence while others do not, different population regulation forces (either parasitism or competitive exclusion) will reduce the success of migration in both directions. Our study shows that co-evolution with parasites can predictably homogenises or isolates host populations, depending on heterogeneity of abiotic conditions, with the second scenario constituting a novel type of 'isolation by adaptation'.

Hot spots become cold spots: coevolution in variable temperature environments

Antagonistic coevolution between hosts and parasites is a key process in the genesis and maintenance of biological diversity. Whereas coevolutionary dynamics show distinct patterns under favourable environmental conditions, the effects of more realistic, variable conditions are largely unknown. We investigated the impact of a fluctuating environment on antagonistic coevolution in experimental microcosms of Pseudomonas fluorescens SBW25 and lytic phage SBWΦ2. High-frequency temperature fluctuations caused no deviations from typical coevolutionary arms race dynamics. However, coevolution was stalled during periods of high temperature under intermediate- and low-frequency fluctuations, generating temporary coevolutionary cold spots. Temperature variation affected population density, providing evidence that eco-evolutionary feedbacks act through variable bacteria-phage encounter rates. Our study shows that environmental fluctuations can drive antagonistic species interactions into and out of coevolutionary cold and hot spots. Whether coevolution persists or stalls depends on the frequency of change and the environmental optima of both interacting players.

Ecological conditions determine extinction risk in co-evolving bacteria-phage populations

Background

Antagonistic coevolution between bacteria and their viral parasites, phage, drives continual evolution of resistance and infectivity traits through recurrent cycles of adaptation and counter-adaptation. Both partners are vulnerable to extinction through failure of adaptation. Environmental conditions may impose unequal abiotic selection pressures on each partner, destabilising the coevolutionary relationship and increasing the extinction risk of one partner. In this study we explore how the degree of population mixing and resource supply affect coevolution-induced extinction risk by coevolving replicate populations of Pseudomonas fluorescens SBW25 with its associated lytic phage SBW25Ф2 under four treatment regimens incorporating low and high resource availability with mixed or static growth conditions.

Results

We observed an increased risk of phage extinction under population mixing, and in low resource conditions. High levels of evolved bacterial resistance promoted phage extinction at low resources under both mixed and static conditions, whereas phage populations could survive when phage susceptible bacterial genotypes rose to high frequency.

Conclusions

These findings demonstrate that phage extinction risk is influenced by multiple abiotic conditions, which together act to destabilise the bacteria-phage coevolutionary relationship. The risk of coevolution-induced extinction is therefore dependent on the ecological context.

Adaptation to abiotic conditions drives local adaptation in bacteria and viruses coevolving in heterogeneous environments

Parasite local adaptation, the greater performance of parasites on their local compared with foreign hosts, has important consequences for the maintenance of diversity and epidemiology. While the abiotic environment may significantly affect local adaptation, most studies to date have failed either to incorporate the effects of the abiotic environment, or to separate them from those of the biotic environment. Here, we tease apart biotic and abiotic components of local adaptation using the bacterium Pseudomonas fluorescens and its viral parasite bacteriophage Φ2. We coevolved replicate populations of bacteria and phages at three different temperatures, and determined their performance against coevolutionary partners from the same and different temperatures. Crucially, we measured performance at different assay temperatures, which allowed us to disentangle adaptation to biotic and abiotic habitat components. Our results show that bacteria and phages are more resistant and infectious, respectively, at the temperature at which they previously coevolved, confirming that local adaptation to abiotic conditions can play a crucial role in determining parasite infectivity and host resistance. Our work underlines the need to assess host–parasite interactions across multiple relevant abiotic environments, and suggests that microbial adaption to local temperatures can create ecological barriers to dispersal across temperature gradients.

Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community

Local adaptation of a species can affect community composition, yet the importance of local adaptation compared with species presence per se is unknown. Here we determine how a compost bacterial community exposed to elevated temperature changes over 2 months as a result of the presence of a focal bacterium, Pseudomonas fluorescens SBW25, that had been pre-adapted or not to the compost for 48 days. The effect of local adaptation on community composition is as great as the effect of species presence per se, with these results robust to the presence of an additional strong selection pressure: an SBW25-specific virus. These findings suggest that evolution occurring over ecological time scales can be a key driver of the structure of natural microbial communities, particularly in situations where some species have an evolutionary head start following large perturbations, such as exposure to antibiotics or crop planting and harvesting.

Though both the presence and traits of a species can influence the dynamics of its ecological community, the effects of these factors are difficult to disentangle. Here, Gómez et al. demonstrate in a microbial mesocosm that local adaptation of a focal species can influence the community as much as the presence of the focal species per se.

Resource-dependent antagonistic coevolution leads to a new paradox of enrichment

The classical, ecological, paradox of enrichment describes a phenomenon that resource enrichment destabilizes predator-prey systems by exacerbating population oscillations. Here we suggest a new, evolutionary, paradox of enrichment. Resource enrichment can lead to more asymmetrical predator-prey coevolution (i.e., extremely high levels of prey defenses against predators) that decreases predator abundances and increases predator extinction risk. A major reason for this is that high resource availability can reduce fitness costs associated with prey defenses. In our experiments with a bacterium and its lytic phage, nutrient-balanced resource enrichment led to patterns in population demography and coevolutionary dynamics consistent with this coevolution-based paradox of enrichment; in particular, phage population extinction events were observed under nutrient-rich, not nutrient-poor, conditions. Consistent with ecological studies, carbon-biased resource enrichment (with carbon availability disproportionately increased relative to other nutrients) did not destabilize dynamics, and the asymmetry of coevolution was not altered in this context. Our work highlights the importance of integrating ecological and evolutionary thinking for studies of the consequences of nutrient pollution and other types of environmental changes.

Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton

Understanding the mechanisms that determine how phytoplankton adapt to warming will substantially improve the realism of models describing ecological and biogeochemical effects of climate change. Here, we quantify the evolution of elevated thermal tolerance in the phytoplankton, Chlorella vulgaris. Initially, population growth was limited at higher temperatures because respiration was more sensitive to temperature than photosynthesis meaning less carbon was available for growth. Tolerance to high temperature evolved after ≈ 100 generations via greater down-regulation of respiration relative to photosynthesis. By down-regulating respiration, phytoplankton overcame the metabolic constraint imposed by the greater temperature sensitivity of respiration and more efficiently allocated fixed carbon to growth. Rapid evolution of carbon-use efficiency provides a potentially general mechanism for thermal adaptation in phytoplankton and implies that evolutionary responses in phytoplankton will modify biogeochemical cycles and hence food web structure and function under warming. Models of climate futures that ignore adaptation would usefully be revisited.

Pre-adapting parasitic phages to a pathogen leads to increased pathogen clearance and lowered resistance evolution with Pseudomonas aeruginosa cystic fibrosis bacterial isolates

Recent years have seen renewed interest in phage therapy--the use of viruses to specifically kill disease-causing bacteria--because of the alarming rise in antibiotic resistance. However, a major limitation of phage therapy is the ease at with bacteria can evolve resistance to phages. Here, we determined whether in vitro experimental coevolution can increase the efficiency of phage therapy by limiting the resistance evolution of intermittent and chronic cystic fibrosis Pseudomonas aeruginosa lung isolates to four different phages. We first pre-adapted all phage strains against all bacterial strains and then compared the efficacy of pre-adapted and nonadapted phages against ancestral bacterial strains. We found that evolved phages were more efficient in reducing bacterial densities than ancestral phages. This was primarily because only 50% of bacterial strains were able to evolve resistance to evolved phages, whereas all bacteria were able to evolve some level of resistance to ancestral phages. Although the rate of resistance evolution did not differ between intermittent and chronic isolates, it incurred a relatively higher growth cost for chronic isolates when measured in the absence of phages. This is likely to explain why evolved phages were more effective in reducing the densities of chronic isolates. Our data show that pathogen genotypes respond differently to phage pre-adaptation, and as a result, phage therapies might need to be individually adjusted for different patients.

Parasite and nutrient enrichment effects on Daphnia interspecific competition

Increased productivity due to nutrient enrichment is hypothesized to affect density-dependent processes, such as transmission success of horizontally transmitting parasites. Changes in nutrient availability can also modify the stoichiometry and condition of individual hosts, which may affect their susceptibility for parasites as well as the growth conditions for parasites within the host. Consequently, if not balanced by increased host immuno-competence or life history responses, changes in the magnitude of parasite effects with increasing nutrient availability are expected. If these parasite effects are host-species specific, this may lead to shifts in the host community structure. We here used the Daphnia- parasite model system to study the effect of nutrient enrichment on parasite-mediated competition in experimental mesocosms. In the absence of parasites, D. magna was competitively dominant to D. pulex at both low and high nutrient levels. Introduction of parasites resulted in infections of D. magna, but not of D. pulex and, as such, reversed the competitive hierarchy between these two species. Nutrient addition resulted in an increased prevalence and infection intensity of some of the parasites on D. magna. However, there was no evidence that high nutrient levels enhanced negative effects of parasites on the hosts. Costs associated with parasite infections may have been compensated by better growth conditions for D. magna in the presence of high nutrient levels.

Evolutionary rescue can be impeded by temporary environmental amelioration

Rapid evolutionary adaptation has the potential to rescue from extinction populations experiencing environmental changes. Little is known, however, about the impact of short-term environmental fluctuations during long-term environmental deterioration, an intrinsic property of realistic environmental changes. Temporary environmental amelioration arising from such fluctuations could either facilitate evolutionary rescue by allowing population recovery (a positive demographic effect) or impede it by relaxing selection for beneficial mutations required for future survival (a negative population genetic effect). We address this uncertainty in an experiment with populations of a bacteriophage virus that evolved under deteriorating conditions (gradually increasing temperature). Periodic environmental amelioration (short periods of reduced temperature) caused demographic recovery during the early phase of the experiment, but ultimately reduced the frequency of evolutionary rescue. These experimental results suggest that environmental fluctuations could reduce the potential of evolutionary rescue.

Experimental evolution can unravel the complex causes of natural selection in clinical infections

It is increasingly clear that rapid evolutionary dynamics are an important process in microbial ecology. Experimental evolution, wherein microbial evolution is observed in real-time, has revealed many instances of appreciable evolutionary change occurring on very short timescales of a few days or weeks in response to a variety of biotic and abiotic selection pressures. From clinical infections, including the chronic bacterial lung infections associated with cystic fibrosis that form a focus of my research, there is now abundant evidence suggesting that rapid evolution by infecting microbes contributes to host adaptation, treatment failure and worsening patient prognosis. However, disentangling the drivers of natural selection in complex infection environments is extremely challenging and limits our understanding of the selective pressures acting upon microbes in infections. Controlled evolution experiments can make a vital contribution to this by determining the causal links between predicted drivers of natural selection and the evolutionary responses of microbes. Integration of experimental evolution into studies of clinical infections is a key next step towards a better understanding of the causes and consequences of rapid microbial evolution in infections, and discovering how these evolutionary processes might be influenced to improve patient health.A video of this Prize Lecture, presented at the Society for General Microbiology Annual Conference 2015, can be viewed via this link: Michael A. Brockhurst https://www.youtube.com/watch?v=N1bodVSl27E.

Coevolution with bacteriophages drives genome-wide host evolution and constrains the acquisition of abiotic-beneficial mutations

Studies of antagonistic coevolution between hosts and parasites typically focus on resistance and infectivity traits. However, coevolution could also have genome-wide effects on the hosts due to pleiotropy, epistasis, or selection for evolvability. Here, we investigate these effects in the bacterium Pseudomonas fluorescens SBW25 during approximately 400 generations of evolution in the presence or absence of bacteriophage (coevolution or evolution treatments, respectively). Coevolution resulted in variable phage resistance, lower competitive fitness in the absence of phages, and greater genome-wide divergence both from the ancestor and between replicates, in part due to the evolution of increased mutation rates. Hosts from coevolution and evolution treatments had different suites of mutations. A high proportion of mutations observed in coevolved hosts were associated with a known phage target binding site, the lipopolysaccharide (LPS), and correlated with altered LPS length and phage resistance. Mutations in evolved bacteria were correlated with higher fitness in the absence of phages. However, the benefits of these growth-promoting mutations were completely lost when these bacteria were subsequently coevolved with phages, indicating that they were not beneficial in the presence of resistance mutations (consistent with negative epistasis). Our results show that in addition to affecting genome-wide evolution in loci not obviously linked to parasite resistance, coevolution can also constrain the acquisition of mutations beneficial for growth in the abiotic environment.

Effects of epistasis on infectivity range during host-parasite coevolution

Understanding how parasites adapt to changes in host resistance is crucial to evolutionary epidemiology. Experimental studies have demonstrated that parasites are more capable of adapting to gradual, rather than sudden changes in host phenotype, as the latter may require multiple mutations that are unlikely to arise simultaneously. A key, but as yet unexplored factor is precisely how interactions between mutations (epistasis) affect parasite evolution. Here, we investigate this phenomenon in the context of infectivity range, where parasites may experience selection to infect broader sets of genotypes. When epistasis is strongly positive, we find that parasites are unlikely to evolve broader infectivity ranges if hosts exhibit sudden, rather than gradual changes in phenotype, in close agreement with empirical observations. This is due to a low probability of fixing multiple mutations that individually confer no immediate advantage. When epistasis is weaker, parasites are more likely to evolve broader infectivity ranges if hosts make sudden changes in phenotype, which can be explained by a balance between mutation supply and selection. Thus, we demonstrate that both the rate of phenotypic change in hosts and the form of epistasis between mutations in parasites are crucial in shaping the evolution of infectivity range.

Coevolution and the effects of climate change on interacting species

BACKGROUND

Recent studies suggest that environmental changes may tip the balance between interacting species, leading to the extinction of one or more species. While it is recognized that evolution will play a role in determining how environmental changes directly affect species, the interactions among species force us to consider the coevolutionary responses of species to environmental changes.

METHODOLOGY/PRINCIPLE FINDINGS

We use simple models of competition, predation, and mutualism to organize and synthesize the ways coevolution modifies species interactions when climatic changes favor one species over another. In cases where species have conflicting interests (i.e., selection for increased interspecific interaction strength on one species is detrimental to the other), we show that coevolution reduces the effects of climate change, leading to smaller changes in abundances and reduced chances of extinction. Conversely, when species have nonconflicting interests (i.e., selection for increased interspecific interaction strength on one species benefits the other), coevolution increases the effects of climate change.

CONCLUSIONS/SIGNIFICANCE

Coevolution sets up feedback loops that either dampen or amplify the effect of environmental change on species abundances depending on whether coevolution has conflicting or nonconflicting effects on species interactions. Thus, gaining a better understanding of the coevolutionary processes between interacting species is critical for understanding how communities respond to a changing climate. We suggest experimental methods to determine which types of coevolution (conflicting or nonconflicting) drive species interactions, which should lead to better understanding of the effects of coevolution on species adaptation. Conducting these experiments across environmental gradients will test our predictions of the effects of environmental change and coevolution on ecological communities.

The interplay between microevolution and community structure in microbial populations

The structure of microbial communities is key to their functionality. However, this structure is likely to be influenced by adaptive genetic change in members of the community, which can occur over a matter of days. Changes in community structure can in turn influence the evolutionary trajectories of species within the community, further altering community structure. Microbial communities provide evidence for this interplay between rapid evolution and community structure. To date, studies are primarily limited to simple in vitro systems, but we suggest similar processes are inevitably operating in both natural and derived communities, which are important for biotechnology.

Real-time microbial adaptive diversification in soil

Bacteria undergo adaptive diversification over a matter of days in test tubes, but the relevance to natural populations remains unclear. Here, we report real-time adaptive diversification of the bacterium Pseudomonas fluorescens in its natural environment, soil. Crucially, adaptive diversification was much greater in the absence of the established natural microbial community, suggesting that resident diversity is likely to inhibit, rather than promote, adaptive radiations in natural environments. Rapid diversification is therefore likely to play an important role in the population and community dynamics of microbes in environments where resident communities are perturbed, such as by agriculture, pollution and antibiotics.

How competition affects evolutionary rescue

Populations facing novel environments can persist by adapting. In nature, the ability to adapt and persist will depend on interactions between coexisting individuals. Here we use an adaptive dynamic model to assess how the potential for evolutionary rescue is affected by intra- and interspecific competition. Intraspecific competition (negative density-dependence) lowers abundance, which decreases the supply rate of beneficial mutations, hindering evolutionary rescue. On the other hand, interspecific competition can aid evolutionary rescue when it speeds adaptation by increasing the strength of selection. Our results clarify this point and give an additional requirement: competition must increase selection pressure enough to overcome the negative effect of reduced abundance. We therefore expect evolutionary rescue to be most likely in communities which facilitate rapid niche displacement. Our model, which aligns to previous quantitative and population genetic models in the absence of competition, provides a first analysis of when competitors should help or hinder evolutionary rescue.

The probability of evolutionary rescue: towards a quantitative comparison between theory and evolution experiments

Evolutionary rescue occurs when a population genetically adapts to a new stressful environment that would otherwise cause its extinction. Forecasting the probability of persistence under stress, including emergence of drug resistance as a special case of interest, requires experimentally validated quantitative predictions. Here, we propose general analytical predictions, based on diffusion approximations, for the probability of evolutionary rescue. We assume a narrow genetic basis for adaptation to stress, as is often the case for drug resistance. First, we extend the rescue model of Orr & Unckless (Am. Nat. 2008 172, 160-169) to a broader demographic and genetic context, allowing the model to apply to empirical systems with variation among mutation effects on demography, overlapping generations and bottlenecks, all common features of microbial populations. Second, we confront our predictions of rescue probability with two datasets from experiments with Saccharomyces cerevisiae (yeast) and Pseudomonas fluorescens (bacterium). The tests show the qualitative agreement between the model and observed patterns, and illustrate how biologically relevant quantities, such as the per capita rate of rescue, can be estimated from fits of empirical data. Finally, we use the results of the model to suggest further, more quantitative, tests of evolutionary rescue theory.

Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory

Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause 'evolutionary suicide'. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called 'evolutionary trapping'. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps.

What Can Phages Tell Us about Host-Pathogen Coevolution?

The outcomes of host-parasite interactions depend on the coevolutionary forces acting upon them, but because every host-parasite relation is enmeshed in a web of biotic and abiotic interactions across a heterogeneous landscape, host-parasite coevolution has proven difficult to study. Simple laboratory phage-bacteria microcosms can ameliorate this difficulty by allowing controlled, well-replicated experiments with a limited number of interactors. Genetic, population, and life history data obtained from these studies permit a closer examination of the fundamental correlates of host-parasite coevolution. In this paper, I describe the results of phage-bacteria coevolutionary studies and their implications for the study of host-parasite coevolution. Recent experimental studies have confirmed phage-host coevolutionary dynamics in the laboratory and have shown that coevolution can increase parasite virulence, specialization, adaptation, and diversity. Genetically, coevolution frequently proceeds in a manner best described by the Gene for Gene model, typified by arms race dynamics, but certain contexts can result in Red Queen dynamics according to the Matching Alleles model. Although some features appear to apply only to phage-bacteria systems, other results are broadly generalizable and apply to all instances of antagonistic coevolution. With laboratory host-parasite coevolutionary studies, we can better understand the perplexing array of interactions that characterize organismal diversity in the wild.

Investigating climate change and reproduction: experimental tools from evolutionary biology

It is now generally acknowledged that climate change has wide-ranging biological consequences, potentially leading to impacts on biodiversity. Environmental factors can have diverse and often strong effects on reproduction, with obvious ramifications for population fitness. Nevertheless, reproductive traits are often neglected in conservation considerations. Focusing on animals, recent progress in sexual selection and sexual conflict research suggests that reproductive costs may pose an underestimated hurdle during rapid climate change, potentially lowering adaptive potential and increasing extinction risk of certain populations. Nevertheless, regime shifts may have both negative and positive effects on reproduction, so it is important to acquire detailed experimental data. We hence present an overview of the literature reporting short-term reproductive consequences of exposure to different environmental factors. From the enormous diversity of findings, we conclude that climate change research could benefit greatly from more coordinated efforts incorporating evolutionary approaches in order to obtain cross-comparable data on how individual and population reproductive fitness respond in the long term. Therefore, we propose ideas and methods concerning future efforts dealing with reproductive consequences of climate change, in particular by highlighting the advantages of multi-generational experimental evolution experiments.

Egg phenotype matching by cuckoos in relation to discrimination by hosts and climatic conditions

Although parasites and their hosts often coexist in a set of environmentally differentiated populations connected by gene flow, few empirical studies have considered a role of environmental variation in shaping correlations between traits of hosts and parasites. Here, we studied for the first time the association between the frequency of adaptive parasitic common cuckoo Cuculus canorus phenotypes in terms of egg matching and level of defences exhibited by its reed warbler Acrocephalus scirpaceus hosts across seven geographically distant populations in Europe. We also explored the influence of spring climatic conditions experienced by cuckoos and hosts on cuckoo-host egg matching. We found that between-population differences in host defences against cuckoos (i.e. rejection rate) covaried with between-population differences in degree of matching. Between-population differences in host egg phenotype were associated with between-population differences in parasitism rate and spring climatic conditions, but not with host level of defences. Between-population differences in cuckoo egg phenotype covaried with between-population differences in host defences and spring climatic conditions. However, differences in host defences still explained differences in mimicry once differences in climatic conditions were controlled, suggesting that selection exerted by host defences must be strong relative to selection imposed by climatic factors on egg phenotypes.

Bacteria-virus coevolution

Phages, viruses of bacteria, are ubiquitous. Many phages require host cell death to successfully complete their life cycle, resulting in reciprocal evolution of bacterial resistance and phage infectivity (antagonistic coevolution). Such coevolution can have profound consequences at all levels of biological organisation. Here, we review genetic and ecological factors that contribute to determining coevolutionary dynamics between bacteria and phages. We also consider some of the consequences of bacteria-phage coevolution, such as determining rates of molecular evolution and structuring communities, and how these in turn feedback into driving coevolutionary dynamics.