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

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

Population structure inhibits evolutionary diversification under competition for resources

A model is presented that explores how population structure affects the evolutionary outcome of ecological competition for resources. The model assumes that competition for resources occurs within groups of a finite number of individuals (interaction groups), and that limited dispersal of individuals between groups (according to Wright's island model of population structure) results in genetic structuring of the population. It is found that both finite-sized interaction groups and limited dispersal can have substantial effects on the evolution of resource exploitation strategies as compared to models with a single, infinitely large, well-mixed interaction group. Both effects, in general, tend to select for less aggressive competitive strategies. Moreover, both effects also tend to reduce the likelihood of the evolutionary diversification of resource exploitation strategies that often occurs in models of resource competition with infinite populations. The results are discussed in the context of theories of the evolutionary diversification of resource exploitation strategies and speciation.     

Evolutionary rescue under demographic and environmental stochasticity

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

Ecological bistability and evolutionary reversals under asymmetrical competition

Abstract How does the process of life‐history evolution interplay with population dynamics? Almost all models that have addressed this question assume that any combination of phenotypic traits uniquely determine the ecological population state. Here we show that if multiple ecological equilibria can exist, the evolution of a trait that relates to competitive performance can undergo adaptive reversals that drive cyclic alternation between population equilibria. The occurrence of evolutionary reversals requires neither environmentally driven changes in selective forces nor the coevolution of interactions with other species. The mechanism inducing evolutionary reversals is twofold. First, there exist phenotypes near which mutants can invade and yet fail to become fixed; although these mutants are eventually eliminated, their transitory growth causes the resident population to switch to an alternative ecological equilibrium. Second, asymmetrical competition causes the direction of selection to revert between high and low density. When ecological conditions for evolutionary reversals are not satisfied, the population evolves toward a steady state of either low or high abundance, depending on the degree of competitive asymmetry and environmental parameters. A sharp evolutionary transition between evolutionary stasis and evolutionary reversals and cycling can occur in response to a smooth change in ecological parameters, and this may have implications for our understanding of size‐abundance patterns.     

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.     

On evolution under asymmetric competition

The evolutionary consequences of asymmetric competition between species are poorly understood in comparison with symmetric competition. A model for evolution of body size under asymmetric competition within and between species is described. The model links processes operating at the scale of the individual to that of macroscopic evolution through a stochastic mutation–selection process. Phase portraits of evolution in a phenotype space characteristically show character convergence and parallel character shifts, with character divergence being relatively uncommon. The asymptotic states of evolution depend very much on the properties of asymmetric competition. Given relatively weak asymmetries between species, a single equilibrium point exists; this is a local attractor, and its position is determined by the intra- and interspecific asymmetries. When the asymmetries are made stronger, several fixed points may come about, creating further equilibrium points which are local attractors. It is also possible for periodic attractors to occur; such attractors comprise Red Queen dynamics with phenotype values that continue to change without ever settling down to constant values. From certain initial conditions, evolution leading to extinction of one of the species is also a likely outcome.     

Limited evolutionary rescue of locally adapted populations facing climate change

Dispersal is a key determinant of a population''s evolutionary potential. It facilitates the propagation of beneficial alleles throughout the distributional range of spatially outspread populations and increases the speed of adaptation. However, when habitat is heterogeneous and individuals are locally adapted, dispersal may, at the same time, reduce fitness through increasing maladaptation. Here, we use a spatially explicit, allelic simulation model to quantify how these equivocal effects of dispersal affect a population''s evolutionary response to changing climate. Individuals carry a diploid set of chromosomes, with alleles coding for adaptation to non-climatic environmental conditions and climatic conditions, respectively. Our model results demonstrate that the interplay between gene flow and habitat heterogeneity may decrease effective dispersal and population size to such an extent that substantially reduces the likelihood of evolutionary rescue. Importantly, even when evolutionary rescue saves a population from extinction, its spatial range following climate change may be strongly narrowed, that is, the rescue is only partial. These findings emphasize that neglecting the impact of non-climatic, local adaptation might lead to a considerable overestimation of a population''s evolvability under rapid environmental change.     

Overcoming Allee effects through evolutionary,genetic, and demographic rescue

Despite the amplified threats of extinction facing small founder populations, successful colonization sometimes occurs, bringing devastating ecological and economic consequences. One explanation may be rapid evolution, which can increase mean fitness in populations declining towards extinction, permitting persistence and subsequent expansion. Such evolutionary rescue may be particularly important, given Allee effects. When a population is introduced at low density, individuals often experience a reduction in one or more components of fitness due to novel selection pressures that arise from diminished intraspecific interactions and positive density dependence (i.e. component Allee effects). A population can avoid extinction if it can adapt and recover on its own (i.e. evolutionary rescue), or if additional immigration sustains the population (i.e. demographic rescue) or boosts its genetic variation that facilitates adaptation (i.e. genetic rescue). These various forms of rescue have often been invoked as possible mechanisms for specific invasions, but their relative importance to invasion is not generally understood. Within a spatially explicit modelling framework, we consider the relative impact of each type of rescue on the probability of successful colonization, when there is evolution of a multi-locus quantitative trait that influences the strength of component Allee effects. We demonstrate that when Allee effects are important, the effect of demographic rescue via recurrent immigration overall provides the greatest opportunity for success. While highlighting the role of evolution in the invasion process, we underscore the importance of the ecological context influencing the persistence of small founder populations.     

Compensatory adaptation and diversification subsequent to evolutionary rescue in a model adaptive radiation

Biological populations may survive lethal environmental stress through evolutionary rescue. The rescued populations typically suffer a reduction in growth performance and harbor very low genetic diversity compared with their parental populations. The present study addresses how population size and within‐population diversity may recover through compensatory evolution, using the experimental adaptive radiation of bacterium Pseudomonas fluorescens. We exposed bacterial populations to an antibiotic treatment and then imposed a one‐individual‐size population bottleneck on those surviving the antibiotic stress. During the subsequent compensatory evolution, population size increased and leveled off very rapidly. The increase of diversity was of slower paces and persisted longer. In the very early stage of compensatory evolution, populations of large sizes had a greater chance to diversify; however, this productivity–diversification relationship was not observed in later stages. Population size and diversity from the end of the compensatory evolution was not contingent on initial population growth performance. We discussed the possibility that our results be explained by the emergence of a “holey” fitness landscape under the antibiotic stress.     

Ecological and evolutionary principles in immunology

Experimental immunology has given rise to detailed insights into how immune cells react to infectious agents and fight pathogens. At the same time, however, the interplay between infectious agents and immune responses can be viewed as an ecological system in vivo . This is characterized by complex interactions between species of immune cells and populations of pathogens. This review discusses how an understanding of the immune system can be aided by the application of ecological and evolutionary principles: competition, predation, and the evolution of viruses in vivo . These concepts can shed light onto important immunological concepts such as the correlates of efficient virus control, immunodominance, the relationship between viral evolution and the development of pathology, as well as the ability of the immune system to control immunosuppressive infections.     

Cooperation can promote rescue or lead to evolutionary suicide during environmental change

The adaptation of populations to changing conditions may be affected by interactions between individuals. For example, when cooperative interactions increase fecundity, they may allow populations to maintain high densities and thus keep track of moving environmental optima. Simultaneously, changes in population density alter the marginal benefits of cooperative investments, creating a feedback loop between population dynamics and the evolution of cooperation. Here we model how the evolution of cooperation interacts with adaptation to changing environments. We hypothesize that environmental change lowers population size and thus promotes the evolution of cooperation, and that this, in turn, helps the population keep up with the moving optimum. However, we find that the evolution of cooperation can have qualitatively different effects, depending on which fitness component is reduced by the costs of cooperation. If the costs decrease fecundity, cooperation indeed speeds adaptation by increasing population density; if, in contrast, the costs decrease viability, cooperation may instead slow adaptation by lowering the effective population size, leading to evolutionary suicide. Thus, cooperation can either promote or—counterintuitively—hinder adaptation to a changing environment. Finally, we show that our model can also be generalized to other social interactions by discussing the evolution of competition during environmental change.     

用动态模型研究森林群落中物种间的竞争

研究了以过程为基础的模型在物种竞争试验模型及实践中的应用。应用森林动态林窗模型模拟了群落内物种竞争规律。结果表明：同一群落中具有不同生物、生态学特征的物种竞争过程与环境条件有密切关系。由此确定,竞争是与外部条件密切相关的,不是一个单独稀量物种特征的指标;具有相似生物和生态学特性的物种,在森林植被发育过程中,存在绝对竞争,具有较弱更新与生长能力的物种,始终处于竞争劣热,不宜于在这样的群落中生长,而且有较强更新和生长的树种在群落中处于优势地位。     

A macroecological approach to evolutionary rescue and adaptation to climate change

Despite the widespread use of ecological niche models (ENMs) for predicting the responses of species to climate change, these models do not explicitly incorporate any population‐level mechanism. On the other hand, mechanistic models adding population processes (e.g. biotic interactions, dispersal and adaptive potential to abiotic conditions) are much more complex and difficult to parameterize, especially if the goal is to predict range shifts for many species simultaneously. In particular, the adaptive potential (based on genetic adaptations, phenotypic plasticity and behavioral adjustments for physiological responses) of local populations has been a less studied mechanism affecting species’ responses to climatic change so far. Here, we discuss and apply an alternative macroecological framework to evaluate the potential role of evolutionary rescue under climate change based on ENMs. We begin by reviewing eco‐evolutionary models that evaluate the maximum sustainable evolutionary rate under a scenario of environmental change, showing how they can be used to understand the impact of temperature change on a Neotropical anuran species, the Schneider's toad Rhinella diptycha. Then we show how to evaluate spatial patterns of species’ geographic range shift using such models, by estimating evolutionary rates at the trailing edge of species distribution estimated by ENMs and by recalculating the relative amount of total range loss under climate change. We show how different models can reduce the expected range loss predicted for the studied species by potential ecophysiological adaptations in some regions of the trailing edge predicted by ENMs. For general applications, we believe that parameters for large numbers of species and populations can be obtained from macroecological generalizations (e.g. allometric equations and ecogeographical rules), so our framework coupling ENMs with eco‐evolutionary models can be applied to achieve a more accurate picture of potential impacts from climate change and other threats to biodiversity.     

No evidence for competition between cytotoxic T-lymphocyte responses in HIV-1 infection

Strong competition between cytotoxic T-lymphocytes (CTLs) specific for different epitopes in human immunodeficiency virus (HIV) infection would have important implications for the design of an HIV vaccine. To investigate evidence for this type of competition, we analysed CTL response data from 97 patients with chronic HIV infection who were frequently sampled for up to 96 weeks. For each sample, CTL responses directed against a range of known epitopes in gag, pol and nef were measured using an enzyme-linked immunospot assay. The Lotka–Volterra model of competition was used to predict patterns that would be expected from these data if competitive interactions materially affect CTL numbers. In this application, the model predicts that when hosts make responses to a larger number of epitopes, they would have diminished responses to each epitope and that if one epitope-specific response becomes dramatically smaller, others would increase in size to compensate; conversely if one response grows, others would shrink. Analysis of the experimental data reveals results that are wholly inconsistent with these predictions. In hosts who respond to more epitopes, the average epitope-specific response tends to be larger, not smaller. Furthermore, responses to different epitopes almost always increase in unison or decrease in unison. Our findings are therefore inconsistent with the hypothesis that there is competition between CTL responses directed against different epitopes in HIV infection. This suggests that vaccines that elicit broad responses would be favourable because they would direct a larger total response against the virus, in addition to being more robust to the effects of CTL escape.     

Evolutionary rescue in randomly mating,selfing, and clonal populations

Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations.     

Trade-offs between and within scales: environmental persistence and within-host fitness of avian influenza viruses

Trade-offs between different components of a pathogen''s replication and transmission cycle are thought to be common. A number of studies have identified trade-offs that emerge across scales, reflecting the tension between strategies that optimize within-host proliferation and large-scale population spread. Most of these studies are theoretical in nature, with direct experimental tests of such cross-scale trade-offs still rare. Here, we report an analysis of avian influenza A viruses across scales, focusing on the phenotype of temperature-dependent viral persistence. Taking advantage of a unique dataset that reports both environmental virus decay rates and strain-specific viral kinetics from duck challenge experiments, we show that the temperature-dependent environmental decay rate of a strain does not impact within-host virus load. Hence, for this phenotype, the scales of within-host infection dynamics and between-host environmental persistence do not seem to interact: viral fitness may be optimized on each scale without cross-scale trade-offs. Instead, we confirm the existence of a temperature-dependent persistence trade-off on a single scale, with some strains favouring environmental persistence in water at low temperatures while others reduce sensitivity to increasing temperatures. We show that this temperature-dependent trade-off is a robust phenomenon and does not depend on the details of data analysis. Our findings suggest that viruses might employ different environmental persistence strategies, which facilitates the coexistence of diverse strains in ecological niches. We conclude that a better understanding of the transmission and evolutionary dynamics of influenza A viruses probably requires empirical information regarding both within-host dynamics and environmental traits, integrated within a combined ecological and within-host framework.     

适应性实验室进化技术在微生物育种中的应用进展

适应性实验室进化(Adaptive laboratory evolution,ALE)技术已成为微生物学基础研究和工业微生物育种的强大工具,被广泛用来研究影响菌株表型、性能和稳定性的进化潜力以及快速获取含有有益突变的工业生产菌株。近年来,随着基因组测序技术的进步,关于微生物新陈代谢机理和动力学方面的研究变得更加广泛和深入,这也极大促进了适应性实验室进化技术的快速发展。文中主要介绍了长期、短期适应性实验室进化技术在微生物育种方面的应用实例,并总结归纳了该技术在快速高效构建优良菌株过程中的方式与作用。最后分析了目前ALE技术面临的瓶颈问题及其可能的解决方法,以期能够为该技术的未来发展提供有价值的参考依据。