Evolutionary and plastic rescue in multitrophic model communities

Under changing environmental conditions, intraspecific variation can potentially rescue populations from extinction. There are two principal sources of variation that may ultimately lead to population rescue: genetic diversity and phenotypic plasticity. We compared the potential for evolutionary rescue (through genetic diversity) and plastic rescue (through phenotypic plasticity) by analysing their differential ability to produce dynamical stability and persistence in model food webs. We also evaluated how rescue is affected by the trophic location of variation. We tested the following hypotheses: (i) plastic communities are more likely to exhibit stability and persistence than communities in which genetic diversity provides the same range of traits. (ii) Variation at the lowest trophic level promotes stability and persistence more than variation at higher levels. (iii) Communities with variation at two levels have greater probabilities of stability and persistence than communities with variation at only one level. We found that (i) plasticity promotes stability and persistence more than genetic diversity; (ii) variation at the second highest trophic level promotes stability and persistence more than variation at the autotroph level; and (iii) more than variation at two trophic levels. Our study shows that proper evaluation of the rescue potential of intraspecific variation critically depends on its origin and trophic location.     

Evolutionary rescue and the coexistence of generalist and specialist competitors: an experimental test

Competition for resources is thought to play a critical role in both the origins and maintenance of biodiversity. Although numerous laboratory evolution experiments have confirmed that competition can be a key driver of adaptive diversification, few have demonstrated its role in the maintenance of the resulting diversity. We investigate the conditions that favour the origin and maintenance of alternative generalist and specialist resource-use phenotypes within the same population. Previously, we confirmed that competition for hosts among φ6 bacteriophage in a mixed novel (non-permissive) and ancestral (permissive) host microcosm triggered the evolution of a generalist phenotype capable of infecting both hosts. However, because the newly evolved generalists tended to competitively exclude the ancestral specialists, coexistence between the two phenotypes was rare. Here, we show that reducing the relative abundance of the novel host slowed the increase in frequency of the generalist phenotype, allowing sufficient time for the specialist to further adapt to the ancestral host. This adaptation resulted in ‘evolutionary rescue’ of the specialists, preventing their competitive exclusion by the generalists. Thus, our results suggest that competition promotes both the origin and maintenance of biodiversity when it is strong enough to favour a novel resource-use phenotype, but weak enough to allow adaptation of both the novel and ancestral phenotypes to their respective niches.     

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.     

Evolutionary rescue in vertebrates: evidence,applications and uncertainty

The current rapid rate of human-driven environmental change presents wild populations with novel conditions and stresses. Theory and experimental evidence for evolutionary rescue present a promising case for species facing environmental change persisting via adaptation. Here, we assess the potential for evolutionary rescue in wild vertebrates. Available information on evolutionary rescue was rare and restricted to abundant and highly fecund species that faced severe intentional anthropogenic selective pressures. However, examples from adaptive tracking in common species and genetic rescues in species of conservation concern provide convincing evidence in favour of the mechanisms of evolutionary rescue. We conclude that low population size, long generation times and limited genetic variability will result in evolutionary rescue occurring rarely for endangered species without intervention. Owing to the risks presented by current environmental change and the possibility of evolutionary rescue in nature, we suggest means to study evolutionary rescue by mapping genotype → phenotype → demography → fitness relationships, and priorities for applying evolutionary rescue to wild populations.     

Evolutionary Change and Epistemology

This paper is concerned with the debate in evolutionary epistemology about the nature of the evolutionary process at work in the development of science: whether it is Darwinian or Lamarckian. It is claimed that if we are to make progress through the many arguments that have grown up around this issue, we must return to an examination of the concepts of change and evolution, and examine the basic kinds of mechanism capable of bringing evolution about. This examination results in two kinds of processes being identified, dubbed direct and indirect, and these are claimed to exhaust all possibilities. These ideas are then applied to a selection of the debates within evolutionary epistemology. It is shown that while arguments about the pattern and rate of evolutionary change are necessarily inconclusive, those concerning the origin of novel variations and the mode of inheritance can be resolved by means of the distinctions made here. It is claimed that the process of selection in the evolution of science can also be clarified. The conclusion is that the main process producing the evolution of science is a direct or Lamarckian one although, if realism is correct, an indirect or Darwinian process plays a vital role.     

Two Explanations of Evolutionary Progress

Natural selection explains how living forms are fitted to theirconditions of life. Darwin argued that selection also explains what hecalled the gradual advancement of the organisation, i.e.evolutionary progress. Present-day selectionists disagree. In theirview, it is happenstance that sustains conditions favorable to progress,and therefore happenstance, not selection, that explains progress. Iargue that the disagreement here turns not on whether there exists aselection-based condition bias – a belief now attributed to Darwin – but on whether there needs to be such a bias for selection to count as explaining progress. In Darwin's own view, selection explained progressso far as more complex organisms have the selective advantage whenselection operates unimpeded. I show that these two explanations ofevolutionary progress, selection and happenstance, answer for theirobjectivity to different standards, and for their truth or falsehood todifferent features of the world.     

Stress and limits to adaptation: Sexual ornaments

Limits to adaptation of sexual ornaments are discussed in the context of the stressful environments of free-living populations. A trade-off occurs whereby the energetic demands from the development and maintenance of sexual ornaments of increasing size are countered by (1) the energetic cost of stress in particular from parasites and climatic extremes, and (2) a lack of energy from nutritional inadequacy. Furthermore, at times of environmental deterioration followed by high extinction rates, sexually dimorphic species should be particularly vulnerable. However, at these unfavourable times, individuals carrying genes for stress resistance should have the potential for developing the most extreme ornaments.     

Evolutionary dynamics in structured populations

Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces.     

Evolutionary rescue and adaptation to abrupt environmental change depends upon the history of stress

Whether evolution will be rapid enough to rescue declining populations will depend upon population size, the supply of genetic variation, the degree of maladaptation and the historical direction of selection. We examined whether the level of environmental stress experienced by a population prior to abrupt environmental change affects the probability of evolutionary rescue (ER). Hundreds of populations of two species of yeast, Saccharomyces cerevisiae and Saccharomyces paradoxus were exposed to a range of sublethal concentrations of salt for approximately a hundred generations before transfer to a concentration of salt lethal to the ancestor (150 g l^–1 NaCl). The fitness of surviving populations of both species was a quadratic function of yield: fitness was greatest for large populations that had been selected on low salt concentrations (less than 20 g l⁻¹ NaCl) and small populations that had adapted to high salt (more than 80 g l⁻¹ NaCl). However, differences occurred between species in the probability of ER. The frequency of ER was positively correlated with salt concentration for S. cerevisiae, but negatively correlated with salt concentration in S. paradoxus. These results not only demonstrate that past environmental conditions can determine the probability of ER after abrupt environmental change, but also suggest that there may even be differences between closely related species that are worth further exploration.     

Developmental variability and the limits of adaptation: Interactions with stress

1. Little evolutionary change may occur at species borders since the cost of accommodating environmental stresses is high. Extreme examples of such stasis include cave animals in stable stressed environments and ‘living fossils’ in widely fluctuating stressed environments. 2. Variability from the molecular to the organismic level tends to be high under extreme stress. At the developmental level, the fitness of such variants may be low. This means that much developmental variability in natural populations may have little evolutionary significance. 3. Rapid evolutionary change of morphological traits is most likely to be based upon genes acting late in a developmental pathway under conditions which are ecologically and energetically permissive. 4. Although some increases in resistance to temperature extremes have been recorded in laboratory selection experiments, major extensions of extremes in natural populations appear difficult to achieve. The energetic costs of surviving extremes at species borders implies that the evolution of major developmental and morphological shifts is more likely to be a feature of populations of more equable habitats.     

Isolation of transgenic progeny of maize by embryo rescue under selective conditions

Summary Fertile transgenic maize plants (T₀) and progeny (T₁) were obtained using microprojectile bombardment and callus selection on hygromycin B. To quickly identify progeny expressing the transgene, embryos from T3 generation kernels were excised 20 days after pollination and exposed to different concentrations of hygromycin B. Surviving and non-surviving embryos were assayed for the presence of the hygromycin phosphotransferase (aphIV) gene using polymerase chain reaction. Embryos that germinated and survived on 25, 50, or 100 mg/liter hygromycin possessed theaphIV gene. Embryos that did not germinate lacked the gene. Progeny surviving selection were transferred to the greenhouse and tested for expression of the gene using a leaf disc assay. The results demonstrated that the gene construct was expressed in both embryo and leaf tissue and that selection during germination successfully eliminated progeny lacking the gene of interest. This method is also useful for rapid-cycling of maize generations.     

Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses

In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments.     

Evolutionary Dynamics of Seed Size and Seedling Competitive Ability

We present a model for the evolutionary dynamics of seed size when there is a trade-off between seed size and seed number, and seedlings from large seeds are better competitors and have a higher precompetitive survival than seedlings from small seeds. We find that strong competitive asymmetry, high resource levels, and intermediate harshness of the precompetitive environment favor coexistence of plants with different seed sizes. If the evolution of seed size is mutation-limited and single mutations have only a small phenotypic effect, then an initially monomorphic population reaches the final evolutionarily stable polymorphic state through one or more discrete evolutionary branching events. At each such branching event, a given lineage already present in the population divides into two phenotypically diverging daughter lines, each with its own seed size. If the precompetitive survival of seeds and seedlings is high for small and large seeds alike, however, evolutionary branching may be followed by the extinction of one or more lineages. Various results presented here are model-independent and point the way to a more general evolutionary bifurcation theory describing how the number and stability properties of evolutionary equilibria may change as a consequence of changes in model parameters.     

Evolutionary rescue by beneficial mutations in environments that change in space and time

A factor that may limit the ability of many populations to adapt to changing conditions is the rate at which beneficial mutations can become established. We study the probability that mutations become established in changing environments by extending the classic theory for branching processes. When environments change in time, under quite general conditions, the establishment probability is approximately twice the ‘effective selection coefficient’, whose value is an average that gives most weight to a mutant''s fitness in the generations immediately after it appears. When fitness varies along a gradient in a continuous habitat, increased dispersal generally decreases the chance a mutation establishes because mutations move out of areas where they are most adapted. When there is a patch of favourable habitat that moves in time, there is a maximum speed of movement above which mutations cannot become established, regardless of when and where they first appear. This critical speed limit, which is proportional to the mutation''s maximum selective advantage, represents an absolute constraint on the potential of locally adapted mutations to contribute to evolutionary rescue.     

Evolutionary dynamics of human retroviruses investigated through full-genome scanning

To test hypotheses on the differences in retroviral genetic diversity, we compared the evolutionary dynamics of the human immunodeficiency virus type 1 (HIV-1) group M and the primate T-cell lymphotropic virus (PTLV) using a full-genome analysis. Evolutionary rates and nonsynonymous/synonymous substitution rate ratios were estimated across the genome using a maximum likelihood sliding window approach, and molecular clock properties were investigated. We confirm a remarkable difference in genetic stability and selective pressure at the interhost level. While there is evidence for adaptive evolution in HIV-1, the evolution of PTLV is almost exclusively characterized by negative selection or nearly neutral processes. For both retroviruses, evolutionary rate estimates across the genome reflect the differential selective constraints. However, based on the relationship between evolutionary rate and selective pressure and based on the comparison of synonymous substitution rates, the differences in rate between HIV-1 and PTLV cannot be explained by selective forces only. Several evolutionary and statistical assumptions, examined using a Bayesian coalescent method, were shown to have little influence on our inference.     

鸟类羽色多态现象：概念及其进化机制假说

多态现象对了解物种的遗传、变异和进化有着重要意义,鸟类羽色多态现象的进化机制,是多态现象研究中非常重要的内容。鸟类羽色多态现象的进化机制假说主要有：分化选择假说、异类选择假说和非随机性交配假说等。本文对鸟类羽色多态现象的概念和以上进化机制假说进行了综述,并针对鸟类羽色多态现象进化机制研究中存在争议的问题及研究的不足提出了自己的看法。     

Evolutionary and Ecological Effects of Multi-Generational Exposures to Anthropogenic Stressors

Biological and ecological responses to stress are dictated by duration and frequency, as well as instantaneous magnitude. Conditional compensatory responses at the physiological and behavioral levels, referred to as ‘acclimation’, may mitigate effects on individuals experiencing brief or infrequent periods of moderate stress. However, even modest stress over extended periods may reduce the fitness of some or all exposed individuals. In this way, specific stress that persists over multiple generations will increase probabilities for extinction of populations composed of sensitive individuals. For populations whose members demonstrate variance and heritability for stressor response, this selective loss of sensitive individuals may result in populations dominated by resistant individuals. The formation of these ‘adapted’ populations may be considered an ecological compensatory mechanism to multi-generational stress. Paradoxically, the biological costs to individuals of toxicity and physiological acclimation may result in obvious signs of stress in affected wildlife populations while the costs of genetic adaptation may be more covert. It is important to consider such costs because recent evidence suggests that anthropogenic stressors have acted as powerful selection agents that have modified the composition of wildlife populations subjected for successive generational exposures to specific stressors. This essay focuses on a case study where adaptation has been demonstrated in fish populations with a history of chronic exposure to persistent, bioaccumulative and toxic environmental contaminants. Because the magnitude, breadth and long-term outcomes of such changes are unknown, ecological risk assessments that are limited in focus to short-term exposures and consequences may seriously underestimate the ecological and evolutionary impacts of anthropogenic stressors.     

Evolutionary rates for multivariate traits: the role of selection and genetic variation

A fundamental question in evolutionary biology is the relative importance of selection and genetic architecture in determining evolutionary rates. Adaptive evolution can be described by the multivariate breeders'' equation (), which predicts evolutionary change for a suite of phenotypic traits () as a product of directional selection acting on them (β) and the genetic variance–covariance matrix for those traits (G). Despite being empirically challenging to estimate, there are enough published estimates of G and β to allow for synthesis of general patterns across species. We use published estimates to test the hypotheses that there are systematic differences in the rate of evolution among trait types, and that these differences are, in part, due to genetic architecture. We find some evidence that sexually selected traits exhibit faster rates of evolution compared with life-history or morphological traits. This difference does not appear to be related to stronger selection on sexually selected traits. Using numerous proposed approaches to quantifying the shape, size and structure of G, we examine how these parameters relate to one another, and how they vary among taxonomic and trait groupings. Despite considerable variation, they do not explain the observed differences in evolutionary rates.