TEMPORAL VARIATION FAVORS THE EVOLUTION OF GENERALISTS IN EXPERIMENTAL POPULATIONS OF DROSOPHILA MELANOGASTER

In variable environments, selection should favor generalists that maintain fitness across a range of conditions. However, costs of adaptation may generate fitness trade‐offs and lead to some compromise between specialization and generalization that maximizes fitness. Here, we evaluate the evolution of specialization and generalization in 20 populations of Drosophila melanogaster experimentally evolved in constant and variable thermal environments for 3 years. We developed genotypes from each population at two temperatures after which we measured fecundity across eight temperatures. We predicted that constant environments would select for thermal specialists and that variable environments would select for thermal generalists. Contrary to our predictions, specialists and generalists did not evolve in constant and spatially variable environments, respectively. However, temporal variation produced a type of generalist that has rarely been considered by theoretical models of developmental plasticity. Specifically, genotypes from the temporally variable selective environment were more fecund across all temperatures than were genotypes from other environments. These patterns suggest certain allelic effects and should inspire new directions for modeling adaptation to fluctuating environments.     

Experimental demography and the vital rates of generalist and specialist insect herbivores on native and novel host plants

1. Colonization success of species when confronted with novel environments is of interest in ecological, evolutionary and conservation contexts. Such events may represent the first step for ecological diversification. They also play an important role in adaptive divergence and speciation. 2. A species that is able to do well across a range of environments has a higher plasticity than one whose success is restricted to a single or few environments. The breadth of environments in which a species can succeed is ultimately determined by the full pattern of its vital rates in each environment. 3. Examples of organisms colonizing novel environments are insect herbivores expanding their diets to novel host plants. One expectation for insect herbivores is that species with specialized diets may display less plasticity when faced with novel hosts than generalist species. 4. We examine this hypothesis for two generalist and two specialist neotropical beetles (genus Cephaloleia: Chrysomelidae) currently expanding their diets from native to novel plants of the order Zingiberales. Using an experimental approach, we estimated changes in vital rates, life-history traits and lifetime fitness for each beetle species when feeding on native or novel host plants. 5. We did not find evidence supporting more plasticity for generalists than for specialists. Instead, we found similar patterns of survival and fecundity for all herbivores. Larvae survived worse on novel hosts; adults survived at least as well or better, but reproduced less on the novel host than on natives. 6. Some of the novel host plants represent challenging environments where population growth was negative. However, in four novel plant-herbivore interactions, instantaneous population growth rates were positive. 7. Positive instantaneous population growth rates during initial colonization of novel host plants suggest that both generalist and specialist Cephaloleia beetles may be pre-adapted to feed on some novel hosts. This plasticity in host use is a key factor for successful colonization of novel hosts. Future success or failure in the colonization of these novel hosts will depend on the demographic rates described in this research, natural selection and the evolutionary responses of life-history traits in novel environments.     

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.     

Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6

ABSTRACT: BACKGROUND: Viruses are exceedingly diverse in their evolved strategies to manipulate hosts for viral replication. However, despite these differences, most virus populations will occasionally experience two commonly-encountered challenges: growth in variable host environments, and growth under fluctuating population sizes. We used the segmented RNA bacteriophage [GREEK PHI SYMBOL]6 as a model for studying the evolutionary genomics of virus adaptation in the face of host switches and parametrically varying population sizes. To do so, we created a bifurcating deme structure that reflected lineage splitting in natural populations, allowing us to test whether phylogenetic algorithms could accurately resolve this 'known phylogeny'. The resulting tree yielded 32 clones at the tips and internal nodes; these strains were fully sequenced and measured for phenotypic changes in selected traits (fitness on original and novel hosts). RESULTS: We observed that RNA segment size was negatively correlated with the extent of molecular change in the imposed treatments; molecular substitutions tended to cluster on the Small and Medium RNA chromosomes of the virus, and not on the Large segment. Our study yielded a very large molecular and phenotypic dataset, fostering possible inferences on genotype-phenotype associations. Using further experimental evolution, we confirmed an inference on the unanticipated role of an allelic switch in a viral assembly protein, which governed viral performance across host environments. CONCLUSIONS: Our study demonstrated that varying complexities can be simultaneously incorporated into experimental evolution, to examine the combined effects of population size, and adaptation in novel environments. The imposed bifurcating structure revealed that some methods for phylogenetic reconstruction failed to resolve the true phylogeny, owing to a paucity of molecular substitutions separating the RNA viruses that evolved in our study.     

No need for speed: slow development of fungi in extreme environments

Microbial growth under extreme conditions is often slow. This is partly because large amounts of energy are diverted into cellular mechanisms that allow survival under hostile conditions. Because this challenge is universal and diversity in extreme environments is low compared to non-extreme environments, slow-growing microorganisms are not overgrown by other species. In some cases, especially when nutrients are scarce, slow growth was even shown to increase stress tolerance. And in at least some species of extremotolerant and extremophilic fungi, growth rate appears to be coupled with their very unusual morphologies, which in turn may be an adaptation to extreme conditions. However, there is more than one strategy of survival in extreme environments. Fungi that thrive in extremes can be divided into (i) ubiquitous and polyextremotolerant generalists and (ii) rarely isolated specialists with narrow ecological amplitudes. While generalists can compete with mesophilic species, specialists cannot. When adapting to extreme conditions, the risk of an evolutionary trade-off in the form of reduced fitness under mesophilic conditions may limit the maximum stress tolerance achievable by polyextremotolerant generalists. At the same time, specialists are rarely found in mesophilic environments, which allows them to evolve to ever greater extremotolerance, since a reduction of mesophilic fitness is likely to have little impact on their evolutionary success.     

Rapid specialization of counter defenses enables two-spotted spider mite to adapt to novel plant hosts

Genetic adaptation, occurring over a long evolutionary time, enables host-specialized herbivores to develop novel resistance traits and to efficiently counteract the defenses of a narrow range of host plants. In contrast, physiological acclimation, leading to the suppression and/or detoxification of host defenses, is hypothesized to enable broad generalists to shift between plant hosts. However, the host adaptation mechanisms used by generalists composed of host-adapted populations are not known. Two-spotted spider mite (TSSM; Tetranychus urticae) is an extreme generalist herbivore whose individual populations perform well only on a subset of potential hosts. We combined experimental evolution, Arabidopsis thaliana genetics, mite reverse genetics, and pharmacological approaches to examine mite host adaptation upon the shift of a bean (Phaseolus vulgaris)-adapted population to Arabidopsis. We showed that cytochrome P450 monooxygenases are required for mite adaptation to Arabidopsis. We identified activities of two tiers of P450s: general xenobiotic-responsive P450s that have a limited contribution to mite adaptation to Arabidopsis and adaptation-associated P450s that efficiently counteract Arabidopsis defenses. In approximately 25 generations of mite selection on Arabidopsis plants, mites evolved highly efficient detoxification-based adaptation, characteristic of specialist herbivores. This demonstrates that specialization to plant resistance traits can occur within the ecological timescale, enabling the TSSM to shift to novel plant hosts.

Mites can evolve highly efficient detoxification-based adaptation in approximately 25 generations on an initially unfavorable plant host, revealing that specialization can occur within the ecological timescale.     

Experimental evolution for generalists and specialists reveals multivariate genetic constraints on thermal reaction norms

Theory predicts the emergence of generalists in variable environments and antagonistic pleiotropy to favour specialists in constant environments, but empirical data seldom support such generalist–specialist trade‐offs. We selected for generalists and specialists in the dung fly Sepsis punctum (Diptera: Sepsidae) under conditions that we predicted would reveal antagonistic pleiotropy and multivariate trade‐offs underlying thermal reaction norms for juvenile development. We performed replicated laboratory evolution using four treatments: adaptation at a hot (31 °C) or a cold (15 °C) temperature, or under regimes fluctuating between these temperatures, either within or between generations. After 20 generations, we assessed parental effects and genetic responses of thermal reaction norms for three correlated life‐history traits: size at maturity, juvenile growth rate and juvenile survival. We find evidence for antagonistic pleiotropy for performance at hot and cold temperatures, and a temperature‐mediated trade‐off between juvenile survival and size at maturity, suggesting that trade‐offs associated with environmental tolerance can arise via intensified evolutionary compromises between genetically correlated traits. However, despite this antagonistic pleiotropy, we found no support for the evolution of increased thermal tolerance breadth at the expense of reduced maximal performance, suggesting low genetic variance in the generalist–specialist dimension.     

Combining mathematics and empirical data to predict emergence of RNA viruses that differ in reservoir use

RNA viruses may be particularly capable of contributing to the increasing biomedical problem of infectious disease emergence. Empirical studies and epidemiological models are informative for the understanding of evolutionary processes that promote pathogen emergence, but rarely are these approaches combined in the same study. Here, we used an epidemiology model containing observations of pathogen productivity in reservoirs, as a means to predict which pathogens should be most prone to emerge in a primary host such as humans. We employed as a model system a collection of vesicular stomatitis virus populations that had previously diverged in host-use strategy: specialists, directly selected generalists and indirectly selected (fortuitous) generalists. Using data from experiments where these viral strategists were challenged to grow on unencountered novel hosts in vitro, logistic growth models determined that the directly selected generalist viruses tended to grow best on model reservoirs. Furthermore, when we used the growth data to estimate average reproductive rate across secondary reservoirs, we showed that the combined approach could be used to estimate relative success of the differing virus strategists when encountering a primary host. Our study suggests that synergistic approaches combining epidemiological modelling with empirical data from experimental evolution may be useful for developing efforts to predict which types of pathogens pose the greatest probability of emerging in the future.     

Extremotolerance in fungi: evolution on the edge

Our planet offers many opportunities for life on the edge: high and low temperatures, high salt concentrations, acidic and basic conditions and toxic environments, to name but a few extremes. Recent studies have revealed the diversity of fungi that can occur in stressful environments that are hostile to most eukaryotes. We review these studies here, with the additional purpose of proposing some mechanisms that would allow for the evolutionary adaptation of eukaryotic microbial life under extreme conditions. We focus, in particular, on life in ice and life at high salt concentrations, as there is a surprising similarity between the fungal populations in these two kinds of environments, both of which are characterized by low water activity. We propose steps of evolution of generalist species towards the development of specialists in extreme habitats. We argue that traits present in some fungal groups, such as asexuality, synthesis of melanin-like pigments and a flexible morphology, are preadaptations that facilitate persistence and eventual adaptation to conditions on the ecological edge, as well as biotope switches. These processes are important for understanding the evolution of extremophiles; moreover, they have implications for the emergence of novel fungal pathogens.     

Dengue Virus RNA Structure Specialization Facilitates Host Adaptation

Many viral pathogens cycle between humans and insects. These viruses must have evolved strategies for rapid adaptation to different host environments. However, the mechanistic basis for the adaptation process remains poorly understood. To study the mosquito-human adaptation cycle, we examined changes in RNA structures of the dengue virus genome during host adaptation. Deep sequencing and RNA structure analysis, together with fitness evaluation, revealed a process of host specialization of RNA elements of the viral 3’UTR. Adaptation to mosquito or mammalian cells involved selection of different viral populations harvesting mutations in a single stem-loop structure. The host specialization of the identified RNA structure resulted in a significant viral fitness cost in the non-specialized host, posing a constraint during host switching. Sequence conservation analysis indicated that the identified host adaptable stem loop structure is duplicated in dengue and other mosquito-borne viruses. Interestingly, functional studies using recombinant viruses with single or double stem loops revealed that duplication of the RNA structure allows the virus to accommodate mutations beneficial in one host and deleterious in the other. Our findings reveal new concepts in adaptation of RNA viruses, in which host specialization of RNA structures results in high fitness in the adapted host, while RNA duplication confers robustness during host switching.     

Generalized selection to overcome innate immunity selects for host breadth in an RNA virus

Virus‐host coevolution has selected for generalized host defense against viruses, exemplified by interferon production/signaling and other innate immune function in eukaryotes such as humans. Although cell‐surface binding primarily limits virus infection success, generalized adaptation to counteract innate immunity across disparate hosts may contribute to RNA virus emergence potential. We examined this idea using vesicular stomatitis virus (VSV) populations previously evolved on strictly immune‐deficient (HeLa) cells, strictly immune competent (MDCK) cells, or on alternating deficient/competent cells. By measuring viral fitness in unselected human cancer cells of differing innate immunity, we confirmed that HeLa‐adapted populations were specialized for innate immune‐deficient hosts, whereas MDCK‐adapted populations were relatively more generalized for fitness on hosts of differing innate immune capacity and of different species origin. We also confirmed that HeLa‐evolved populations maintained fitness in immune‐deficient nonhuman primate cells. These results suggest that innate immunity is more prominent than host species in determining viral fitness at the host‐cell level. Finally, our prediction was inexact that selection on alternating deficient/competent hosts should produce innate viral generalists. Rather, fitness differences among alternating host‐evolved VSV populations indicated variable capacities to evade innate immunity. Our results suggest that the evolutionary history of innate immune selection can affect whether RNA viruses evolve greater host‐breadth.     

Specialist and generalist herbivores exert opposing selection on a chemical defense

* Plant defense traits often show high levels of genetic variation, despite clear impacts on plant fitness. This variation may be partly maintained by trade-offs in the defense against multiple herbivore species, for example between generalists and coevolved specialists. Despite a long-standing discussion in the literature on the subject, no study to date has specifically manipulated specialist and generalist herbivores independently of one another to determine whether the two guilds exert opposing selection pressures on specific defensive traits. * In two separate experiments, the dominant specialist and generalist herbivores of Brassica nigra were independently manipulated to test whether the composition of the herbivore community altered the direction of selection on a major defensive trait of the plant, sinigrin concentration. * It was found that generalist damage was negatively correlated but specialist loads were positively correlated with increasing sinigrin concentrations; and sinigrin concentration was favored when specialists were removed, disfavored (past an intermediate point) when generalists were removed and selectively neutral when plants faced both generalists and specialists.     

Partial host fidelity in nest selection by the shiny cowbird (Molothrus bonariensis), a highly generalist avian brood parasite

Obligate avian brood parasites can be host specialists or host generalists. In turn, individual females within generalist brood parasites may themselves be host specialists or generalists. The shiny cowbird Molothrus bonariensis is an extreme generalist, but little is known about individual female host fidelity. We examined variation in mitochondrial control region sequences from cowbird chicks found in nests of four common Argentinean hosts. Haplotype frequency distributions differed among cowbird chicks from nests of these hosts, primarily because eggs laid in nests of house wrens Troglodytes aedon differed genetically from those laid in nests of the other three hosts (chalk-browed mockingbird Mimus saturninus, brown-and-yellow marshbird Pseudoleistes virescens, and rufous-collared sparrow Zonotrichia capensis). These differences in a maternally inherited marker indicate the presence of a nonrandom laying behaviour in the females of this otherwise generalist brood parasite, which may be guided by choice for nest type, as house wrens nest in cavities whereas the other three species are open cup nesters.     

Host specificity in phytophagous insects: selection pressure from generalist predators

The narrow host range of insect herbivores is noted, and some of the reasons why specificity has evolved are reviewed. Works indicating the need for new approaches are pointed out including the possibility that generalist predators provide a suitable pressure. Experiments to test the hypothesis that generalists are more vulnerable than specialists to predators are described. They involved a vespid wasp and over thirty species pairs of caterpillars, matched for size and density. Overall, generalists were taken more readily than specialists: some but not all reasons could be detected. The results are discussed in ecological and evolutionary terms.     

Constraints on adaptation of Escherichia coli to mixed‐resource environments increase over time

Can a population evolved in two resources reach the same fitness in both as specialist populations evolved in each of the individual resources? This question is central to theories of ecological specialization, the maintenance of genetic variation, and sympatric speciation, yet relatively few experiments have examined costs of generalism over long‐term adaptation. We tested whether selection in environments containing two resources limits a population's ability to adapt to the individual resources by comparing the fitness of replicate Escherichia coli populations evolved for 6000 generations in the presence of glucose or lactose alone (specialists), or in varying presentations of glucose and lactose together (generalists). We found that all populations had significant fitness increases in both resources, though the magnitude and rate of these increases differed. For the first 4000 generations, most generalist populations increased in fitness as quickly in the individual resources as the corresponding specialist populations. From 5000 generations, however, a widespread cost of adaptation affected all generalists, indicating a growing constraint on their abilities to adapt to two resources simultaneously. Our results indicate that costs of generalism are prevalent, but may influence evolutionary trajectories only after a period of cost‐free adaptation.     

Specialized avian Haemosporida trade reduced host breadth for increased prevalence

Parasite specialization on one or a few host species leads to a reduction in the total number of available host individuals, which may decrease transmission. However, specialists are thought to be able to compensate by increased prevalence in the host population and increased success in each individual host. Here, we use variation in host breadth among a community of avian Haemosporida to investigate consequences of generalist and specialist strategies on prevalence across hosts. We show that specialist parasites are more prevalent than generalist parasites in host populations that are shared between them. Moreover, the total number of infections of generalist and specialist parasites within the study area did not vary significantly with host breadth. This suggests that specialists can infect a similar number of host individuals as generalists, thus compensating for a reduction in host availability by achieving higher prevalence in a single host species. Specialist parasites also tended to infect older hosts, whereas infections by generalists were biased towards younger hosts. We suggest that this reflects different abilities of generalists and specialists to persist in hosts following infection. Higher abundance and increased persistence in hosts suggest that specialists are more effective parasites than generalists, supporting the existence of a trade‐off between host breadth and average host use among these parasites.     

Genetic and phenotypic influences on clone-level success and host specialization in a generalist parasite

Studying resource specialization at the individual level can identify factors constraining the evolution of generalism. We quantified genotypic and phenotypic variability among infective stages of 20 clones of the parasitic trematode Maritrema novaezealandensis and measured their infection success and post-infection fitness (growth, egg output) in several crabs and amphipods. First, different clones varied in their infection success of different crustaceans. Second, neither genetic nor phenotypic traits had consistent effects on infection success across all host species. Although the results suggest a relationship between infection success and phenotypic variability, phenotypically variable clones were not better at infecting more host species than less variable ones. Third, genetic and phenotypic traits also showed no consistent correlations with post-infection fitness measures. Overall, we found no consistent clone-level specialization, with some clones acting as specialists and others, generalists. The trematode population therefore maintains an overall generalist strategy by comprising a mixture of clone-level specialists and generalists.     

Geographic variation in performance of a widespread generalist insect herbivore

1. Generalist herbivores are often widespread and occur in a variety of environments. Due to their broad distribution, it is likely that some populations of generalists will encounter host plants with geographic variation in traits that could affect the herbivore's growth and survival (i.e. performance). However, the geographic pattern of performance has rarely been studied for generalists, especially across large geographic ranges. 2. This study used one of the most generalist herbivore species known, the fall webworm (Hyphantria cunea Drury 1773, Erebidae, Lepidoptera), to experimentally test how the performance of a local population of fall webworms varies with increasing geographic distance of the host plant population from the local herbivore population. Specifically, a transplant experiment was used to compare the performance of one fall webworm population feeding on its local host plants with its performance on host populations from two other locations, 1300 and 2600 km away. 3. It was found that fall webworms performed better on their local host plant populations than on populations from other regions, with performance at its lowest when reared on hosts of the same species from the farthest region. It was also found that local fall webworms do not perform well on hosts commonly used by fall webworms at the other two, more distant sites. 4. This study helps to elucidate how the performance of generalist herbivores varies along their geographic range and suggests possible local adaptation to different sets of hosts across sites.     

Rate of novel host invasion affects adaptability of evolving RNA virus lineages

Although differing rates of environmental turnover should be consequential for the dynamics of adaptive change, this idea has been rarely examined outside of theory. In particular, the importance of RNA viruses in disease emergence warrants experiments testing how differing rates of novel host invasion may impact the ability of viruses to adaptively shift onto a novel host. To test whether the rate of environmental turnover influences adaptation, we experimentally evolved 144 Sindbis virus lineages in replicated tissue-culture environments, which transitioned from being dominated by a permissive host cell type to a novel host cell type. The rate at which the novel host ‘invaded’ the environment varied by treatment. The fitness (growth rate) of evolved virus populations was measured on each host type, and molecular substitutions were mapped via whole genome consensus sequencing. Results showed that virus populations more consistently reached high fitness levels on the novel host when the novel host ‘invaded’ the environment more gradually, and gradual invasion resulted in less variable genomic outcomes. Moreover, virus populations that experienced a rapid shift onto the novel host converged upon different genotypes than populations that experienced a gradual shift onto the novel host, suggesting a strong effect of historical contingency.     

ROLE OF EVOLVED HOST BREADTH IN THE INITIAL EMERGENCE OF AN RNA VIRUS

Understanding how evolution promotes pathogen emergence would aid disease management, and prediction of future host shifts. Increased pathogen infectiousness of different hosts may occur through direct selection, or fortuitously via indirect selection. However, it is unclear which type of selection tends to produce host breadth promoting pathogen emergence. We predicted that direct selection for host breadth should foster emergence by causing higher population growth on new hosts, lower among‐population variance in growth on new hosts, and lower population variance in growth across new hosts. We tested the predictions using experimentally evolved vesicular stomatitis virus populations, containing groups of host‐use specialists, directly selected generalists, and indirectly selected generalists. In novel‐host challenges, viruses directly selected for generalism showed relatively higher or equivalent host growth, lower among‐population variance in host growth, and lower population variance in growth across hosts. Thus, two of three outcomes supported our prediction that directly selected host breadth should favor host colonization. Also, we observed that indirectly selected generalists were advantaged over specialist viruses, indicating that fortuitous changes in host breadth may also promote emergence. We discuss evolution of phenotypic plasticity versus environmental robustness in viruses, virus avoidance of extinction, and surveillance of pathogen niche breadth to predict future likelihood of emergence.