Host-parasite fluctuating selection in the absence of specificity

Pathogen evolution following spillover from a resident to a migrant host population depends on interactions between host pace of life and tolerance to infection

Changes to migration routes and phenology create novel contact patterns among hosts and pathogens. These novel contact patterns can lead to pathogens spilling over between resident and migrant populations. Predicting the consequences of such pathogen spillover events requires understanding how pathogen evolution depends on host movement behaviour. Following spillover, pathogens may evolve changes in their transmission rate and virulence phenotypes because different strategies are favoured by resident and migrant host populations. There is conflict in current theoretical predictions about what those differences might be. Some theory predicts lower pathogen virulence and transmission rates in migrant populations because migrants have lower tolerance to infection. Other theoretical work predicts higher pathogen virulence and transmission rates in migrants because migrants have more contacts with susceptible hosts. We aim to understand how differences in tolerance to infection and host pace of life act together to determine the direction of pathogen evolution following pathogen spillover from a resident to a migrant population. We constructed a spatially implicit model in which we investigate how pathogen strategy changes following the addition of a migrant population. We investigate how differences in tolerance to infection and pace of life between residents and migrants determine the effect of spillover on pathogen evolution and host population size. When the paces of life of the migrant and resident hosts are equal, larger costs of infection in the migrants lead to lower pathogen transmission rate and virulence following spillover. When the tolerance to infection in migrant and resident populations is equal, faster migrant paces of life lead to increased transmission rate and virulence following spillover. However, the opposite can also occur: when the migrant population has lower tolerance to infection, faster migrant paces of life can lead to decreases in transmission rate and virulence. Predicting the outcomes of pathogen spillover requires accounting for both differences in tolerance to infection and pace of life between populations. It is also important to consider how movement patterns of populations affect host contact opportunities for pathogens. These results have implications for wildlife conservation, agriculture and human health.

The impact of sterility-mortality tolerance and recovery-transmission trade-offs on host-parasite coevolution

Understanding the coevolutionary dynamics of hosts and their parasites remains a major focus of much theoretical literature. Despite empirical evidence supporting the presence of sterility-mortality tolerance trade-offs in hosts and recovery-transmission trade-offs in parasites, none of the current models have explored the potential outcomes when both trade-offs are considered within a coevolutionary framework. In this study, we consider a model where the host evolves sterility tolerance at the cost of increased mortality and the parasite evolves higher transmission rate at the cost of increased recovery rate (reduced infection duration), and use adaptive dynamics to predict the coevolutionary outcomes under such trade-off assumptions. We particularly aim to understand how our coevolutionary dynamics compare with single species evolutionary models. We find that evolutionary branching in the host can drive the parasite population to branch, but that cycles in the population dynamics can prevent the coexisting strains from reaching their extremes. We also find that varying crowding does not impact the recovery rate when only the parasite evolves, yet coevolution reduces recovery as crowding intensifies. We conclude by discussing how different host and parasite trade-offs shape coevolutionary outcomes, underscoring the pivotal role of trade-offs in coevolution.

How do fluctuating ecological dynamics impact the evolution of hosts and parasites?

Theoretical models of the evolution of parasites and their hosts have shaped our understanding of infectious disease dynamics for over 40 years. Many theoretical models assume that the underlying ecological dynamics are at equilibrium or constant, yet we know that in a great many systems there are fluctuations in the ecological dynamics owing to a variety of intrinsic or extrinsic factors. Here, we discuss the challenges presented when modelling evolution in systems with fluctuating ecological dynamics and summarize the main approaches that have been developed to study host-parasite evolution in such systems. We provide an in-depth guide to one of the methods by applying it to two worked examples of host evolution that have not previously been studied in the literature: when cycles occur owing to seasonal forcing in competition, and when the presence of a free-living parasite causes cycles, with accompanying interactive Python code provided. We review the findings of studies that have explored host-parasite evolution when ecological dynamics fluctuate, and point to areas of future research. Throughout we stress the importance of feedbacks between the ecological and evolutionary dynamics in driving the outcomes of infectious disease systems. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.

Spillover and genome selection of the gut parasite Nosema ceranae between honey bee species

Nosema ceranae is a honey bee gut parasite that has recently spilled to another honey bee host through trading. The impact of infection on the native host is minor, which is substantial in the novel host. In this study, artificial inoculation simulated the parasite transmission from the native to the novel host. We found that the parasite initiated proliferation earlier in the novel host than in the native host. Additionally, parasite gene expression was significantly higher when infecting the novel host compared with the native host, leading to a significantly higher number of spores. Allele frequencies were similar for spores of parasites infecting both native and novel hosts. This suggests that the high number of spores found in the novel host was not caused by a subset of more fit spores from native hosts. Native hosts also showed a higher number of up-regulated genes in response to infection when compared with novel hosts. Our data further showed that native hosts suppressed parasite gene expression and arguably sacrificed cells to limit the parasite. The results provide novel insights into host defenses and gene selection during a parasite spillover event.

Coevolutionary theory of hosts and parasites

Host and parasite evolution are closely intertwined, with selection for adaptations and counter-adaptations forming a coevolutionary feedback loop. Coevolutionary dynamics are often difficult to intuit due to these feedbacks and are hard to demonstrate empirically in most systems. Theoretical models have therefore played a crucial role in shaping our understanding of host-parasite coevolution. Theoretical models vary widely in their assumptions, approaches and aims, and such variety makes it difficult, especially for non-theoreticians and those new to the field, to: (1) understand how model approaches relate to one another; (2) identify key modelling assumptions; (3) determine how model assumptions relate to biological systems; and (4) reconcile the results of different models with contrasting assumptions. In this review, we identify important model features, highlight key results and predictions and describe how these pertain to model assumptions. We carry out a literature survey of theoretical studies published since the 1950s (n = 219 papers) to support our analysis. We identify two particularly important features of models that tend to have a significant qualitative impact on the outcome of host-parasite coevolution: population dynamics and the genetic basis of infection. We also highlight the importance of other modelling features, such as stochasticity and whether time proceeds continuously or in discrete steps, that have received less attention but can drastically alter coevolutionary dynamics. We finish by summarizing recent developments in the field, specifically the trend towards greater model complexity, and discuss likely future directions for research.

Leapfrog dynamics in phage‐bacteria coevolution revealed by joint analysis of cross‐infection phenotypes and whole genome sequencing

Viruses and their hosts can undergo coevolutionary arms races where hosts evolve increased resistance and viruses evolve counter-resistance. Given these arms race dynamics (ARD), both players are predicted to evolve along a single trajectory as more recently evolved genotypes replace their predecessors. By coupling phenotypic and genomic analyses of coevolving populations of bacteriophage λ and Escherichia coli, we find conflicting evidence for ARD. Virus-host infection phenotypes fit the ARD model, yet genomic analyses revealed fluctuating selection dynamics. Rather than coevolution unfolding along a single trajectory, cryptic genetic variation emerges and is maintained at low frequency for generations until it eventually supplants dominant lineages. These observations suggest a hybrid 'leapfrog' dynamic, revealing weaknesses in the predictive power of standard coevolutionary models. The findings shed light on the mechanisms that structure coevolving ecological networks and reveal the limits of using phenotypic or genomic data alone to differentiate coevolutionary dynamics.

An Ecologically Framed Comparison of The Potential for Zoonotic Transmission of Non-Human and Human-Infecting Species of Malaria Parasite

The threats, both real and perceived, surrounding the development of new and emerging infectious diseases of humans are of critical concern to public health and well-being. Among these risks is the potential for zoonotic transmission to humans of species of the malaria parasite, Plasmodium, that have been considered historically to infect exclusively non-human hosts. Recently observed shifts in the mode, transmission, and presentation of malaria among several species studied are evidenced by shared vectors, atypical symptoms, and novel host-seeking behavior. Collectively, these changes indicate the presence of environmental and ecological pressures that are likely to influence the dynamics of these parasite life cycles and physiological make-up. These may be further affected and amplified by such factors as increased urban development and accelerated rate of climate change. In particular, the extended host-seeking behavior of what were once considered non-human malaria species indicates the specialist niche of human malaria parasites is not a limiting factor that drives the success of blood-borne parasites. While zoonotic transmission of non-human malaria parasites is generally considered to not be possible for the vast majority of Plasmodium species, failure to consider the feasibility of its occurrence may lead to the emergence of a potentially life-threatening blood-borne disease of humans. Here, we argue that recent trends in behavior among what were hitherto considered to be non-human malaria parasites to infect humans call for a cross-disciplinary, ecologically-focused approach to understanding the complexities of the vertebrate host/mosquito vector/malaria parasite triangular relationship. This highlights a pressing need to conduct a multi-species investigation for which we recommend the construction of a database to determine ecological differences among all known Plasmodium species, vectors, and hosts. Closing this knowledge gap may help to inform alternative means of malaria prevention and control.

Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system

Bacterial viruses are widespread and abundant across natural and engineered habitats. They influence ecosystem functioning through interactions with their hosts. Laboratory studies of phage-host pairs have advanced our understanding of phenotypic and genetic diversification in bacteria and phages. However, the dynamics of phage-host interactions have been seldom recorded in complex natural environments. We conducted an observational metagenomic study of the dynamics of interaction between Gordonia and their phages using a three-year data series of samples collected from a full-scale wastewater treatment plant. The aim was to obtain a comprehensive picture of the coevolution dynamics in naturally evolving populations at relatively high time resolution. Coevolution was followed by monitoring changes over time in the CRISPR loci of Gordonia metagenome-assembled genome, and reciprocal changes in the viral genome. Genome-wide analysis indicated low strain variability of Gordonia, and almost clonal conservation of the trailer end of the CRISPR loci. Incorporation of newer spacers gave rise to multiple coexisting bacterial populations. The host population carrying a shorter CRISPR locus that contain only ancestral spacers, which has not acquired newer spacers against the coexisting phages, accounted for more than half of the total host abundance in the majority of samples. Phages genome co-evolved by introducing directional changes, with no preference for mutations within the protospacer and PAM regions. Metagenomic reconstruction of time-resolved variants of host and viral genomes revealed how the complexity at the population level has important consequences for bacteria-phage coexistence.

Salmon immunological defence and interplay with the modulatory capabilities of its ectoparasite Lepeophtheirus salmonis

The salmon louse Lepeophtheirus salmonis (Lsal) is an ectoparasitic copepod that exerts immunomodulatory and physiological effects on its host Atlantic salmon. Over 30 years of research on louse biology, control, host responses and the host-parasite relationship has provided a plethora of information on the intricacies of host resistance and parasite adaptation. Atlantic salmon exhibit temporal and spatial impairment of the immune system and wound healing ability during infection. This immunosuppression may render Atlantic salmon less tolerant to stress and other confounders associated with current management strategies. Contrasting susceptibility of salmonid hosts exists, and early pro-inflammatory Th1 type responses are associated with resistance. Rapid cellular responses to larvae appear to tip the balance of the host-parasite relationship in favour of the host, preventing severe immune-physiological impacts of the more invasive adults. Immunological, transcriptomic, genomic and proteomic evidence suggests pathological impacts occur in susceptible hosts through modulation of host immunity and physiology via pharmacologically active molecules. Co-evolutionary and farming selection pressures may have incurred preference of Atlantic salmon as a host for Lsal reflected in their interactome. Here, we review host-parasite interactions at the primary attachment/feeding site, and the complex life stage-dependent molecular mechanisms employed to subvert host physiology and immune responses.

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.

How long do Red Queen dynamics survive under genetic drift? A comparative analysis of evolutionary and eco-evolutionary models

Background

Red Queen dynamics are defined as long term co-evolutionary dynamics, often with oscillations of genotype abundances driven by fluctuating selection in host-parasite systems. Much of our current understanding of these dynamics is based on theoretical concepts explored in mathematical models that are mostly (i) deterministic, inferring an infinite population size and (ii) evolutionary, thus ecological interactions that change population sizes are excluded. Here, we recall the different mathematical approaches used in the current literature on Red Queen dynamics. We then compare models from game theory (evo) and classical theoretical ecology models (eco-evo), that are all derived from individual interactions and are thus intrinsically stochastic. We assess the influence of this stochasticity through the time to the first loss of a genotype within a host or parasite population.

Results

The time until the first genotype is lost (“extinction time”), is shorter when ecological dynamics, in the form of a changing population size, is considered. Furthermore, when individuals compete only locally with other individuals extinction is even faster. On the other hand, evolutionary models with a fixed population size and competition on the scale of the whole population prolong extinction and therefore stabilise the oscillations. The stabilising properties of intra-specific competitions become stronger when population size is increased and the deterministic part of the dynamics gain influence. In general, the loss of genotype diversity can be counteracted with mutations (or recombination), which then allow the populations to recurrently undergo negative frequency-dependent selection dynamics and selective sweeps.

Conclusion

Although the models we investigated are equal in their biological motivation and interpretation, they have diverging mathematical properties both in the derived deterministic dynamics and the derived stochastic dynamics. We find that models that do not consider intraspecific competition and that include ecological dynamics by letting the population size vary, lose genotypes – and thus Red Queen oscillations – faster than models with competition and a fixed population size.

Host migration strategy is shaped by forms of parasite transmission and infection cost

Most studies on the evolution of migration focus on food, mates and/or climate as factors influencing these movements, whereas negative species interactions such as predators, parasites and pathogens are often ignored. Although infection and its associated costs clearly have the potential to influence migration, thoroughly studying these interactions is challenging without a solid theoretical framework from which to develop testable predictions in natural systems. Here, we aim to understand when parasites favour the evolution of migration. We develop a general model which enables us to explore a broad range of biological conditions and to capture population and infection dynamics over both ecological and evolutionary time-scales. We show that when migration evolves depends on whether the costs of migration and infection are paid in reduced fecundity or survival. Also important are the parasite transmission mode and spatiotemporal dynamics of infection and recovery (if it occurs). Finally, we find that partial migration (where only a fraction of the population migrates) can evolve but only when parasite transmission is density-dependent. Our results highlight the critical, if overlooked, role of parasites in shaping long-distance movement patterns, and suggest that infection should be considered alongside more traditional drivers of migration in both empirical and theoretical studies.

Coevolutionary dynamics shape the structure of bacteria-phage infection networks

Coevolution-reciprocal evolutionary change among interacting species driven by natural selection-is thought to be an important force in shaping biodiversity. This ongoing process takes place within tangled networks of species interactions. In microbial communities, evolutionary change between hosts and parasites occurs at the same time scale as ecological change. Yet, we still lack experimental evidence of the role of coevolution in driving changes in the structure of such species interaction networks. Filling this gap is important because network structure influences community persistence through indirect effects. Here, we quantified experimentally to what extent coevolutionary dynamics lead to contrasting patterns in the architecture of bacteria-phage infection networks. Specifically, we look at the tendency of these networks to be organized in a nested pattern by which the more specialist phages tend to infect only a proper subset of those bacteria infected by the most generalist phages. We found that interactions between coevolving bacteria and phages become less nested over time under fluctuating dynamics, and more nested under arms race dynamics. Moreover, when coevolution results in high average infectivity, phages and bacteria differ more from each other over time under arms race dynamics than under fluctuating dynamics. The tradeoff between the fitness benefits of evolving resistance/infectivity traits and the costs of maintaining them might explain these differences in network structure. Our study shows that the interaction pattern between bacteria and phages at the community level depends on the way coevolution unfolds.

Ecological and Evolutionary Processes Shaping Viral Genetic Diversity

The contemporary genomic diversity of viruses is a result of the continuous and dynamic interaction of past ecological and evolutionary processes. Thus, genome sequences of viruses can be a valuable source of information about these processes. In this review, we first describe the relevant processes shaping viral genomic variation, with a focus on the role of host–virus coevolution and its potential to give rise to eco-evolutionary feedback loops. We further give a brief overview of available methodology designed to extract information about these processes from genomic data. Short generation times and small genomes make viruses ideal model systems to study the joint effect of complex coevolutionary and eco-evolutionary interactions on genetic evolution. This complexity, together with the diverse array of lifetime and reproductive strategies in viruses ask for extensions of existing inference methods, for example by integrating multiple information sources. Such integration can broaden the applicability of genetic inference methods and thus further improve our understanding of the role viruses play in biological communities.

Fueling Defense: Effects of Resources on the Ecology and Evolution of Tolerance to Parasite Infection

Resource availability is a key environmental constraint affecting the ecology and evolution of species. Resources have strong effects on disease resistance, but they can also affect the other main parasite defense strategy, tolerance. A small but growing number of animal studies are beginning to investigate the effects of resources on tolerance phenotypes. Here, we review how resources affect tolerance strategies across animal taxa ranging from fruit flies to frogs to mice. Surprisingly, resources (quality and quantity) can increase or reduce tolerance, dependent upon the particular host-parasite system. To explore this seeming contradiction, we recast predictions of models of sterility tolerance and mortality tolerance in a resource-dependent context. Doing so reveals that resources can have very different epidemiological and evolutionary effects, depending on what aspects of the tolerance phenotype are affected. Thus, it is critical to consider both sterility and mortality in future empirical studies of how behavioral and environmental resource availability affect tolerance to infection.

Host-pathogen coevolution in the presence of predators: fluctuating selection and ecological feedbacks

Host-pathogen coevolution is central to shaping natural communities and is the focus of much experimental and theoretical study. For tractability, the vast majority of studies assume the host and pathogen interact in isolation, yet in reality, they will form one part of complex communities, with predation likely to be a particularly key interaction. Here, I present, to my knowledge, the first theoretical study to assess the impact of predation on the coevolution of costly host resistance and pathogen transmission. I show that fluctuating selection is most likely when predators selectively prey upon infected hosts, but that saturating predation, owing to large handling times, dramatically restricts the potential for fluctuations. I also show how host evolution may drive either enemy to extinction, and demonstrate that while predation selects for low host resistance and high pathogen infectivity, ecological feedbacks mean this results in lower infection rates when predators are present. I emphasize the importance of accounting for varying population sizes, and place the models in the context of recent experimental studies.