Scale-dependent effects of host patch traits on species composition in a stickleback parasite metacommunity

The Dominance of Coinfecting Parasites' Indirect Genetic Effects on Host Traits

AbstractIndirect genetic effects (IGEs) exist when there is heritable variation in one organism's ability to alter a second organism's traits. For example, parasites have antigens that can induce a host immune response, as well as disparate strategies to evade or suppress host immunity; among-parasite genetic variation in these antigens generates among-host variation in immune traits. Here, we experimentally show that the cestode parasite Schistocephalus solidus exerts an IGE on an immune trait (peritoneal fibrosis) in its threespine stickleback host: stickleback developed strong fibrosis after exposure to some parasite genotypes but not others. A complication arises during coinfection, when two or more parasite genotypes may impose conflicting IGEs on the same host trait. What parasite-controlled trait will the host express? Will the host trait reflect the more immune-stimulatory parasite genotype or the more immune-evasive genotype? These alternatives can be quantified by estimating the dominance coefficient, as if a coinfected host were a heterozygote. We experimentally estimated the dominance of S. solidus IGEs by coinjecting antigens from different parasite genotypes. Contrary to our a priori hypotheses, coinjected antigens induced an overdominant effect, stronger than either parasite's antigens alone. We present a mathematical model showing that the value of this IGE dominance is biologically important, affecting the evolutionary dynamics of parasites in a density- and frequency-dependent manner. The model indicates that overdominance would be detrimental to immigrants when resident prevalence is high. This combination of experimental data and modeling provides an example of a parasite IGE on host traits and the evolutionary significance of IGE dominance.

Is the local environment more important than within-host interactions in determining coinfection?

Host populations often vary in the magnitude of coinfection they experience across environmental gradients. Furthermore, coinfection often occurs sequentially, with a second parasite infecting the host after the first has established a primary infection. Because the local environment and interactions between coinfecting parasites can both drive patterns of coinfection, it is important to disentangle the relative contributions of environmental factors and within-host interactions to patterns of coinfection. Here, we develop a conceptual framework and present an empirical case study to disentangle these facets of coinfection. Across multiple lakes, we surveyed populations of five damselfly (host) species and quantified primary parasitism by aquatic, ectoparasitic water mites and secondary parasitism by terrestrial, endoparasitic gregarines. We first asked if coinfection is predicted by abiotic and biotic factors within the local environment, finding that the probability of coinfection decreased for all host species as pH increased. We then asked if primary infection by aquatic water mites mediated the relationship between pH and secondary infection by terrestrial gregarines. Contrary to our expectations, we found no evidence for a water mite-mediated relationship between pH and gregarines. Instead, the intensity of gregarine infection correlated solely with the local environment, with the magnitude and direction of these relationships varying among environmental predictors. Our findings emphasize the role of the local environment in shaping infection dynamics that set the stage for coinfection. Although we did not detect within-host interactions, the approach herein can be applied to other systems to elucidate the nature of interactions between hosts and coinfecting parasites within complex ecological communities.

Destabilized host-parasite dynamics in newly founded populations

When species disperse into previously unoccupied habitats, new populations encounter unfamiliar species interactions such as altered parasite loads. Theory predicts that newly founded populations should exhibit destabilized eco-evolutionary fluctuations in infection rates and immune traits. However, to understand founder effects biologists typically rely on retrospective studies of range expansions, missing early-generation infection dynamics. To remedy this, we experimentally founded whole-lake populations of threespine stickleback. Infection rates were temporally stable in native source lakes. In contrast, newly founded populations exhibit destabilized host-parasite dynamics: high starting infection rates led to increases in a heritable immune trait (peritoneal fibrosis), suppressing infection rates. The resulting temporal auto-correlation between infection and immunity suggest that newly founded populations can exhibit rapid host-parasite eco-evolutionary dynamics.

Elemental content of a host-parasite relationship in the threespine stickleback

Parasite infections are ubiquitous and their effects on hosts could play a role in ecosystem processes. Ecological stoichiometry provides a framework to study linkages between consumers and their resource, such as parasites and their host, and ecosystem process; however, the stoichiometric traits of host-parasite associations are rarely quantified. Specifically, it is unclear whether parasites' elemental ratios closely resemble those of their host or if infection is related to host stoichiometry, especially in vertebrate hosts. To answer such questions, we measured the elemental content (%C, %N, and %P) and molar ratios (C:N, C:P, and N:P) of parasitized and unparasitized Gasterosteus aculeatus (three-spined stickleback) and their cestode parasite, Schistocephalus solidus. Host and parasite elemental content were distinct from each other, and parasites were generally higher in %C and lower in %N and %P. Parasite infections were related to host C:N, with infected hosts being lower in C:N. Parasite elemental content was independent of their host, but parasite body mass and parasite density were important drivers of parasite stoichiometry. Overall, these potential effects of parasite infections on host stoichiometry along with parasites' distinct elemental compositions suggest parasites may further contribute to differences in how individual hosts store and recycle nutrients.

Opening a can of worms: a test of the co-infection facilitation hypothesis

Parasitic infections are a global occurrence and impact the health of many species. Coinfections, where two or more species of parasite are present in a host, are a common phenomenon across species. Coinfecting parasites can interact directly or indirectly via their manipulation of (and susceptibility to) the immune system of their shared host. Helminths, such as the cestode Schistocephalus solidus, are well known to suppress immunity of their host (threespine stickleback, Gasterosteus aculeatus), potentially facilitating other parasite species. Yet, hosts can evolve a more robust immune response (as seen in some stickleback populations), potentially turning facilitation into inhibition. Using wild-caught stickleback from 20 populations with non-zero S. solidus prevalence, we tested an a priori hypothesis that S. solidus infection facilitates infection by other parasites. Consistent with this hypothesis, individuals with S. solidus infections have 18.6% higher richness of other parasites compared to S. solidus-uninfected individuals from the same lakes. This facilitation-like trend is stronger in lakes where S. solidus is particularly successful but is reversed in lakes with sparse and smaller cestodes (indicative of stronger host immunity). These results suggest that a geographic mosaic of host-parasite co-evolution might lead to a mosaic of between-parasite facilitation/inhibition effects.

Host and parasite identity interact in scale-dependent fashion to determine parasite community structure

Understanding the ecological assembly of parasite communities is critical to characterise how changing host and environmental landscapes will alter infection dynamics and outcomes. However, studies frequently assume that (a) closely related parasite species or those with identical life-history strategies are functionally equivalent, and (b) the same factors will drive infection dynamics for a single parasite across multiple host species, oversimplifying community assembly patterns. Here, we challenge these two assumptions using a naturally occurring host-parasite system, with the mussel Anodonta anatina infected by the digenean trematode Echinoparyphium recurvatum, and the snail Viviparus viviparus infected by both E. recurvatum and Echinostoma sp. By analysing the impact of temporal parasite dispersal, host species and size, and the impact of coinfection (moving from broader environmental factors to within-host dynamics), we show that neither assumption holds true, but at different ecological scales. The assumption that closely related parasites can be functionally grouped is challenged when considering dispersal to the host (i.e. larger scales), while the assumption that the same factors will drive infection dynamics for a single parasite across multiple host species is challenged when considering within-host interspecific competition (i.e. smaller scales). Our results demonstrate that host identity, parasite identity and ecological scale require simultaneous consideration in studies of parasite community composition and transmission.

Host-parasite interactions in perpetual darkness: Macroparasite diversity in the cavefish Astyanax mexicanus

Astyanax mexicanus has repeatedly colonized cave environments, displaying evolutionary parallelisms in many troglobitic traits. Despite being a model system for the study of adaptation to life in perpetual darkness, the parasites that infect cavefish are practically unknown. In this study, we investigated the macroparasite communities in 18 cavefish populations from independent lineages and compared them with the parasite diversity found in their sister surface fish populations, with the aim of better understanding the role that parasites play in the colonization of new environments. Within the cavefish populations, we identified 13 parasite taxa, including a subset of 10 of the 27 parasite taxa known for the surface populations. Parasites infecting the cavefish belong to five taxonomic groups, including trematodes, monogeneans, nematodes, copepods, and acari. Monogeneans are the most dominant group, found in 14 caves. The macroparasites include species with direct life cycles and trophic transmission, including invasive species. Surprisingly, paired comparisons indicate higher parasite richness in the cavefish than in the surface fish. Spatial variation in parasite composition across the caves suggests historical and geographical contingencies in the host-parasite colonization process and potential evolution of local adaptations. This base-line data on parasite diversity in cavefish populations of A. mexicanus provides a foundation to explore the role of divergent parasite infections under contrasting ecological pressures (cave vs. surface environments) in the evolution of cave adaptive traits.

Opening a can of worms: a test of the coinfection facilitation hypothesis

Parasitic infections are a global occurrence and impact the health of many species. Coinfections, where two or more species of parasite are present in a host, are a common phenomenon across species. Coinfecting parasites can interact directly, or indirectly via their manipulation of (and susceptibility to) the immune system of their shared host. Helminths, such as the cestode Schistocephalus solidus , are well known to suppress immunity of their host (threespine stickleback, Gasterosteus aculeatus ), potentially facilitating other parasite species. Yet, hosts can evolve a more robust immune response (as seen in some stickleback populations), potentially turning facilitation into inhibition. Using wild-caught stickleback from 21 populations with non-zero S. solidus prevalence, we tested an a priori hypothesis that S. solidus infection facilitates infection by other parasites. Consistent with this hypothesis, individuals with S. solidus infections have 18.6% higher richness of other parasites, compared to S. solidus -uninfected individuals from the same lakes. This facilitation-like trend is stronger in lakes where S. solidus is particularly successful but is reversed in lakes with sparse and smaller cestodes (indicative of stronger host immunity). These results suggest that a geographic mosaic of host-parasite coevolution might lead to a mosaic of between-parasite facilitation/inhibition effects.

Single-Cell RNA Sequencing Reveals Microevolution of the Stickleback Immune System

The risk and severity of pathogen infections in humans, livestock, or wild organisms depend on host immune function, which can vary between closely related host populations or even among individuals. This immune variation can entail between-population differences in immune gene coding sequences, copy number, or expression. In recent years, many studies have focused on population divergence in immunity using whole-tissue transcriptomics. But, whole-tissue transcriptomics cannot distinguish between evolved differences in gene regulation within cells, versus changes in cell composition within the focal tissue. Here, we leverage single-cell transcriptomic approaches to document signatures of microevolution of immune system structure in a natural system, the three-spined stickleback (Gasterosteus aculeatus). We sampled nine adult fish from three populations with variability in resistance to a cestode parasite, Schistocephalus solidus, to create the first comprehensive immune cell atlas for G. aculeatus. Eight broad immune cell types, corresponding to major vertebrate immune cells, were identified. We were also able to document significant variation in both abundance and expression profiles of the individual immune cell types among the three populations of fish. Furthermore, we demonstrate that identified cell type markers can be used to reinterpret traditional transcriptomic data: we reevaluate previously published whole-tissue transcriptome data from a quantitative genetic experimental infection study to gain better resolution relating infection outcomes to inferred cell type variation. Our combined study demonstrates the power of single-cell sequencing to not only document evolutionary phenomena (i.e., microevolution of immune cells) but also increase the power of traditional transcriptomic data sets.

Factors at multiple scales drive parasite community structure

Understanding how ecological communities are assembled remains a key goal of ecosystem ecology. Because communities are hierarchical, factors acting at multiple scales can contribute to patterns of community structure. Parasites provide a natural system to explore this idea, as they exist as discrete communities within host individuals, which are themselves part of a community and metacommunity. We aimed to understand the relative contribution of multi-scale drivers in parasite community assembly and assess how patterns at one level may mask those occurring at another. Specifically, we wanted to disentangle patterns caused by passive sampling from those determined by ecological drivers, and how these vary with scale. We applied a Markov Random Fields model and assessed measures of β-diversity and nestedness for 420 replicate parasite infracommunities (parasite assemblages in host individuals) across two freshwater mussel host species, three sites and two time periods, comparing our results to simulations from four different ecologically relevant null models. We showed that β-diversity between sites (explaining 25% of variation in parasite distribution) and host species (41%) is greater than expected, and β-diversity between individual hosts is smaller than expected, even after accounting for parasite prevalence and characteristics of host individuals. Furthermore, parasite communities were significantly less nested than expected once parasite prevalence and host characteristics were both accounted for, but more nested than expected otherwise, suggesting a degree of modularity at the within-host level that is masked if underlying host and parasite characteristics are not taken into account. The Markov Random Fields model provided evidence for possible competitive within-host parasite interactions, providing a mechanism for the observed infracommunity modularity. An integrative approach that examines factors at multiple scales is necessary to understand the composition of ecological communities. Furthermore, patterns at one level can alter the interpretation of ecologically important drivers at another if variation at higher scales is not accounted for.

Historical contingency in parasite community assembly: Community divergence results from early host exposure to symbionts and ecological drift

Host individuals are commonly coinfected with multiple parasite species that may interact to shape within-host parasite community structure. In addition to within-host species interactions, parasite communities may also be structured by other processes like dispersal and ecological drift. The timing of dispersal (in particular, the temporal sequence in which parasite species infect a host individual) can alter within-host species interactions, setting the stage for historical contingency by priority effects, but how persistently such effects drive the trajectory of parasite community assembly is unclear, particularly under continued dispersal and ecological drift. We tested the role of species interactions under continued dispersal and ecological drift by simultaneously inoculating individual plants of tall fescue with a factorial combination of three symbionts (two foliar fungal parasites and a mutualistic endophyte), then deploying the plants in the field and tracking parasite communities as they assembled within host individuals. In the field, hosts were exposed to continued dispersal from a common pool of parasites, which should promote convergence in the structure of within-host parasite communities. Yet, analysis of parasite community trajectories found no signal of convergence. Instead, parasite community trajectories generally diverged from each other, and the magnitude of divergence depended on the initial composition of symbionts within each host, indicating historical contingency. Early in assembly, parasite communities also showed evidence of drift, revealing another source of among-host divergence in parasite community structure. Overall, these results show that both historical contingency and ecological drift contributed to divergence in parasite community assembly within hosts.

Evolutionary gain and loss of a pathological immune response to parasitism

Parasites impose fitness costs on their hosts. Biologists often assume that natural selection favors infection-resistant hosts. Yet, when the immune response itself is costly, theory suggests that selection may sometimes favor loss of resistance, which may result in alternative stable states where some populations are resistant and others are tolerant. Intraspecific variation in immune costs is rarely surveyed in a manner that tests evolutionary patterns, and there are few examples of adaptive loss of resistance. Here, we show that when marine threespine stickleback colonized freshwater lakes, they gained resistance to the freshwater-associated cestode Schistocephalus solidus. Extensive peritoneal fibrosis and inflammation are a commonly observed phenotype that contributes to suppression of cestode growth and viability but also imposes a substantial cost on fecundity. Combining genetic mapping and population genomics, we find that opposing selection generates immune system differences between tolerant and resistant populations, consistent with divergent optimization.

Altered within- and between-host transmission under coinfection underpin parasite co-occurrence patterns in the wild

Interactions among parasite species coinfecting the same host individual can have far reaching consequences for parasite ecology and evolution. How these within-host interactions affect epidemics may depend on two non-exclusive mechanisms: parasite growth and reproduction within hosts, and parasite transmission between hosts. Yet, how these two mechanisms operate under coinfection, and how sensitive they are to the composition of the coinfecting parasite community, remains poorly understood. Here, we test the hypothesis that the relationship between within- and between-host transmission of the fungal pathogen, Phomopsis subordinaria, is affected by co-occurring parasites infecting the host plant, Plantago lanceolata. We conducted a field experiment manipulating the parasite community of transmission source plants, then tracked P. subordinaria within-host transmission, as well as between-host transmission to naïve recipient plants. We find that coinfection with the powdery mildew pathogen, Podosphaera plantaginis, causes increased between-host transmission of P. subordinaria by affecting the number of infected flower stalks in the source plants, resulting from altered auto-infection. In contrast, coinfection with viruses did not have an effect on either within- or between-host transmission. We then analyzed data on the occurrence of P. subordinaria in 2018 and the powdery mildew in a multi-year survey data set from natural host populations to test whether the positive association predicted by our experimental results is evident in field epidemiological data. Consistent with our experimental findings, we observed a positive association in the occurrence of P. subordinaria and historical powdery mildew persistence. Jointly, our experimental and epidemiological results suggest that within- and between-host transmission of P. subordinaria depends on the identity of coinfecting parasites, with potentially far-reaching effects on disease dynamics and parasite co-occurrence patterns in wild populations.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10682-022-10182-9.

Life history mediates the association between parasite abundance and geographic features

Though parasites are ubiquitous in marine ecosystems, predicting the abundance of parasites present within marine ecosystems has proven challenging due to the unknown effects of multiple interacting environmental gradients and stressors. Furthermore, parasites often are considered as a uniform group within ecosystems despite their significant diversity. We aim to determine the potential importance of multiple predictors of parasite abundance in coral reef ecosystems, including reef area, island area, human population density, chlorophyll-a, host diversity, coral cover, host abundance, and island isolation. Using a model selection approach within a database of more than 1200 individual fish hosts and their parasites from 11 islands within the Pacific Line Islands archipelago, we reveal that geographic gradients, including island area and island isolation, emerged as the best predictors of parasite abundance. Life history moderated the relationship; parasites with complex life cycles increased in abundance with increasing island isolation, while parasites with direct life cycles decreased with increasing isolation. Direct life cycle parasites increased in abundance with increasing island area, though complex life cycle parasite abundance was not associated with island area. This novel analysis of a unique dataset indicates that parasite abundance in marine systems cannot be predicted precisely without accounting for the independent and interactive effects of each parasite's life history and environmental conditions.

Elevated corticosterone levels are associated with increased immunocompetence in male toads, both when calling and under experimental conditions

Circulating androgens can influence immune responses and sexual traits in male vertebrates. However, in the last 20 years, glucocorticoids have also been implicated as a possible source of variation in male sexual traits and immunocompetence. In this context, we studied the relations between male vocal mating display, immunity, androgens, and glucocorticoids in the explosive breeding toad Rhinella granulosa. In the field, males with high calling effort display either high- or low-corticosterone (CORT) plasma levels, but only males with both high calling effort and high CORT plasma levels showed high bacterial killing ability (BKA), suggesting that the acute CORT elevation can be immunostimulatory. CORT treatments increased BKA in laboratory experiments, confirming the functional relationship observed in the field. However, toads treated with a low dose of CORT increased BKA for 10 h after the treatment, while toads that received a high dose increased BKA for only 1 h after the treatment. These results indicate that different CORT doses can result in temporal differences in the immune response. We did not find any relationship between calling effort, immune response (BKA and PHA swelling response), and testosterone plasma levels in the field, or any effects of testosterone treatment on immunocompetence. Our results suggest a complex relationship between calling effort and immunity, mediated by CORT plasma levels.

Between-population differences in constitutive and infection-induced gene expression in threespine stickleback

Vertebrate immunity is a complex system consisting of a mix of constitutive and inducible defences. Furthermore, host immunity is subject to selective pressure from a range of parasites and pathogens which can produce variation in these defences across populations. As populations evolve immune responses to parasites, they may adapt via a combination of (1) constitutive differences, (2) shared inducible responses, or (3) divergent inducible responses. Here, we leverage a powerful natural host‐parasite model system (Gasterosteus aculeatus and Schistochephalus solidus) to tease apart the relative contributions of these three types of adaptations to among‐population divergence in response to parasites. Gene expression analyses revealed limited evidence of significant divergence in constitutive expression of immune defence, and strong signatures of conserved inducible responses to the parasite. Furthermore, our results highlight a handful of immune‐related genes which show divergent inducible responses which may contribute disproportionately to functional differences in infection success or failure. In addition to investigating variation in evolutionary adaptation to parasite selection, we also leverage this unique data set to improve understanding of cellular mechanisms underlying a putative resistance phenotype (fibrosis). Combined, our results provide a case study in evolutionary immunology showing that a very small number of genes may contribute to genotype differences in infection response.

Sick of eating: Eco-evo-immuno dynamics of predators and their trophically acquired parasites

When predators consume prey, they risk becoming infected with their prey's parasites, which can then establish the predator as a secondary host. A predator population's diet therefore influences what parasites it is exposed to, as has been repeatedly shown in many species such as threespine stickleback (Gasterosteus aculeatus) (more benthic‐feeding individuals obtain nematodes from oligocheate prey, whereas limnetic‐feeding individuals catch cestodes from copepod prey). These differing parasite encounters, in turn, determine how natural selection acts on the predator's immune system. We might therefore expect that ecoevolutionary dynamics of a predator's diet (as determined by its ecomorphology) should drive correlated evolution of its immune traits. Conversely, the predator's immunity to certain parasites might alter the relative costs and benefits of different prey, driving evolution of its ecomorphology. To evaluate the potential for ecological morphology to drive evolution of immunity, and vice versa, we use a quantitative genetics framework coupled with an ecological model of a predator and two prey species (the diet options). Our analysis reveals fundamental asymmetries in the evolution of ecomorphology and immunity. When ecomorphology rapidly evolves, it determines how immunity evolves, but not vice versa. Weak trade‐offs in ecological morphology select for diet generalists despite strong immunological trade‐offs, but not vice versa. Only weak immunological trade‐offs can explain negative diet‐infection correlations across populations. The analysis also reveals that eco‐evo‐immuno feedbacks destabilize population dynamics when trade‐offs are sufficiently weak and heritability is sufficiently high. Collectively, these results highlight the delicate interplay between multivariate trait evolution and the dynamics of ecological communities.

What evolutionary processes maintain MHC IIꞵ diversity within and among populations of stickleback?

Major Histocompatibility Complex (MHC) genes code for proteins that recognize foreign protein antigens to initiate T-cell-mediated adaptive immune responses. They are often the most polymorphic genes in vertebrate genomes. How evolution maintains this diversity remains of debate. Three main hypotheses seek to explain the maintenance of MHC diversity by invoking pathogen-mediated selection: heterozygote advantage, frequency-dependent selection, and fluctuating selection across landscapes or through time. Here, we use a large-scale field parasite survey in a stickleback metapopulation to test predictions derived from each of these hypotheses. We identify over 1000 MHC IIβ variants (alleles spanning paralogous genes) and find that many of them covary positively or negatively with parasite load, suggesting that these genes contribute to resistance or susceptibility. However, despite our large sample-size, we find no evidence for the widely cited stabilizing selection on MHC heterozygosity, in which individuals with an intermediate number of MHC variants have the lowest parasite burden. Nor do we observe a rare-variant advantage, or widespread fluctuating selection across populations. In contrast, we find that MHC diversity is best predicted by neutral genome-wide heterozygosity and between-population genomic divergence, suggesting neutral processes are important in shaping the pattern of metapopulation MHC diversity. Thus, although MHC IIβ is highly diverse and relevant to the type and intensity of macroparasite infection in these populations of stickleback, the main models of MHC evolution still provide little explanatory power in this system.

Scale-dependent effects of host patch traits on species composition in a stickleback parasite metacommunity

A core goal of ecology is to understand the abiotic and biotic variables that regulate species distributions and community composition. A major obstacle is that the rules governing species distributions can change with spatial scale. Here, we illustrate this point using data from a spatially nested metacommunity of parasites infecting a metapopulation of threespine stickleback fish from 34 lakes on Vancouver Island, British Columbia. Like most parasite metacommunities, the composition of stickleback parasites differs among host individuals within each host population, and differs between host populations. The distribution of each parasite taxon depends, to varying degrees, on individual host traits (e.g., mass, diet) and on host-population characteristics (e.g., lake size, mean host mass, mean diet). However, in most cases in this data set, a given parasite was regulated by different factors at the host-individual and host-population scales, leading to scale-dependent patterns of parasite-species co-occurrence.