Evolutionary gain and loss of a pathological immune response to parasitism

Effect of parasite infections on fish body condition: a systematic review and meta-analysis

Using host body condition indices (BCIs) based on the relationship between host body mass and length is a general and pervasive approach to assess the negative effects of parasites on host health. Although many researchers, especially fish biologists and fisheries managers, commonly utilize BCIs, the overall general patterns among BCI - infection relationships remain unclear. Here, we first systematically reviewed 985 fish BCI - infection relationships from 216 publications and investigated the factors affecting the strength and directionality of effects in BCI - infection relationships. We specifically predicted that the BCI measure used, parasite taxonomic group, and the infection measure used would influence the observed effect size and directionality of BCI - infection relationships. We found that most studies were heavily biased towards specific BCI measures such as Fulton's BCI and Relative BCI. Furthermore, studies using Fulton's BCI were more likely to report significant results compared with those using other BCI measures, suggesting that index choice could lead to an overestimation of the negative effects of parasites. Our meta-regressions uncovered that the use of parasite intensity as an infection measure and studies based on experimental rather than natural infections were more likely to report significant negative effects, however there were no differences among parasite taxonomic groups. Surprisingly, many studies, especially field studies, did not report significant negative correlations between BCI and infection, contrary to widespread expectations among researchers that parasites would negatively affect fish health. We discuss potential mechanisms underlying these results. Finally, we make several recommendations for the use of BCI - infection relationships in future studies.

A spectral framework to map QTLs affecting joint differential networks of gene co-expression

Studying the mechanisms underlying the genotype-phenotype association is crucial in genetics. Gene expression studies have deepened our understanding of the genotype  →  expression  →  phenotype mechanisms. However, traditional expression quantitative trait loci (eQTL) methods often overlook the critical role of gene co-expression networks in translating genotype into phenotype. This gap highlights the need for more powerful statistical methods to analyze genotype  →  network  →  phenotype mechanism. Here, we develop a network-based method, called spectral network quantitative trait loci analysis (snQTL), to map quantitative trait loci affecting gene co-expression networks. Our approach tests the association between genotypes and joint differential networks of gene co-expression via a tensor-based spectral statistics, thereby overcoming the ubiquitous multiple testing challenges in existing methods. We demonstrate the effectiveness of snQTL in the analysis of three-spined stickleback (Gasterosteus aculeatus) data. Compared to conventional methods, our method snQTL uncovers chromosomal regions affecting gene co-expression networks, including one strong candidate gene that would have been missed by traditional eQTL analyses. Our framework suggests the limitation of current approaches and offers a powerful network-based tool for functional loci discoveries.

Host Disease Tolerance Predicts Transmission Probability for a Songbird Pathogen

Disease tolerance reduces the per-pathogen fitness costs of infection for hosts and is an important component of host adaptation to pathogens. However, how disease tolerance affects host transmission potential is not well understood, especially because there are many potential mechanisms that facilitate host tolerance. For example, tissue-specific host tolerance leads to the reduction of host pathology, regardless of pathogen load. Hosts may also exhibit behavioral tolerance, where normal behaviors are maintained even while harboring high pathogen loads. Here, we examined the impacts that tissue-specific and behavioral tolerance have on transmission in house finches (Haemorhous mexicanus) infected with a common and highly transmissible bacterial pathogen, Mycoplasma gallisepticum (MG). MG causes conjunctivitis in house finches and severely reduces population numbers after it arrives in a new area. Wild house finch populations differ in tissue-specific tolerance to MG and here we assessed how this variation in tolerance influences transmission success. We inoculated wild-captured, MG-naïve individuals from two populations that are on the extremes of tissue-specific tolerance to MG and determined the likelihood of these "index" individuals transmitting MG to an uninfected, susceptible cagemate. Higher tissue-specific tolerance results in reduced conjunctivitis, which is associated with decreased deposition and spread of MG. Thus, we predicted that individuals with high tissue-specific tolerance would be less likely to transmit MG. In contrast, we predicted that behavioral tolerance would be linked to higher transmission, as more tolerant individuals spent more time on a feeder shared with a susceptible individual despite high pathogen loads. In agreement with our prediction, individuals with high tissue-specific tolerance were less likely to transmit MG. However, there was no effect of behavioral tolerance on the likelihood of MG transmission. Our results highlight that it is key to consider how different mechanisms of tolerance affect transmission and, therefore, host-pathogen coevolution and epidemic dynamics.

Dynamics of infection and immunity over 50 years as marine stickleback adapt to freshwater

When a species colonizes a new environment, it may encounter new parasites to which its immune system is poorly adapted. After an initial spike in infection rates in the naïve founder population, the host may subsequently evolve increased immunity thereby reducing infection rates. Here, we present an example of this eco-evolutionary process, in a population of threespine stickleback (Gasterosteus aculeatus) that was founded in Heisholt Quarry, a man-made quarry pond, in 1967. Marine stickleback rarely encounter Schistocephalus solidus tapeworms (which require freshwater to hatch), and so remain highly susceptible to infection. Initially, introduced marine fish were heavily infected by S.solidus. They exhibited low levels of fibrosis, a heritable immune trait which some genotypes activate in response to infection, thereby suppressing tapeworm growth and viability. By the 1990's, the Heisholt Quarry population exhibited high rates of fibrosis, which partly suppressed S.solidus infection. This increased immune response led to reduced infection rates and the tapeworm was apparently extirpated by 2021. Because fibrosis has a strong genetic basis in other stickleback populations, we infer that the newly founded stickleback-parasite interaction exhibit an eco-evolutionary process of increased immunity that effectively reduced infection. The infection and immune dynamics documented here closely match those expected from a simple eco-evo dynamic model presented here.

Diversity of trematodes (Platyhelminthes) in Mexico with an assessment of the availability of genetic data for their conservation

Trematodes are one of the most abundant and diverse groups of platyhelminths. They parasitize all major groups of vertebrates as definitive hosts and therefore play an important role in ecosystem composition. It is estimated that 18,000 to 25,000 species of trematodes exist worldwide, of which 685 have been reported in Mexico. Although this group is an integral part of ecosystems, there are still no studies that highlight the importance of parasites, especially in conservation approaches. Here, we recompiled information on the occurrence and available genetic data of trematodes in Mexico to estimate the specific richness of their representation across the Protected Areas (PAs) and provinces of Mexico. We consulted national and international databases (e.g., GBIF, CONABIO, CNHE-UNAM) and genetic repositories (e.g., GenBank) to generate curated datasets. We obtained 6,780 records that represent 99% of species reported in Mexico (680 species), of which only 10.2% are included in PAs. For genetic data, we found information from five nuclear regions (28S, 18S, ITS1, ITS2 and 5.8S) and two mitochondrial genes (COI and NAD1) for 118 species, of which only 3.5% were associated with PAs. With these results, we provide a spatial distribution of records (occurrence and genetic data) of trematodes present in Mexico and its PAs and identify poorly represented biogeographic provinces (e.g., Sierra Madre del Sur). We also highlight that this is the first study in Mexico to include this group in a conservation approach, and we record valuable information for future studies.

Macroevolutionary changes in gene expression response to an immune stimulus across the diversity of fishes

Our understanding of the vertebrate immune system is dominated by a few model organisms such as mice. This use of a few model systems is reasonable if major features of the immune systems evolve slowly and are conserved across most vertebrates, but may be problematic if there is substantial macroevolutionary change in immune responses. Here, we present a test of the macroevolutionary stability, across 15 species of jawed fishes, of the transcriptomic response to a standardized immune challenge. Intraperitoneal injection of an immune adjuvant (alum) induces a fibrosis response in nearly all jawed fishes, which in some species contributes to anti-helminth resistance. Despite this conserved phenotypic response, the underlying transcriptomic response is highly inconsistent across species. Although many gene orthogroups exhibit differential expression between saline versus alum-injected fish in at least one species, few orthogroups exhibit consistent differential expression across species. This result suggests that although the phenotypic response to alum (fibrosis) is highly conserved, the underlying gene regulatory architecture is very flexible and cannot readily be extrapolated from any one species to fishes (or vertebrates) more broadly. The vertebrate immune response is remarkably changeable over macroevolutionary time, requiring a diversity of model organisms to describe effectively.

Rates of evolution differ between cell types identified by single-cell RNAseq in threespine stickleback

Rates of evolutionary change vary by gene. While some broad gene categories are highly conserved with little divergence over time, others undergo continuous selection pressure and are highly divergent. Here, we combine single-cell RNA sequencing (scRNAseq) with evolutionary genomics to understand whether certain cell types exhibit faster evolutionary divergence (using their characteristic genes), than other types of cells. Merging scRNAseq with population genomic data, we show that cell types differ in the rate at which their characteristic genes evolve, as measured by allele frequency divergence among many populations (F ST ) and between species (dN/dS ratios). Neutrophils, B cells, and fibroblasts exhibit elevated F ST at characteristic genes, while eosinophils in the intestine and thrombocytes in the head kidney exhibit lower F ST than the average for 1000 random genes. Gene network centrality also differed between immune- and non-immune-associated genes, and closeness centrality was positively related to gene F ST . These results highlight the value of merging single cell RNA sequencing technology with evolutionary population genomic data, and reveal that genes which define immune cell types exhibit especially rapid evolution.

Does Motility-Restricting Fibrosis Influence Dispersal? An Experiment in Nature With Threespine Stickleback

Dispersal can affect individual-level fitness and population-level ecological and evolutionary processes. Factors that affect dispersal could therefore have important eco-evolutionary implications. Here, we investigated the extent to which an inflammation and tissue repair response-peritoneal fibrosis-which is known to restrict movement, could influence dispersal by conducting a mark-recapture experiment in a lake in Alaska with threespine stickleback (Gasterosteus aculatus). A subset of captured stickleback were injected with aluminium phosphate to experimentally induce fibrosis ('treatment group'), and another subset were injected with saline or received no injection-both of which do not induce fibrosis ('control group'). We released all fish at one introduction point and re-sampled stickleback throughout the lake for 8 days. We recaptured 123 individuals (n = 47 fibrosis treatment; n = 76 control) and dissected them to determine fibrosis levels. Overall, fibrosis did not affect dispersal. Some compelling (but not statistically significant) trends suggest that early-stage inflammation may affect dispersal, providing opportunities for future work. By showing that effects on dispersal are not important side effects of fibrosis, these findings improve our understanding of the ecological implications of immune responses.

Noninvasive Methods Unveil the Trophic Transmission of the Tapeworm Ligula intestinalis in Gull-Billed Terns

Recent developments in microscopic and molecular tools have allowed the implementation of new approaches for assessing parasitic infections in wildlife populations. This is particularly important for the noninvasive detection and quantification of endoparasites in live animals. Here, we combined copromicroscopic (Mini-FLOTAC) and molecular (qPCR) techniques to detect the infection of the macroparasite Ligula intestinalis (Cestoda, Pseudophyllidea) in fresh droppings of Gull-billed Terns Gelochelidon nilotica (Charadriiformes, Laridae) breeding in southwestern Spain. Additionally, we sequenced the cytochrome b gene in parasite isolates from Gull-billed Terns (definitive host) and Common Bleak Alburnus alburnus (second intermediate host) sampled around tern colonies to explore potential genetic differences between the isolates. The qPCR test showed a higher prevalence (18%; in 13/73 samples) than Mini-FLOTAC (9%; in 8/88 samples), indicating that qPCR was more sensitive for diagnostic purposes than fecal flotation alone. Although the agreement between both techniques was substantial (84.2%) mainly due to the large number of uninfected samples, only Mini-FLOTAC allowed us to quantify parasite shedding. When combining techniques, the prevalence of infection did not differ between adults and chicks, suggesting frequent trophic transmission from parents to their offspring via food provisioning. Phylogenetic analyses identified four haplotypes in the isolates from Gull-billed Terns and Bleak, all of which were placed within a European clade composed of tapeworms recovered exclusively from phylogenetically derived cyprinid fish. This, combined with the short lifespan of mature tapeworms, suggests that Gull-billed Terns became infected after consuming infected fish around their breeding colonies rather than on their West African wintering grounds. Altogether, our results represent the first record of L. intestinalis in Gull-billed Terns and the first molecular characterization of the parasite in the Iberian Peninsula. This integrative coprodiagnostic protocol can be applied to other host-parasite systems, allowing researchers to study helminth infections in wild populations using a noninvasive approach.

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.

Among-Population Differentiation in the Tapeworm Proteome through Prediction of Excretory/Secretory and Transmembrane Proteins in Schistocephalus solidus

Background

Parasites secrete and excrete a variety of molecules evolve to help establish and sustain infections within hosts. Parasite adaptation to their host may lead to between-population divergence in these excretory and secretory products (ESPs), but few studies have tested for intraspecific variation in helminth proteomes.

Methods

Schistocephalus solidus is a cestode that parasitizes three spined stickleback, Gasterosteus aculeatus . We used an ultra-performance liquid chromatography-mass spectrometry protocol to characterize the ESP and whole-body proteome of S. solidus. Specifically, we characterized the proteome of S. solidus at the plerocercoid stage from wild caught stickleback from three lakes on Vancouver Island (British Columbia, Canada) and one lake in Alaska (United States). We tested for differences in proteome composition among the four populations and specifically between ESPs and body tissue.

Results

Overall, we identified 1362 proteins in the total proteome of S. solidus, with 542 of the 1362 proteins detected exclusively in the ESPs. Of the ESP proteins, we found signaling peptides and transmembrane proteins that were previously not detected or characterized in S. solidus. We also found protein spectrum counts greatly varied between all lake populations.

Conclusions

These population-level differences were observed in both ESP and tissue types. Our study suggests that S. solidus can excrete and secrete a wide range of proteins which are distinct among populations. These differences might reflect plastic responses to host genotype differences, or evolved adaptations by Schistocephalus to different local host populations.

Tapeworm infection affects sleep-like behavior in three-spined sticklebacks

Sleep is a complex and conserved biological process that affects several body functions and behaviors. Evidence suggests that there is a reciprocal interaction between sleep and immunity. For instance, fragmented sleep can increase the probability of parasitic infections and reduce the ability to fight infections. Moreover, viral and bacterial infections alter the sleep patterns of infected individuals. However, the effects of macro-parasitic infections on sleep remain largely unknown, and measuring sleep in non-model organisms remains challenging. In this study, we investigated whether macro-parasite infections could alter sleep-like behavior of their hosts. We experimentally infected three-spined sticklebacks (Gasterosteus aculeatus), a freshwater fish, with the tapeworm Schistocephalus solidus and used a hidden Markov model to characterize sleep-like behavior in sticklebacks. One to four days after parasite exposure, infected fish showed no difference in sleep-like behavior compared with non-exposed fish, and fish that were exposed-but-not-infected only showed a slight reduction in sleep-like behavior during daytime. Twenty-nine to 32 days after exposure, infected fish showed more sleep-like behavior than control fish, while exposed-but-not-infected fish showed overall less sleep-like behavior. Using brain transcriptomics, we identified immune- and sleep-associated genes that potentially underlie the observed behavioral changes. These results provide insights into the complex association between macro-parasite infection, immunity, and sleep in fish and may thus contribute to a better understanding of reciprocal interactions between sleep and immunity.

GPCR-MAPK signaling pathways underpin fitness trade-offs in whitefly

Trade-offs between evolutionary gain and loss are prevalent in nature, yet their genetic basis is not well resolved. The evolution of insect resistance to insecticide is often associated with strong fitness costs; however, how the fitness trade-offs operates remains poorly understood. Here, we show that the mitogen-activated protein kinase (MAPK) pathway and its upstream and downstream actors underlie the fitness trade-offs associated with insecticide resistance in the whitefly Bemisia tabaci. Specifically, we find a key cytochrome P450 gene CYP6CM1, that confers neonicotinoids resistance to in B. tabaci, is regulated by the MAPKs p38 and ERK through their activation of the transcription factor cAMP-response element binding protein. However, phosphorylation of p38 and ERK also leads to the activation of the transcription repressor Cap "n" collar isoform C (CncC) that negatively regulates exuperantia (Ex), vasa (Va), and benign gonial cell neoplasm (Bg), key genes involved in oogenesis, leading to abnormal ovary growth and a reduction in female fecundity. We further demonstrate that the transmembrane G protein-coupled receptor (GPCR) neuropeptide FF receptor 2 (NPFF2) triggers the p38 and ERK pathways via phosphorylation. Additionally, a positive feedback loop between p38 and NPFF2 leads to the continuous activation of the MAPK pathways, thereby constitutively promoting neonicotinoids resistance but with a significant reproductive cost. Collectively, these findings provide fundamental insights into the role of cis-trans regulatory networks incurred by GPCR-MAPK signaling pathways in evolutionary trade-offs and applied knowledge that can inform the development of strategies for the sustainable pest control.

Assessing immune phenotypes using simple proxy measures: promise and limitations

The study of immune phenotypes in wild animals is beset by numerous methodological challenges, with assessment of detailed aspects of phenotype difficult to impossible. This constrains the ability of disease ecologists and ecoimmunologists to describe immune variation and evaluate hypotheses explaining said variation. The development of simple approaches that allow characterization of immune variation across many populations and species would be a significant advance. Here we explore whether serum protein concentrations and coarse-grained white blood cell profiles, immune quantities that can easily be assayed in many species, can predict, and therefore serve as proxies for, lymphocyte composition properties. We do this in rewilded laboratory mice, which combine the benefits of immune phenotyping of lab mice with the natural context and immune variation found in the wild. We find that easily assayed immune quantities are largely ineffective as predictors of lymphocyte composition, either on their own or with other covariates. Immunoglobulin G (IgG) concentration and neutrophil-lymphocyte ratio show the most promise as indicators of other immune traits, but their explanatory power is limited. Our results prescribe caution in inferring immune phenotypes beyond what is directly measured, but they do also highlight some potential paths forward for the development of proxy measures employable by ecoimmunologists.

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.

Designing eco-evolutionary experiments for restoration projects: Opportunities and constraints revealed during stickleback introductions

Eco-evolutionary experiments are typically conducted in semi-unnatural controlled settings, such as mesocosms; yet inferences about how evolution and ecology interact in the real world would surely benefit from experiments in natural uncontrolled settings. Opportunities for such experiments are rare but do arise in the context of restoration ecology-where different "types" of a given species can be introduced into different "replicate" locations. Designing such experiments requires wrestling with consequential questions. (Q1) Which specific "types" of a focal species should be introduced to the restoration location? (Q2) How many sources of each type should be used-and should they be mixed together? (Q3) Which specific source populations should be used? (Q4) Which type(s) or population(s) should be introduced into which restoration sites? We recently grappled with these questions when designing an eco-evolutionary experiment with threespine stickleback (Gasterosteus aculeatus) introduced into nine small lakes and ponds on the Kenai Peninsula in Alaska that required restoration. After considering the options at length, we decided to use benthic versus limnetic ecotypes (Q1) to create a mixed group of colonists from four source populations of each ecotype (Q2), where ecotypes were identified based on trophic morphology (Q3), and were then introduced into nine restoration lakes scaled by lake size (Q4). We hope that outlining the alternatives and resulting choices will make the rationales clear for future studies leveraging our experiment, while also proving useful for investigators considering similar experiments in the future.

Population-level immunologic variation in wild threespine stickleback (Gasterosteusaculeatus)

Wild organisms are regularly exposed to a wide range of parasites, requiring the management of an effective immune response while avoiding immunopathology. Currently, our knowledge of immunoparasitology primarily derives from controlled laboratory studies, neglecting the genetic and environmental diversity that contribute to immune phenotypes observed in wild populations. To gain insight into the immunologic variability in natural settings, we examined differences in immune gene expression of two Alaskan stickleback (Gasterosteus aculeatus) populations with varying susceptibility to infection by the cestode Schistocephalus solidus. Between these two populations, we found distinct immune gene expression patterns at the population level in response to infection with fish from the high-infection population displaying signs of parasite-driven immune manipulation. Further, we found significant differences in baseline immune gene profiles between the populations, with uninfected low-infection population fish showing signatures of inflammation compared to uninfected high-infection population fish. These results shed light on divergent responses of wild populations to the same parasite, providing valuable insights into host-parasite interactions in natural ecosystems.

Natural selection directing molecular evolution in vertebrate viral sensors

Diseases caused by pathogens contribute to molecular adaptations in host immunity. Variety of viral pathogens challenging animal immunity can drive positive selection diversifying receptors recognising the infections. However, whether distinct virus sensing systems differ across animals in their evolutionary modes remains unclear. Our review provides a comparative overview of natural selection shaping molecular evolution in vertebrate viral-binding pattern recognition receptors (PRRs). Despite prevailing negative selection arising from the functional constraints, multiple lines of evidence now suggest diversifying selection in the Toll-like receptors (TLRs), NOD-like receptors (NLRs), RIG-I-like receptors (RLRs) and oligoadenylate synthetases (OASs). In several cases, location of the positively selected sites in the ligand-binding regions suggests effects on viral detection although experimental support is lacking. Unfortunately, in most other PRR families including the AIM2-like receptor family, C-type lectin receptors (CLRs), and cyclic GMP-AMP synthetase studies characterising their molecular evolution are rare, preventing comparative insight. We indicate shared characteristics of the viral sensor evolution and highlight priorities for future research.

Protozoan-Derived Cytokine-Transgenic Macrophages Reverse Hepatic Fibrosis

Macrophage therapy for liver fibrosis is on the cusp of meaningful clinical utility. Due to the heterogeneities of macrophages, it is urgent to develop safer macrophages with a more stable and defined phenotype for the treatment of liver fibrosis. Herein, a new macrophage-based immunotherapy using macrophages stably expressing a pivotal cytokine from Toxoplasma gondii, a parasite that infects ≈ 2 billion people is developed. It is found that Toxoplasma gondii macrophage migration inhibitory factor-transgenic macrophage (Mφtgmif) shows stable fibrinolysis and strong chemotactic capacity. Mφtgmif effectively ameliorates liver fibrosis and deactivates aHSCs by recruiting Ly6Chi macrophages via paracrine CCL2 and polarizing them into the restorative Ly6Clo macrophage through the secretion of CX3CL1. Remarkably, Mφtgmif exhibits even higher chemotactic potential, lower grade of inflammation, and better therapeutic effects than LPS/IFN-γ-treated macrophages, making macrophage-based immune therapy more efficient and safer. Mechanistically, TgMIF promotes CCL2 expression by activating the ERK/HMGB1/NF-κB pathway, and this event is associated with recruiting endogenous macrophages into the fibrosis liver. The findings do not merely identify viable immunotherapy for liver fibrosis but also suggest a therapeutic strategy based on the evolutionarily designed immunomodulator to treat human diseases by modifying the immune microenvironment.

A spectral framework to map QTLs affecting joint differential networks of gene co-expression

Studying the mechanisms underlying the genotype-phenotype association is crucial in genetics. Gene expression studies have deepened our understanding of the genotype → expression → phenotype mechanisms. However, traditional expression quantitative trait loci (eQTL) methods often overlook the critical role of gene co-expression networks in translating genotype into phenotype. This gap highlights the need for more powerful statistical methods to analyze genotype → network → phenotype mechanism. Here, we develop a network-based method, called snQTL, to map quantitative trait loci affecting gene co-expression networks. Our approach tests the association between genotypes and joint differential networks of gene co-expression via a tensor-based spectral statistics, thereby overcoming the ubiquitous multiple testing challenges in existing methods. We demonstrate the effectiveness of snQTL in the analysis of three-spined stickleback (Gasterosteus aculeatus) data. Compared to conventional methods, our method snQTL uncovers chromosomal regions affecting gene co-expression networks, including one strong candidate gene that would have been missed by traditional eQTL analyses. Our framework suggests the limitation of current approaches and offers a powerful network-based tool for functional loci discoveries.

Interwoven processes in fish development: microbial community succession and immune maturation

Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer's investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish's life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis.

Varying conjunctival immune response adaptations of house finch populations to a rapidly evolving bacterial pathogen

Pathogen adaptations during host-pathogen co-evolution can cause the host balance between immunity and immunopathology to rapidly shift. However, little is known in natural disease systems about the immunological pathways optimised through the trade-off between immunity and self-damage. The evolutionary interaction between the conjunctival bacterial infection Mycoplasma gallisepticum (MG) and its avian host, the house finch (Haemorhous mexicanus), can provide insights into such adaptations in immune regulation. Here we use experimental infections to reveal immune variation in conjunctival tissue for house finches captured from four distinct populations differing in the length of their co-evolutionary histories with MG and their disease tolerance (defined as disease severity per pathogen load) in controlled infection studies. To differentiate contributions of host versus pathogen evolution, we compared house finch responses to one of two MG isolates: the original VA1994 isolate and a more evolutionarily derived one, VA2013. To identify differential gene expression involved in initiation of the immune response to MG, we performed 3'-end transcriptomic sequencing (QuantSeq) of samples from the infection site, conjunctiva, collected 3-days post-infection. In response to MG, we observed an increase in general pro-inflammatory signalling, as well as T-cell activation and IL17 pathway differentiation, associated with a decrease in the IL12/IL23 pathway signalling. The immune response was stronger in response to the evolutionarily derived MG isolate compared to the original one, consistent with known increases in MG virulence over time. The host populations differed namely in pre-activation immune gene expression, suggesting population-specific adaptations. Compared to other populations, finches from Virginia, which have the longest co-evolutionary history with MG, showed significantly higher expression of anti-inflammatory genes and Th1 mediators. This may explain the evolution of disease tolerance to MG infection in VA birds. We also show a potential modulating role of BCL10, a positive B- and T-cell regulator activating the NFKB signalling. Our results illuminate potential mechanisms of house finch adaptation to MG-induced immunopathology, contributing to understanding of the host evolutionary responses to pathogen-driven shifts in immunity-immunopathology trade-offs.

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.

Locomotor effects of a fibrosis-based immune response in stickleback fish

The vertebrate immune system provides an impressively effective defense against parasites and pathogens. However, these benefits must be balanced against a range of costly side-effects including energy loss and risks of auto-immunity. These costs might include biomechanical impairment of movement, but little is known about the intersection between immunity and biomechanics. Here, we show that a fibrosis immune response to Schistocephalus solidus infection in freshwater threespine stickleback (Gasterosteus aculeatus) has collateral effects on their locomotion. Although fibrosis is effective at reducing infection, some populations of stickleback actively suppress this immune response, possibly because the costs of fibrosis outweigh the benefits. We quantified the locomotor effects of the fibrosis immune response in the absence of parasites to investigate whether there are incidental costs of fibrosis that could help explain why some fish forego this effective defense. To do this, we induced fibrosis in stickleback and then tested their C-start escape performance. Additionally, we measured the severity of fibrosis, body stiffness and body curvature during the escape response. We were able to estimate performance costs of fibrosis by including these variables as intermediates in a structural equation model. This model revealed that among control fish without fibrosis, there is a performance cost associated with increased body stiffness. However, fish with fibrosis did not experience this cost but rather displayed increased performance with higher fibrosis severity. This result demonstrates that the adaptive landscape of immune responses can be complex with the potential for wide-reaching and unexpected fitness consequences.

Genes, Morphology, Performance, and Fitness: Quantifying Organismal Performance to Understand Adaptive Evolution

To understand the complexities of morphological evolution, we must understand the relationships between genes, morphology, performance, and fitness in complex traits. Genomicists have made tremendous progress in finding the genetic basis of many phenotypes, including a myriad of morphological characters. Similarly, field biologists have greatly advanced our understanding of the relationship between performance and fitness in natural populations. However, the connection from morphology to performance has primarily been studied at the interspecific level, meaning that in most cases we lack a mechanistic understanding of how evolutionarily relevant variation among individuals affects organismal performance. Therefore, functional morphologists need methods that will allow for the analysis of fine-grained intraspecific variation in order to close the path from genes to fitness. We suggest three methodological areas that we believe are well suited for this research program and provide examples of how each can be applied within fish model systems to build our understanding of microevolutionary processes. Specifically, we believe that structural equation modeling, biological robotics, and simultaneous multi-modal functional data acquisition will open up fruitful collaborations among biomechanists, evolutionary biologists, and field biologists. It is only through the combined efforts of all three fields that we will understand the connection between evolution (acting at the level of genes) and natural selection (acting on fitness).

Locomotor effects of a fibrosis-based immune response in stickleback fish

The vertebrate immune system provides an impressively effective defense against parasites and pathogens. However, these benefits must be balanced against a range of costly side-effects including energy loss and risks of auto-immunity. These costs might include biomechanical impairment of movement, but little is known about the intersection between immunity and biomechanics. Here, we show that a fibrosis immune response in threespine stickleback (Gasterosteus aculeatus) has collateral effects on their locomotion. When freshwater stickleback are infected with the tapeworm parasite Schistocephalus solidus, they face an array of fitness consequences ranging from impaired body condition and fertility to an increased risk of mortality. To fight the infection, some stickleback will initiate a fibrosis immune response in which they produce excess collagenous tissue in their coelom. Although fibrosis is effective at reducing infection, some populations of stickleback actively suppress this immune response, possibly because the costs of fibrosis outweigh the benefits. Here we quantify the locomotor effects of the fibrosis immune response in the absence of parasites to investigate whether there are collateral costs of fibrosis that could help explain why some fish forego this effective defense. To do this, we induce fibrosis in stickleback and then test their C-start escape performance. Additionally, we measure the severity of fibrosis, body stiffness, and body curvature during the escape response. We were able to estimate performance costs of fibrosis by including these variables as intermediates in a structural equation model. This model reveals that among control fish without fibrosis, there is a performance cost associated with increased body stiffness. However, fish with fibrosis did not experience this cost but rather displayed increased performance with higher fibrosis severity. This result demonstrates that the adaptive landscape of immune responses can be complex with the potential for wide reaching and unexpected fitness consequences.

Rapid adaptation to a novel pathogen through disease tolerance in a wild songbird

Animal hosts can adapt to emerging infectious disease through both disease resistance, which decreases pathogen numbers, and disease tolerance, which limits damage during infection without limiting pathogen replication. Both resistance and tolerance mechanisms can drive pathogen transmission dynamics. However, it is not well understood how quickly host tolerance evolves in response to novel pathogens or what physiological mechanisms underlie this defense. Using natural populations of house finches (Haemorhous mexicanus) across the temporal invasion gradient of a recently emerged bacterial pathogen (Mycoplasma gallisepticum), we find rapid evolution of tolerance (<25 years). In particular, populations with a longer history of MG endemism have less pathology but similar pathogen loads compared with populations with a shorter history of MG endemism. Further, gene expression data reveal that more-targeted immune responses early in infection are associated with tolerance. These results suggest an important role for tolerance in host adaptation to emerging infectious diseases, a phenomenon with broad implications for pathogen spread and evolution.

Understanding the evolution of immune genes in jawed vertebrates

Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.

Local adaptation and host specificity to copepod intermediate hosts by the tapeworm Schistocephalus solidus

Host-parasite coevolution may lead to patterns of local adaptation in either the host or parasite. For parasites with complex multi-host life cycles, this coevolution may be more challenging as they must adapt to multiple geographically varying hosts. The tapeworm Schistocephalus solidus exhibits some local adaptation to its second intermediate host, threespine stickleback, to which the parasite is strictly specialized. However, the tapeworm's adaptation to its first intermediate host (any of a number of copepod species) is not documented. We investigated if there was local adaptation and host specify in the tapeworm Schistocephalus solidus to its copepod first intermediate hosts. We exposed copepods from five lakes in Vancouver Island (BC, Canada) to local (i.e. same lake) and foreign tapeworms in a reciprocal exposure experiment. Results indicate that the tapeworm is not locally adapted to the copepods. Instead, we observed moderate-effect host specificity, infection rates being higher in certain copepod species than in others. Infection rates also varied among cestode populations. These results show that although S. solidus infects multiple copepod genera, they are not equally competent hosts. Differences in S. solidus epidemiology among lakes is likely to be driven more by this partial specialization, than by local adaptation to first intermediate hosts.

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.

The dominance of coinfecting parasites' indirect effects on host traits

Indirect genetic effects (IGEs) exist when there is heritable variation in one species' ability to alter a second species' traits. For example, parasites can evolve disparate strategies to manipulate host immune response, whether by evading detection or suppressing immunity. A complication arises during coinfection, when two or more parasite genotypes may try to impose distinct IGEs on the same host trait: which parasite's IGE will be dominant? Here, we apply the notion of dominance to IGEs during coinfection. Using a mathematical model we show that the dominance of IGEs can alter the evolutionary dynamics of parasites. We consider a resident parasite population receiving rare immigrants with a different immune manipulation trait. These immigrants' relative fitness depends on resident prevalence (e.g., the probability immigrants are alone in a host, or coinfecting with a native), and the dominance of the immigrant's IGE on host immunity. Next, we show experimentally that the cestode Schistocephalus solidus exerts an IGE on a host immune trait: parasite antigens from different populations produced different intensities of fibrosis. We then evaluated IGE dominance, finding evidence for overdominance (coinjected antigens induced an even stronger host immune response) which would be detrimental to immigrants when resident prevalence is high. This combination of experimental and modeling results shows that parasites do exhibit IGEs on host traits, and that the dominance of these IGEs during coinfection can substantially alter parasite evolution.

A Call For More Ecologically And Evolutionarily Relevant Studies of Immune Costs

What are the relative costs and benefits of mounting immune responses? Practitioners of ecoimmunology have grappled with this central question since the field's inception with the main tension being how to make tractable methodological choices that maintain the ecological relevance of induced and measured immune costs. Here, we point out two methodological approaches that we feel are underrepresented in the field, describe risks associated with neglecting these methods, and suggest modern techniques that maximize both the diversity and ecological relevance of collected data. First, it is commonly assumed that frequently used and experimentally convenient immune stimulants will induce ecologically relevant immune responses in study organisms. This can be a dangerous assumption. Even if a stimulant's general immune response properties are well characterized, it is critical to also measure the type and scale of immune responses induced by live pathogens. Second, patterns of immune defenses evolve like other traits, thus a comparative approach is essential to understand what forces shape immune variation. Finally, we describe modern genetic and immunological approaches that will soon become essential tools for ecoimmunologists, and present case studies that exemplify the utility of our recommendations.

Anisakis Infection in the Spotted Flounder Citharus linguatula (Pleuronectiformes: Citharidae) Caught in the Gulf of Cadiz (Area FAO 27-ICES IXa) Appears to Negatively Affect Fish Growth

Spotted flounder (Citharus linguatula L.) caught in the Gulf of Cadiz (area FAO 27 ICES IXa) were examined for Anisakis larvae and to assess the possible risk of anisakiasis in humans through consumption of this fish. Larvae of the genera Anisakis and Hysterothylacium were identified in the analysis of 128 purchased fish specimens. All Anisakis larvae corresponded to type I. Molecular analysis showed the presence of A. pegreffii, A. simplex s.s., and recombinant genotype between the two. The prevalence of Anisakis was 9.4% with a mean intensity of 1.42, while for Hysterothylacium the values were 12.5% and 1.06. The length and weight of the fish, but not Fulton's condition factor, varied significantly between infected and uninfected fish. The prevalence of Anisakis increased with fish length, with no fish parasitized with Anisakis measuring less than 15.5 cm (2-2.5 years old), which is probably related to the reported dietary change of these fish at around 2 years of age. Fish not parasitized with any of these nematodes showed positive allometric growth, while those parasitized only with Anisakis showed negative allometric growth. When comparing both groups including only fish ≥ 15.5 cm (the smallest size of Anisakis-infected fish), the difference is shown to be statistically significant (p = 0.01), suggesting that Anisakis infection of spotted flounder negatively affects fish growth even when parasite intensity is low, which may have important economic repercussions. Finally, the low prevalence and, above all, intensity of Anisakis in these fish, as well as the habit of consuming this fish fried in oil in our geographical area, means that the risk of acquiring anisakiasis through consumption of this fish is low.