Evolution of pathogens in a man-made world

Evolution of parasites in the Anthropocene: new pressures, new adaptive directions

The Anthropocene is seeing the human footprint rapidly spreading to all of Earth's ecosystems. The fast-changing biotic and abiotic conditions experienced by all organisms are exerting new and strong selective pressures, and there is a growing list of examples of human-induced evolution in response to anthropogenic impacts. No organism is exempt from these novel selective pressures. Here, we synthesise current knowledge on human-induced evolution in eukaryotic parasites of animals, and present a multidisciplinary framework for its study and monitoring. Parasites generally have short generation times and huge fecundity, features that predispose them for rapid evolution. We begin by reviewing evidence that parasites often have substantial standing genetic variation, and examples of their rapid evolution both under conditions of livestock production and in serial passage experiments. We then present a two-step conceptual overview of the causal chain linking anthropogenic impacts to parasite evolution. First, we review the major anthropogenic factors impacting parasites, and identify the selective pressures they exert on parasites through increased mortality of either infective stages or adult parasites, or through changes in host density, quality or immunity. Second, we discuss what new phenotypic traits are likely to be favoured by the new selective pressures resulting from altered parasite mortality or host changes; we focus mostly on parasite virulence and basic life-history traits, as these most directly influence the transmission success of parasites and the pathology they induce. To illustrate the kinds of evolutionary changes in parasites anticipated in the Anthropocene, we present a few scenarios, either already documented or hypothetical but plausible, involving parasite taxa in livestock, aquaculture and natural systems. Finally, we offer several approaches for investigations and real-time monitoring of rapid, human-induced evolution in parasites, ranging from controlled experiments to the use of state-of-the-art genomic tools. The implications of fast-evolving parasites in the Anthropocene for disease emergence and the dynamics of infections in domestic animals and wildlife are concerning. Broader recognition that it is not only the conditions for parasite transmission that are changing, but the parasites themselves, is needed to meet better the challenges ahead.

Emerging contaminants: A One Health perspective

Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.

Novel typing scheme reveals emergence and genetic diversity of Chlamydia pecorum at the local management scale across two koala populations

To overcome shortcomings in discriminating Chlamydia pecorum strains infecting the koala (Phascolarctos cinereus) at the local level, we developed a novel genotyping scheme for this pathogen to inform koala management at a fine-scale subpopulation level. We applied this scheme to two geographically distinct koala populations in New South Wales, Australia: the Liverpool Plains and the Southern Highlands to South-west Sydney (SHSWS). Our method provides greater resolution than traditional multi-locus sequence typing, and can be used to monitor strain emergence, movement, and divergence across a range of fragmented habitats. Within the Liverpool Plains population, suspected recent introduction of a novel strain was confirmed by an absence of genetic diversity at the earliest sampling events and limited diversity at recent sampling events. Across the partially fragmented agricultural landscape of the Liverpool Plains, diversity within a widespread sequence type suggests that this degree of fragmentation may hinder but not prevent spread. In the SHSWS population, our results suggest movement of a strain from the south, where diverse strains exist, into a previously Chlamydia-free area in the north, indicating the risk of expansion towards an adjacent Chlamydia-negative koala population in South-west Sydney. In the south of the SHSWS where koala subpopulations appear segregated, we found evidence of divergent strain evolution. Our tool can be used to infer the risks of strain introduction across fragmented habitats in population management, particularly through practices such as wildlife corridor constructions and translocations.

Resource asynchrony and landscape homogenization as drivers of virulence evolution: The case of a directly transmitted disease in a social host

Throughout the last decades, the emergence of zoonotic diseases and the frequency of disease outbreaks have increased substantially, fuelled by habitat encroachment and vectors overlapping with more hosts due to global change. The virulence of pathogens is one key trait for successful invasion. In order to understand how global change drivers such as habitat homogenization and climate change drive pathogen virulence evolution, we adapted an established individual-based model of host-pathogen dynamics. Our model simulates a population of social hosts affected by a directly transmitted evolving pathogen in a dynamic landscape. Pathogen virulence evolution results in multiple strains in the model that differ in their transmission capability and lethality. We represent the effects of global change by simulating environmental changes both in time (resource asynchrony) and space (homogenization). We found an increase in pathogenic virulence and a shift in strain dominance with increasing landscape homogenization. Our model further indicated that lower virulence is dominant in fragmented landscapes, although pulses of highly virulent strains emerged under resource asynchrony. While all landscape scenarios favoured co-occurrence of low- and high-virulent strains, the high-virulence strains capitalized on the possibility for transmission when host density increased and were likely to become dominant. With asynchrony likely to occur more often due to global change, our model showed that a subsequent evolution towards lower virulence could lead to some diseases becoming endemic in their host populations.

Evolution of pathogens with cross-immunity in response to healthcare interventions

Cross-immunity, as an evolutionary driver, can contribute to pathogen evolution, particularly pathogen diversity. Healthcare interventions aimed at reducing disease severity or transmission are commonly used to control diseases and can also induce pathogen evolution. Understanding pathogen evolution in the context of cross-immunity and healthcare interventions is crucial for infection control. This study starts by modelling cross-immunity, the extent of which is determined by strain traits and host characteristics. Given that all hosts have the same characteristics, full cross-immunity between residents and mutants occurs when mutation step sizes are small enough. Cross-immunity can be partial when the step size is large. The presence of partial cross-immunity reduces pathogen load and shortens the infectious period inside hosts, reducing transmission between hosts and improving host population survival and recovery. This study focuses on how pathogens evolve through small and large mutational steps and how healthcare interventions affect pathogen evolution. Using the theory of adaptive dynamics, we found that when mutational steps are small (only full cross-immunity is present), pathogen diversity cannot occur because it maximises the basic reproduction number. This results in intermediate values for both pathogen growth and clearance rates. However, when large mutational steps are allowed (with full and partial cross-immunity present), pathogens can evolve into multiple strains and induce pathogen diversity. The study also shows that different healthcare interventions can have varying effects on pathogen evolution. Generally, low levels of intervention are more likely to induce strain diversity, while high levels are more likely to result in strain reduction.

Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador

Human movement may be an important driver of transmission dynamics for enteric pathogens but has largely been underappreciated except for international 'travelers' diarrhea or cholera. Phylodynamic methods, which combine genomic and epidemiological data, are used to examine rates and dynamics of disease matching underlying evolutionary history and biogeographic distributions, but these methods often are not applied to enteric bacterial pathogens. We used phylodynamics to explore the phylogeographic and evolutionary patterns of diarrheagenic E. coli in northern Ecuador to investigate the role of human travel in the geographic distribution of strains across the country. Using whole genome sequences of diarrheagenic E. coli isolates, we built a core genome phylogeny, reconstructed discrete ancestral states across urban and rural sites, and estimated migration rates between E. coli populations. We found minimal structuring based on site locations, urban vs. rural locality, pathotype, or clinical status. Ancestral states of phylogenomic nodes and tips were inferred to have 51% urban ancestry and 49% rural ancestry. Lack of structuring by location or pathotype E. coli isolates imply highly connected communities and extensive sharing of genomic characteristics across isolates. Using an approximate structured coalescent model, we estimated rates of migration among circulating isolates were 6.7 times larger for urban towards rural populations compared to rural towards urban populations. This suggests increased inferred migration rates of diarrheagenic E. coli from urban populations towards rural populations. Our results indicate that investments in water and sanitation prevention in urban areas could limit the spread of enteric bacterial pathogens among rural populations.

Plant disease risk is modified by multiple global change drivers

Plant diseases are strongly influenced by host biodiversity, spatial structure, and abiotic conditions. All of these are undergoing rapid change, as the climate is warming, habitats are being lost, and nitrogen deposition is changing nutrient dynamics of ecosystems with ensuing consequences for biodiversity. Here, I review examples of plant-pathogen associations to demonstrate how our ability to understand, model and predict disease dynamics is becoming increasingly difficult, as both plant and pathogen populations and communities are undergoing extensive change. The extent of this change is influenced via both direct and combined effects of global change drivers, and especially the latter are still poorly understood. Change at one trophic level is expected to drive change also at the other, and hence feedback loops between plants and their pathogens are expected to drive changes in disease risk both through ecological as well as evolutionary mechanisms. Many of the examples discussed here demonstrate an increase in disease risk as a result of ongoing change, suggesting that unless we successfully mitigate global environmental change, plant disease is going to become an increasingly heavy burden on our societies with far-reaching consequences for food security and functioning of ecosystems.

Modular DNA Circuits for Point-of-Care Colorimetric Assay of Infectious Pathogens

Accurate, specific, and inexpensive detection of multiple infectious pathogens simultaneously is a significant goal for human health and safety. Herein we present a rationally designed modular DNA circuit for point-of-care (POC) detection of a variety of infectious pathogens based on nucleic acid isothermal amplification technology and DNAzyme-mediated colorimetric readout. A modular DNA circuit was constructed with a fixed module and a flexible module and was rationally designed according to genetic targets. On this basis, the platform could detect multiple genetic targets corresponding to infectious pathogens simultaneously. Signal amplification properties of the DNA circuit and the peroxidase-like DNAzyme enable the detection limits to reach the picomolar level. By urea treatment and magnetic separation, the fixed module can be reused at least five times, which makes this assay more economical and environmentally friendly. The detection of genetic infectious pathogens should be accomplished in 2 h with naked-eye observation and may provide an efficient tool for POC analysis of multiple infectious pathogens, especially in resource-poor areas.

Tissues: the unexplored frontier of antibody mediated immunity

Pathogen-specific immunity evolves in the context of the infected tissue. However, current immune correlates analyses and vaccine efficacy metrics are based on immune functions from peripheral cells. Less is known about tissue-resident mechanisms of immunity. While antibodies represent the primary correlate of immunity following most clinically approved vaccines, how antibodies interact with localized, compartment-specific immune functions to fight infections, remains unclear. Emerging data demonstrate a unique community of immune cells that reside within different tissues. These tissue-specific immunological communities enable antibodies to direct both expected and unexpected local attack strategies to control, disrupt, and eliminate infection in a tissue-specific manner. Defining the full breadth of antibody effector functions, how they selectively contribute to control at the site of infection may provide clues for the design of next-generation vaccines able to direct the control, elimination, and prevention of compartment specific diseases of both infectious and non-infectious etiologies.

Internet of medical things (IoMT)-integrated biosensors for point-of-care testing of infectious diseases

On global scale, the current situation of pandemic is symptomatic of increased incidences of contagious diseases caused by pathogens. The faster spread of these diseases, in a moderately short timeframe, is threatening the overall population wellbeing and conceivably the economy. The inadequacy of conventional diagnostic tools in terms of time consuming and complex laboratory-based diagnosis process is a major challenge to medical care. In present era, the development of point-of-care testing (POCT) is in demand for fast detection of infectious diseases along with “on-site” results that are helpful in timely and early action for better treatment. In addition, POCT devices also play a crucial role in preventing the transmission of infectious diseases by offering real-time testing and lab quality microbial diagnosis within minutes. Timely diagnosis and further treatment optimization facilitate the containment of outbreaks of infectious diseases. Presently, efforts are being made to support such POCT by the technological development in the field of internet of medical things (IoMT). The IoMT offers wireless-based operation and connectivity of POCT devices with health expert and medical centre. In this review, the recently developed POC diagnostics integrated or future possibilities of integration with IoMT are discussed with focus on emerging and re-emerging infectious diseases like malaria, dengue fever, influenza A (H1N1), human papilloma virus (HPV), Ebola virus disease (EVD), Zika virus (ZIKV), and coronavirus (COVID-19). The IoMT-assisted POCT systems are capable enough to fill the gap between bioinformatics generation, big rapid analytics, and clinical validation. An optimized IoMT-assisted POCT will be useful in understanding the diseases progression, treatment decision, and evaluation of efficacy of prescribed therapy.

Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene

Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.

The spreading of parasites by human migratory activities

The global spread of parasites is unquestionably linked with human activities. Migration in all its different forms played a major role in the introduction of parasites into new areas. In ancient times, mass migrations were the main causes for the spread of parasites while in the recent past and present, emigration, immigration, displacement, external and internal migration, and labor migration were the reasons for the dispersal of parasites. With the advent of seagoing ships, long-distance trading became another important mode of spreading parasites. This review summarizes the spread of parasites using notable examples. In addition, the different hypotheses explaining the arrival of Plasmodium vivax and soil-transmitted helminths in pre-Columbian America are also discussed.

Evolution in the Anthropocene: Informing Governance and Policy

The Anthropocene biosphere constitutes an unprecedented phase in the evolution of life on Earth with one species, humans, exerting extensive control. The increasing intensity of anthropogenic forces in the twenty-first century has widespread implications for attempts to govern both human-dominated ecosystems and the last remaining wild ecosystems. Here, we review how evolutionary biology can inform governance and policies in the Anthropocene, focusing on five governance challenges that span biodiversity, environmental management, food and other biomass production, and human health. The five challenges are: ( a) evolutionary feedbacks, ( b) maintaining resilience, ( c) alleviating constraints, ( d) coevolutionary disruption, and ( e) biotechnology. Strategies for governing these dynamics will themselves have to be coevolutionary, as eco-evolutionary and social dynamics change in response to each other.

Microsatellite markers reveal two genetic groups in European populations of the carrot cyst nematode Heterodera carotae

The cyst nematode Heterodera carotae, which parasitizes carrot roots, has been recorded in many countries in Europe (Italy, The Netherlands, Switzerland, France, Denmark, …), in South Africa and in North America (Canada, USA). To date, there is a lack of knowledge about the genetic structure of the populations of this economically important nematode. The aim of this work was to study the structuration of the genetic diversity of the carrot cyst nematode at the European scale. We have developed a set of thirteen polymorphic microsatellite markers and used it to genotype seventeen European populations of H. carotae coming from France, Switzerland, Italy, Denmark and one non-European population from Canada. As previously showed for other cyst nematode species, the H. carotae populations were characterised by a strong heterozygote deficit. A Bayesian clustering analysis revealed two distinct genetic clusters, with one group located in the north of Europe and a second one located in the south of Europe. Moreover, our results highlighted rather limited gene flow at small spatial scale and some events of long distance migration. This first investigation of the genetic diversity of H. carotae populations would be useful to develop sustainable control strategies.

Patterns of avian haemosporidian infections vary with time, but not habitat, in a fragmented Neotropical landscape

Habitat loss has the potential to alter vertebrate host populations and their interactions with parasites. Theory predicts a decrease in parasite diversity due to the loss of hosts in such contexts. However, habitat loss could also increase parasite infections as a result of the arrival of new parasites or by decreasing host immune defenses. We investigated the effect of habitat loss and other habitat characteristics on avian haemosporidian infections in a community of birds within a fragmented landscape in northwest Ecuador. We estimated Plasmodium and Haemoproteus parasite infections in 504 individual birds belonging to 8 families and 18 species. We found differences in infection status among bird species, but no relationship between forest fragment characteristics and infection status was observed. We also found a temporal effect, with birds at the end of the five-month study (which ran from the end of the rainy season thru the dry season), being less infected by Plasmodium parasites than individuals sampled at the beginning. Moreover, we found a positive relationship between forest area and Culicoides abundance. Taken as a whole, these findings indicate little effect of fragment characteristics per se on infection, although additional sampling or higher infection rates would have offered more power to detect potential relationships.

Impacts of human development index and climate conditions on prevalence of Blastocystis: A systematic review and meta-analysis

Blastocystis is a prevalent eukaryotic microorganism that has been frequently reported from the stool samples of human and animals, all over the world. The prevalence of this parasite has close correlation with the climate and hygiene situation of studied populations. For the current study, English and Persian databases were searched for the following terms: "Blastocystis hominis", "Blastocystis sp.", "Intestinal Parasites", "Prevalence" and "Iran". In order to data analysis and assess the possibility of publication bias, STATA v11 and Begg's Funnel plot were employed respectively. From 605 searched cases, 86 publications met our criteria for the analysis. The pooled prevalence of Blastocystis was 9.1% (95%CI: 8.2%, 10.1%). The results represented that the prevalence of the parasite using molecular techniques or cultivation followed by molecular techniques (20.89%) was higher than only microscopical examination (8.96%). The prevalence rate of Blastocystis according to human development index was 7.6%, 7.2%, 11.9%, 13.4%, and 3.3% for ranks 1 to 5, respectively. This is the first study signifying the prevalence of Blastocystis regarding the human development index and climate conditions. The findings represented that although human development index, low levels of socioeconomic situations together with appropriate climate such as sufficient humidity and high temperature increase the chance of transmission of Blastocystis in a society.

Turning natural adaptations to oncogenic factors into an ally in the war against cancer

Both field and experimental evolution studies have demonstrated that organisms naturally or artificially exposed to environmental oncogenic factors can, sometimes rapidly, evolve specific adaptations to cope with pollutants and their adverse effects on fitness. Although numerous pollutants are mutagenic and carcinogenic, little attention has been given to exploring the extent to which adaptations displayed by organisms living in oncogenic environments could inspire novel cancer treatments, through mimicking the processes allowing these organisms to prevent or limit malignant progression. Building on a substantial knowledge base from the literature, we here present and discuss this progressive and promising research direction, advocating closer collaboration between the fields of medicine, ecology, and evolution in the war against cancer.

A pedigree-based experiment reveals variation in salinity and thermal tolerance in the salmon louse, Lepeophtheirus salmonis

The salmon louse is a highly abundant ectoparasitic copepod of salmonids in the North Pacific and Atlantic. Widespread and rapid development of resistance to chemical agents used to delouse salmonids on marine farms is now threatening the continued development of the aquaculture industry and have served as a potent catalyst for the development of alternative pest management strategies. These include freshwater and warm-water treatments to which the louse is sensitive. However, given the well-documented evolutionary capacity of this species, the risk of developing tolerance towards these environmental treatments cannot be dismissed. Two common-garden experiments were performed using full-sibling families of lice identified by DNA parentage testing to investigate whether one of the fundamental premises for evolution, in this context genetic variation in the capacity of coping with fresh or warm water, exists within this species. Significant differences in survival were observed among families in both experiments, although for the salinity experiment, it was not possible to unequivocally disentangle background mortality from treatment-induced mortality. Thus, our data demonstrate genetic variation in tolerance of warm water and are suggestive of genetic variation in salinity tolerance. We conclude that extensive use of these environmental-based treatments to delouse salmonids on commercial farms may drive lice towards increased tolerance.

Invest more and die faster: The life history of a parasite on intensive farms

Organisms are expected to respond to alterations in their survival by evolutionary changes in their life history traits. As agriculture and aquaculture have become increasingly intensive in the past decades, there has been growing interest in their evolutionary effects on the life histories of agri‐ and aquacultural pests, parasites, and pathogens. In this study, we used salmon lice (Lepeophtheirus salmonis) to explore how modern farming might have affected life history evolution in parasites. We infected salmon hosts with lice from either farmed or unfarmed locations, and monitored life history traits of those parasites in laboratory conditions. Our results show that compared to salmon lice from areas unaffected by salmon farming, those from farmed areas produced more eggs in their first clutch, and less eggs later on; they achieved higher infestation intensities in early adulthood, but suffered higher adult mortality. These results suggest that salmon lice on farms may have been selected for increased investment in early reproduction, at the expense of later fecundity and survival. This call for further empirical studies of the extent to which farming practices may alter the virulence of agricultural parasites.

Parasite fecundity decreases with increasing parasite load in the salmon louse Lepeophtheirus salmonis infecting Atlantic salmon Salmo salar

Aggregation is common amongst parasites, where a small number of hosts carry a large proportion of parasites. This could result in density-dependent effects on parasite fitness. In a laboratory study, we explored whether parasite load affected parasite fecundity and survival, using ectoparasitic salmon lice (Lepeophtheirus salmonis Krøyer, 1837) infecting Atlantic salmon (Salmo salar) hosts. We found a significant reduction in fecundity with higher parasite load, but no significant effect on survival. Together with previous findings, this suggests that stronger competition amongst female lice under high parasite load is a more likely explanation than increased host immune response.

Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift

Studying wild pathogen populations in natural ecosystems offers the opportunity to better understand the evolutionary dynamics of biotic diseases in crops and to enhance pest control strategies. We used simulations and genetic markers to investigate the spatial and temporal population genetic structure of wild populations of the beet cyst nematode Heterodera schachtii on a wild host plant species, the sea beet (Beta vulgaris spp. maritima), the wild ancestor of cultivated beets. Our analysis of the variation of eight microsatellite loci across four study sites showed that (i) wild H. schachtii populations displayed fine-scaled genetic structure with no evidence of substantial levels of gene flow beyond the scale of the host plant, and comparisons with simulations indicated that (ii) genetic drift substantially affected the residual signals of isolation-by-distance processes, leading to departures from migration-drift equilibrium. In contrast to what can be suspected for (crop) field populations, this showed that wild cyst nematodes have very low dispersal capabilities and are strongly disconnected from each other. Our results provide some key elements for designing pest control strategies, such as decreasing passive dispersal events to limit the spread of virulence among field nematode populations.

Elucidating the spatio-temporal dynamics of an emerging wildlife pathogen using approximate Bayesian computation

Emerging pathogens constitute a severe threat for human health and biodiversity. Determining the status (native or non-native) of emerging pathogens, and tracing back their spatio-temporal dynamics, is crucial to understand the eco-evolutionary factors promoting their emergence, to control their spread and mitigate their impacts. However, tracing back the spatio-temporal dynamics of emerging wildlife pathogens is challenging because (i) they are often neglected until they become sufficiently abundant and pose socio-economical concerns and (ii) their geographical range is often little known. Here, we combined classical population genetics tools and approximate Bayesian computation (i.e. ABC) to retrace the dynamics of Tracheliastes polycolpus, a poorly documented pathogenic ectoparasite emerging in Western Europe that threatens several freshwater fish species. Our results strongly suggest that populations of T. polycolpus in France emerged from individuals originating from a unique genetic pool that were most likely introduced in the 1920s in central France. From this initial population, three waves of colonization occurred into peripheral watersheds within the next two decades. We further demonstrated that populations remained at low densities, and hence undetectable, during 10 years before a major demographic expansion occurred, and before its official detection in France. These findings corroborate and expand the few historical records available for this emerging pathogen. More generally, our study demonstrates how ABC can be used to determine the status, reconstruct the colonization history and infer key evolutionary parameters of emerging wildlife pathogens with low data availability, and for which samples from the putative native area are inaccessible.

Host manipulation in the face of environmental changes: Ecological consequences

Several parasite species, particularly those having complex life-cycles, are known to induce phenotypic alterations in their hosts. Most often, such alterations appear to increase the fitness of the parasites at the expense of that of their hosts, a phenomenon known as “host manipulation”. Host manipulation can have important consequences, ranging from host population dynamics to ecosystem engineering. So far, the importance of environmental changes for host manipulation has received little attention. However, because manipulative parasites are embedded in complex systems, with many interacting components, changes in the environment are likely to affect those systems in various ways. Here, after reviewing the ecological importance of manipulative parasites, we consider potential causes and consequences of changes in host manipulation by parasites driven by environmental modifications. We show that such consequences can extend to trophic networks and population dynamics within communities, and alter the ecological role of manipulative parasites such as their ecosystem engineering. We suggest that taking them into account could improve the accuracy of predictions regarding the effects of global change. We also propose several directions for future studies.

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Environmental changes can affect ecosystems in various ways.

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Manipulative parasites are known to play numerous roles within ecosystems.

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However, the effects of environmental changes on manipulation has been overlooked.

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We review those effects and their potential consequences on larger scales.

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We conclude with suggestions on the direction of future studies.

The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus

Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by conducting a Q_ST/F_ST analysis using agricultural populations of the barley pathogen Rhynchosporium commune. Population divergence for eight quantitative traits (Q_ST) was compared with divergence at eight neutral microsatellite loci (F_ST) for 126 pathogen strains originating from nine globally distributed field populations to infer the effects of genetic drift and types of selection acting on each trait. Our analyses indicated that five of the eight traits had Q_ST values significantly lower than F_ST, consistent with stabilizing selection, whereas one trait, growth under heat stress (22°C), showed evidence of diversifying selection and local adaptation (Q_ST>F_ST). Estimates of heritability were high for all traits (means ranging between 0.55–0.84), and average heritability across traits was negatively correlated with microsatellite gene diversity. Some trait pairs were genetically correlated and there was significant evidence for a trade-off between spore size and spore number, and between melanization and growth under benign temperature. Our findings indicate that many ecologically and agriculturally important traits are under stabilizing selection in R. commune and that high within-population genetic variation is maintained for these traits.

A common-garden experiment to quantify evolutionary processes in copepods: the case of emamectin benzoate resistance in the parasitic sea louse Lepeophtheirus salmonis

BACKGROUND

The development of pesticide resistance represents a global challenge to food production. Specifically for the Atlantic salmon aquaculture industry, parasitic sea lice and their developing resistance to delousing chemicals is challenging production. In this study, seventeen full sibling families, established from three strains of Lepeophtheirus salmonis displaying differing backgrounds in emamectin benzoate (EB) tolerance were produced and quantitatively compared under a common-garden experimental design. Lice surviving to the preadult stage were then exposed to EB and finally identified through the application of DNA parentage testing.

RESULTS

With the exception of two families (19 and 29%), survival from the infectious copepod to preadult stage was very similar among families (40-50%). In contrast, very large differences in survival following EB exposure were observed among the families (7.9-74%). Family survival post EB exposure was consistent with the EB tolerance characteristics of the strains from which they were established and no negative effect on infection success were detected in association with increased EB tolerance. Two of the lice families that displayed reduced sensitivity to EB were established from a commercial farm that had previously used this chemical. This demonstrates that resistant alleles were present on this farm even though the farm had not reported treatment failure.

CONCLUSIONS

To our knowledge, this represents the first study where families of any multi-cellular parasite have been established and compared in performance under communal rearing conditions in a common-garden experiment. The system performed in a predictable manner and permitted, for the first time, elucidation of quantitative traits among sea lice families. While this experiment concentrated on, and provided a unique insight into EB sensitivity among lice families, the experimental design represents a novel methodology to experimentally address both resistance development and other evolutionary questions in parasitic copepods.

Avian blood parasite infection during the non-breeding season: an overlooked issue in declining populations?

Background

Pathogens and parasites can have major impacts on host population dynamics, both through direct mortality and via indirect effects. Both types of effect may be stronger in species whose populations are already under pressure. We investigated the potential for blood parasites to impact upon their hosts at the immunological, physiological and population level during the non-breeding season using a declining population of yellowhammers Emberiza citrinella as a model.

Results

Yellowhammers infected by Haemoproteus spp. showed both a reduced heterophil to lymphocyte (H:L) ratio, and an elevated standardised white blood cell (WBC) count compared to uninfected birds, indicating an immunological response to infection. Infected birds had shorter wings during the first winter of sampling but not during the second, colder, winter; survival analysis of 321 birds sampled across four winters indicated that increased wing length conferred a survival advantage.

Conclusions

We suggest that the potential impacts of blood parasite infections on over-wintering birds may have been underestimated. Further research should consider the potential impacts of sub-clinical parasite infections on the dynamics of vulnerable populations, and we suggest using declining populations as model systems within which to investigate these relationships as well as examining interactions between sub-clinical disease and other environmental stressors.

JEL Code

Q5

Cancer: a missing link in ecosystem functioning?

Cancer is a disease that affects the majority of metazoan species and, before directly causing host death, is likely to influence the competitive abilities of individuals, their susceptibility to pathogens, their vulnerability to predators, and their ability to disperse. Despite the potential importance of these ecological impacts, cancer is rarely incorporated into model ecosystems. We describe here the diversity of ways in which oncogenic phenomena, from precancerous lesions to generalized metastatic cancers, may affect ecological processes that govern biotic interactions. We argue that oncogenic phenomena, despite their complexity, can have significant and sometimes predictable ecological consequences. Our aim is to provide a new perspective on the ecological and evolutionary significance of cancer in wildlife, and to stimulate research on this topic.

Connecting the study of wild influenza with the potential for pandemic disease

Continuing outbreaks of pathogenic (H5N1) and pandemic (SOIVH1N1) influenza have underscored the need to understand the origin, characteristics, and evolution of novel influenza A virus (IAV) variants that pose a threat to human health. In the last 4-5years, focus has been placed on the organization of large-scale surveillance programs to examine the phylogenetics of avian influenza virus (AIV) and host-virus relationships in domestic and wild animals. Here we review the current gaps in wild animal and environmental surveillance and the current understanding of genetic signatures in potentially pandemic strains.

Recent cases of invasive alien mites and ticks in Japan: why is a regulatory framework needed?

Japan's economy depends on the importation of natural resources, and as a result, Japan is subjected to a high risk of biological invasion. Although Japan has quarantine systems to protect ecosystems, agriculture, forestry, fisheries, and human health against alien species, economic globalization has resulted in an ever-increasing risk of invasion. Mite invasion is no exception. Alien species that impact natural ecosystems are regulated in Japan by the Invasive Alien Species Act. However, the law focuses only on visibly recognizable species, so that species too small to see, such as viruses, bacteria, fungi, and mites, are beyond the scope of this law. The Plant Protection Law has limited the introduction of alien pests, including mites, that are harmful to agricultural crops. Recently, the liberalization of global trade policies have increased pressure to loosen regulations on various pests, including spider mites. Infectious diseases and their causative species are quarantined under the Rabies Prevention Law, the Domestic Animal Infectious Diseases Control Law, and the Human Infectious Diseases Control Law, but these laws do not cover wildlife diseases. The most serious problem is that wild reptiles, which can be carriers of ticks and tick-borne diseases, can be freely introduced to Japan. These loopholes in Japan's regulatory system have resulted in mite and tick invasions, which affect not only wildlife communities and human society but also endemism and biological diversity of natural mite populations.

Genes under positive selection in a model plant pathogenic fungus, Botrytis

The rapid evolution of particular genes is essential for the adaptation of pathogens to new hosts and new environments. Powerful methods have been developed for detecting targets of selection in the genome. Here we used divergence data to compare genes among four closely related fungal pathogens adapted to different hosts to elucidate the functions putatively involved in adaptive processes. For this goal, ESTs were sequenced in the specialist fungal pathogens Botrytis tulipae and Botrytis ficariarum, and compared with genome sequences of Botrytis cinerea and Sclerotinia sclerotiorum, responsible for diseases on over 200 plant species. A maximum likelihood-based analysis of 642 predicted orthologs detected 21 genes showing footprints of positive selection. These results were validated by resequencing nine of these genes in additional Botrytis species, showing they have also been rapidly evolving in other related species. Twenty of the 21 genes had not previously been identified as pathogenicity factors in B. cinerea, but some had functions related to plant-fungus interactions. The putative functions were involved in respiratory and energy metabolism, protein and RNA metabolism, signal transduction or virulence, similarly to what was detected in previous studies using the same approach in other pathogens. Mutants of B. cinerea were generated for four of these genes as a first attempt to elucidate their functions.

Host shifts and molecular evolution of H7 avian influenza virus hemagglutinin

Evolutionary consequences of host shifts represent a challenge to identify the mechanisms involved in the emergence of influenza A (IA) viruses. In this study we focused on the evolutionary history of H7 IA virus in wild and domestic birds, with a particular emphasis on host shifts consequences on the molecular evolution of the hemagglutinin (HA) gene. Based on a dataset of 414 HA nucleotide sequences, we performed an extensive phylogeographic analysis in order to identify the overall genetic structure of H7 IA viruses. We then identified host shift events and investigated viral population dynamics in wild and domestic birds, independently. Finally, we estimated changes in nucleotide substitution rates and tested for positive selection in the HA gene. A strong association between the geographic origin and the genetic structure was observed, with four main clades including viruses isolated in North America, South America, Australia and Eurasia-Africa. We identified ten potential events of virus introduction from wild to domestic birds, but little evidence for spillover of viruses from poultry to wild waterbirds. Several sites involved in host specificity (addition of a glycosylation site in the receptor binding domain) and virulence (insertion of amino acids in the cleavage site) were found to be positively selected in HA nucleotide sequences, in genetically unrelated lineages, suggesting parallel evolution for the HA gene of IA viruses in domestic birds. These results highlight that evolutionary consequences of bird host shifts would need to be further studied to understand the ecological and molecular mechanisms involved in the emergence of domestic bird-adapted viruses.

Context-dependent effects of ranaviral infection on northern leopard frog life history traits

Pathogens have important effects on host life-history traits, but the magnitude of these effects is often strongly context-dependent. The outcome of an interaction between a host and an infectious agent is often associated with the level of stress experienced by the host. Ranavirus causes disease and mortality in amphibian populations in various locations around the world, but most known cases of ranaviral infection have occurred in North America and the United Kingdom. While Ranavirus virulence has been investigated, the outcome of Ranavirus infection has seldom been related to the host environment. In a factorial experiment, we exposed Northern leopard frog (Lithobates pipiens, formerly Rana pipiens) tadpoles to different concentrations of Ranavirus and investigated the effect of host density on certain life-history traits, namely survival, growth rate, developmental stage and number of days from virus exposure to death. Our results suggest a prominent role of density in driving the direction of the interaction between L. pipiens tadpoles and Ranavirus. We showed that increasing animal holding density is detrimental for host fitness as mortality rate is higher, day of death earlier, development longer and growth rate significantly lower in high-density tanks. We observed a linear increase of detrimental effects when Ranavirus doses increased in low-density conditions, with control tadpoles having a significantly higher overall relative fitness. However, this pattern was no longer observed in high-density conditions, where the effects of increasing Ranavirus dose were limited. Infected and control animals fitness were consequently similar. We speculate that the host may eventually diverts the energy required for a metabolic/immune response triggered by the infection (i.e., direct costs of the infection) to better cope with the increase in environmental "stress" associated with high density (i.e., indirect benefits of the infection). Our results illustrate how the net fitness of organisms may be shaped by ecological context and emphasize the necessity of examining the direct/indirect costs and benefits balance to fully understand host-pathogen interactions.

Persistence of highly pathogenic avian influenza viruses in natural ecosystems

Differences in virus evolution may explain virulence heterogeneity.

Understanding of ecologic factors favoring emergence and maintenance of highly pathogenic avian influenza (HPAI) viruses is limited. Although low pathogenic avian influenza viruses persist and evolve in wild populations, HPAI viruses evolve in domestic birds and cause economically serious epizootics that only occasionally infect wild populations. We propose that evolutionary ecology considerations can explain this apparent paradox. Host structure and transmission possibilities differ considerably between wild and domestic birds and are likely to be major determinants of virulence. Because viral fitness is highly dependent on host survival and dispersal in nature, virulent forms are unlikely to persist in wild populations if they kill hosts quickly or affect predation risk or migratory performance. Interhost transmission in water has evolved in low pathogenic influenza viruses in wild waterfowl populations. However, oropharyngeal shedding and transmission by aerosols appear more efficient for HPAI viruses among domestic birds.

Intensive Farming: Evolutionary Implications for Parasites and Pathogens

An increasing number of scientists have recently raised concerns about the threat posed by human intervention on the evolution of parasites and disease agents. New parasites (including pathogens) keep emerging and parasites which previously were considered to be ‘under control’ are re-emerging, sometimes in highly virulent forms. This re-emergence may be parasite evolution, driven by human activity, including ecological changes related to modern agricultural practices. Intensive farming creates conditions for parasite growth and transmission drastically different from what parasites experience in wild host populations and may therefore alter selection on various traits, such as life-history traits and virulence. Although recent epidemic outbreaks highlight the risks associated with intensive farming practices, most work has focused on reducing the short-term economic losses imposed by parasites, such as application of chemotherapy. Most of the research on parasite evolution has been conducted using laboratory model systems, often unrelated to economically important systems. Here, we review the possible evolutionary consequences of intensive farming by relating current knowledge of the evolution of parasite life-history and virulence with specific conditions experienced by parasites on farms. We show that intensive farming practices are likely to select for fast-growing, early-transmitted, and hence probably more virulent parasites. As an illustration, we consider the case of the fish farming industry, a branch of intensive farming which has dramatically expanded recently and present evidence that supports the idea that intensive farming conditions increase parasite virulence. We suggest that more studies should focus on the impact of intensive farming on parasite evolution in order to build currently lacking, but necessary bridges between academia and decision-makers.

Global Warming and Trans-Boundary Movement of Waterborne Microbial Pathogens

Potential ramifications of climate change, as they relate to waterborne pathogens (primarily viruses, bacterial and parasitic protozoa), are the focus of this chapter. It seems clear that climate change will impact on waterborne pathogens in various ways (Rose et al. 2001), pertinent to transboundary issues are: (1) increases in intense storm events (increasing sewage/animal waste flows into waterways/aquifers) (Charron et al. 2004; Schijven and de Roda Husman 2005; Yang and Goodrich 2009; De Toffol et al. 2009; Richardson et al. 2009); (2) warmer surface water temperatures or salinity changes (for increased autochthonous pathogen growth) (Niemi et al. 2004; Koelle et al. 2005; Lebarbenchon et al. 2008); and (3) changes in food production, as most obvious in animal diseases (Lightner et al. 1997; Rapoport and Shimshony 1997), but also of concern with zoonoses and from changes in social behavior (Schwab et al. 1998; Nancarrow et al. 2008; CDC 2009a). When considering trans-boundary effects on waterborne pathogens, it is therefore the flow of pathogens in surface water (fresh and marine) and in groundwater, as well as in the varying ways water is used/reused in association with human activities (e.g., food production) that are the trans-boundary issues discussed in this chapter (examples in Table 5.1). Changes in infectious and vector-borne diseases associated with rising sea levels, losses of habitat, international travel etc. are not addressed in this chapter.