Does genetic diversity protect host populations from parasites? A meta-analysis across natural and agricultural systems

Haitian coffee agroforestry systems harbor complex arabica variety mixtures and under-recognized genetic diversity

Though facing significant challenges, coffee (Coffea arabica) grown in Haitian agroforestry systems are important contributors to rural livelihoods and provide several ecosystem services. However, little is known about their genetic diversity and the variety mixtures used. In light of this, there is a need to characterize Haitian coffee diversity to help inform revitalization of this sector. We sampled 28 diverse farms in historically important coffee growing regions of northern and southern Haiti. We performed KASP-genotyping of SNP markers and HiPlex multiplex amplicon sequencing for haplotype calling on our samples, as well as several Ethiopian and commercial accessions from international collections. This allowed us to assign Haitian samples to varietal groups. Our analyses revealed considerable genetic diversity in Haitian farms, higher in fact than many farmers realized. Notably, genetic structure analyses revealed the presence of clusters related to Typica, Bourbon, and Catimor groups, another group that was not represented in our reference accession panel, and several admixed individuals. Across the study areas, we found both mixed-variety farms and monovarietal farms with the historical and traditional Typica variety. This study is, to our knowledge, the first to genetically characterize Haitian C. arabica variety mixtures, and report the limited cultivation of C. canephora (Robusta coffee) in the study area. Our results show that some coffee farms are repositories of historical, widely-abandoned varieties while others are generators of new diversity through genetic mixing.

Loss of species and genetic diversity during colonization: Insights from acanthocephalan parasites in northern European seals

Studies on host-parasite systems that have experienced distributional shifts, range fragmentation, and population declines in the past can provide information regarding how parasite community richness and genetic diversity will change as a result of anthropogenic environmental changes in the future. Here, we studied how sequential postglacial colonization, shifts in habitat, and reduced host population sizes have influenced species richness and genetic diversity of Corynosoma (Acanthocephala: Polymorphidae) parasites in northern European marine, brackish, and freshwater seal populations. We collected Corynosoma population samples from Arctic, Baltic, Ladoga, and Saimaa ringed seal subspecies and Baltic gray seals, and then applied COI barcoding and triple-enzyme restriction-site associated DNA (3RAD) sequencing to delimit species, clarify their distributions and community structures, and elucidate patterns of intraspecific gene flow and genetic diversity. Our results showed that Corynosoma species diversity reflected host colonization histories and population sizes, with four species being present in the Arctic, three in the Baltic Sea, two in Lake Ladoga, and only one in Lake Saimaa. We found statistically significant population-genetic differentiation within all three Corynosoma species that occur in more than one seal (sub)species. Genetic diversity tended to be high in Corynosoma populations originating from Arctic ringed seals and low in the landlocked populations. Our results indicate that acanthocephalan communities in landlocked seal populations are impoverished with respect to both species and intraspecific genetic diversity. Interestingly, the loss of genetic diversity within Corynosoma species seems to have been less drastic than in their seal hosts, possibly due to their large local effective population sizes resulting from high infection intensities and effective intra-host population mixing. Our study highlights the utility of genomic methods in investigations of community composition and genetic diversity of understudied parasites.

Host genetic identity determines parasite community structure across time and space in oyster restoration

Intraspecific variation in host susceptibility to individual parasite species is common, yet how these effects scale to mediate the structure of diverse parasite communities in nature is less well understood. To address this knowledge gap, we tested how host genetic identity affects parasite communities on restored reefs seeded with juvenile oysters from different sources-a regional commercial hatchery or one of two wild progenitor lines. We assessed prevalence and intensity of three micro- and two macroparasite species for 4 years following restoration. Despite the spatial proximity of restored reefs, oyster source identity strongly predicted parasite community prevalence across all years, with sources varying in their relative susceptibility to different parasites. Oyster seed source also predicted reef-level parasite intensities across space and through time. Our results highlight that host intraspecific variation can shape parasite community structure in natural systems, and reinforce the importance of considering source identity and diversity in restoration design.

Mechanistic models to meet the challenge of climate change in plant-pathogen systems

Evidence that climate change will impact the ecology and evolution of individual plant species is growing. However, little, as yet, is known about how climate change will affect interactions between plants and their pathogens. Climate drivers could affect the physiology, and thus demography, and ultimately evolutionary processes affecting both plant hosts and their pathogens. Because the impacts of climate drivers may operate in different directions at different scales of infection, and, furthermore, may be nonlinear, abstracting across these processes may mis-specify outcomes. Here, we use mechanistic models of plant-pathogen interactions to illustrate how counterintuitive outcomes are possible, and we introduce how such framing may contribute to understanding climate effects on plant-pathogen systems. We discuss the evidence-base derived from wild and agricultural plant-pathogen systems that could inform such models, specifically in the direction of estimates of physiological, demographic and evolutionary responses to climate change. We conclude by providing an overview of knowledge gaps and directions for future research in this important area. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.

Genomic Underpinnings of Population Persistence in Isle Royale Moose

Island ecosystems provide natural laboratories to assess the impacts of isolation on population persistence. However, most studies of persistence have focused on a single species, without comparisons to other organisms they interact with in the ecosystem. The case study of moose and gray wolves on Isle Royale allows for a direct contrast of genetic variation in isolated populations that have experienced dramatically differing population trajectories over the past decade. Whereas the Isle Royale wolf population recently declined nearly to extinction due to severe inbreeding depression, the moose population has thrived and continues to persist, despite having low genetic diversity and being isolated for ∼120 years. Here, we examine the patterns of genomic variation underlying the continued persistence of the Isle Royale moose population. We document high levels of inbreeding in the population, roughly as high as the wolf population at the time of its decline. However, inbreeding in the moose population manifests in the form of intermediate-length runs of homozygosity suggestive of historical inbreeding and purging, contrasting with the long runs of homozygosity observed in the smaller wolf population. Using simulations, we confirm that substantial purging has likely occurred in the moose population. However, we also document notable increases in genetic load, which could eventually threaten population viability over the long term. Overall, our results demonstrate a complex relationship between inbreeding, genetic diversity, and population viability that highlights the use of genomic datasets and computational simulation tools for understanding the factors enabling persistence in isolated populations.

High Temporal Variability in Late Blight Pathogen Diversity, Virulence, and Fungicide Resistance in Potato Breeding Fields: Results from a Long-Term Monitoring Study

Long-term site-specific studies describing changes in the phenotypic variability of Phytophthora infestans populations allow quantitative predictions of pathogen spread and possible outbreaks of epidemics, and provide key input for regional resistance breeding programs. Late blight samples were collected from potato (Solanum tuberosum) breeding fields in Estonia during a twelve-year study period between 2001 and 2014. In total, 207 isolates were assessed for mating type and 235 isolates for metalaxyl resistance and 251 isolates for virulence factors. The frequency of mating types strongly fluctuated across the years, whereas the later period of 2010–2014 was dominated by the A2 mating. Despite fluctuations, both mating types were recorded in the same fields in most years, indicating sustained sexual reproduction of P. infestans with oospore production. Metalaxyl-resistant and intermediately resistant strains dominated in the first years of study, but with the progression of the study, metalaxyl-sensitive isolates became dominant, reaching up to 88%. Racial diversity, characterized by normalized Shannon diversity index decreased in time, varying from 1.00 in 2003 to 0.43 in 2013. The frequency of several virulence factors changed in a time-dependent manner, with R2 increasing and R6, R8, and R9 decreasing in time. Potato cultivar resistance background did not influence the frequency of P. infestans mating type, response to metalaxyl, and racial diversity. However, the diversity index decreased in time among isolates collected from resistant and susceptible cultivars, and remained at a high level in moderately resistant cultivars. These data demonstrate major time-dependent changes in racial diversity, fungicide resistance, and virulence factors in P. infestans, consistent with alterations in the control strategies and popularity of potato cultivars with different resistance.

Genetic composition and diversity of Arabica coffee in the crop's center of origin and its impact on four major fungal diseases

Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the sixty sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels.

Challenging a host-pathogen paradigm: Susceptibility to chytridiomycosis is decoupled from genetic erosion

The putatively positive association between host genetic diversity and the ability to defend against pathogens has long attracted the attention of evolutionary biologists. Chytridiomycosis, a disease caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), has emerged in recent decades as a cause of dramatic declines and extinctions across the amphibian clade. Bd susceptibility can vary widely across populations of the same species, but the relationship between standing genetic diversity and susceptibility has remained notably underexplored so far. Here, we focus on a putatively Bd‐naive system of two mainland and two island populations of the common toad (Bufo bufo) at the edge of the species’ range and use controlled infection experiments and dd‐RAD sequencing of >10 000 SNPs across 95 individuals to characterize the role of host population identity, genetic variation and individual body mass in mediating host response to the pathogen. We found strong genetic differentiation between populations and marked variation in their susceptibility to Bd. This variation was not, however, governed by isolation‐mediated genetic erosion, and individual heterozygosity was even found to be negatively correlated with survival. Individual survival during infection experiments was strongly positively related to body mass, which itself was unrelated to population of origin or heterozygosity. Our findings underscore the general importance of context‐dependency when assessing the role of host genetic variation for the ability of defence against pathogens.

Genetic diversity and disease: The past, present, and future of an old idea

Why do infectious diseases erupt in some host populations and not others? This question has spawned independent fields of research in evolution, ecology, public health, agriculture, and conservation. In the search for environmental and genetic factors that predict variation in parasitism, one hypothesis stands out for its generality and longevity: genetically homogeneous host populations are more likely to experience severe parasitism than genetically diverse populations. In this perspective piece, I draw on overlapping ideas from evolutionary biology, agriculture, and conservation to capture the far-reaching implications of the link between genetic diversity and disease. I first summarize the development of this hypothesis and the results of experimental tests. Given the convincing support for the protective effect of genetic diversity, I then address the following questions: (1) Where has this idea been put to use, in a basic and applied sense, and how can we better use genetic diversity to limit disease spread? (2) What new hypotheses does the established disease-diversity relationship compel us to test? I conclude that monitoring, preserving, and augmenting genetic diversity is one of our most promising evolutionarily informed strategies for buffering wild, domesticated, and human populations against future outbreaks.

Genotype diversity promotes the persistence of Daphnia populations exposed to severe copper stress

When environmental stressors of high intensity are sustained for long periods of time, populations face high probabilities of being extirpated. However, depending on the intensity of the stressor, large populations with sufficient genetic diversity may persist. We report the results of an experiment that tracked the persistence of Daphnia populations exposed to copper contamination. We assessed whether genotypic diversity reduced the risk of extinction. We created monoclonal and multiclonal populations and monitored their population sizes during a 32-week experiment. Cu was applied at a sub-lethal concentration and then increased every week until the population sizes dropped to about 10% of the carrying capacity (Cu at 180 μg/L). The concentration was then increased up to 186 μg/L and held stable until the end of the experiment. A survival analysis showed that clonal diversity extended the persistence of Daphnia populations, but copper contamination caused a substantial genetic erosion followed by population extirpation. However, some Cu-treated populations, mostly multiclonal, showed U-shaped patterns of growth consistent with evolutionary rescue but these did not lead to lasting population recovery. These results highlight the importance of genetic variation for population persistence, but they also show how quickly it can be lost in contaminated environments.

Infectious disease in an era of global change

The twenty-first century has witnessed a wave of severe infectious disease outbreaks, not least the COVID-19 pandemic, which has had a devastating impact on lives and livelihoods around the globe. The 2003 severe acute respiratory syndrome coronavirus outbreak, the 2009 swine flu pandemic, the 2012 Middle East respiratory syndrome coronavirus outbreak, the 2013-2016 Ebola virus disease epidemic in West Africa and the 2015 Zika virus disease epidemic all resulted in substantial morbidity and mortality while spreading across borders to infect people in multiple countries. At the same time, the past few decades have ushered in an unprecedented era of technological, demographic and climatic change: airline flights have doubled since 2000, since 2007 more people live in urban areas than rural areas, population numbers continue to climb and climate change presents an escalating threat to society. In this Review, we consider the extent to which these recent global changes have increased the risk of infectious disease outbreaks, even as improved sanitation and access to health care have resulted in considerable progress worldwide.

Optimizing Plant Disease Management in Agricultural Ecosystems Through Rational In-Crop Diversification

Biodiversity plays multifaceted roles in societal development and ecological sustainability. In agricultural ecosystems, using biodiversity to mitigate plant diseases has received renewed attention in recent years but our knowledge of the best ways of using biodiversity to control plant diseases is still incomplete. In term of in-crop diversification, it is not clear how genetic diversity per se in host populations interacts with identifiable resistance and other functional traits of component genotypes to mitigate disease epidemics and what is the best way of structuring mixture populations. In this study, we created a series of host populations by mixing different numbers of potato varieties showing different late blight resistance levels in different proportions. The amount of naturally occurring late blight disease in the mixture populations was recorded weekly during the potato growing seasons. The percentage of disease reduction (PDR) in the mixture populations was calculated by comparing their observed late blight levels relative to that expected when they were planted in pure stands. We found that PDR in the mixtures increased as the number of varieties and the difference in host resistance (DHR) between the component varieties increased. However, the level of host resistance in the potato varieties had little impact on PDR. In mixtures involving two varieties, the optimum proportion of component varieties for the best PDR depended on their DHR, with an increasing skewness to one of the component varieties as the DHR between the component varieties increased. These results indicate that mixing crop varieties can significantly reduce disease epidemics in the field. To achieve the best disease mitigation, growers should include as many varieties as possible in mixtures or, if only two component mixtures are possible, increase DHR among the component varieties.

Causation without correlation: parasite-mediated frequency-dependent selection and infection prevalence

Parasite-mediated selection is thought to maintain host genetic diversity for resistance. We might thus expect to find a strong positive correlation between host genetic diversity and infection prevalence across natural populations. Here, we used computer simulations to examine host-parasite coevolution in 20 simi-isolated clonal populations across a broad range of values for both parasite virulence and parasite fecundity. We found that the correlation between host genetic diversity and infection prevalence can be significantly positive for intermediate values of parasite virulence and fecundity. But the correlation can also be weak and statistically non-significant, even when parasite-mediated frequency-dependent selection is the sole force maintaining host diversity. Hence correlational analyses of field populations, while useful, might underestimate the role of parasites in maintaining host diversity.

Mosaic vaccination: How distributing different vaccines across a population could improve epidemic control

Although vaccination has been remarkably effective against some pathogens, for others, rapid antigenic evolution results in vaccination conferring only weak and/or short‐lived protection. Consequently, considerable effort has been invested in developing more evolutionarily robust vaccines, either by targeting highly conserved components of the pathogen (universal vaccines) or by including multiple immunological targets within a single vaccine (multi‐epitope vaccines). An unexplored third possibility is to vaccinate individuals with one of a number of qualitatively different vaccines, creating a “mosaic” of individual immunity in the population. Here we explore whether a mosaic vaccination strategy can deliver superior epidemiological outcomes to “conventional” vaccination, in which all individuals receive the same vaccine. We suppose vaccine doses can be distributed between distinct vaccine “targets” (e.g., different surface proteins against which an immune response can be generated) and/or immunologically distinct variants at these targets (e.g., strains); the pathogen can undergo antigenic evolution at both targets. Using simple mathematical models, here we provide a proof‐of‐concept that mosaic vaccination often outperforms conventional vaccination, leading to fewer infected individuals, improved vaccine efficacy, and lower individual risks over the course of the epidemic.

Plant-plant communication in variety mixtures plays on disease susceptibility and immunity

This article comments on: Pélissier R, Buendia L, Brousse A, Temple C, Ballini E, Fort F, Violle C, Morel JB. 2021. Plant neighbour-modulated susceptibility to pathogens in intraspecific mixtures. Journal of Experimental Botany 72, 6570–6580.

Dilution effects in disease ecology

For decades, people have reduced the transmission of pathogens by adding low‐quality hosts to managed environments like agricultural fields. More recently, there has been interest in whether similar ‘dilution effects’ occur in natural disease systems, and whether these effects are eroded as diversity declines. For some pathogens of plants, humans and other animals, the highest‐quality hosts persist when diversity is lost, so that high‐quality hosts dominate low‐diversity communities, resulting in greater pathogen transmission. Meta‐analyses reveal that these natural dilution effects are common. However, studying them remains challenging due to limitations on the ability of researchers to manipulate many disease systems experimentally, difficulties of acquiring data on host quality and confusion about what should and should not be considered a dilution effect. Because dilution effects are widely used in managed disease systems and have been documented in a variety of natural disease systems, their existence should not be considered controversial. Important questions remain about how frequently they occur and under what conditions to expect them. There is also ongoing confusion about their relationships to both pathogen spillover and general biogeographical correlations between diversity and disease, which has resulted in an inconsistent and confusing literature. Progress will require rigorous and creative research.

Functional immunogenetic variation, rather than local adaptation, predicts ectoparasite infection intensity in a model fish species

Natural host populations differ in their susceptibility to infection by parasites, and these intrapopulation differences are still an incompletely understood component of host‐parasite dynamics. In this study, we used controlled infection experiments with wild‐caught guppies (Poecilia reticulata) and their ectoparasite Gyrodactylus turnbulli to investigate the roles of local adaptation and host genetic composition (immunogenetic and neutral) in explaining differences in susceptibility to infection. We found differences between our four study host populations that were consistent between two parasite source populations, with no indication of local adaptation by either host or parasite at two tested spatial scales. Greater values of host population genetic variability metrics broadly aligned with lower population mean infection intensity, with the best alignments associated with major histocompatibility complex (MHC) “supertypes”. Controlling for intrapopulation differences and potential inbreeding variance, we found a significant negative relationship between individual‐level functional MHC variability and infection: fish carrying more MHC supertypes experienced infections of lower severity, with limited evidence for supertype‐specific effects. We conclude that population‐level differences in host infection susceptibility probably reflect variation in parasite selective pressure and/or host evolutionary potential, underpinned by functional immunogenetic variation.