Genomic evidence for population‐specific responses to co‐evolving parasites in a New Zealand freshwater snail

Reciprocal co‐evolving interactions between hosts and parasites are a primary source of strong selection that can promote rapid and often population‐ or genotype‐specific evolutionary change. These host–parasite interactions are also a major source of disease. Despite their importance, very little is known about the genomic basis of co‐evolving host–parasite interactions in natural populations, especially in animals. Here, we use gene expression and sequence evolution approaches to take critical steps towards characterizing the genomic basis of interactions between the freshwater snail Potamopyrgus antipodarum and its co‐evolving sterilizing trematode parasite, Microphallus sp., a textbook example of natural coevolution. We found that Microphallus‐infected P. antipodarum exhibit systematic downregulation of genes relative to uninfected P. antipodarum. The specific genes involved in parasite response differ markedly across lakes, consistent with a scenario where population‐level co‐evolution is leading to population‐specific host–parasite interactions and evolutionary trajectories. We also used an F_ST‐based approach to identify a set of loci that represent promising candidates for targets of parasite‐mediated selection across lakes as well as within each lake population. These results constitute the first genomic evidence for population‐specific responses to co‐evolving infection in the P. antipodarum‐Microphallus interaction and provide new insights into the genomic basis of co‐evolutionary interactions in nature.     

The influence of parasitic water mites on the instantaneous death rate of their hosts

Summary The effect of 2 species of water mites on the instantaneous death rate of their hosts was measured on the basis of laboratory experiments. In both parasite-host association — the parasitic water mite Hydryphantes tenuabilis on the aquatic insect host Hydrometra australis and the parasitic water mite Arrenurus pseudotenuicollis on the mosquito Anopheles crucians — the effect of mite load on the instantaneous death rate of the host appeared to be linear. Also, the impact of a single parasite on the host's death rate was apparently related to the ratio of parasite to host body weight. The results of this study are in general agreement with recent theoretical investigations of the regulation of host populations by parasites.     

Genetic structure and host–parasite co‐divergence: evidence for trait‐specific local adaptation

Host–parasite co‐evolution can lead to genetic differentiation among isolated host–parasite populations and local adaptation between parasites and their hosts. However, tests of local adaptation rarely consider multiple fitness‐related traits although focus on a single component of fitness can be misleading. Here, we concomitantly examined genetic structure and co‐divergence patterns of the trematode Coitocaecum parvum and its crustacean host Paracalliope fluviatilis among isolated populations using the mitochondrial cytochrome oxidase I gene (COI). We then performed experimental cross‐infections between two genetically divergent host–parasite populations. Both hosts and parasites displayed genetic differentiation among populations, although genetic structure was less pronounced in the parasite. Data also supported a co‐divergence scenario between C. parvum and P. fluviatilis potentially related to local co‐adaptation. Results from cross‐infections indicated that some parasite lineages seemed to be locally adapted to their sympatric (home) hosts in which they achieved higher infection and survival rates than in allopatric (away) amphipods. However, local, intrinsic host and parasite characteristics (host behavioural or immunological resistance to infections, parasite infectivity or growth rate) also influenced patterns of host–parasite interactions. For example, overall host vulnerability to C. parvum varied between populations, regardless of parasite origin (local vs. foreign), potentially swamping apparent local co‐adaptation effects. Furthermore, local adaptation effects seemed trait specific; different components of parasite fitness (infection and survival rates, growth) responded differently to cross‐infections. Overall, data show that genetic differentiation is not inevitably coupled with local adaptation, and that the latter must be interpreted with caution in a multi‐trait context.     

PARASITE CO‐TRANSMISSION AND THE EVOLUTIONARY EPIDEMIOLOGY OF VIRULENCE

Hosts are often co‐infected by several parasite genotypes of the same species or even by different species and this is known to affect virulence evolution. However, epidemiological models typically assume that only one of the co‐infecting strains can be transmitted at the same time, which is often at odds with the observed biology. Here, I study the effect of co‐transmission on virulence evolution in a case where parasites compete for host resources. For co‐infections by strains of the same species, increased co‐transmission selects for less virulent strains. This is because co‐transmission aligns the interests of co‐infecting strains, thus decreasing the selective pressure for increased within‐host competitiveness. For co‐infection caused by different parasite species, the evolutionary outcome depends on the respective virulence of the two parasite species. Finally, I investigate asymmetric scenarios, for example that of plant viruses that require “helper” molecules produced by viruses from another species to be transmitted. These results show that even if parasite strains compete for host resources, the prevalence of co‐infections can be a poor predictor of virulence evolution.     

Mites as biological tags of their hosts

Movements and spatial distribution of host populations are expected to shape the genetic structure of their parasite populations. Comparing the genetic patterns of both interacting species may improve our understanding of their evolutionary history. Moreover, genetic analyses of parasites with horizontal transmission may serve as indicators of historical events or current demographic processes that are not apparent in the genetic signature of their hosts. Here, we compared mitochondrial variation in populations of the ectoparasitic mite Spinturnix myoti with the genetic pattern of its host, the Maghrebian bat Myotis punicus in North Africa and in the islands of Corsica and Sardinia. Mite mitochondrial differentiation among populations was correlated with both host mitochondrial and nuclear differentiation, suggesting spatial co‐differentiation of the lineages of the two interacting species. Therefore our results suggest that parasite dispersal is exclusively mediated by host movements, with open water between landmasses as a main barrier for host and parasite dispersal. Surprisingly the unique presence of a continental European mite lineage in Corsica was inconsistent with host phylogeographical history and strongly suggests the former presence of European mouse‐eared bats on this island. Parasites may thus act as biological tags to reveal the presence of their now locally extinct host.     

Host phenology regulates parasite–host demographic cycles and eco‐evolutionary feedbacks

Parasite–host interactions can drive periodic population dynamics when parasites overexploit host populations. The timing of host seasonal activity, or host phenology, determines the frequency and demographic impact of parasite–host interactions, which may govern whether parasites sufficiently overexploit hosts to drive population cycles. We describe a mathematical model of a monocyclic, obligate‐killer parasite system with seasonal host activity to investigate the consequences of host phenology on host–parasite dynamics. The results suggest that parasites can reach the densities necessary to destabilize host dynamics and drive cycling as they adapt, but only in some phenological scenarios such as environments with short seasons and synchronous host emergence. Furthermore, only parasite lineages that are sufficiently adapted to phenological scenarios with short seasons and synchronous host emergence can achieve the densities necessary to overexploit hosts and produce population cycles. Host‐parasite cycles also generate an eco‐evolutionary feedback that slows parasite adaptation to the phenological environment as rare advantageous phenotypes can be driven extinct due to a population bottleneck depending on when they are introduced in the cycle. The results demonstrate that seasonal environments can drive population cycling in a restricted set of phenological patterns and provide further evidence that the rate of adaptive evolution depends on underlying ecological dynamics.     

The impact of host genetic diversity on virus evolution and emergence

Accumulating evidence indicates that biodiversity has an important impact on parasite evolution and emergence. The vast majority of studies in this area have only considered the diversity of species within an environment as an overall measure of biodiversity, overlooking the role of genetic diversity within a particular host species. Although theoretical models propose that host genetic diversity in part shapes that of the infecting parasite population, and hence modulates the risk of parasite emergence, this effect has seldom been tested empirically. Using Rabies virus (RABV) as a model parasite, we provide evidence that greater host genetic diversity increases both parasite genetic diversity and the likelihood of a host being a donor in RABV cross‐species transmission events. We conclude that host genetic diversity may be an important determinant of parasite evolution and emergence.     

Evolutionary transition to a semelparous life history in the socially parasitic ant Acromyrmex insinuator

The recently discovered social parasite Acromyrmex insinuator ( 25 ) exploits colonies of the leafcutter ant A. echinatior. We document that A. insinuator represents a rare early stage in the evolution of social parasitism, because a worker caste is still partially present and mating phenology has remained at least partially similar to that of the host. A. insinuator is tolerant of host queens, and sexual offspring produced in parasitized colonies can be either exclusively A. insinuator or a mix of A. insinuator and A. echinatior. The remarkably high abundance of A. insinuator in nests of the investigated Panamanian host population and the fact that A. insinuator colonies readily reproduce under laboratory conditions allowed us to test evolutionary predictions on reproductive life history evolution that are not possible in most other socially parasitic ants. We show that (1) A. insinuator has a semelparous ‘big bang’ reproductive life history which exploits host colonies without leaving reserves for survival; (2) social parasite sexuals are significantly smaller than A. echinatior host sexuals, but still large compared to host workers, confirming an evolutionary scenario of gradual size reduction and loss of the worker caste after transition towards a socially parasitic life history; (3) major changes in the life history of ants can evolve relatively quickly compared to adaptations in morphology, caste differentiation and mating phenology.     

Experimental evolution with a multicellular host causes diversification within and between microbial parasite populations—Differences in emerging phenotypes of two different parasite strains

Host‐parasite coevolution is predicted to have complex evolutionary consequences, potentially leading to the emergence of genetic and phenotypic diversity for both antagonists. However, little is known about variation in phenotypic responses to coevolution between different parasite strains exposed to the same experimental conditions. We infected Caenorhabditis elegans with one of two strains of Bacillus thuringiensis and either allowed the host and the parasite to experimentally coevolve (coevolution treatment) or allowed only the parasite to adapt to the host (one‐sided parasite adaptation). By isolating single parasite clones from evolved populations, we found phenotypic diversification of the ancestral strain into distinct clones, which varied in virulence toward ancestral hosts and competitive ability against other parasite genotypes. Parasite phenotypes differed remarkably not only between the two strains, but also between and within different replicate populations, indicating diversification of the clonal population caused by selection. This study highlights that the evolutionary selection pressure mediated by a multicellular host causes phenotypic diversification, but not necessarily with the same phenotypic outcome for different parasite strains.     

Biogeography of parasitism in freshwater fish: spatial patterns in hot spots of infection

Contrary to species occurrence, little is known about the determinants of spatial patterns of intraspecific variation in abundance, particularly for parasitic organisms. In this study, we provide a multi‐faceted overview of spatial patterns in parasite abundance and examine several potential underlying processes. We first tested for a latitudinal gradient in local abundance of the regionally most common parasite species and whether these species achieve higher abundances at the same localities (shared hot spots of infection). Secondly, we tested whether intraspecific similarity in local abundance between sites follows a spatial distance decay pattern or is better explained by variation in extrinsic biotic and abiotic factors between localities related to local parasite transmission success. We examined the infection landscape of a model fish host system (common and upland bullies, genus Gobiomorphus: Eleotridae) across its entire distributional range. We applied general linear models to test the effect of latitude on each species local abundance independently, including the abundance of each co‐infecting species as another predictor. We computed multiple regressions on distance matrices among localities based on abundance of each of the four most common trematode species, as well as for geographic distance, biotic and abiotic distinctness of the localities. Our results showed that the most widely distributed parasites of bullies also achieve the highest mean local abundances, following the abundance – occupancy relationship. Variation in local abundance of any focal parasite species was independent of latitude, the abundance of co‐occurring species and spatial distance or disparity in biotic attributes between localities. For only one parasite species, similarity of abundance between sites covaried with the extent of abiotic differences between sites. The lack of association between hot spots of infection for co‐occurring species reinforces the geographic mosaic scenario in which hosts and parasites coevolve by suggesting non‐deterministic, species‐specific variation in parasite abundance across space.     

Selection for outbreeding in Varroa parasitising resistant honey bee (Apis mellifera) colonies

Parasitism is expected to select for counter‐adaptations in the host: driving a coevolutionary arms race. However, human interference between honey bees (Apis mellifera) and Varroa mites removes the effect of natural selection and restricts the evolution of host counter‐adaptations. With full‐sibling mating common among Varroa, this can rapidly select for virulent, highly inbred, Varroa populations. We investigated how the evolution of host resistance could affect the infesting population of Varroa mites. We screened a Varroa‐resistant honey bee population near Toulouse, France, for a Varroa resistance trait: the inhibition of Varroa's reproduction in drone pupae. We then genotyped Varroa which had co‐infested a cell using microsatellites. Across all resistant honey bee colonies, Varroa's reproductive success was significantly higher in co‐infested cells but the distribution of Varroa between singly and multiply infested cells was not different from random. While there was a trend for increased reproductive success when Varroa of differing haplotypes co‐infested a cell, this was not significant. This suggests local mate competition, through the presence of another Varroa foundress in a pupal cell, may be enough to help Varroa overcome host resistance traits; with a critical mass of infesting Varroa overwhelming host resistance. However, the fitness trade‐offs associated with preferentially co‐infesting cells may be too high for Varroa to evolve a mechanism to identify already‐infested cells. The increased reproductive success of Varroa when co‐infesting resistant pupal cells may act as a release valve on the selective pressure for the evolution of counter resistance traits: helping to maintain a stable host–parasite relationship.     

Parasite evolution and extinctions

We examine the evolution of diseases that show the frequency‐dependent transmission process that is commonly applied to sexually and vector‐transmitted infections. As is commonly found, the basic reproductive ratio (R₀) of the parasite is maximized by evolution. This has important implications, as it implies that for a wide range of circumstances diseases that show frequency‐dependent transmission may be selected to evolve towards driving their hosts to extinction. This contrasts with the results obtained in spatially explicit models where although parasite‐driven host extinction may occur, it is unlikely to evolve. We further show that an evolutionary constraint between transmission and virulence is required for evolution to lead to an endemic coexistence of both the host and the disease. Furthermore, this constraint needs to be saturating, such that transmission is ‘bought’ at an increasing cost in terms of virulence, to avoid evolution to extinction.     

Escaping the matrix: a new algorithm for phylogenetic comparative studies of co-evolution

An algorithm for generating host cladograms from parasite‐host cladograms derived from parasite phylogenies, Phylogenetic Analysis for Comparing Trees (PACT), is described. PACT satisfies Assumption 0, that all the information in each parasite‐host cladogram must be used in a co‐evolutionary analysis, and that the host relationships depicted in the final host cladogram must be logically consistent with the phylogenetic relationships depicted in every part of every parasite‐host cladogram used to construct the host cladogram. It accounts for cases of speciation by host switching and expansion of host range, and reticulated host relationships, in addition to co‐speciation, sympatric speciation, and extinction in all input parasite‐host cladograms, and does so without a priori weighting schemes and without a posteriori manipulation of the data.     

Host–parasite interactions and vectors in the barn swallow in relation to climate change

Recent climate change has affected the phenology of numerous species, and such differential changes may affect host–parasite interactions. Using information on vectors (louseflies, mosquitoes, blackflies) and parasites (tropical fowl mite Ornithonyssus bursa, the lousefly Ornithomyia avicularia, a chewing louse Brueelia sp., two species of feather mites Trouessartia crucifera and Trouessartia appendiculata, and two species of blood parasites Leucozytozoon whitworthi and Haemoproteus prognei) of the barn swallow Hirundo rustica collected during 1971–2008, I analyzed temporal changes in emergence and abundance, relationships with climatic conditions, and changes in the fitness impact of parasites on their hosts. Temperature and rainfall during the summer breeding season of the host increased during the study. The intensity of infestation by mites decreased, but increased for the lousefly during 1982–2008. The prevalence of two species of blood parasites increased during 1988–2008. The timing of first mass emergence of mosquitoes and blackflies advanced. These temporal changes in phenology and abundance of parasites and vectors could be linked to changes in temperature, but less so to changes in precipitation. Parasites had fitness consequences for hosts because intensity of the mite and the chewing louse was significantly associated with delayed breeding of the host, while a greater abundance of feather mites was associated with earlier breeding. Reproductive success of the host decreased with increasing abundance of the chewing louse. The temporal decrease in mite abundance was associated with advanced breeding of the host, while the increase in abundance of the lousefly was associated with earlier breeding. Virulence by the tropical fowl mite decreased with increasing temperature, independent of confounding factors. These findings suggest that climate change affects parasite species differently, hence altering the composition of the parasite community, and that climate change causes changes in the virulence of parasites. Because the changing phenology of different species of parasites had both positive and negative effects on their hosts, and because the abundance of some parasites increased, while that of other decreased, there was no consistent temporal change in host fitness during 1971–2008.     

Species and sex biases in ectoparasitism of dragonflies by mites

An important problem in understanding the evolution of parasite host range is determining the extent to which parasite fitness varies among host species and the factors affecting that fitness variation. We present a detailed investigation on the patterns of host use and successful parasitism of two dragonfly species by the ectoparasitic water mite, Limnochares americana Lundblad. In our field surveys, we found both species biases and sex biases in parasitism by mites, which appear explained by differences in exposure. Differential habitat use by dragonflies helped explain male biases in parasitism in both host species, but was not useful in explaining species biases in parasitism. Species biases in parasitism may be explained by more subtle variation in habitat use not explored in this study, or perhaps by differences in timing of emergence, as we found for the two dragonfly species. Despite species differences in parasitism in nature, we found that mites attached equally successfully to both dragonfly species during experimental infestations. However, mites failed to engorge more often on the dragonfly species less often used as a host in nature. This host species also was more likely to have dead mites in natural infestations as compared to the other host species, which was more often and more heavily parasitized. Our results are consistent with previous research suggesting parasites are less successful on less often used hosts. Such research has implications for understanding determinants of host range for animal parasites.     

Migration highways and migration barriers created by host–parasite interactions

Co‐evolving parasites may play a key role in host migration and population structure. Using co‐evolving bacteria and viruses, we test general hypotheses as to how co‐evolving parasites affect the success of passive host migration between habitats that can support different intensities of host–parasite interactions. First, we show that parasites aid migration from areas of intense to weak co‐evolutionary interactions and impede migration in the opposite direction, as a result of intraspecific apparent competition mediated via parasites. Second, when habitats show qualitative difference such that some environments support parasite persistence while others do not, different population regulation forces (either parasitism or competitive exclusion) will reduce the success of migration in both directions. Our study shows that co‐evolution with parasites can predictably homogenises or isolates host populations, depending on heterogeneity of abiotic conditions, with the second scenario constituting a novel type of ‘isolation by adaptation’.     

EVALUATING PATTERNS OF CONVERGENT EVOLUTION AND TRANS‐SPECIES POLYMORPHISM AT MHC IMMUNOGENES IN TWO SYMPATRIC STICKLEBACK SPECIES

The immunologically important major histocompatibility complex (MHC) harbors some of the most polymorphic genes in vertebrates. These genes presumably evolve under parasite‐mediated selection and frequently show inconsistent allelic genealogies, where some alleles are more similar between species than within species. This phenomenon is thought to arise either from convergent evolution under parallel selection or from the preservation of ancient allelic lineages beyond speciation events (trans‐species polymorphism, TSP). Here, we examine natural populations of two sympatric stickleback species (Gasterosteus aculeatus and Pungitius pungitius) to investigate the contribution of these two mechanisms to the evolution of inconsistent allelic genealogies at the MHC. Overlapping parasite taxa between the two host species in three different habitats suggest contemporary parallel selection on the MHC genes. Accordingly, we detected a lack of species‐specific phylogenetic clustering in the immunologically relevant antigen‐binding residues of the MHC IIB genes which contrasted with the rest of the coding and noncoding sequence. However, clustering was not habitat‐specific and a codon‐usage analysis revealed patterns of similarity by descent. In this light, common descent via TSP, in combination with intraspecies gene conversion, rather than convergent evolution is the more strongly supported scenario for the inconsistent genealogy at the MHC.     

Climate,host phylogeny and the connectivity of host communities govern regional parasite assembly

Aim

Identifying barriers that govern parasite community assembly and parasite invasion risk is critical to understand how shifting host ranges impact disease emergence. We studied regional variation in the phylogenetic compositions of bird species and their blood parasites (Plasmodium and Haemoproteus spp.) to identify barriers that shape parasite community assembly.

Location

Australasia and Oceania.

Methods

We used a data set of parasite infections from >10,000 host individuals sampled across 29 bioregions. Hierarchical models and matrix regressions were used to assess the relative influences of interspecies (host community connectivity and local phylogenetic distinctiveness), climate and geographic barriers on parasite local distinctiveness and composition.

Results

Parasites were more locally distinct (co‐occurred with distantly related parasites) when infecting locally distinct hosts, but less distinct (co‐occurred with closely related parasites) in areas with increased host diversity and community connectivity (a proxy for parasite dispersal potential). Turnover and the phylogenetic symmetry of parasite communities were jointly driven by host turnover, climate similarity and geographic distance.

Main conclusions

Interspecies barriers linked to host phylogeny and dispersal shape parasite assembly, perhaps by limiting parasite establishment or local diversification. Infecting hosts that co‐occur with few related species decreases a parasite's likelihood of encountering related competitors, perhaps increasing invasion potential but decreasing diversification opportunity. While climate partially constrains parasite distributions, future host range expansions that spread distinct parasites and diminish barriers to host shifting will likely be key drivers of parasite invasions.     

Frequency-dependent host selection by parasitic mites: a model and a case study

Previous studies on frequency-dependent food selection (changing food preferences in response to changes in relative food abundance) have focused on predators and parasitoids. These organisms utilize several victims during their lifetime. We introduce the case of parasites which, having accepted a host, do not change it. We propose two alternative models to explain the biased occurrence of parasites on different host types: (1) through the option of rejecting less-preferred hosts prior to accepting one of them; (2) by differential parasite survival on different host types. These models predict that host rejection, but not differential survival, can create frequency-dependent parasitism (FDP). Unlike previously described factors responsible for frequency dependence of food selection, which act through changing the foraging behaviour of individual predators or parasitoids, FDP involves no adjustment of parasite foraging strategy according to previous feeding experience. The mite Hemisarcoptes coccophagus is an obligate parasite of armoured scale insects (Homptera: Diaspididae). Our field data show that H. coccophagus is found more frequently on ovipositing than on young host females. Our model, combining the effects of host rejection and differential survival, is used to estimate the relative contribution of these factors to parasite biased occurrence on different hosts. The contribution of differential survival was dominant in H. coccophagus, and overode any effect of host rejection. Nevertheless, our prediction that FDP may be found in parasites is supported by literature data about a parasitic water mite.     

Host‐specific variation in off‐host performance of a temperate ectoparasite

Antagonistic host–parasite interactions are rarely considered from an ecological perspective of the parasite. We used a blood‐feeding ectoparasite of boreal cervids, the deer ked (Lipoptena cervi L., Hippoboscidae), to study host‐dependent variation in a parasite's ability to cope with an abiotic environment during the free‐living stage(s) in two allopatric Fennoscandian populations. We found that a strongly host‐specific deer ked population in eastern Fennoscandia, exploiting only moose (Alces alces), produced the largest offspring that were the most cold‐tolerant and emerged the earliest as adults, when compared with the western Fennoscandian population that exploited two hosts efficiently. Within the western population, however, offspring produced on roe deer (Capreolus capreolus) were significantly larger, more cold‐tolerant, and had higher survival than those produced on moose in the same area. We discuss potential causes for both host‐specific and geographical differences in off‐host performance: (1) maternal host directly affects the offspring survival prospects; (2) divergent co‐evolution with local main host(s) has shaped the parasite's life history; and/or (3) off‐host performance is shaped by adaptation to the local abiotic environment. In conclusion, this study increases our understanding of the evolution of host–parasite interactions by demonstrating how geographical differences in host exploitation may result in differences in survival prospects outside the host.