Parasites promote host gene flow in a metapopulation

Near chromosome-level genome assembly of the microsporidium Hamiltosporidium tvaerminnensis

Microsporidia are intracellular parasitic fungi whose genomes rank among the smallest of all known eukaryotes. A number of outstanding questions remain concerning the evolution of their large-scale variation in genome architecture, responsible for genome size variation of more than an order of magnitude. This genome report presents the first near-chromosomal assembly of a large-genome microsporidium, Hamiltosporidium tvaerminnensis. Combined Oxford Nanopore, Pacific Biosciences (PacBio), and Illumina sequencing led to a genome assembly of 17 contigs, 11 of which represent complete chromosomes. Our assembly is 21.64 Mb in length, has an N50 of 1.44 Mb, and consists of 39.56% interspersed repeats. We introduce a novel approach in microsporidia, PacBio Iso-Seq, as part of a larger annotation pipeline for obtaining high-quality annotations of 3,573 protein-coding genes. Based on direct evidence from the full-length Iso-Seq transcripts, we present evidence for alternative polyadenylation and variation in splicing efficiency, which are potential regulation mechanisms for gene expression in microsporidia. The generated high-quality genome assembly is a necessary resource for comparative genomics that will help elucidate the evolution of genome architecture in response to intracellular parasitism.

Parasite-mediated selection in a natural metapopulation of Daphnia magna

Parasite-mediated selection varying across time and space in metapopulations is expected to result in host local adaptation and the maintenance of genetic diversity in disease-related traits. However, nonadaptive processes like migration and extinction-(re)colonization dynamics might interfere with adaptive evolution. Understanding how adaptive and nonadaptive processes interact to shape genetic variability in life-history and disease-related traits can provide important insights into their evolution in subdivided populations. Here we investigate signatures of spatially fluctuating, parasite-mediated selection in a natural metapopulation of Daphnia magna. Host genotypes from infected and uninfected populations were genotyped at microsatellite markers, and phenotyped for life-history and disease traits in common garden experiments. Combining phenotypic and genotypic data a Q_ST -F_ST -like analysis was conducted to test for signatures of parasite mediated selection. We observed high variation within and among populations for phenotypic traits, but neither an indication of host local adaptation nor a cost of resistance. Infected populations have a higher gene diversity (Hs) than uninfected populations and Hs is strongly positively correlated with fitness. These results suggest a strong parasite effect on reducing population level inbreeding. We discuss how stochastic processes related to frequent extinction-(re)colonization dynamics as well as host and parasite migration impede the evolution of resistance in the infected populations. We suggest that the genetic and phenotypic patterns of variation are a product of dynamic changes in the host gene pool caused by the interaction of colonization bottlenecks, inbreeding, immigration, hybrid vigor, rare host genotype advantage and parasitism. Our study highlights the effect of the parasite in ameliorating the negative fitness consequences caused by the high drift load in this metapopulation.

Metapopulations revisited: the area-dependence of dispersal matters

The metapopulation concept initiated a paradigm shift in ecology and conservation biology, recognizing the eminent role of dispersal and colonization as fundamental processes contributing to species' long-term persistence. Early models made ad hoc assumptions about a positive area dependency of dispersal (i.e., total number of emigrants), which persisted in the theoretical literature; however, numerous empirical examples of negative area dependencies of dispersal have been reported. Here, we first give a qualitative overview for different area dependencies of dispersal in empirical systems. Then, using a spatially realistic Levins model, we show that extending assumptions on the area dependence of dispersal (ADD) to include all empirically supported parameter space, specifically also negative ADD, alters predictions on several conservation-relevant patterns. Importantly, we find that small patches could be of similar importance as large ones if dispersal decreases inversely with patch area, a result contrasting with previous findings based on a positive ADD. This leads to context-dependent strategies to preserve metapopulations. If dispersal is positively correlated with patch area, efforts should be devoted to preserving large patches and the total habitat area. If dispersal is negatively correlated with patch area, the most efficient strategy is to preserve a high number of patches, including small ones. Our results have direct implications for management decisions in the context of destruction, deterioration, and protection of habitat patches.

The integration of climate change, spatial dynamics, and habitat fragmentation: A conceptual overview

A growing number of studies have looked at how climate change alters the effects of habitat fragmentation and degradation on both single and multiple species; some raise concern that biodiversity loss and its effects will be exacerbated. The published literature on spatial dynamics (such as dispersal and metapopulation dynamics), habitat fragmentation and climate change requires synthesis and a conceptual framework to simplify thinking. We propose a framework that integrates how climate change affects spatial population dynamics and the effects of habitat fragmentation in terms of: (i) habitat quality, quantity and distribution; (ii) habitat connectivity; and (iii) the dynamics of habitat itself. We use the framework to categorize existing autecological studies and investigate how each is affected by anthropogenic climate change. It is clear that a changing climate produces changes in the geographic distribution of climatic conditions, and the amount and quality of habitat. The most thorough published studies show how such changes impact metapopulation persistence, source-sink dynamics, changes in species' geographic range and community composition. Climate-related changes in movement behavior and quantity, quality and distribution of habitat have also produced empirical changes in habitat connectivity for some species. An underexplored area is how habitat dynamics that are driven by climatic processes will affect species that live in dynamic habitats. We end our discussion by suggesting ways to improve current attempts to integrate climate change, spatial population dynamics and habitat fragmentation effects, and suggest distinct areas of study that might provide opportunities for more fully integrative work.

Genetic architecture of resistance in Daphnia hosts against two species of host-specific parasites

Understanding the genetic architecture of host resistance is key for understanding the evolution of host-parasite interactions. Evolutionary models often assume simple genetics based on few loci and strong epistasis. It is unknown, however, whether these assumptions apply to natural populations. Using a quantitative trait loci (QTL) approach, we explore the genetic architecture of resistance in the crustacean Daphnia magna to two of its natural parasites: the horizontally transmitted bacterium Pasteuria ramosa and the horizontally and vertically transmitted microsporidium Hamiltosporidium tvaerminnensis. These two systems have become models for studies on the evolution of host-parasite interactions. In the QTL panel used here, Daphnia's resistance to P. ramosa is controlled by a single major QTL (which explains 50% of the observed variation). Resistance to H. tvaerminnensis horizontal infections shows a signature of a quantitative trait based in multiple loci with weak epistatic interactions (together explaining 38% variation). Resistance to H. tvaerminnensis vertical infections, however, shows only one QTL (explaining 13.5% variance) that colocalizes with one of the QTLs for horizontal infections. QTLs for resistance to Pasteuria and Hamiltosporidium do not colocalize. We conclude that the genetics of resistance in D. magna are drastically different for these two parasites. Furthermore, we infer that based on these and earlier results, the mechanisms of coevolution differ strongly for the two host-parasite systems. Only the Pasteuria-Daphnia system is expected to follow the negative frequency-dependent selection (Red Queen) model. How coevolution works in the Hamiltosporidium-Daphnia system remains unclear.

Global warming will reshuffle the areas of high prevalence and richness of three genera of avian blood parasites

The importance of parasitism for host populations depends on local parasite richness and prevalence: usually host individuals face higher infection risk in areas where parasites are most diverse, and host dispersal to or from these areas may have fitness consequences. Knowing how parasites are and will be distributed in space and time (in a context of global change) is thus crucial from both an ecological and a biological conservation perspective. Nevertheless, most research articles focus just on elaborating models of parasite distribution instead of parasite diversity. We produced distribution models of the areas where haemosporidian parasites are currently highly diverse (both at community and at within-host levels) and prevalent among Iberian populations of a model passerine host: the blackcap Sylvia atricapilla; and how these areas are expected to vary according to three scenarios of climate change. On the basis of these models, we analysed whether variation among populations in parasite richness or prevalence are expected to remain the same or change in the future, thereby reshuffling the geographic mosaic of host-parasite interactions as we observe it today. Our models predict a rearrangement of areas of high prevalence and richness of parasites in the future, with Haemoproteus and Leucocytozoon parasites (today the most diverse genera in blackcaps) losing areas of high diversity and Plasmodium parasites (the most virulent ones) gaining them. Likewise, the prevalence of multiple infections and parasite infracommunity richness would be reduced. Importantly, differences among populations in the prevalence and richness of parasites are expected to decrease in the future, creating a more homogeneous parasitic landscape. This predicts an altered geographic mosaic of host-parasite relationships, which will modify the interaction arena in which parasite virulence evolves.

Transport distance of invertebrate environmental DNA in a natural river

Environmental DNA (eDNA) monitoring is a novel molecular technique to detect species in natural habitats. Many eDNA studies in aquatic systems have focused on lake or ponds, and/or on large vertebrate species, but applications to invertebrates in river systems are emerging. A challenge in applying eDNA monitoring in flowing waters is that a species' DNA can be transported downstream. Whether and how far eDNA can be detected due to downstream transport remains largely unknown. In this study we tested for downstream detection of eDNA for two invertebrate species, Daphnia longispina and Unio tumidus, which are lake dwelling species in our study area. The goal was to determine how far away from the source population in a lake their eDNA could be detected in an outflowing river. We sampled water from eleven river sites in regular intervals up to 12.3 km downstream of the lake, developed new eDNA probes for both species, and used a standard PCR and Sanger sequencing detection method to confirm presence of each species' eDNA in the river. We detected D. longispina at all locations and across two time points (July and October); whereas with U. tumidus, we observed a decreased detection rate and did not detect its eDNA after 9.1 km. We also observed a difference in detection for this species at different times of year. The observed movement of eDNA from the source amounting to nearly 10 km for these species indicates that the resolution of an eDNA sample can be large in river systems. Our results indicate that there may be species' specific transport distances for eDNA and demonstrate for the first time that invertebrate eDNA can persist over relatively large distances in a natural river system.

Single-nucleotide polymorphisms of two closely related microsporidian parasites suggest a clonal population expansion after the last glaciation

The mode of reproduction of microsporidian parasites has remained puzzling since many decades. It is generally accepted that microsporidia are capable of sexual reproduction, and that some species have switched to obligate asexuality, but such process had never been supported with population genetic evidence. We examine the mode of reproduction of Hamiltosporidium tvaerminnensis and Hamiltosporidium magnivora, two closely related microsporidian parasites of the widespread freshwater crustacean Daphnia magna, based on a set of 129 single-nucleotide polymorphisms distributed across 16 genes. We analyse 20 H. tvaerminnensis isolates from localities representative of the entire species' geographic distribution along the Skerry Island belt of the Baltic Sea. Five isolates of the sister species H. magnivora were used for comparison. We estimate the recombination rates in H. tvaerminnensis to be at least eight orders of magnitude lower than in H. magnivora and not significantly different from zero. This is corroborated by the higher divergence between H. tvaerminnensis alleles (including fixed heterozygosity), as compared to H. magnivora. Our study confirms that sexual recombination is present in microsporidia, that it can be lost, and that asexuals may become epidemic.

Converging seasonal prevalence dynamics in experimental epidemics

Background

Regular seasonal changes in prevalence of infectious diseases are often observed in nature, but the mechanisms are rarely understood. Empirical tests aiming at a better understanding of seasonal prevalence patterns are not feasible for most diseases and thus are widely lacking. Here, we set out to study experimentally the seasonal prevalence in an aquatic host-parasite system. The microsporidian parasite Hamiltosporidium tvärminnensis exhibits pronounced seasonality in natural rock pool populations of its host, Daphnia magna with a regular increase of prevalence during summer and a decrease during winter. An earlier study was, however, unable to test if different starting conditions (initial prevalence) influence the dynamics of the disease in the long term. Here, we aim at testing how the starting prevalence affects the regular prevalence changes over a 4-year period in experimental populations.

Results

In an outdoor experiment, populations were set up to include the extremes of the prevalence spectrum observed in natural populations: 5% initial prevalence mimicking a newly invading parasite, 100% mimicking a rock pool population founded by infected hosts only, and 50% prevalence which is commonly observed in natural populations in spring. The parasite exhibited similar prevalence changes in all treatments, but seasonal patterns in the 100% treatment differed significantly from those in the 5% and 50% treatments. Populations started with 5% and 50% prevalence exhibited strong and regular seasonality already in the first year. In contrast, the amplitude of changes in the 100% treatment was low throughout the experiment demonstrating the long-lasting effect of initial conditions on prevalence dynamics.

Conclusions

Our study shows that the time needed to approach the seasonal changes in prevalence depends strongly on the initial prevalence. Because individual D. magna populations in this rock pool metapopulation are mostly short lived, only few populations might ever reach a point where the initial conditions are not visible anymore.

Effects of connectivity and recurrent local disturbances on community structure and population density in experimental metacommunities

Metacommunity theory poses that the occurrence and abundance of species is a product of local factors, including disturbance, and regional factors, like dispersal among patches. While metacommunity ideas have been broadly tested there is relatively little work on metacommunities subject to disturbance. We focused on how localized disturbance and dispersal interact to determine species composition in metacommunities. Experiments conducted in simple two-patch habitats containing eight protozoa and rotifer species tested how dispersal altered community composition in both communities that were disturbed and communities that connected to refuge communities not subject to disturbance. While disturbance lowered population densities, in disturbed patches connected to undisturbed patches this was ameliorated by immigration. Furthermore, species with high dispersal abilities or growth rates showed the fastest post-disturbance recovery in presence of immigration. Connectivity helped to counteract the negative effect of disturbances on local populations, allowing mass-effect-driven dispersal of individuals from undisturbed to disturbed patches. In undisturbed patches, however, local population sizes were not significantly reduced by emigration. The absence of a cost of dispersal for undisturbed source populations is consistent with a lack of complex demography in our system, such as age- or sex-specific emigration. Our approach provides an improved way to separate components of population growth from organisms' movement in post-disturbance recovery of (meta)communities. Further studies are required in a variety of ecosystems to investigate the transient dynamics resulting from disturbance and dispersal.

The expression of virulence during double infections by different parasites with conflicting host exploitation and transmission strategies

In many natural populations, hosts are found to be infected by more than one parasite species. When these parasites have different host exploitation strategies and transmission modes, a conflict among them may arise. Such a conflict may reduce the success of both parasites, but could work to the benefit of the host. For example, the less-virulent parasite may protect the host against the more-virulent competitor. We examine this conflict using the waterflea Daphnia magna and two of its sympatric parasites: the blood-infecting bacterium Pasteuria ramosa that transmits horizontally and the intracellular microsporidium Octosporea bayeri that can concurrently transmit horizontally and vertically after infecting ovaries and fat tissues of the host. We quantified host and parasite fitness after exposing Daphnia to one or both parasites, both simultaneously and sequentially. Under conditions of strict horizontal transmission, Pasteuria competitively excluded Octosporea in both simultaneous and sequential double infections, regardless of the order of exposure. Host lifespan, host reproduction and parasite spore production in double infections resembled those of single infection by Pasteuria. When hosts became first vertically (transovarilly) infected with O. bayeri, Octosporea was able to withstand competition with P. ramosa to some degree, but both parasites produced less transmission stages than they did in single infections. At the same time, the host suffered from reduced fecundity and longevity. Our study demonstrates that even when competing parasite species utilize different host tissues to proliferate, double infections lead to the expression of higher virulence and ultimately may select for higher virulence. Furthermore, we found no evidence that the less-virulent and vertically transmitting O. bayeri protects its host against the highly virulent P. ramosa.

Cytological and molecular description of Hamiltosporidium tvaerminnensis gen. et sp. nov., a microsporidian parasite of Daphnia magna, and establishment of Hamiltosporidium magnivora comb. nov

We describe the new microsporidium Hamiltosporidium tvaerminnensis gen. et sp. nov. with an emphasis on its ultrastructural characteristics and phylogenetic position as inferred from the sequence data of SSU rDNA, alpha- and beta-tubulin. This parasite was previously identified as Octosporea bayeri Jírovec, 1936 and has become a model system to study the ecology, epidemiology, evolution and genomics of microsporidia - host interactions. Here, we present evidence that shows its differences from O. bayeri. Hamiltosporidium tvaerminnensis exclusively infects the adipose tissue, the ovaries and the hypodermis of Daphnia magna and is found only in host populations located in coastal rock pool populations in Finland and Sweden. Merogonial stages of H. tvaerminnensis have isolated nuclei; merozoites are formed by binary fission or by the cleaving of a plasmodium with a small number of nuclei. A sporogonial plasmodium with isolated nuclei yields 8 sporoblasts. Elongated spores are generated by the most finger-like plasmodia. The mature spores are polymorphic in shape and size. Most spores are pyriform (4·9–5·6×2·2–2·3 μm) and have their polar filament arranged in 12–13 coils. A second, elongated spore type (6·8–12·0×1·6–2·1 μm) is rod-shaped with blunt ends and measures 6·8–12·0×1·6–2·1 μm. The envelope of the sporophorous vesicle is thin and fragile, formed at the beginning of the sporogony. Cytological and molecular comparisons with Flabelliforma magnivora, a parasite infecting the same tissues in the same host species, reveal that these two species are very closely related, yet distinct. Moreover, both cytological and molecular data indicate that these species are quite distant from F. montana, the type species of the genus Flabelliforma. We therefore propose that F. magnivora also be placed in Hamiltosporidium gen. nov.

Desiccation of rock pool habitats and its influence on population persistence in a Daphnia metacommunity

Habitat instability has an important influence on species' occurrence and community composition. For freshwater arthropods that occur in ephemeral rock pools, the most drastic habitat instabilities are droughts and the intermittent availability of water. However, although the desiccation of a rock pool is detrimental for planktonic populations, it may also bring certain benefits: the exclusion of predators or parasites, for example, or the coexistence of otherwise competitively exclusive species. The commonness of drought resistant resting stages in many aquatic organisms shows the ecological significance of droughts. We measured daily evaporation in 50 rock pools inhabited by three Daphnia species D. magna, D. longispina and D. pulex over one summer. Daily evaporation and ultimately desiccation showed significantly seasonally influenced correlation with pool surface area, presence of vegetation, ambient temperature, wind and standardized evaporation measures. We used the estimates from this analysis to develop a simulation model to predict changes in the water level in 530 individual pools on a daily basis over a 25-year period. Eventually, hydroperiod lengths and desiccation events could be predicted for all of these rock pools. We independently confirmed the validity of this simulation by surveying desiccation events in the 530 rock pools over a whole season in 2006. In the same 530 rock pools, Daphnia communities had been recorded over the 25 years the simulation model considered. We correlated pool-specific occupation lengths of the three species with pool-specific measures of desiccation risk. Occupation lengths of all three Daphnia species were positively correlated with maximum hydroperiod length and negatively correlated with the number of desiccation events. Surprisingly, these effects were not species-specific.

Expression of parasite virulence at different host population densities under natural conditions

It has recently been suggested that the expression of parasite virulence depends on host population density, such that infected hosts have a higher sensitivity to density, and thus reach their carrying capacity earlier than uninfected hosts. In this scenario, parasite-induced reduction in fitness (i.e., virulence) increases with host density. We tested this hypothesis experimentally, using outdoor mesocosm populations of Daphnia magna infected by the microsporidian Octosporea bayeri. Contrary to the prediction, virulence was independent of host density. In a competition experiment with initial prevalence of 50%, O. bayeri reduced the competitive ability of infected Daphnia within the asexual growth phase independent of initial host population density. In an additional experiment we set up populations with 100% and 0% prevalence and followed their population dynamics over the whole season. Consistent with the competition experiment, we found no difference in population dynamics within the asexual growth phase of the host, suggesting that infected hosts are not more sensitive to density than uninfected hosts. The additional experiment, however, included more than the initial growth phase as did the competition experiment. Eventually, after 100 days, 100% infected populations assumed a reduced carrying capacity compared to uninfected populations. We identify and discuss three reasons for the discrepancy between our experiment and the predictions.

The influence of pool volume and summer desiccation on the production of the resting and dispersal stage in a Daphnia metapopulation

Dispersal is a key process in metapopulations, as migrants genetically connect populations and enable the colonization of empty habitat patches. Sub-populations may differ in their numerical contribution of migrants within a metapopulation. This has strong implications on evolutionary and ecological dynamics and has led to two different hypotheses about the Daphnia metapopulation studied here: the assessment by some authors is that sub-populations contribute equally to the production of migrants, while others have postulated long-lived core populations in large "mainland" habitat patches as the dominant source of migrants. We have studied the resting and dispersal stage (ephippium) in a natural Daphnia metapopulation and in mesocosm experiments, and tested for effects of habitat size and summer desiccation. We found that a 1,000-fold increase in rock pool volume resulted on average in only in a 2.8-fold increase in ephippium production. Mesocosm experiments confirmed these results: a 1,000-fold increase of the mesocosms' volume resulted in a 7.2-fold increase in ephippium production. Additionally, we showed that ephippium production did not depend on the initial population size. Thus, populations in small pools may contribute only marginal fewer potential migrants in the whole metapopulation than populations in large pools. In a second mesocosm experiment we found that summer desiccation, which is a typical occurrence in small pools, is not detrimental for the populations. Daphnia hatched out of ephippia that were produced earlier within the same season and built up viable populations again. The substantial production of ephippia by populations in small pools suggests that these populations might be important for both the dynamics and global stability of metapopulations.

Genetic diversity of Daphnia magna populations enhances resistance to parasites

The diversity-disease hypothesis states that decreased genetic diversity in host populations increases the incidence of diseases caused by pathogens (= monoculture effect) and eventually influences ecosystem functioning. The monoculture effect is well-known from crop studies and may be partially specific to the artificial situation in agriculture. The effect received little attention in animal populations of different diversities. Compared with plants, animals are mobile and exhibiting social interactions. We followed the spread of a microsporidian parasite in semi-natural outdoor Daphnia magna populations of low and high genetic diversity. We used randomly selected, naturally occurring host genotypes. Host populations of low diversity were initially monoclonal, while the host populations of high diversity started with 10 genotypes per replicate. We found that the parasite spread significantly better in host populations of low diversity compared with host populations of high diversity, independent of parasite diversity. The difference was visible over a 3-year period. Host genotypic diversity did not affect host population density. Our experiment demonstrated a monoculture effect in independently replicated semi-natural zooplankton populations, indicating that the monoculture effect may be relevant beyond agriculture.

Male-biased sex-ratio distortion caused by Octosporea bayeri, a vertically and horizontally-transmitted parasite of Daphnia magna

Female-biased sex-ratio distortion is often observed in hosts infected with vertically-transmitted microsporidian parasites. This bias is assumed to benefit the spread of the parasite, because male offspring usually do not transmit the parasite further. The present study reports on sex-ratio distortion in a host-parasite system with both horizontal and vertical parasite transmission: the microsporidium Octosporea bayeri and its host, the planktonic cladoceran Daphnia magna. In laboratory and field experiments, we found an overall higher proportion of male offspring in infected than in uninfected hosts. In young males, there was no parasite effect on sperm production, but, later in life, infected males produced significantly less sperm than uninfected controls. This shows that infected males are fertile. As males are unlikely to transmit the parasite vertically, an increase in male production could be advantageous to the host during phases of sexual reproduction, because infected mothers may obtain uninfected grandchildren through their sons. Life-table experiments showed that, overall, sons harboured more parasite spores than their sisters, although they reached a smaller body size and died earlier. Male production may thus be beneficial for the parasite when horizontal transmission has a large pay-off as males may contribute more effectively to parasite spread than females.

The genotype specific competitive ability does not correlate with infection in natural Daphnia magna populations

BACKGROUND

Different evolutionary hypotheses predict a correlation between the fitness of a genotype in the absence of infection and the likelihood to become infected. The cost of resistance hypothesis predicts that resistant genotypes pay a cost of being resistant and are less fit in the absence of parasites. The inbreeding-infection hypothesis predicts that the susceptible individuals are less fit due to inbreeding depression.

METHODS AND RESULTS

Here we tested if a host's natural infection status was associated with its fitness. First, we experimentally confirmed that cured but formerly infected Daphnia magna are genetically more susceptible to reinfections with Octosporea bayeri than naturally uninfected D. magna. We then collected from each of 22 populations both uninfected and infected D. magna genotypes. All were treated against parasites and kept in their asexual phase. We estimated their relative fitness in an experiment against a tester genotype and in another experiment in direct competition. Consistently, we found no difference in competitive abilities between uninfected and cured but formerly infected genotypes. This was the case both in the presence as well as in the absence of sympatric parasites during the competition trials.

CONCLUSIONS

Our data do not support the inbreeding-infection hypothesis. They also do not support a cost of resistance, however ignoring other parasite strains or parasite species. We suggest as a possible explanation for our results that resistance genes might segregate largely independently of other fitness associated genes in this system.