The ecoresponsive genome of Daphnia pulex

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.

Blowing in the wind: a field test of overland dispersal and colonization by aquatic invertebrates

Despite the importance of dispersal to ecology, accurate estimates of dispersal rates are often difficult to obtain, especially for organisms that rely on passive dispersal of propagules to colonize new sites. To investigate potential dispersal vectors and relative colonization rates of zooplankton, we conducted a field experiment in which we restricted potential dispersal vectors (insects, birds, amphibians) from transporting zooplankton to mesocosms. Twenty-six non-insect invertebrate taxa invaded our array during 2 years. Colonization rates of organisms varied considerably, with some species appearing several weeks after the experiment began and others appearing after a year. We observed no difference in colonization rates among treatments, suggesting that species were transported to our experiment primarily by wind or rain, rather than by animal vectors. The absence of an additional 13 zooplankton species common in ponds immediately adjacent to the array either occurred because of dispersal limitation or an inability to invade the existing communities. Ecologists generally assume that all zooplankton are rapidly dispersed hence the potential for dispersal limitation is generally ignored. Our results suggest that zooplankton vary in their dispersal and colonization ability. Hence, increased attention should be focused on the potential role of dispersal limitation and its importance for understanding the structure and function of aquatic communities.

Natural selection for grazer resistance to toxic cyanobacteria: evolution of phenotypic plasticity?

We studied the selection response of the freshwater grazing zooplankter, Daphnia galeata, to increased abundance of cyanobacteria in its environment. Cyanobacteria are a poor-quality and often toxic food. Distinct genotypes of D. galeata were hatched from diapausing eggs extracted from three time horizons in the sediments of Lake Constance, Europe, covering the period 1962 to 1997, a time of change in both the prevalence of planktonic cyanobacteria and levels of phosphorus pollution. We assessed whether the grazers evolved to become more resistant to dietary cyanobacteria by exposing genetically distinct clones to two diets, one composed only of the nutritious green alga, Scenedesmus obliquus (good food), and the other a mixture of S. obliquus and the toxic cyanobacterium Microcvstis aeruginosa (poor food). Genotype performance was measured as the specific rate of weight gain from neonate to maturity (gj). We evaluated evolutionary change in the Daphnia population using an analysis of reaction norms based on relative (log-transformed) changes in gj. Log(gj) is a measure of the proportional effect of dietary cyanobacteria on other fitness components of the Daphnia phenotype. For comparison, we also analyze absolute (i.e., nontransformed) changes in gj and discuss the interpretations of the two approaches. Statistical results using a general linear model demonstrate a significant effect of genotype (showing differences in gj among genotypes), a significant genotype x food-type interaction (showing differences in phenotypic plasticity among genotypes), and, in the case of log-transformed data, a significant sediment-genotype-age x food-type interaction. The latter shows that phenotypic plasticity evolved over the period studied. Two constraints act on response to selection in the D. galeata-Lake Constance system. First, gj on a diet containing poor food is highly correlated with gj on a diet of good food, thus evolving resistance also meant evolving an increase in gj on both diets. Second, because genotypes with a high gj also grow to a large adult body size, which in turn increases Daphnia vulnerability to fish predation, we suggest that selection only acted to favor genotypes possessing a high potential gj after cyanobacteria became prevalent. The presence of cyanobacteria depressed realized gj and led to animals of small adult body size even if their genotypes had the potential for high gj and large size. With realized gj reduced, genotypes with an inherently high value could be selected even in the presence of predatory fish. The joint action of selection by dietary cyanobacteria and vulnerability to fish predation provides an explanation for the observed evolution of resistance to poor food through reduced phenotypic plasticity.

Temporal variation, dormancy, and coexistence: a field test of the storage effect

Theoretical models suggest that overlapping generations, in combination with a temporally fluctuating environment, may allow the persistence of competitors that otherwise would not coexist. Despite extensive theoretical development, this "storage effect" hypothesis has received little empirical attention. Herein I present the first explicit mathematical analysis of the contribution of the storage effect to the dynamics of competing natural populations. In Oneida Lake, NY, data collected over the past 30 years show a striking negative correlation between the water-column densities of two species of suspension-feeding zooplankton, Daphnia galeata mendotae and Daphnia pulicaria. I have demonstrated competition between these two species and have shown that both possess long-lived eggs that establish overlapping generations. Moreover, recruitment to this long-lived stage varies annually, so that both daphnids have years in which they are favored (for recruitment) relative to their competitor. When the long-term population growth rates are calculated both with and without the effects of a variable environment, I show that D. galeata mendotae clearly cannot persist without the environmental variation and prolonged dormancy (i.e., storage effect) whereas D. pulicaria persists through consistently high per capita recruitment to the long-lived stage.

Eating yourself sick: transmission of disease as a function of foraging ecology

Species interactions may profoundly influence disease outbreaks. However, disease ecology has only begun to integrate interactions between hosts and their food resources (foraging ecology) despite that hosts often encounter their parasites while feeding. A zooplankton-fungal system illustrated this central connection between foraging and transmission. Using experiments that varied food density for Daphnia hosts, density of fungal spores and body size of Daphnia, we produced mechanistic yet general models for disease transmission rate based on broadly applicable components of feeding biology. Best performing models could explain why prevalence of infection declined at high food density and rose sharply as host size increased (a pattern echoed in nature). In comparison, the classic mass-action model for transmission performed quite poorly. These foraging-based models should broadly apply to systems in which hosts encounter parasites while eating, and they will catalyse future integration of the roles of Daphnia as grazer and host.

Acceptability of pre-exposure prophylaxis as an HIV prevention strategy: barriers and facilitators to pre-exposure prophylaxis uptake among at-risk Peruvian populations

This study examined pre-exposure prophylaxis (PrEP) acceptability among female sex workers, male-to-female transgendered persons and men who have sex with men in Lima, Peru. Focus groups explored social issues associated with PrEP acceptability and conjoint analysis assessed preferences among eight hypothetical PrEP scenarios with varying attribute profiles and their relative impact on acceptability. Conjoint analysis revealed that PrEP acceptability ranged from 19.8 to 82.5 out of a possible score of 100 across the eight hypothetical PrEP scenarios. Out-of-pocket cost had the greatest impact on PrEP acceptability (25.2, P < 0.001), followed by efficacy (21.4, P < 0.001) and potential side-effects (14.7, P < 0.001). Focus group data supported these findings, and also revealed that potential sexual risk disinhibition, stigma and discrimination associated with PrEP use, and mistrust of health-care professionals were also concerns. These issues will require careful attention when planning for PrEP roll-out.

Selective Predation and Productivity Jointly Drive Complex Behavior in Host‐Parasite Systems

Successful invasion of a parasite into a host population and resulting host-parasite dynamics can depend crucially on other members of a host's community such as predators. We do not fully understand how predation intensity and selectivity shape host-parasite dynamics because the interplay between predator density, predator foraging behavior, and ecosystem productivity remains incompletely explored. By modifying a standard susceptible-infected model, we show how productivity can modulate complex behavior induced by saturating and selective foraging behavior of predators in an otherwise stable host-parasite system. When predators strongly prefer parasitized hosts, the host-parasite system can oscillate, but predators can also create alternative stable states, Allee effects, and catastrophic extinction of parasites. In the latter three cases, parasites have difficulty invading and/or persisting in ecosystems. When predators are intermediately selective, these more complex behaviors become less important, but the host-parasite system can switch from stable to oscillating and then back to stable states along a gradient of predator control. Surprisingly, at higher productivity, predators that neutrally select or avoid parasitized hosts can catalyze extinction of both hosts and parasites. Thus, synergy between two enemies can end disastrously for the host. Such diverse outcomes underscore the crucial importance of the community and ecosystem context in which host-parasite interactions occur.

Quality matters: resource quality for hosts and the timing of epidemics

Epidemiologists increasingly realize that species interactions (e.g. selective predation) can determine when epidemics start and end. We hypothesize here that resource quality can also strongly influence disease dynamics: epidemics can be inhibited when resource quality for hosts is too poor and too good. In three lakes, resource quality for the zooplankton host (Daphnia dentifera) was poor when fungal epidemics (Metschnikowia bicuspidata) commenced and increased as epidemics waned. Experiments using variation in algal food showed that resource quality had conflicting effects on underlying epidemiology: high-quality food induced large production of infective propagules (spores) and high birth rate but also reduced transmission. A model then illustrated how these underlying correlations can inhibit the start of epidemics (when spore production/birth rate are too low) but also catalyse their end (when transmission becomes too low). This resource quality mechanism is likely to interface with other ones controlling disease dynamics and warrants closer evaluation.

Resource ecology of virulence in a planktonic host-parasite system: an explanation using dynamic energy budgets

Parasites steal resources that a host would otherwise direct toward its own growth and reproduction. We use this fundamental notion to explain resource-dependent virulence in a fungal parasite (Metschnikowia)-zooplankton host (Daphnia) system and in a variety of other disease systems with invertebrate hosts. In an experiment, well-fed hosts died faster and produced more parasites than did austerely fed ones. This resource-dependent variation in virulence and other experimental results (involving growth and reproduction rate/timing of hosts) readily emerged from a model based on dynamic energy budgets. This model follows energy flow through the host, from ingestion of food, to internal energy storage, to allocation toward growth and reproduction or to a parasite that consumes these reserves. Acting as a consumer, the parasite catalyzes its own extinction, persistence with an energetically compromised host, or death of the host. In this last case, more resources for the host inadvertently fuels faster parasite growth, thereby accelerating the demise of the host (although the opposite result arises with different resource kinetics of the parasite). Thus, this model can explain how resource supply drives variation in virulence. This ecological dependence of virulence likely rivals and/or interacts with genetic mechanisms that often garner more attention in the literature on disease.

Parasitic castration: a perspective from a model of dynamic energy budgets

Models of the evolution of virulence have typically focused on increased mortality, one of two negative effects that parasites can inflict on their host. Those that consider the other effect, fecundity reduction, can predict that parasites should completely sterilize their hosts. Although this prediction seems extreme, sterilization features prominently in a fascinating strategy, parasitic castration. Such castration can be accompanied by gigantism (unusually large growth of infected hosts), long infectious periods, and fecundity compensation (where, before heavy parasite burdens ensue, newly infected hosts reproduce earlier/more than they would if not infected). Using a model of dynamic energy budgets (DEB), we show how these results readily emerge, assuming that parasites consume energy reserves of the host. The simple, but mechanistic, DEB model follows energy flow though hosts and parasites, starting with ingestion, and continuing with storage of assimilated energy, and use of those reserves for growth and reproduction, as allocated by the host according to the "κ-rule". Using this model, we compare and contrast two strategies for parasites. "Consumers" only steal energy from their hosts, thereby indirectly altering allocation of energy to growth and reproduction, reducing fecundity, and enhancing mortality. "Castrators" steal energy but also directly modify the scheme by which hosts allocate reserve energy, shunting resources from reproduction to growth. Not surprisingly, the model predicts that this strategy should promote gigantism, but it also forecasts longer infectious periods and fecundity compensation. Thus, commonly observed characteristics of parasitic castration readily emerge from a mechanistic model of energy flow using a minimal number of assumptions. Finally, the DEB model for both "consumers" and "castrators" highlight that variation in resources supplied to hosts promotes variation in virulence in a given host-parasite system, holding all else equal. Such predictions highlight the potential importance of resource ecology for virulence in disease systems.

Friendly competition: evidence for a dilution effect among competitors in a planktonic host-parasite system

The "dilution effect" concept in disease ecology offers the intriguing possibility that clever manipulation of less competent hosts could reduce disease prevalence in populations of more competent hosts. The basic concept is straightforward: host species vary in suitability (competence) for parasites, and disease transmission decreases when there are more incompetent hosts interacting with vectors or removing free-living stages of a parasite. However, host species also often interact with each other in other ecological ways, e.g., as competitors for resources. The net result of these simultaneous, multiple interactions (disease dilution and resource competition) is challenging to predict. Nonetheless, we see the signature of both roles operating concurrently in a planktonic host-parasite system. We document pronounced spatiotemporal variation in the size of epidemics of a virulent fungus (Metschnikowia bicuspidata) in Midwestern U.S. lake populations of a dominant crustacean grazer (Daphnia dentifera). We show that some of this variation is captured by changes in structure of Daphnia assemblages. Lake-years with smaller epidemics were characterized by assemblages dominated by less suitable hosts ("diluters," D. pulicaria and D. retrocurva, whose suitabilties were determined in lab experiments and field surveys) at the start of epidemics. Furthermore, within a season, less suitable hosts increased as epidemics declined. These observations are consistent with a dilution effect. However, more detailed time series analysis (using multivariate autoregressive models) of three intensively sampled epidemics show the signature of a likely interaction between dilution and resource competition between these Daphnia species. The net outcome of this interaction likely promoted termination of these fungal outbreaks. Should this outcome always arise in "friendly competition" systems where diluting hosts compete with more competent hosts? The answers to this question lie at a frontier of disease ecology.

WARMER DOES NOT HAVE TO MEAN SICKER: TEMPERATURE AND PREDATORS CAN JOINTLY DRIVE TIMING OF EPIDEMICS

Ecologists and epidemiologists worry that global warming will increase disease prevalence. These fears arise because several direct and indirect mechanisms link warming to disease, and because parasite outbreaks are increasing in many taxa. However, this outcome is not a foregone conclusion, as physiological and community-interaction-based mechanisms may inhibit epidemics at warmer temperatures. Here, we explore this thermal-community-ecology-based mechanism, centering on fish predators that selectively prey upon Daphnia infected with a fungal parasite. We used an interplay between a simple model built around this system's biology and laboratory experiments designed to parameterize the model. Through this data-model interaction, we found that a given density of predators can inhibit epidemics as temperatures rise when thermal physiology of the predator scales more steeply than that of the host. This case is met in our fish-Daphnia-fungus system. Furthermore, the combination of steeply scaling parasite physiology and predation-induced mortality can inhibit epidemics at lower temperatures. This effect may terminate fungal epidemics of Daphnia as lakes cool in autumn. Thus, predation and physiology could constrain epidemics to intermediate temperatures (a pattern that we see in our system). More generally, these results accentuate the possibility that warmer temperatures might actually enhance predator control of parasites.

Estimating the number of men who have sex with men in low and middle income countries

OBJECTIVES

To collect and analyse published and unpublished surveillance and research data on the prevalence of same sex sexual activity among male adults (including male-to-female transgenders and sex workers) in low and middle income countries.

METHODS

Key indicators were operationalised (ever sex with a man, sex with a man last year, high risk sex last year (as defined by unprotected anal sex or commercial sex)) and a database was designed for data collection. Searches were conducted (PubMed, databases (US Census Bureau, World Bank, conferences)) and regional informants helped. Reference reports were used to assess the methodology and quality of information in each record. The best data available per region were identified and indicator estimates were used to propose regional range estimates.

RESULTS

Of 561 studies on male sexual behaviour and/or MSM population characteristics, 67 addressed prevalence of sex between men, with diverse numbers per region and virtual unavailability in sub-Saharan Africa, Middle East/North Africa, and the English speaking Caribbean. Overall, data on lifetime prevalence of sex with men (among males) yielded figures of 3-5% for East Asia, 6-12% for South and South East Asia, 6-15% for Eastern Europe, and 6-20% for Latin America. Last year figures were approximately half of lifetime figures, and prevalence of high risk sex among MSM last year was approximately 40-60% in all regions except South Asia, where it is 70-90%.

CONCLUSIONS

Data available on the prevalence of male same sex sexual activity across regions are scarce (non-existent in some areas), with validity and comparability problems. In South and South East Asia, Eastern Europe, and Latin America, a lifetime prevalence of 6-20% was estimated, with smaller figures in East Asia. A cross cultural analysis of terminology and practices is needed, as is continued work on epidemiological and social analysis of male-male sexual practices in societies across regions.

Variation in resource acquisition and use among host clones creates key epidemiological trade‐offs

Parasites can certainly harm host fitness. Given such virulence, hosts should evolve strategies to resist or tolerate infection. But what governs those strategies and the costs that they incur? This study illustrates how a fecundity‐susceptibility trade‐off among clonally reared genotypes of a zooplankton (Daphnia dentifera) infected by a fungal parasite (Metschnikowia) arises due to variation in resource acquisition and use by hosts. To make these connections, we used lab experiments and theoretical models that link feeding with susceptibility, energetics, and fecundity of hosts. These feeding‐based mechanisms also produced a fecundity‐survivorship trade‐off. Meanwhile, a parasite spore yield–fecundity trade‐off arose from variation in juvenile growth rate among host clones (another index of resource use), a result that was readily anticipated and explained by the models. Thus, several key epidemiological trade‐offs stem from variation in resource acquisition and use among clones. This connection should catalyze the creation of new theory that integrates resource‐ and gene‐based responses of hosts to disease.

Segregating variation in the transcriptome: cis regulation and additivity of effects

Properties of genes underlying variation in complex traits are largely unknown, especially for variation that segregates within populations. Here, we evaluate allelic effects, cis and trans regulation, and dominance patterns of transcripts that are genetically variable in a natural population of Drosophila melanogaster. Our results indicate that genetic variation due to the third chromosome causes mainly additive and nearly additive effects on gene expression, that cis and trans effects on gene expression are numerically about equal, and that cis effects account for more genetic variation than do trans effects. We also evaluated patterns of variation in different functional categories and determined that genes involved in metabolic processes are overrepresented among variable transcripts, but those involved in development, transcription regulation, and signal transduction are underrepresented. However, transcripts for proteins known to be involved in protein-protein interactions are proportionally represented among variable transcripts.

Success, failure and ambiguity of the dilution effect among competitors

It remains challenging to predict variation in the magnitude of disease outbreaks. The dilution effect seeks to explain this variation by linking multiple host species to disease transmission. It predicts that disease risk increases for a focal host when host species diversity declines. However, when an increase in species diversity does not reduce disease, we are often unable to diagnose why. Here, we increase mechanistic and predictive clarity of the dilution effect with a general trait-based model of disease transmission in multi-host communities. Then, we parameterise and empirically test our model with a multi-generational case study of planktonic disease. The model-experiment combination shows that hosts that vary in competitive ability (R*) and potential to spread disease (R0 ) can produce three qualitatively disparate outcomes of dilution on disease: the dilution effect can succeed, fail, or be ambiguous/irrelevant.

Parasite-mediated disruptive selection in a natural Daphnia population

Background

A mismatch has emerged between models and data of host-parasite evolution. Theory readily predicts that parasites can promote host diversity through mechanisms such as disruptive selection. Yet, despite these predictions, empirical evidence for parasite-mediated increases in host diversity remains surprisingly scant.

Results

Here, we document parasite-mediated disruptive selection on a natural Daphnia population during a parasite epidemic. The mean susceptibility of clones collected from the population before and after the epidemic did not differ, but clonal variance and broad-sense heritability of post-epidemic clones were significantly greater, indicating disruptive selection and rapid evolution. A maximum likelihood method that we developed for detecting selection on natural populations also suggests disruptive selection during the epidemic: the distribution of susceptibilities in the population shifted from unimodal prior to the epidemic to bimodal after the epidemic. Interestingly, this same bimodal distribution was retained after a generation of sexual reproduction.

Conclusion

These results provide rare empirical support for parasite-driven increases in host genetic diversity, and suggest that this increase can occur rapidly.

Solar radiation decreases parasitism in Daphnia

Climate change and variation in atmospheric ozone are influencing the intensity of ultraviolet radiation (UVR) reaching ecosystems. Changing UVR regimes, in turn, may alter epidemics of infectious disease. This possibility hinges on the sensitivity of epidemiologically relevant traits of host and parasite to UVR. We address this issue using a planktonic system (a zooplankton host, Daphnia dentifera, and its virulent fungal parasite, Metschnikowia bicuspidata). Controlled laboratory experiments, coupled with in situ field incubations of spores, revealed that quite low levels of UVR (as well as longer wavelength light) sharply reduced the infectivity of fungal spores but did not affect host susceptibility to infection. The parasite's sensitivity to solar radiation may underlie patterns in a lake survey: higher penetration of solar radiation into lakes correlated with smaller epidemics that started later in autumn (as incident sunlight declined). Thus, solar radiation, by diminishing infectivity of the parasite, may potently reduce disease.