Parameterising a public good: how experiments on predation can be used to predict cheat frequencies

Chemical defence is superficially easy to understand as a means for individuals to protect themselves from enemies. The evolution of chemical defence is however potentially complex because such defences may cause the generation of a public good, protecting members of the population as a whole as well as individuals that deploy toxins defensively. If a public good of protection exists, it may be exploited and degraded by “cheats” that do not invest in defence. This can in turn lead to complex frequency (and density) dependent effects in toxin evolution. To investigate this we used ecologically relevant predators (Great tits, Parus major) and examined how individual and public benefits vary depending on the frequency of non-defended “cheating” prey and their spatial distribution. We found that the public benefit, of reduced attack probability, increased with increasing frequency of defended individuals. In contrast the individual benefit of chemical defence, measured as increased chance of rejection during an attack before injury, did not vary with the frequency of defended forms. Hence the selective dynamics of these two levels of benefits responded differently to the frequency of defended forms. Surprisingly, given the strong associations of chemical defences and grouping in animals, large aggregations did not help individuals in the group regardless of their defence status. The explanation for the result, may be that in our experiment birds did not have information about other potential aggregations (i.e. set up was sequential) and thus their giving up density was lower compared to the situations where set ups were simultaneous. We use behavioural data of our predators to construct a simple model of toxin evolution which can make quantitative predictions about the frequencies to which defence cheats evolve. We use this model to discuss how toxin evolution can be investigated in the wild and in laboratory settings.     

BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data

The structure and function of diverse microbial communities is underpinned by ecological interactions that remain uncharacterized. With rapid adoption of next-generation sequencing for studying microbiomes, data-driven inference of microbial interactions based on abundance correlations is widely used, but with the drawback that ecological interpretations may not be possible. Leveraging cross-sectional microbiome datasets for unravelling ecological structure in a scalable manner thus remains an open problem. We present an expectation-maximization algorithm (BEEM-Static) that can be applied to cross-sectional datasets to infer interaction networks based on an ecological model (generalized Lotka-Volterra). The method exhibits robustness to violations in model assumptions by using statistical filters to identify and remove corresponding samples. Benchmarking against 10 state-of-the-art correlation based methods showed that BEEM-Static can infer presence and directionality of ecological interactions even with relative abundance data (AUC-ROC>0.85), a task that other methods struggle with (AUC-ROC<0.63). In addition, BEEM-Static can tolerate a high fraction of samples (up to 40%) being not at steady state or coming from an alternate model. Applying BEEM-Static to a large public dataset of human gut microbiomes (n = 4,617) identified multiple stable equilibria that better reflect ecological enterotypes with distinct carrying capacities and interactions for key species.ConclusionBEEM-Static provides new opportunities for mining ecologically interpretable interactions and systems insights from the growing corpus of microbiome data.     

feedr and animalnexus.ca: A paired R package and user‐friendly Web application for transforming and visualizing animal movement data from static stations

Radio frequency identification (RFID) provides a simple and inexpensive approach for examining the movements of tagged animals, which can provide information on species behavior and ecology, such as habitat/resource use and social interactions. In addition, tracking animal movements is appealing to naturalists, citizen scientists, and the general public and thus represents a tool for public engagement in science and science education. Although a useful tool, the large amount of data collected using RFID may quickly become overwhelming. Here, we present an R package (feedr) we have developed for loading, transforming, and visualizing time‐stamped, georeferenced data, such as RFID data collected from static logger stations. Using our package, data can be transformed from raw RFID data to visits, presence (regular detections by a logger over time), movements between loggers, displacements, and activity patterns. In addition, we provide several conversion functions to allow users to format data for use in functions from other complementary R packages. Data can also be visualized through static or interactive maps or as animations over time. To increase accessibility, data can be transformed and visualized either through R directly, or through the companion site: http://animalnexus.ca , an online, user‐friendly, R‐based Shiny Web application. This system can be used by professional and citizen scientists alike to view and study animal movements. We have designed this package to be flexible and to be able to handle data collected from other stationary sources (e.g., hair traps, static very high frequency (VHF) telemetry loggers, observations of marked individuals in colonies or staging sites), and we hope this framework will become a meeting point for science, education, and community awareness of the movements of animals. We aim to inspire citizen engagement while simultaneously enabling robust scientific analysis.     

Microscopy images as interactive tools in cell modeling and cell biology education

The advent of genomics, proteomics, and microarray technology has brought much excitement to science, both in teaching and in learning. The public is eager to know about the processes of life. In the present context of the explosive growth of scientific information, a major challenge of modern cell biology is to popularize basic concepts of structures and functions of living cells, to introduce people to the scientific method, to stimulate inquiry, and to analyze and synthesize concepts and paradigms. In this essay we present our experience in mixing science and education in Brazil. For two decades we have developed activities for the science education of teachers and undergraduate students, using microscopy images generated by our work as cell biologists. We describe open-air outreach education activities, games, cell modeling, and other practical and innovative activities presented in public squares and favelas. Especially in developing countries, science education is important, since it may lead to an improvement in quality of life while advancing understanding of traditional scientific ideas. We show that teaching and research can be mutually beneficial rather than competing pursuits in advancing these goals.     

Evaluating the efficacy of antimicrobial cycling programmes and patient isolation on dual resistance in hospitals

Antibiotic-resistant bacteria cause a number of infections in hospitals and are considered a threat to public health. A strategy suggested to curb the development of resistant hospital-acquired infections is antimicrobial cycling, in which antibiotic classes are alternated over time. This can be compared with a mixing programme in which, when given two drugs, half of the physicians prescribe one drug over the other. A mathematical model of antimicrobial cycling in a hospital population setting is developed to evaluate the efficacy of a cycling programme with an emphasis on reducing the emergence and significance of dual resistance. The model also considers the effects of physician compliance and isolating patients harbouring dual-resistant bacteria. Simulation results show that the optimal antimicrobial drug usage programme in hospital populations depends upon the type of resistance being targeted for treatment; a cycling programme is more effective against dual resistance compared with mixing. Patient isolation and high compliance to a cycling programme is also shown to dramatically decrease dual resistance in hospitalized populations. Ultimately, the exclusive use of antimicrobials in fighting nosocomial infection does not solve the problem but just slows down what appears to be a losing battle against drug resistance. We hope that this paper serves to instigate discussion on the many dimensions of the complex problem of drug resistance in hospital settings.     

Evaluating the efficacy of antimicrobial cycling programmes and patient isolation on dual resistance in hospitals

Antibiotic-resistant bacteria cause a number of infections in hospitals and are considered a threat to public health. A strategy suggested to curb the development of resistant hospital-acquired infections is antimicrobial cycling, in which antibiotic classes are alternated over time. This can be compared with a mixing programme in which, when given two drugs, half of the physicians prescribe one drug over the other. A mathematical model of antimicrobial cycling in a hospital population setting is developed to evaluate the efficacy of a cycling programme with an emphasis on reducing the emergence and significance of dual resistance. The model also considers the effects of physician compliance and isolating patients harbouring dual-resistant bacteria. Simulation results show that the optimal antimicrobial drug usage programme in hospital populations depends upon the type of resistance being targeted for treatment; a cycling programme is more effective against dual resistance compared with mixing. Patient isolation and high compliance to a cycling programme is also shown to dramatically decrease dual resistance in hospitalized populations. Ultimately, the exclusive use of antimicrobials in fighting nosocomial infection does not solve the problem but just slows down what appears to be a losing battle against drug resistance. We hope that this paper serves to instigate discussion on the many dimensions of the complex problem of drug resistance in hospital settings.     

Experimentalist Meets Theoretician: A Tale of Two Scientific Cultures

This is the story of how a small team of experimentalists and theoreticians collaborated to develop a theoretical model for vesicle formation during endocytosis. In telling our story, we hope to distil some general conclusions about the purpose and value of theoretical models and how best to navigate collaborations between experimentalists and theoreticians. We encountered challenges in building and publishing our model, but through our experiences we gained insight into how such collaborations can be profitably conducted. We also developed opinions about how theoretical models should be evaluated by peer reviewers and editors. During the evolution of our theoretical model, we educated each other, organized our thoughts and our data, developed a conceptual framework for understanding the mechanochemistry of endocytosis, and generated testable hypotheses that stimulated new experiments.     

Movement toward better environments and the evolution of rapid diffusion

We study a reaction-diffusion-advection model for two ecologically equivalent competitors with different dispersal strategies inhabiting a spatially heterogeneous environment. The competitors represent different phenotypes of the same species. One is assumed to disperse by simple diffusion, the other by diffusion together with directed movement toward more favorable environments. We show that under suitable conditions on the underlying spatial domain, the competitor that moves toward more favorable environments may have a competitive advantage even if it diffuses more rapidly than the other competitor. This is in contrast with the case in which both competitors disperse by pure diffusion, where the competitor that diffuses more slowly always has the advantage. We determine competitive advantage by examining the invasibility, i.e. stability or instability, of steady states with only one competitor present. The mathematical approach is a perturbation analysis of principal eigenvalues.     

Evaluating the risks of public health programs: Rational antibiotic use and antimicrobial resistance

Existing ethical frameworks for public health provide insufficient guidance on how to evaluate the risks of public health programs that compromise the best clinical interests of present patients for the benefit of others. Given the relevant similarity of such programs to clinical research, we suggest that insights from the long‐standing debate about acceptable risk in clinical research can helpfully inform and guide the evaluation of risks posed by public health programs that compromise patients’ best clinical interests. We discuss how lessons learned regarding the ethics of risk in one context can be fruitfully transferred to the other, using the example of a so‐called ‘rational antibiotic use’ guideline that limits antimicrobial prescribing in order to curb antimicrobial resistance.     

A genetic interpretation of ecologically dependent isolation

Hybrids may suffer a reduced fitness both because they fall between ecological niches (ecologically dependent isolation) and as a result of intrinsic genetic incompatibilities between the parental genomes (ecologically independent isolation). Whereas genetic incompatibilities are common to all theories of speciation, ecologically dependent isolation is a unique prediction of the ecological model of speciation. This prediction can be tested using reciprocal transplants in which the fitness of various genotypes is evaluated in both parental habitats. Here we expand a quantitative genetic model of Lynch (1991) to include two parental environments. We ask whether a sufficient experimental design exists for detecting ecologically dependent isolation. Analysis of the model reveals that by using both backcrosses in both parental environments, environment-specific additive genetic effects can be estimated while correcting for any intrinsic genetic isolation. Environment-specific dominance effects can also be estimated by including the F1 and F2 in the reciprocal transplant. In contrast, a reciprocal transplant comparing only F1s or F2s to the parental species cannot separate ecologically dependent from intrinsic genetic isolation. Thus, a reduced fitness of F1 or F2 hybrids relative to the parental species is not sufficient to demonstrate ecological speciation. The model highlights the importance of determining the contribution of genetic and ecological mechanisms to hybrid fitness if inferences concerning speciation mechanisms are to be made.     

Japanese Honeysuckle (Lonicera japonica) as an Invasive Species; History,Ecology, and Context

Japanese honeysuckle (Lonicera japonica) was introduced outside of Asia in the early 19th century and is now invasive to varying degrees on every continent, except Anarctica, and many archipelagos. The basic ecology and life history of Japanese honeysuckle are well known and described here; however, research needs on the underlying causes of the voracity and subsequent ecological impacts of this species are many. Virtually all ecological experimentation with Japanese honeysuckle has been conducted in the southeastern U.S., thus more data are needed in other regions, particularly South America and Africa. Although Japanese honeysuckle is naturalized in many areas where it has been introduced, there still may be hope for the control of local infestations and its further spread in areas that have a fairly recent introduction history. Japanese honeysuckle may be secure throughout much of its introduced range, but land management principles that discourage its use and public education to prevent further dispersal are recommended strongly.     

Multiple infections and the evolution of virulence

Infections that consist of multiple parasite strains or species are common in the wild and are a major public health concern. Theory suggests that these infections have a key influence on the evolution of infectious diseases and, more specifically, on virulence evolution. However, we still lack an overall vision of the empirical support for these predictions. We argue that within‐host interactions between parasites largely determine how virulence evolves and that experimental data support model predictions. Then, we explore the main limitation of the experimental study of such ‘mixed infections’, which is that it draws conclusions on evolutionary outcomes from studies conducted at the individual level. We also discuss differences between coinfections caused by different strains of the same species or by different species. Overall, we argue that it is possible to make sense out of the complexity inherent to multiple infections and that experimental evolution settings may provide the best opportunity to further our understanding of virulence evolution.     

Disentangling interactions between adaptive divergence and gene flow when ecology drives diversification

Adaptive diversification is driven by selection in ecologically different environments. In absence of geographical barriers to dispersal, this adaptive divergence (AD) may be constrained by gene flow (GF). And yet the reverse may also be true, with AD constraining GF (i.e. 'ecological speciation'). Both of these causal effects have frequently been inferred from the presence of negative correlations between AD and GF in nature - yet the bi-directional causality warrants caution in such inferences. We discuss how the ability of correlative studies to infer causation might be improved through the simultaneous measurement of multiple ecological and evolutionary variables. On the one hand, inferences about the causal role of GF can be made by examining correlations between AD and the potential for dispersal. On the other hand, inferences about the causal role of AD can be made by examining correlations between GF and environmental differences. Experimental manipulations of dispersal and environmental differences are a particularly promising approach for inferring causation. At present, the best studies find strong evidence that GF constrains AD and some studies also find the reverse. Improvements in empirical approaches promise to eventually allow general inferences about the relative strength of different causal interactions during adaptive diversification.     

Predicting impacts of lionfish (<Emphasis Type="Italic">Pterois volitans</Emphasis>) invasion in a coastal ecosystem of southern Brazil

The opportunistic feeder Pterois volitans is a voracious invader, causing large impacts in marine food-webs. We have used a Ecopath-with-Ecosim model to hypothesize an invasion by lionfish and to predict the likely impact of this potential generalist mesopredator in a subtropical food-web model. With thirty-three functional groups, the initial Ecopath model was balanced with a low biomass of lionfish (0.07 t/km²). In Ecosim, three scenarios of different vulnerability settings for the linkages between the introduced fish and its prey were tested, representing the default setting, a top-down control, and an extreme top-down control. The scenarios were tested using different assumptions on the ability of the invasive fish to change the proportions of prey consumed according to prey availability. Our model predicted that the hypothesized lionfish invasion would have a strong impact on this subtropical marine food web: (1) by reducing prey populations and, consequently, food for native predators, and; (2) by predating on key species, causing direct impacts and possibly cascading trophic effects. Reef fish were the most affected, including some groups ecologically and economically important, like lutjanids and groupers. However, some adaptations in the fishing strategy of fishermen are expected which may affect other fish groups. Stakeholders should be warned of the potential ecological and socio-economic impacts that may arise from a lionfish invasion and various strategies and policy options should be immediately developed and applied (1) to prevent the arrival and establishment of the lionfish, and; (2) to make the ecosystem more resilient to this and other possible exotic species.     

Octosporea bayeri: fumidil B inhibits vertical transmission in Daphnia magna

Microsporidia are a highly successful and ecologically diverse group of parasites, and thus represent interesting model systems for research on host-parasite interactions. However, such research often requires the ability to cure hosts of infections, a difficult task, given the short lifespan of most invertebrates and the efficient vertical transmission of some parasites. To our knowledge, few treatments are available to cure microsporidiosis in invertebrate hosts, and protocols have not yet been developed to inhibit vertical transmission and thereby cure host lines. We present a protocol for inhibiting vertical transmission of the microsporidian parasite Octosporea bayeri in the freshwater crustacean Daphnia magna. We used 100 mg/L Fumidil B dissolved in the culture medium of the host. This technique allowed Daphnia to survive and reproduce and inhibited vertical transmission of the parasite. The method presented here may be of general interest for other aquatic host-parasite systems involving microsporidia.     

Approaches to Selecting Native Plant Replacements for Fleshy-Fruited Invasive Species

Invasive plants are a serious threat to biodiversity. Yet, in some cases, they may play an important ecological role in heavily modified landscapes, such as where fleshy‐fruited invasive plants support populations of native frugivores. How can such conservation conflicts be managed? We advocate an approach in which native fleshy‐fruited plants are ranked on their ability to provide the fruit food resources for native frugivores currently being provided by invasive plants. If these native taxa are preferentially used, where ecologically appropriate, in plantings for restoration and in park and garden settings, they could help support native frugivore populations in the event of extensive invasive plant control. We develop and critically examine six approaches to selecting candidate native plant taxa: a multivariate approach based on the frugivore assemblage, a scoring model, and several multivariate approaches (including trait combinations having the greatest correlation with the diet of the native frugivore assemblage) based on the functional traits of fruit morphology, phenology, conspicuousness, and accessibility. To illustrate these approaches, we use a case study with Bitou bush (Chrysanthemoides monilifera subsp. rotundata) (Asteraceae), an Australian Weed of National Significance. The model using a dissimilarity value generated from all available traits identified a set of species used by the frugivores of C. monilifera more than null models. A replacement approach using species ranked by either all traits available or the frugivore community appears best suited to guide selection of plants in restoration practice.     

Tailoring science outreach through E-matching using a community-based participatory approach

In an effort to increase science exposure for pre-college (K-12) students and as part of the science education reform agenda, many biomedical research institutions have established university-community partnerships. Typically, these science outreach programs consist of pre-structured, generic exposure for students, with little community engagement. However, the use of a medium that is accessible to both teachers and scientists, electronic web-based matchmaking (E-matching) provides an opportunity for tailored outreach utilizing a community-based participatory approach (CBPA), which involves all stakeholders in the planning and implementation of the science outreach based on the interests of teachers/students and scientists. E-matching is a timely and urgent endeavor that provides a rapid connection for science engagement between teachers/students and experts in an effort to fill the science outreach gap. National Lab Network (formerly National Lab Day), an ongoing initiative to increase science equity and literacy, provides a model for engaging the public in science via an E-matching and hands-on learning approach. We argue that science outreach should be a dynamic endeavor that changes according to the needs of a target school. We will describe a case study of a tailored science outreach activity in which a public school that serves mostly under-represented minority students from disadvantaged backgrounds were E-matched with a university, and subsequently became equal partners in the development of the science outreach plan. In addition, we will show how global science outreach endeavors may utilize a CBPA, like E-matching, to support a pipeline to science among under-represented minority students and students from disadvantaged backgrounds. By merging the CBPA concept with a practical case example, we hope to inform science outreach practices via the lens of a tailored E-matching approach.     

Do fires in savannas consume woody biomass? A comment on approaches to modeling savanna dynamics

Savanna ecosystems have long been fertile ground for mathematical modeling of vegetation structure and the role of resources and disturbance in tree-grass coexistence. In recent years, several authors have presented models that explore how savanna fires suppress the woody community, alter ecosystem dynamics, and promote grass persistence. We argue, however, that the assumption that fires influence savanna dynamics by consuming woody biomass may be wrong because, in reality, fires kill seedlings and saplings that constitute little biomass relative to adult trees. We present a simple alternative that separates the woody community into a subadult (fire-sensitive) class and an adult (fire-resistant) class and explore how this ecologically more realistic, but still simplified, model may provide better simulations of demographic processes and response to fires in savannas.     

Closing the Gap: Inverting the Genetics Curriculum to Ensure an Informed Public

Over the past 20 years, the focus of national efforts to improve K-12 science education has ranged from curriculum and professional development of teachers to the adoption of science standards and high-stakes testing. In spite of this work, students in the United States continue to lag behind their peers in other countries. This underperformance is true for genetics, as well as for science and math in general, and is particularly worrisome given the accelerating need for scientists and engineers in our increasingly technology-driven economy. A scientifically literate public is essential if citizens are to engage effectively with policymakers on issues of scientific importance. Perhaps nowhere is this conjunction more personally meaningful than in human genetics and medicine. Rapid changes in our field have the potential to revolutionize healthcare, but the public is ill prepared to participate in this transformation. One potential solution is to modernize the genetics curriculum so that it matches the science of the 21^st century. This paper highlights changes in human genetics that support a curricular reorganization, outlines the problems with current genetics instruction, and proposes a new genetics curriculum.