Modelling small groundwater systems: experiences from the Braunton Burrows and Ainsdale coastal dune systems,UK

Coastal dunes are delicate systems that are under threat from a variety of human and natural influences. Groundwater modelling can provide a better understanding of how these systems operate and can be a useful tool towards the effective management of a coastal dune system, e.g. by identifying strategically important locations for flora and fauna and guiding the planning of management operations through predicting impacts from climatic change, sea level rise and land use management. Most dune systems are small, typically of the size 10–100 km², compared with inland groundwater systems. Applying conventional groundwater modelling approaches to these small systems presents a number of challenges due to the local scale of the system and the fact that the system boundaries (sea, drains, ponds etc.) are close to the main body of the aquifer. In this paper, two case studies will be presented using different modelling approaches to understand the groundwater balance in two dune systems in the UK. The studies demonstrate that, although conventional hydraulic models can describe the general system behaviour, a fuller understanding of the recharge mechanisms and system boundaries is needed to represent adequately system dynamics of small groundwater systems.     

Adaptive prey behavior and the dynamics of intraguild predation systems

Intraguild predation constitutes a widespread interaction occurring across different taxa, trophic positions and ecosystems, and its endogenous dynamical properties have been shown to affect the abundance and persistence of the involved populations as well as those connected with them within food webs. Although optimal foraging decisions displayed by predators are known to exert a stabilizing influence on the dynamics of intraguild predation systems, few is known about the corresponding influence of adaptive prey decisions in spite of its commonness in nature. In this study, we analyze the effect that adaptive antipredator behavior exerts on the stability and persistence of the populations involved in intraguild predation systems. Our results indicate that adaptive prey behavior in the form of inducible defenses act as a stabilizing mechanism and show that, in the same direction that adaptive foraging, enhances the parameter space in which species can coexist through promoting persistence of the IG-prey. At high levels of enrichment, the intraguild predation system exhibits unstable dynamics and zones of multiples attractors. In addition, we show that the equilibrium density of the IG-predator could be increased at intermediate values of defense effectiveness. Finally we conclude that adaptive prey behavior is an important mechanism leading to species coexistence in intraguild predation systems and consequently enhancing stability of food webs.     

Ecological boundary detection using Bayesian areal wombling

The study of ecological boundaries and their dynamics is of fundamental importance to much of ecology, biogeography, and evolution. Over the past two decades, boundary analysis (of which wombling is a subfield) has received considerable research attention, resulting in multiple approaches for the quantification of ecological boundaries. Nonetheless, few methods have been developed that can simultaneously (1) analyze spatially homogenized data sets (i.e., areal data in the form of polygons rather than point-reference data); (2) account for spatial structure in these data and uncertainty associated with them; and (3) objectively assign probabilities to boundaries once detected. Here we describe the application of a Bayesian hierarchical framework for boundary detection developed in public health, which addresses these issues but which has seen limited application in ecology. As examples, we analyze simulated spread data and the historic pattern of spread of an invasive species, the hemlock woolly adelgid (Adelges tsugae), using county-level summaries of the year of first reported infestation and several covariates potentially important to influencing the observed spread dynamics. Bayesian areal wombling is a promising approach for analyzing ecological boundaries and dynamics related to changes in the distributions of native and invasive species.     

State-specific detection probabilities and disease prevalence.

Investigations of disease dynamics in wild animal populations often use estimated prevalence or incidence as a measure of true disease frequency. Such indices, almost always based solely on raw counts of infected and uninfected individuals, are often used as the basis for analysis of temporal and spatial dynamics of diseases. Generally, such studies do not account for potential differences in observer detection probabilities of host individuals stratified by biotic and/or abiotic factors. We demonstrate the potential effects of heterogeneity in state-specific detection probabilities on estimated disease prevalence using mark-recapture data from previous work in a House Finch (Carpodacus mexicanus) and Mycoplasma gallisepticum system. In this system, detection probabilities of uninfected finches were generally higher than infected individuals. We show that the magnitude and seasonal pattern of variation in estimated prevalence, corrected for differences in detection probabilities, differed markedly from uncorrected (apparent) prevalence. When the detection probability of uninfected individuals is higher than infected individuals (as in our study), apparent prevalence is negatively biased, and vice versa. In situations where state-specific detection probabilities strongly interact over time, we show that the magnitude and pattern of apparent prevalence can change dramatically; in such cases, observed variations in prevalence may be completely spurious artifacts of variation in detection probability, rather than changes in underlying disease dynamics. Accounting for differential detection probabilities in estimates of disease frequency removes a potentially confounding factor in studies seeking to identify biotic and/or abiotic drivers of disease dynamics. Given that detection probabilities of different groups of individuals are likely to change temporally and spatially in most field studies, our results underscore the importance of estimating and incorporating detection probabilities in estimated disease prevalence (specifically), and more generally, any ecological index used to estimate some parameter of interest. While a mark-recapture approach makes it possible to estimate detection probabilities, it is not always practical, especially at large scales. We discuss several alternative approaches and categorize the assumptions under which analysis of uncorrected prevalence may be acceptable.     

Measuring the impact of dynamic antipredator traits on predator-prey-resource interactions

This article analyzes the limitations of the most widely used method for quantifying the impact of dynamic antipredator traits on food chain dynamics and discusses alternative approaches. The standard method for a predator-prey-resource chain estimates the effects of the prey's defensive behavior by comparing population densities or fitness measures in a "predator cue" treatment to those in a no-predator treatment. This design has been interpreted as providing a measure of the "nonconsumptive effect" of the predator on the prey and the "trait-mediated indirect effect" of the predator on the resource. Other approaches involve measurements of the impact of the behavior in the presence of functional predators. The questions addressed here are: (1) How consistent are the results of different approaches? (2) How time-dependent are their results? (3) How well do they correspond to theoretical measures of effect size? (4) How useful are the measurements in understanding system dynamics? A model of a tritrophic system in which the prey species adjusts a defensive trait adaptively is used to evaluate the experimental designs. Measures of changes in prey fitness or population density in a cue treatment generally include offsetting effects of the cost of the behavior and the benefit of more resources. This means that the sign of the effect, as well as its magnitude, may change depending on when the experiment is terminated. Because predation is not present in the cue treatment, few conclusions can be drawn about the impact of the behavior on population densities or fitness of the prey in a natural setting with predators. Cue experiments often do not accurately separate trait-mediated from density-mediated effects on the resource. Most scalar measures of effects are sensitive to experimental duration and initial densities. Use of a wider range of experimental designs to measure trait-related effects is called for.     

Ecological Attributes of Extinction-Prone Species: Loss of Freshwater Fishes of Virginia

I examined patterns of extirpation among Virginia's 197 historically native freshwater fish species to address the following questions: (1) Are extinction-prone species ecologically distinct? and (2) Are distinctive features similar to those identified for extinction-prone species in terrestrial systems? All species were assigned to categories for a series of attributes reflecting geographical distribution, habitat use, trophic habits, life history, size, and reproductive behavior. Associations between species that had been extirpated and those that had not were examined for each attribute. Univariate associations were observed between extirpation and three ecological attributes: diadromy, limited physiographic range, and limited range of water sizes. Species specialized with respect to multiple ecological attributes also were especially likely to be extirpated. These associations reflected the effects of reduced habitat area and increased isolation (insularization), which are also important determinants of extinction in terrestrial systems. Multivariate analyses suggested that extirpated species were ecologically similar to each other, but were not completely distinct from the nonextirpated fauna. My results suggest that ecological knowledge of species can help identify extinction-prone species and provide a basis for proactive conservation. Current approaches to conservation, which are largely reactive and piecemeal, are inadequate to protect biodiversity. Because aquatic degradation is complex and pervasive, conservation of aquatic biodiversity requires proactive comprehensive approaches to water resource management, including emphasis on protecting the ecological integrity of entire systems.     

Modelling coral reef ecosystems with limited observational data

Ecosystem models represent potentially powerful tools for coral reef ecosystem managers. They can provide insight into ecosystem dynamics not achievable through alternative means allowing coral reef managers to assess the potential outcome of any given management decision. One of the main limitations in the applicability of ecosystem models is that they often require detailed empirical data and this can restrict their applicability to ecosystems that are either currently well studied or have the resources available to collect the required data. This study describes the development of a coral reef ecosystem model that can be calibrated to an ecosystem with limited empirical data. Based on the assumption that coral reef ecological structure is generic across all tropical coral reefs and that the magnitude of the interactions between ecological components is reef specific, the dynamics of the ecosystem can be replicated based on limited empirical data. The model successfully replicated the dynamics of three individual reef systems including an inshore and oceanic reef within the Great Barrier Reef and a Caribbean reef system. It highlighted the importance of understanding the specific dynamics of a given reef and that a positive management intervention in one system may result in a negative outcome for another. The model was also used to assess the importance of various interactions within coral reef ecosystems. It identified the interactions between hard corals and other non-algal benthic components as being an important (but currently understudied) facet of coral reef ecology. The development of this modelling approach provides access to ecosystem modelling tools for coral reef managers previously excluded due to a lack of resources or technical expertise.     

Assessment of prey vulnerability through analysis of wolf movements and kill sites.

Within predator-prey systems behavior can heavily influence spatial dynamics, and accordingly, the theoretical study of how spatial dynamics relate to stability within these systems has a rich history. However, our understanding of these behaviors in large mammalian systems is poorly developed. To address the relationship between predator selection patterns, prey density, and prey vulnerability, we quantified selection patterns for two fine-scale behaviors of a recovering wolf (Canis lupus) population in Yellowstone National Park, Wyoming, USA. Wolf spatial data were collected between November and May from 1998-1999 until 2001-2002. Over four winters, 244 aerial locations, 522 ground-based telemetry locations, 1287 km of movement data from snow tracking, and the locations of 279 wolf kill sites were recorded. There was evidence that elk (Cervus elaphus) and bison (Bison bison) densities had a weak effect on the sites where wolves traveled and made kills. Wolf movements showed a strong selection for geothermal areas, meadows, and areas near various types of habitat edges. Proximity to edge and habitat class also had a strong influence on the locations where elk were most vulnerable to predation. There was little evidence that wolf kill sites differed from the places where wolves traveled, indicating that elk vulnerability influenced where wolves selected to travel. Our results indicate that elk are more vulnerable to wolves under certain conditions and that wolves are capable of selecting for these conditions. As such, vulnerability plays a central role in predator-prey behavioral games and can potentially impact the systems to which they relate.     

Compartmental systems. An appealing class for kinetic modeling and identification of metabolic processes

Problems which arise in quantitative studies on the kinetics of exogenous and endogenous chemical substances within the organism are examined together with approaches for their resolution. Linear and nonlinear compartmental mathematical models are presented and their relevant role for interpreting stimulus‐response experimental data is outlined. Available approaches are then discussed for the resolution of the system identification problem, including a priori and a posteriori identifiability, parameter estimation from test measurement data and optimum design of kinetic experiments. Finally, approaches to the problem of validation are reviewed.     

Climate change and forests of the future: managing in the face of uncertainty.

We offer a conceptual framework for managing forested ecosystems under an assumption that future environments will be different from present but that we cannot be certain about the specifics of change. We encourage flexible approaches that promote reversible and incremental steps, and that favor ongoing learning and capacity to modify direction as situations change. We suggest that no single solution fits all future challenges, especially in the context of changing climates, and that the best strategy is to mix different approaches for different situations. Resources managers will be challenged to integrate adaptation strategies (actions that help ecosystems accommodate changes adaptively) and mitigation strategies (actions that enable ecosystems to reduce anthropogenic influences on global climate) into overall plans. Adaptive strategies include resistance options (forestall impacts and protect highly valued resources), resilience options (improve the capacity of ecosystems to return to desired conditions after disturbance), and response options (facilitate transition of ecosystems from current to new conditions). Mitigation strategies include options to sequester carbon and reduce overall greenhouse gas emissions. Priority-setting approaches (e.g., triage), appropriate for rapidly changing conditions and for situations where needs are greater than available capacity to respond, will become increasingly important in the future.     

Analyzing the tradeoffs among ecological and fishing effects on an example fish community: A multispecies (fisheries) production model

Species interactions such as predation or competition can have notable implications for fish population dynamics. Stock status and associated biological reference points can be misrepresented if these interactions are not considered. Here we present a multispecies, biomass production model (MS-PROD) developed by incorporating modifications to the Schaefer production model. The modifications explicitly emphasize a functional group approach, highlighting the effects of species interactions that include competition between species within a group, competition between groups, and predation. The mathematical formulation also includes constraints on carrying capacity for both the entire system and for individual groups. We applied the model as initialized to the Northeast U.S. Large Marine Ecosystem finfish community. We then executed simulations designed to explore the behavior of the model with respect to fishery exploitation and ecological interactions. Collectively, the results demonstrated the utility, and the need, for incorporating ecological effects into fisheries models.     

Defining an ecological thermodynamics using discrete simulation approaches

New insights into interdisciplinary engineering endeavors, from classical modeling to nano–macroscale extrapolation and critical evaluation, weigh heavily on the pervasive nature of thermodynamics in the physical world. Just as statistical thermodynamic approaches provide a beneficial complement to a process-based macroscale thermodynamic approaches with physical systems, a Lagrangian approach to energetics in biological systems can, we believe, provide a beneficial complement to popular Eulerian approaches. Statistical thermodynamics is used as a springboard for some analogies that are similarly used to leap into the ecological scale. The Lagrangian simulation, a discrete simulation, is implemented with a spreadsheet approach, a discrete simulation approach, and a new stochastic differential equation solution approach. The Lagrangian approach complements the more widely used continuous (or Eulerian) simulation approaches such as STELLA or Environ theory approaches. The Lagrangian approach decomposes energy into small packets or ecological quanta. An ecological entropy is computed based on nodal contacts in the network, with the notion that nodal contact is analogous to molecular speed. In the cases shown, the results of ecological entropy appear generally consistent with thermodynamic entropy. A newly available simulation package (ECONET) enabled an easy Lagrangian approach to analyzing the Cone Springs and Oyster ecological models. An analogy between nodal contact numbers and molecular speed was developed to enable computation of an ecological entropy. There is a similarity between classical and ecological entropy based on similarity in shape of the Maxwell–Boltzmann distributions to the packet-nodal contact numbers. An ecological temperature can be defined based on this similarity. Selected ratios of ecological entropy versus classical macroscopic entropy appeared to have some degree of robustness. Other aspects of ecological thermodynamics remain to be developed. It is felt that the ecological thermodynamics approach presented offers an improved way to combine biochemical and ecological entropy. A sound combination of entropies at multiple scales will help bring together measurements at disparate scales.     

Optimal management with potential regime shifts

We analyze how the threat of a potential future regime shift affects optimal management. We use a simple general growth model to analyze four cases that involve combinations of stock collapse versus changes in system dynamics, and exogenous versus endogenous probabilities of regime shift. Prior work in economics has focused on stock collapse with endogenous probabilities and reaches ambiguous conclusions on whether the potential for regime shift will increase or decrease intensity of resource use and level of resource stock. We show that all other cases yield unambiguous results. In particular, with endogenous probability of regime shift that affects system dynamics the potential for regime shift causes optimal management to become precautionary in the sense of maintaining higher resource stock levels.     

Methods for measuring denitrification: diverse approaches to a difficult problem.

Denitrification, the reduction of the nitrogen (N) oxides, nitrate (NO3-) and nitrite (NO2-), to the gases nitric oxide (NO), nitrous oxide (N2O), and dinitrogen (N2), is important to primary production, water quality, and the chemistry and physics of the atmosphere at ecosystem, landscape, regional, and global scales. Unfortunately, this process is very difficult to measure, and existing methods are problematic for different reasons in different places at different times. In this paper, we review the major approaches that have been taken to measure denitrification in terrestrial and aquatic environments and discuss the strengths, weaknesses, and future prospects for the different methods. Methodological approaches covered include (1) acetylene-based methods, (2) 15N tracers, (3) direct N2 quantification, (4) N2:Ar ratio quantification, (5) mass balance approaches, (6) stoichiometric approaches, (7) methods based on stable isotopes, (8) in situ gradients with atmospheric environmental tracers, and (9) molecular approaches. Our review makes it clear that the prospects for improved quantification of denitrification vary greatly in different environments and at different scales. While current methodology allows for the production of accurate estimates of denitrification at scales relevant to water and air quality and ecosystem fertility questions in some systems (e.g., aquatic sediments, well-defined aquifers), methodology for other systems, especially upland terrestrial areas, still needs development. Comparison of mass balance and stoichiometric approaches that constrain estimates of denitrification at large scales with point measurements (made using multiple methods), in multiple systems, is likely to propel more improvement in denitrification methods over the next few years.     

Interrelationships among shrub encroachment, land management, and litter decomposition in a semidesert grassland.

Encroachment of woody plants into grasslands, and subsequent brush management, are among the most prominent changes to occur in arid and semiarid systems over the past century. Despite the resulting widespread changes in landcover, substantial uncertainty about the biogeochemical impacts of woody proliferation and brush management exists. We explored the role of shrub encroachment and brush management on leaf litter decomposition in a semidesert grassland where velvet mesquite (Prosopis velutina) abundance has increased over the past 100 years. This change in physiognomy may affect decomposition directly, through altered litter quality or quantity, and indirectly through altered canopy structure. To assess the direct and indirect impacts of shrubs on decomposition, we quantified changes in mass, nitrogen, and carbon in litterbags deployed under mesquite canopies and in intercanopy zones. Litterbags contained foliage from mesquite and Lehmann lovegrass (Eragrostis lehmanniana), a widespread, nonnative grass in southern Arizona. To explore short- and long-term influences of brush management on the initial stages of decomposition, litterbags were deployed at sites where mesquite canopies were removed three weeks, 45 years, or 70 years prior to study initiation. Mesquite litter decomposed more rapidly than lovegrass, but negative indirect influences of mesquite canopies counteracted positive direct effects. Decomposition was positively correlated with soil infiltration into litterbags, which varied with microsite placement, and was lowest under canopies. Low under-canopy decomposition was ostensibly due to decreased soil movement associated with high under-canopy herbaceous biomass. Decomposition rates where canopies were removed three weeks prior to study initiation were comparable to those beneath intact canopies, suggesting that decomposition was driven by mesquite legacy effects on herbaceous cover-soil movement linkages. Decomposition rates where shrubs were removed 45 and 70 years prior to study initiation were comparable to intercanopy rates, suggesting that legacy effects persist less than 45 years. Accurate decomposition modeling has proved challenging in arid and semiarid systems but is critical to understanding biogeochemical responses to woody encroachment and brush management. Predicting brush-management effects on decomposition will require information on shrub-grass interactions and herbaceous biomass influences on soil movement at decadal timescales. Inclusion of microsite factors controlling soil accumulation on litter would improve the predictive capability of decomposition models.     

Transient dynamics and the destabilizing effects of prey heterogeneity

The presence of prey heterogeneity and weakly interacting prey species is frequently viewed as a stabilizer of predator-prey dynamics, countering the destabilizing effects of enrichment and reducing the amplitude of population cycles. However, prior model explorations have largely focused on long-term, dynamic attractors rather than transient dynamics. Recent theoretical work shows that the presence of prey that are defended from predation can have strongly divergent effects on dynamics depending on time scale: prey heterogeneity can counteract the destabilizing effects of enrichment on predator-prey dynamics at long time scales but strongly destabilize systems during transient phases by creating long periods of low predator/prey abundance and increasing extinction probability (an effect that is amplified with increasing enrichment). We tested these general predictions using a planktonic system composed of a zooplankton predator and multiple algal prey. We first parameterized a model of our system to generate predictions and tested these experimentally. Our results qualitatively supported several model predictions. During transient phases, presence of defended algal prey increased predator extinctions at low and high enrichment levels compared to systems with only a single edible prey. This destabilizing effect was moderated at higher dilution rates, as predicted by our model. When examining dynamics beyond initial oscillations, presence of the defended prey increased predator-prey temporal variability at high nutrient enrichment but had no effect at low nutrient levels. Our results highlight the importance of considering transient dynamics when assessing the role of stabilizing factors on the dynamics of food webs.     

What can we learn from resource pulses?

An increasing number of studies in a wide range of natural systems have investigated how pulses of resource availability influence ecological processes at individual, population, and community levels. Taken together, these studies suggest that some common processes may underlie pulsed resource dynamics in a wide diversity of systems. Developing a common framework of terms and concepts for the study of resource pulses may facilitate greater synthesis among these apparently disparate systems. Here, we propose a general definition of the resource pulse concept, outline some common patterns in the causes and consequences of resource pulses, and suggest a few key questions for future investigations. We define resource pulses as episodes of increased resource availability in space and time that combine low frequency (rarity), large magnitude (intensity), and short duration (brevity), and emphasize the importance of considering resource pulses at spatial and temporal scales relevant to specific resource-onsumer interactions. Although resource pulses are uncommon events for consumers in specific systems, our review of the existing literature suggests that pulsed resource dynamics are actually widespread phenomena in nature. Resource pulses often result from climatic and environmental factors, processes of spatiotemporal accumulation and release, outbreak population dynamics, or a combination of these factors. These events can affect life history traits and behavior at the level of individual consumers, numerical responses at the population level, and indirect effects at the community level. Consumers show strategies for utilizing ephemeral resources opportunistically, reducing resource variability by averaging over larger spatial scales, and tolerating extended interpulse periods of reduced resource availability. Resource pulses can also create persistent effects in communities through several mechanisms. We suggest that the study of resource pulses provides opportunities to understand the dynamics of many specific systems, and may also contribute to broader ecological questions at individual, population, and community levels.     

Consequences of stage-structured predators: cannibalism, behavioral effects, and trophic cascades

Cannibalistic and asymmetrical behavioral interactions between stages are common within stage-structured predator populations. Such direct interactions between predator stages can result in density- and trait-mediated indirect interactions between a predator and its prey. A set of structured predator-prey models is used to explore how such indirect interactions affect the dynamics and structure of communities. Analyses of the separate and combined effects of stage-structured cannibalism and behavior-mediated avoidance of cannibals under different ecological scenarios show that both cannibalism and behavioral avoidance of cannibalism can result in short- and long-term positive indirect connections between predator stages and the prey, including "apparent mutualism." These positive interactions alter the strength of trophic cascades such that the system's dynamics are determined by the interaction between bottom-up and top-down effects. Contrary to the expectation of simpler models, enrichment increases both predator and prey abundance in systems with cannibalism or behavioral avoidance of cannibalism. The effect of behavioral avoidance of cannibalism, however, depends on how strongly it affects the maturation rate of the predator. Behavioral interactions between predator stages reduce the short-term positive effect of cannibalism on the prey density, but can enhance its positive long-term effects. Both interaction types reduce the destabilizing effect of enrichment. These results suggest that inconsistencies between data and simple models can be resolved by accounting for stage-structured interactions within and among species.     

Ecological mechanisms linking protected areas to surrounding lands.

Land use is expanding and intensifying in the unprotected lands surrounding many of the world's protected areas. The influence of this land use change on ecological processes is poorly understood. The goal of this paper is to draw on ecological theory to provide a synthetic framework for understanding how land use change around protected areas may alter ecological processes and biodiversity within protected areas and to provide a basis for identifying scientifically based management alternatives. We first present a conceptual model of protected areas embedded within larger ecosystems that often include surrounding human land use. Drawing on case studies in this Invited Feature, we then explore a comprehensive set of ecological mechanisms by which land use on surrounding lands may influence ecological processes and biodiversity within reserves. These mechanisms involve changes in ecosystem size, with implications for minimum dynamic area, species-area effect, and trophic structure; altered flows of materials and disturbances into and out of reserves; effects on crucial habitats for seasonal and migration movements and population source/sink dynamics; and exposure to humans through hunting, poaching, exotics species, and disease. These ecological mechanisms provide a basis for assessing the vulnerability of protected areas to land use. They also suggest criteria for designing regional management to sustain protected areas in the context of surrounding human land use. These design criteria include maximizing the area of functional habitats, identifying and maintaining ecological process zones, maintaining key migration and source habitats, and managing human proximity and edge effects.