Ecological Systems Model Research Articles

Representing and managing uncertainty in qualitative ecological models

Ecologists and decision makers need ways to understand systems, test ideas, and make predictions and explanations about systems. However, uncertainty about causes and effects of processes and parameter values is pervasive in models of ecological systems. Uncertainty associated with incomplete knowledge of a phenomenon–and incomplete knowledge of the limits of one's knowledge–is referred to as epistemic uncertainty. Here, we illustrate the use of qualitative reasoning (QR) as a modeling approach that supports simulation despite pervasive epistemic uncertainty in a system. We develop a QR model of a simple plant-resource system to illustrate how six sources of epistemic uncertainty can be expressed, assessed, and managed. These include uncertainty about system structure, quantity vagueness, functional relationships, unknown or exogenous processes, simulation outcomes, and post-diction or explanation of outcomes. We show that QR provides a useful framework for expressing uncertainty due to inexact knowledge about parameter values and for exploring the consequences of different understandings of system structure. Furthermore, uncertainty in parameter values can be expressed and managed using different representations of and constraints on parameter quantity spaces. Compositional modeling supports the creation of alternative models representing different system structures. QR models allow the creation of a full envisionment of all possible outcomes given a set of causal processes, a particular system structure, and starting values. Finally, explicit representation of system structure and causality allows simulation results to be unambiguously explained. These features of QR support ecologists in making explicit their substantial qualitative knowledge about causes and effects in systems to produce models that give rise to insightful simulations of system dynamics.

OBSERVABILITY OF CHAOS AND CYCLES IN ECOLOGICAL SYSTEMS: LESSONS FROM PREDATOR–PREY MODELS

We examine and assess deterministic chaos as an observable. First, we present the development of model ecological systems. We illustrate how to apply the Kolmogorov theorem to obtain limits on the parameters in the system, which assure the existence of either stable equilibrium point or stable limit cycle behavior in the phase space of two-dimensional (2D) dynamical systems. We also illustrate the method of deriving conditions using the linear stability analysis. We apply these procedures on some basic existing model ecological systems. Then, we propose four model ecological systems to study the dynamical chaos (chaos and intermittent chaos) and cycles. Dynamics of two predation and two competition models have been explored. The predation models have been designed by linking two predator–prey communities, which differ from one another in one essential way: the predator in the first is specialist and that in the second is generalist. The two competition models pertain to two distinct competition processes: interference and exploitative competition. The first competition model was designed by linking two predator–prey communities through inter-specific competition. The other competition model assumes that a cycling predator–prey community is successfully invaded by a predator with linear functional response and coexists with the community as a result of differences in the functional responses of the two predators. The main criterion behind the selection of these two model systems for the present study was that they represent diversity of ecological interactions in the real world in a manner which preserves mathematical tractability. For investigating the dynamic behavior of the model systems, the following tools are used: (i) calculation of the basin boundary structures, (ii) performing two-dimensional parameter scans using two of the parameters in the system as base variables, (iii) drawing the bifurcation diagrams, and (iv) performing time series analysis and drawing the phase space diagrams. The results of numerical simulation are used to distinguish between chaotic and cyclic behaviors of the systems.The conclusion that we obtain from the first two model systems (predation models) is that it would be difficult to capture chaos in the wild because ecological systems appear to change their attractors in response to changes in the system parameters quite frequently. The detection of chaos in the real data does not seem to be a possibility as what is present in ecological systems is not robust chaos but short-term recurrent chaos. The first competition model (interference competition) shares this conclusion with those of predation ones. The model with exploitative competition suggests that deterministic chaos may be robust in certain systems, but it would not be observed as the constituent populations frequently execute excursions to extinction-sized densities. Thus, no matter how good the data characteristics and analysis techniques are, dynamical chaos may continue to elude ecologists. On the other hand, the models suggest that the observation of cyclical dynamics in nature is the most likely outcome.

A socio-ecological analysis of Ethiopian immigrants’ interactions with the Israeli healthcare system and its policy and service implications

Objective. Despite receiving full medical care and many social services, many Ethiopian immigrants in Israel feel frustrated, and even alienated, by the care they receive. This study uses a qualitative approach to explore the obstacles Ethiopian immigrants face regarding effective health seeking behavior and optimal interactions with healthcare providers in Israel. Design. We gained a three-cornered perspective by conducting semi-structured interviews with healthcare providers, immigrants, and interpreters who mediate between the two. An ecological system or socio-ecological model guided the data analysis. It allowed organizing the varied and complex relationship between the factors that influence healthcare delivery and receipt among this population. Results. The advanced analysis of our results delineated four themes which we grouped into two domains: the cultural divide and the interpreters. Within each of these themes, we explored influences on health or healthcare at each level of the socio-ecological model. We demonstrated that the problems surrounding health seeking behaviors and receiving treatment stem mainly from a cultural divide. This cultural incongruity and its effects are apparent at multiple levels of the ecological model and must be recognized and addressed programmatically at these levels. Conclusions. Necessary program and service modifications include that cultural mediation become an integral part of health personnel's training for healthcare delivery and a necessary criterion for good practices. We recommend that professionals from within the health system be trained to act as interpreters. Lastly, the integration of traditional healers into the allopathic health system should be considered. These modifications require a system-wide change in policy, structure of services, and practices.

Form, Function and Longevity in Fucoid Thalli: Chlorophyll a Fluorescence Differentiation of Ascophyllum nodosum, Fucus vesiculosus and F. distichus (Phaeophyceae)

Ascophyllum and Fucus are the two most abundant genera of seaweeds in the intertidal zone of rocky shores on cold temperate waters of the North Atlantic (Taylor 1957; Keser et al. 1981; Chapman 1995; Adey and Hayek 2005). This is especially the case in eastern Canada where both genera can achieve high frond densities and cover in a large portion of the intertidal zone (Novaczek and McLachlan 1989; Heaven and Scrosati 2008). Exceptions are the inner reaches of the Bay of Fundy and the Gulf of St. Lawrence where soft substrata predominate or ice abrasion limits intertidal perennial algae (Novaczek and McLachlan 1989; Garbary et al. 1991). Here we examine photosynthetic physiology in three species of fucoids from Nova Scotia: Ascophyllum nodosum (L.) Le Jolis, Fucus distichus L. ssp. distichus and F. vesiculosus L. Fucus and Ascophyllum are among the most widely used model systems in marine ecology (e.g., Chapman 1995; Brawley et al. 1999; Schiel and Foster 2006). Ascophyllum nodosum and F. vesiculosus have similar structure and life history (Fritsch 1945; Bold and Wynne 1985; Schiel and Foster 2006). Their perennial fronds are mostly 0.2 to 1.0 m long. Although both species have dichotomous branching, A. nodosum has much greater development of lateral branches. The fronds of F. vesiculosus are thin and wide, and have a thickened central ridge (midrib) with wings of tissue on either side. The fronds of A. nodosum are more elliptical in cross section and without a midrib. Consequently, the wings in older portions of blades of F. vesiculosus become considerably eroded relative to A. nodosum, where little to no erosion is apparent. Whether this tissue loss is caused by environmental (i.e., abrasion), developmental (i.e., apoptosis; see Garbary and Clarke 2001 for algal example) or biological (e.g., herbivory) factors, the basal branch segments of F. vesiculosus are often highly reduced, and sometimes limited to a wiry remnant. In A. nodosum the single air bladders or vesicles are at regular intervals and Algae Volume 24(2): 93-104, 2009

LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia

BackgroundDaphniids, commonly known as waterfleas, serve as important model systems for ecology, evolution and the environmental sciences. The sequencing and annotation of the Daphnia pulex genome both open future avenues of research on this model organism. As proteomics is not only essential to our understanding of cell function, and is also a powerful validation tool for predicted genes in genome annotation projects, a first proteomic dataset is presented in this article.ResultsA comprehensive set of 701,274 peptide tandem-mass-spectra, derived from Daphnia pulex, was generated, which lead to the identification of 531 proteins. To measure the impact of the Daphnia pulex filtered models database for mass spectrometry based Daphnia protein identification, this result was compared with results obtained with the Swiss-Prot and the Drosophila melanogaster database. To further validate the utility of the Daphnia pulex database for research on other Daphnia species, additional 407,778 peptide tandem-mass-spectra, obtained from Daphnia longicephala, were generated and evaluated, leading to the identification of 317 proteins.ConclusionPeptides identified in our approach provide the first experimental evidence for the translation of a broad variety of predicted coding regions within the Daphnia genome. Furthermore it could be demonstrated that identification of Daphnia longicephala proteins using the Daphnia pulex protein database is feasible but shows a slightly reduced identification rate. Data provided in this article clearly demonstrates that the Daphnia genome database is the key for mass spectrometry based high throughput proteomics in Daphnia.

Silene as a model system in ecology and evolution

The genus Silene, studied by Darwin, Mendel and other early scientists, is re-emerging as a system for studying interrelated questions in ecology, evolution and developmental biology. These questions include sex chromosome evolution, epigenetic control of sex expression, genomic conflict and speciation. Its well-studied interactions with the pathogen Microbotryum has made Silene a model for the evolution and dynamics of disease in natural systems, and its interactions with herbivores have increased our understanding of multi-trophic ecological processes and the evolution of invasiveness. Molecular tools are now providing new approaches to many of these classical yet unresolved problems, and new progress is being made through combining phylogenetic, genomic and molecular evolutionary studies with ecological and phenotypic data.

Integrative assessment of hydrological, ecological, and economic systems for water resources management at river basin scale

This study presents a basin-scale integrative hydrological, ecological, and economic (HEE) modeling system, aimed at evaluating the impact of resources management, especially agricultural water resources management, on the sustainability of regional water resources. The hydrological model in the modeling system was adapted from SWAT, the Soil and Water Assessment Tool, to simulate the water balance in terms of soil moisture, evapotranspiration, and streamflow. An ecological model was integrated into the hydrological model to compute the ecosystem production of biomass production and yield for different land use types. The economic model estimated the monetary values of crop production and water productivity over irrigated areas. The modeling system was primarily integrated and run on a Windows platform and was able to produce simulation results at daily time steps with a spatial resolution of hydrological response unit (HRU). The modeling system was then calibrated over the period from 1983 to 1991 for the upper and middle parts of the Yellow River basin, China. Calibration results showed that the efficiencies of the modeling system in simulating monthly streamflow over 5 hydrological stations were from 0.54 to 0.68 with an average of 0.64, indicating an acceptable calibration. Preliminary simulation results from 1986 to 1995 revealed that water use in the study region has largely reduced the streamflow in many parts of the area except for that in the riverhead. Spatial distribution of biomass production, and crop yield showed a strong impact of irrigation on agricultural production. Water productivity over irrigated cropland ranged from 1 to 1640 USD/(ha·mm−1), indicating a wide variation of the production conditions within the study region and a great potential in promoting water use efficiency in low water productivity areas. Generally, simulation results from this study indicated that the modeling system was capable of tracking the temporal and spatial variability of pertinent water balance variables, ecosystem dynamics, and regional economy, and provided a useful simulation tool in evaluating long-term water resources management strategies in a basin scale.

Carnivory and resource‐based niche differentiation in anuran larvae: implications for food web and experimental ecology

Summary1. Food webs represent the paths of material and energy flow through organisms in an ecosystem. Anuran larvae are important components of pond food webs: they are abundant, consume large quantities of food and serve as prey for many organisms. However, there are very basic uncertainties about the feeding ecology of anuran larvae; for instance, as to which trophic level they belong and whether species differ in resource use. Because anuran larvae have been employed in model systems in experimental ecology for decades, these uncertainties could lead to misinterpretation of published experiments, or inadequate designs of experiments directed at general, conceptual issues in ecology.2. Using13C and15N stable isotope and gut content analyses of free‐ranging and enclosed tadpoles of four ranid species (Lithobates sylvaticus,L. pipiens,L. clamitans,L. catesbeianus) in the food webs of six wetlands, we tested the following null hypotheses: (i) that anuran larvae are strict primary consumers; (ii) that they are non‐selective feeders and therefore exhibit little feeding niche differentiation; (iii) that they are opportunistic consumers and (iv) that their diet remains unchanged through ontogeny.3. All four species consumed and assimilated substantial amounts of animal food; bullfrog larvae, in particular, appear to be predatory. Significant feeding niche differentiation among species occurred with respect to the sources of carbon, consumption of animal matter and nutritional quality of food ingested. We further documented opportunistic feeding habits and ontogenetic shifts in diet.4. Collectively, these studies revealed complex trophic relationships that might require a reconsideration of the role of anuran larvae in pond food webs, as well as a reinterpretation of results of previous studies employing anuran larvae in model experimental systems.

Rate-Independent Hysteresis in Terrestrial Hydrology

The goal of this article is twofold. The first objective is to demonstrate the role of hysteresis in hydrology. The second objective is to describe a class of simple and convenient mathematical models of hydrological systems with hysteresis and to briefly discuss methods for the quantitative and qualitative analysis of such models. This article is organized as follows. In the first section we discuss the role of the Preisach model. We then present an explicit expression for analogues of wetting and drying curves in the Preisach model context. The central role in this section is occupied by special one-parameter classes of Preisach operators which are useful as models of soil-water hysteresis for particular soils. Fitting is discussed in the context of the GRIZZLY database of hysteretic soil-water characteristics. The second section introduces a simple but instructive example of a differential equation coupled with a Preisach nonlinearity. This equation serves as a basis for modeling vegetated soil in terrestrial hydrology. The third section is dedicated to the FEST model, where FEST stands for "fully vegetated slab of soil with transpiring plants". This model describes drainage, transpiration, and infiltration flows in a fully vegetated slab of soil. We demonstrate that hysteresis effects are critical, both on qualitative and quantitative levels, for modeling hydrological systems and flows in soil, while theoretical analysis and numerical implementation of the models raise interesting mathematical questions. To demonstrate the application of this model we use rainfall data gathered in the Feale region in County Kerry, Ireland, covering a period of 19 months between July 2002 and February 2004. The FEST model includes a quantitative description of the dynamics of the plant biomass, which depends on the amount and regularity of precipitation and soil type, including details of soil-water hysteresis. Hence, the FEST model can be used as a component of ecological system models. Finally, the qualitative properties of the FEST model are discussed.

Trait-Based Community Ecology of Phytoplankton

Trait-based approaches are increasingly used in ecology. Phytoplankton communities, with a rich history as model systems in community ecology, are ideally suited for applying and further developing these concepts. Here we summarize the essential components of trait-based approaches and review their historical and potential application to illuminating phytoplankton community ecology. Major ecological axes relevant to phytoplankton include light and nutrient acquisition and use, natural enemy interactions, morphological variation, temperature sensitivity, and modes of reproduction. Trade-offs between these traits play key roles in determining community structure. Freshwater and marine environments may select for a different suite of traits owing to their different physical and chemical properties. We describe mathematical techniques for integrating traits into measures of growth and fitness and predicting how community structure varies along environmental gradients. Finally, we outline challenges and future directions for the application of trait-based approaches to phytoplankton ecology.

Physical activity leisure‐time participation of boys with developmental coordination disorder

Physical activity leisure‐time participation of boys with developmental coordination disorder

Influence of horizontal model grid resolution on the simulated primary production in an embedded primary production model in the Norwegian Sea

The purpose of this paper is to investigate the influence of horizontal grid resolution in a physical model on an embedded primary production model. The area for the experiment was along the west coast of Norway, from 60° N to 70° N, an area of high mesoscale activity. The HYbrid Coordinate Ocean Model was coupled with the NORWegian ECOlogical Model system, and run in a nested system, consisting of three model grids with horizontal resolution of 50 km, 16 km and 4.5 km (hereafter: COARSE, MEDIUM and FINE) in the focus area. Two main results were obtained, first, the composition of the phytoplankton functional groups changed with increasing model grid resolution. In FINE, the diatoms produced a larger part (60%) of the total annual primary production than the flagellates, whereas in COARSE and MEDIUM, the primary production from the two phytoplankton groups was the same. This was explained by a higher transport of silicate into the euphotic layer in FINE compared to the other two. Second, the differences in the primary production first became large when the resolution of the model grid reached the Rossby radius of deformation. Whereas the total net primary production in MEDIUM only was 5% larger than in COARSE, the total net primary production in FINE was 20% higher than in COARSE. This was explained by the models ability to resolve mesoscale activity.

Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing

Next generation sequencing technology affords new opportunities in ecological genetics. This paper addresses how an ecological genetics research program focused on a phenotype of interest can quickly move from no genetic resources to having various functional genomic tools. 454 sequencing and its error rates are discussed, followed by a review of de novo transcriptome assemblies focused on the first successful de novo assembly which happens to be in an ecological model system (the Glanville fritillary butterfly). The potential future developments in 454 sequencing are also covered. Particular attention is paid to the difficulties ecological geneticists are likely to encounter through reviewing relevant studies in both model and non-model systems. Various post-sequencing issues and applications of 454 generated data are presented (e.g. database management, microarray construction, molecular marker and candidate gene development). How to use species with genomic resources to inform study of those without is also discussed. In closing, some of the drawbacks of 454 sequencing are presented along with future prospects of this technology.

Editorial: Ecological complex systems

Main aim of this topical issue is to report recent advances in noisy nonequilibrium processes useful to describe the dynamics of ecological systems and to address the mechanisms of spatio-temporal pattern formation in ecology both from the experimental and theoretical points of view. This is in order to understand the dynamical behaviour of ecological complex systems through the interplay between nonlinearity, noise, random and periodic environmental interactions. Discovering the microscopic rules and the local interactions which lead to the emergence of specific global patterns or global dynamical behaviour and the noise’s role in the nonlinear dynamics is an important, key aspect to understand and then to model ecological complex systems.

A quantitative genetics and ecological model system: understanding the aliphatic glucosinolate biosynthetic network via QTLs

Plants’ sessile nature has led them to develop chemical defenses, secondary metabolites, to directly cope with environmental changes rather than escape to more favorable sites. The diversity and fluctuation in biological stresses faced by a plant have generated extraordinary genetic diversity controlling the synthesis and regulation of secondary metabolites that is only now being explored. The glucosinolate secondary metabolites, amino acid derived thioglucosides specific to the order Capparales, is a model system for understanding the molecular basis of complex quantitative traits and their potential ecological role. This review focuses on the extensive progress being made towards understanding the complete molecular basis underlying the glucosinolate genetic diversity at both biosynthetic and regulatory loci. This has identified a highly interactive genetic network whereby biosynthetic loci have additional functions as regulatory loci and laid the foundation for glucosinolates to be a model system for understanding quantitative traits in a broader context.

Age, Emotion Regulation Strategies, Temperament, Creative Drama, and Preschoolers' Creativity

AbstractBased on Yeh's (2004) Ecological Systems Model of Creativity Development, this study investigated the effects that age, the use of emotion regulation strategies, temperament, and exposure to creative drama instruction have on the development of creativity among preschool children. Participants were 1164‐ to 6‐year‐old preschool children. This study categorized the emotion regulation strategies used by preschool children and developed a creativity test which includes the measurement of usefulness, an indicator of creativity that has, until now, been ignored. The main findings are that (a) 6‐year‐olds outperform 4‐ and 5‐year‐olds in terms of creativity; (b) emotion regulation strategies as well as a positive temperament have positive effects on children's creativity; (c) creative drama instruction contributes to children's creativity; and (d) age group, emotion regulation strategies, temperament, and creative drama instruction can collectively predict children's creativity.

Machine Learning Methods Without Tears: A Primer for Ecologists

Machine learning methods, a family of statistical techniques with origins in the field of artificial intelligence, are recognized as holding great promise for the advancement of understanding and prediction about ecological phenomena. These modeling techniques are flexible enough to handle complex problems with multiple interacting elements and typically outcompete traditional approaches (e.g., generalized linear models), making them ideal for modeling ecological systems. Despite their inherent advantages, a review of the literature reveals only a modest use of these approaches in ecology as compared to other disciplines. One potential explanation for this lack of interest is that machine learning techniques do not fall neatly into the class of statistical modeling approaches with which most ecologists are familiar. In this paper, we provide an introduction to three machine learning approaches that can be broadly used by ecologists: classification and regression trees, artificial neural networks, and evolutionary computation. For each approach, we provide a brief background to the methodology, give examples of its application in ecology, describe model development and implementation, discuss strengths and weaknesses, explore the availability of statistical software, and provide an illustrative example. Although the ecological application of machine learning approaches has increased, there remains considerable skepticism with respect to the role of these techniques in ecology. Our review encourages a greater understanding of machin learning approaches and promotes their future application and utilization, while also providing a basis from which ecologists can make informed decisions about whether to select or avoid these approaches in their future modeling endeavors.

Maintenance of clinal variation for shell colour phenotype in the flat periwinkle Littorina obtusata

Clines can signal spatially varying selection and therefore have long been used to investigate the role of environmental heterogeneity in maintaining genetic variation. However, clinal patterns alone are not sufficient to reject neutrality or to establish the mechanism of selection. Indirect, inferential methods can be used to address neutrality and mechanism, but fully understanding the adaptive significance of clinal variation ultimately requires a direct approach. Ecological model systems such as the rocky intertidal provide a useful context for direct experimentation and can serve as a complement to studies in more traditional genetic model systems. In this study, we use indirect and direct approaches to investigate the role of environmental heterogeneity in the maintenance of shell colour polymorphism in the flat periwinkle snail, Littorina obtusata. We document replicated clines in shell colour morph frequencies over thermal gradients at two spatial scales, contrasting with patterns at previously reported microsatellite loci. In addition, experimental results demonstrate that that shell colour has predictable effects on shell temperature and that these differences in temperature, in turn, coincide with patterns of survivorship under episodic thermal stress. Direct manipulation of shell colour revealed that shell colour, and not a correlated character, was the target of selection. Our study provides evidence that spatially varying selection via thermal regime contributes to the maintenance of shell colour phenotype variation in L. obtusata in the sampled areas of the Gulf of Maine.

Agroforests as Model Systems for Tropical Ecology1

Agroforests as Model Systems for Tropical Ecology¹

Community resilience and contemporary agri‐ecological systems: reconnecting people and food, and people with people

AbstractAlternative agricultural systems that emphasize ecological and community resilience provide a bridge between traditional agriculture and natural resource management. These can be referred to as agri‐ecological systems and include systems such as Organic Agriculture, Biodynamics, Community Supported Agriculture (CSA), Permaculture, Farmers Markets and Community Gardens. This paper reports on current research by the author to explore a range of these systems and how they contribute to agri‐ecological and community resilience. For example, resiliency can be seen as a system's ability to adapt and respond to external impacts on a system, and farmers markets show resiliency to sudden market changes (such as price or consumer preferences toward organics, through direct sale and the involvement of a range of consumers and producers offering a broad range of organic produce). That is, this paper reviews these alternative approaches to food production in relation to key concepts from ecological systems thinking, such as ecological resilience, biodiversity and holism. More specifically, the paper explores how agri‐ecological systems contribute to more sustainable and resilient communities, through community development processes such as relationship building, genuine participation, inclusiveness, resource mobilization and creating space for knowledge sharing. The paper concludes by comparing ecological systems models to agri‐ecological systems, and suggests how ecological systems theories and concepts might contribute to thinking about the future of community‐based agri‐ecological resilience. Copyright © 2008 John Wiley & Sons, Ltd.