A PRIMER ON ECOLOGICAL MODELLING IN LIMNOLOGY Carlos Ruberto Fragoso Jr1; Tiago Finkler Ferreira1; David da Motta Marques1 1 Federal University of Rio Grande do Sul, Hydraulic Research Institute, CP 15029, Porto Alegre, RS, Brazil. crubertofj@hotmail.com, tiagofferreira@hotmail.com, dmm@iph.ufrgs.br LIMNOLOGY AND ECOLOGICAL MODELLING The shared management of natural resources, based on specific knowledge, is the best form of promoting environmental conservation. In aquatic ecosystems, the conservation of water resources depends on specific understanding and management of limnological variables. However the wide range of physical, chemical and biological processes and factors, and their interactions, makes the quantitative analysis of the aquatic ecosystems very difficult. In addition, management of aquatic ecosystems is, by their characteristic, a field of multidisciplinary action, where there is a great number of alternatives on planning and forecasting, considering their uses, availability and preservation (Tucci, 1998).Thus, the diversity of methodological approaches available to quantify processes are essential to acquire higher understanding of the dynamics in natural systems and promoting tools for accurate decision making. One of these approaches is the mathematical ecological modelling applied to limnology. Models focused on ecological themes are thinking pad at the limnologist disposal. It allows the formulation of questions and obtaining answers considering the pre-established outline conditions, it allows the formulation of hypotheses and their test, as well as the development and consolidation or the refutation of theories. A model is the representation of some object or system, in a language easily accessed and used, with the means of understanding and searching for answers according to different inputs. In order to better represent reality, a model must simulate the highest possible number of processes that occur in nature. The larger the number of involved interactions the more complex the systems, and, consequently, the more A primer on Ecological Modelling in Limnology 2 challenging and necessary are the models. In Limnology, a model is a tool developed in order to assist the understanding of an aquatic ecosystem, considering the involved drivers, direct or indirect, and in different scales, including the antropic (e.g. social, economical) and natural (e.g. climatic, chemicals, biological, hydrographic basin, hydrology, hydrodynamic) factors, and their interactions and processes. Ecological models can be applied on the Limnology, e.g., for: (a) evaluation responses of trophic cascading interactions before changes in nutrient concentrations (Janse, 2005; Jeppesen et al., 2002; Jakobsen et al., 2004; Scheffer et al., 1993; Moss, 1990; Moss et al., 1996; Perrow et al., 1994, Ferreira et al., 2008,); (b) prediction of phytoplankton blooming (Fragoso Jr, 2005, Lucas et al. 1999a, 1999b; (c) determination of the trophic state in aquatic ecosystems (Kishia et al., 2007); (d) investigation of ecological concepts in limnology such as the theory of alternative stable states (Van Nes et al., 1999; Ferreira et al., 2008; Fragoso Jr. et al., 2007); (e) assesment of biomanipulation impacts (e.g. fishing or alteration of trophic interactions) on the system (Carpenter & Kitchell, 1993; Hansson et al., 1998; Meijer et al., 1994; Shapiro et al., 1975; Shapiro & Wright, 1984; Van Donk et al., 1990); (f) estimative of gross primary production, community respiration and net production of the ecosystem in terms of carbon (Mukherjee, et al, 2002; Sandberg, 2007); (g) evaluation of pollution levels. A model must not be considered as an objective, but as a tool for reaching a determined goal. It may be utilized with the means of prediction; understanding processes; filling the variables of interest within a period without survey; and the generation of hypotheses, which may be tested experimentally or in situ. It is worthy to emphasize that the modelling should be utilized in partnership with experimental, laboratorial and monitoring works, otherwise its potentiality of application may become fulfilled. There is a wide range of software with restrict access or publicly available (e.g. SWMM, 2004; AQUATOX, 2004; Chapra and Pelletier, 2003), which may be acquired for analyzing a A primer on Ecological Modelling in Limnology 3 determined ecological issue. However, these models manuals, many times, do not disclose an appropriate description of the applied methodology, neither a description of their limitations and advantages. Therefore, this chapter aims at providing conditions of analyzing existent models, supplying a conceptual base for the construction of simple ecological models to the application in environmental problems associated with aquatic ecosystems or in scientific investigations. The application of models for scientific questions is almost compulsory if we want to understand a complex system as an aquatic ecosystem. It is not simple to investigate all the components and their interactions in the ecosystem without using models as a synthesis tool. The use of modelling as a tool for understanding the proprieties of the system has advantages and has been revealing gaps in our knowledge. Perhaps the main contribution provided by a model may be the establishment of research priorities, which may reveal proprieties of the system from scientific hypotheses generated by the model itself. Therefore, the models by simulating the interactions in the aquatic ecosystem not only generate results that may be compared with in situ or experimental observations, but also may serve as a thinking base for important scientific questions. History of the development of models The evolution of modelling may be divided in four great phases (Figure 1). These phases are related to the social interest and the computational capacity offered in the period. The first works on modelling appeared around the 20’s with the urban wastewater problem. The pioneer modelling work was done by Streeter and Phelps (1925) in Ohio River. This work and the subsequent ones were focused on the evaluation of the dissolved oxygen levels in rivers and estuaries. Still without the availability of computers, these applications were limited to linear solutions, with simple geometry and considering a steady state. A primer on Ecological Modelling in Limnology 4 Reaeration 1925 -1960 ( Streeter -Phelps ) Problems: untreated and primary effluent Pollutants: BOD/DO Systems: rivers/estuaries (1D) Kinetics: linear Solu tions: analytical DO BOD P R DO sed 1960 -1970 (computerization) Problems: untreated and primary effluent Pollutants: BOD/DO Systems: rivers/estuaries (1D / 2D) Kinetics: linear Solu tions: analytical and numerical Fish 1970 -1977 (Biology) Problems: eutrophication Pollutants: nutrients Systems: rivers/lakes/estuaries (1D / 2D / 3D) Kinetics: nonlinear Solution: numerical Zoo Phyto NO 3 NH 3 PO4 Porg Norg 1977 - Present (Toxics) Problems: toxics Pollutants: organics and metals - interactions/ Systems: water-sediment food-web interactios (1D / 2D / 3D) Kinetics: nonlinear Solutions: numerical and analytical Solids Toxics Biota water sediment Solids Pore water Benthos Figure 1. Four periods of development of the models for limnology (Adapted from Chapra, 1997). In the 60’s the computers appeared as a widely available tool and this leading to a greater advance of the models and their applications. The oxygen was still the focus, but the computers allowed the solution of more complicated problems, as complex geometries, more detailing of the kinetic reactions and non-steady simulations (dynamic simulations). In the 70’s, another outstanding phase occurred stimulated by the environmental consciousness from the period. The dissolved oxygen problems associated to point sewage sources gave rise to the awareness of eutrophication problems in aquatic ecosystems. In this A primer on Ecological Modelling in Limnology 5 period, the first models that were developed would represent the dynamic of the aquatic food chain, such as the models by Chen (1970) and Di Toro et al. (1971). With the additional computational advances, non-linear and retroactive solutions could be applied in systems with complex domains. The most recent phase of models development turned to issues involving toxic, pathogenic and trace-metal substances, which represent a great threat for the human health and the aquatic ecosystem. This issue has also been effectively marked by generated political debates. However, the past problems still endure theses days, once the computational progress has provided solutions closer to reality. Ecological models An ecological model considers, in its conceptual structure, part or fraction of the processes related to the biota of the ecosystem. In aquatic ecosystems, the ecological model tries to simulate the processes inherent of the aquatic trophic interactions in order to evaluate the organisms’ dynamics (Figure 2). The abiotic and biotic components in the aquatic environment have different processes of development and, therefore, different approximations to be included in the modelling. Empiric or deterministic functions may approximate these processes. The mathematics representation of processes, such as, the primary, secondary production and other eco-physiologic traits, are available in the literature, although many of them depict the reality of temperate ecosystems. A few models can distinguish classes of groups with phytoplankton, macrophyte and fish, and, therefore, generalize the main processes of great groups as a state variable for all. However, currently, there have already been models capable of distinguishing classes of phytoplankton (i.e. cyanobacteria, green algae, diatoms, etc), macrophyte (i.e. A primer on Ecological Modelling in Limnology 6 submerged, emergent and floating) and fish (i.e. piscivorous, omnivorous and planktivorous), considering their stages of life (juvenile and adult) (e.g. Janse, 2005; Fragoso Jr. 2007). In order to depict the high level of functional diversity of the aquatic organisms, the ecological models must include the main processes of each group within modules form that contain a group of differential equations representative of ecological functions and metabolic coefficients related to the biological processes. These coefficients are found in situ or experimentally such as (a) respiration rates, primary and secondary production; (b) limit capacity of support (carrying capacity) of biomass or species density per area or water volume, (c) nutrients assimilation (i.e. phosphorous, nitrogen and silicate) by primary producers, (d) competition by nutrients available in the water column, (e) absorption of photosinthetically active radiation (PAR), growing rates, reproduction and mortality; (f) excretion, biomass loss and decomposition. Currently, with the computational available capacity, the mathematical approaches tend to include, with a greater level of detail, all the elements of the aquatic food-web (i.e. communities, complete cycle of phosphorous, nitrogen, silica, carbon and their interactions among the organisms), which are essential for the evaluation of stocks (e.g. plankton compartments, aquatic macrophyte, fish, and benthos), and system processes and patterns.. A primer on Ecological Modelling in Limnology 7 Figure 2. Simplification of the aquatic food web. The thickness of the arrows indicates the strength of interaction. (Adapted from Carpenter & Kitchell, 1993). MODELLING ELEMENTS A mathematical modelling consists, basically, of four components aiming to represent a specific phenomenon of interest: (a) governing functions or external variables; (b) state variables; (c) mathematical equations; and (d) parameters (Figure 3). These components assist the translation of a determined phenomenon existent in the nature towards a mathematical language. On this section, we will thoroughly describe each component of the mathematical modelling and their inter-relations. A primer on Ecological Modelling in Limnology 8 Phenomenon of interest Parameters Driving forces or external variables Equations State variables Figure 3. Elements of modelling and their inter-relations for explaining a determined phenomenon. Phenomenon of interest The phenomena are patterns found in nature that may be observed or noticed (e.g. precipitation, rivers flow, eutrophication, and alteration of the aquatic trophic structure promoted by some natural or anthropogenic stressors). Typically, the phenomena are described from the pre-established assumptions related to homogeneity, uniformity and universality of the proprieties and their main components, which include temporal and spatial relations descibing the phenomenon. Nevertheless, in order to model the phenomena with the necessary level of realism, these rigid assumptions have been simplified and approximated in such form so that the model may be able to represent (Couclelis, 1997): • The space as a non-homogeneous entity as well in its proprieties as in its structure. • The surroundings as non-estationary relations. • The rules of transition as non-universal rules. • The variation of time as a regular or irregular process. • The system as an open environment to external influences. A primer on Ecological Modelling in Limnology 9 For implementing dynamic spatially ecosystems with the characteristics mentioned above, some basic principles relative to the main elements from these systems must be considered. Among these principles, it must be emphasized: (a) the way of temporal and spatial representation, (b) the structure of the model itself to be utilized for the representation of spatial phenomenon and (c) the computational approach for implementing these principles in an integrated and consistent form. On the next sections, we will discuss on the elements of mathematical modelling utilized for the representation of an interest phenomenon. Driving forces or external variables Functions or variables of nature are the ones that influence the state of the aquatic ecosystem. In the management context, the problem may be formulated in the following way: if some phenomena are variable, which one will influence the state of the ecosystem? In this sense, the model is used for predicting the change in the ecosystem when external variables are altered in time and space. For example, a nutrient input, climate changes, inflow or outflow in the system may be considered as external variables or driving forces. State variable The state variables describe, as the name indicates, the state of the ecosystem. The selection of state variables is crucial for the model structure, but generally, in most cases, this selection is trivial. We may, for example, choose for modelling the state of eutrophication in a lake, where the concentration of phytoplankton and nutrients as state variables is intuitive. The states variables are related to the external variables and may be considered as a model outcome. Depending on the purpose of the application of a model, it will contain more state variables than is necessary, since a state variable may explain others. For instance, in models of eutrophication, A primer on Ecological Modelling in Limnology 10 the zooplankton could be included as a state variable, which promote a grazing control on the phytoplankton concentration. Mathematical equations The physical, chemical, physical and biological processes (e.g. nitrification, primary production, mortality, interactions, sediment nutrients release) are represented in the model through mathematical equations. These equations are the relations between the external variables and state variables. The same process may be found in different aquatic ecosystems, suggesting that the same equation may be used in different models. The relations for each process may be found in the literature or may be obtained directly from field and experimental work (e.g. Jorgensen, 1986; Sheffer, 1998; Chapra, 1997). A determined process can be made of innumerable mathematical equations, and, thereby, the modeler has to decide which equation better represent that process with the smallest number of simplifications. Parameters The parameter is a value that characterizes a process in the ecosystem, and may be considered constant for a particular system or for one part of the system, indicating that a parameter can also be variable in time and space. In ecological models the parameters have a scientific definition, as, for instance, the maximum growth rate of phytoplankton or the grazing rate of zooplankton. The complexity of a model has been represented by the quantity of applied parameters. Simple models have a lower quantity of parameters, while complex models have a larger number. Groups of known or suggested values for specific parameters can be found in the literature. However, the majority of parameters are subjected to adjustments with the means of approximating the maximum outcome of the model to the values observed in the field. A primer on Ecological Modelling in Limnology 11 THE MODELLING STEP BY STEP As a research method modeling has a methodological orientation to be followed. In this sense, different schemes were elaborated aiming to describe the phases concerning a process of Mathematical Modelling. There have been several methods with different number of phases, however, it is important that each method contemplate the specific objectives of the problem. Different objectives need different spatial and temporal scales. A general scheme has been compounded in eight phases (Figure 4). From these phases, some have been very generic and may be particularly treated by each modeler, although others have been considered normative (i.e. pattern) and have deserved a greater detailing, and are described briefly as follows. Definition of the problem Given a real situation, the problem to be studied must be identified. The problem is nothing more than an observed phenomenon that we want to represent mathematically. Subsequently, the elements of modelling, necessary for its solution, have to be specified. There are several problems in Limnology to which a mathematical model might contribute, somehow, in the understanding of processes, prediction, generation of hypotheses, or even in the behavior of variables of interest for periods without observation. (Figure 5). A primer on Ecological Modelling in Limnology Definition of the problem Conceptual model 12 Selection of complexity Association of the problem with time, space and sub-systems Quality of data? Data acquisition Simplification and formulation of hypotheses (conceptual) Deduction of the mathematical model (equations) Resolution of the mathematical problem Demanded Revision Calibration and validation of the model Application Figure 4. An approximation of the modelling procedure (Adapted from Jørgensen, 1986). Eutrophication Cyanobacteria blooms Net ecosystem production Biomanipulation Themes in Limnology Trophic interactions Carbon cycle Fishing Water management Alternative steady states Figure 5. Themes in Limnology that can be evaluated using mathematical models. Simplification and formulation of hypotheses A primer on Ecological Modelling in Limnology 13 In this phase, the modelling elements are examined and selected in order to preserve the characteristics of the problem. For that, it is necessary to simplify the reality and define the the driving functions, processes and state variables representative of the phenomenon of interest. Additionally, the parsimony principle must be applied. This principle advocates the adequate representation of a process and/or system behavior by a model with the possible smaller number of variables and/or parameters. For example, in estuaries where the tides action rules the hydrodynamic of the system, and, consequently, the pollutants transportation, the effect of the wind may be discarded or simplified. In deep lakes or reservoirs, the vertical processes are more important than the horizontal processes. On the other hand, in shallow lakes, where stratification of the water column does not occur, the horizontal processes are more important. In summary, this is a decisive phase for modelling, in which the modeler defines the conceptual model. This conceptual model is a simplified scheme, utilizing blocks and arrows, which shows the involved state variables, the processes and the interactions among the variables of interest. For example, for exploring some basic proprieties of interactions between the phytoplankton and zooplankton, the simple model of prey-predator of Lotka-Volterra is generally utilized (Scheffer, 1998). This example will be adopted for the elaboration of its conceptual scheme. This model considers the phytoplankton and zooplankton biomass as variables of interest (blocks) and the processes of interactions among the organisms as flows (arrows) (Figure 6). The processes or interactions among the variables of interest are mathematically represented by equations. It is up to the modeler to choose the approximation that will be adopted in each process. For example, the production of phytoplankton biomass is a biological process that depends on several factors, such as the distribution of the light through the water column, temperature of water and nutrients availability. The modeler could opt for choosing an equation that would involve all these factors, a combinations of them or, simply, choosing a A primer on Ecological Modelling in Limnology 14 constant rate of daily production that would reduce all the driving factors for the phytoplankton production in only one coefficient (Figure 7). The larger the number of parameters and external variables involved in the calculation of a process the better is the approximation with the reality and greater is the difficulty of their estimation in field or experimentally works. The representation of a process by a constant value may be a gross simplification of reality, however it is a way to condensate all the process through only one parameter (constant rate). Thereby, the understanding and control of such process is facilitated. Figure 6. Scheme representing the prey-predator model of Lotka-Volterra, which the variable of interest is the phytoplanton and zooplankton biomass. The challenge of the modeler is always finding the easiest alternative, considering the complexity of the model (number of involved parameters), to investigate the object of study without missing the approximation with reality (Figure 8). As mentioned previously, at this time it is worthy the application of the parsimony principle that is the adequate representation of the behavior of a system or process, through a model, with a possible smaller number of parameters. A primer on Ecological Modelling in Limnology 15 Production Light L 2,781 f e 1 e 2 ke H Constant rate Temperature T Gmax TT Nutrients 20 N N kN N Figure 7. Possible mathematical representations of the phytoplanktonic biomass production. Complexity Aproximation Optimal number of parameters Number of parameters Figure 8. Model complexity versus solution approximation (difference between real and modeled solutions). The joint of the two curves represents the optimal number of parameters utilized to represent a specific process or phenomenon. Deduction of the mathematical model In this stage, the conceptual language is replaced by a coherent mathematical language. That is, the state variables and flows have been written in mathematical terms. For each state A primer on Ecological Modelling in Limnology 16 variable, a flow balance is checked with means of representing the continuity in an infinitesimal interval of time (dt) (Figure 9). The equation of continuity for a state variable, A, discarding the flows related to transportation and chemical reactions, may be written as: dA input output dt (1) The differentiation of state variable (A) in relation to time (t) represents the balance of the variable of interest in a certain interval of time or its internal variation in that interval. The differential has a flow unit and, thus, the balance of the variable of interest must be also in terms of flows. For example, the prey-predator model mentioned previously could be represented by the following differential equations: dF rF g z FZ production grazing dt (2) dZ e z g z FZ m z Z growth mortality dt (3) The first term on the right side of the Equation 2 represents the quantity of biomass fixed through the photosynthesis within the time interval. The second term describes the losses of phytoplankton biomass (negative flow) due to the consumption by zooplankton. The population of zooplankton converts the ingested food in growing with certain efficiency (ez) and suffers losses due to respiration and mortality for other organisms. The phytoplankton biomass (F) and zooplankton (Z) are the state variables of interest in this model. A primer on Ecological Modelling in Limnology 17 Figure 9. Representation of the input and output flows (processes) for a specific state variable (A). The flows related to transport and chemical reactions could also be included in the model. It is worth to emphasize that the decision of what factors will be included in each term for better representing a determined process is responsibility of the modeler. For example, the primary production is associated with various factors, such as, temperature, light, nutrients, and concentration of the phytoplankton itself, among others. In this simplified model, it was assumed that the primary production would only depend on the phytoplankton concentration and other factors would be neglected. This false supposition may not represent this process at all, but, on the other hand, only one parameter was used (r) in order to minimize the complexity of the model (principle of parsimony). Resolution of the mathematical problem During this phase mathematics and computational resources are used by the modeler aiming the solution of the formulated mathematical problem. The mathematical methods utilized to solve the differential equations may be analytical or numerical. After the equations resolution, the next step is choosing an appropriate computational language for the implementation of the differential equations of the model (Figure10). There are several available softwares that refer to this subject, such as, EXCEL, MAPLE, MATLAB, FORTRAN, C++, DELPHI e TURBO A primer on Ecological Modelling in Limnology 18 PASCAL. The mathematical software choice is directly related to the modeler familiarity with the program, as well as to the complexity of the problem to be resolved. Some mathematical programs have taken advantages in relation to others in terms of processing speed and availability of pre-built functions. The model code is an important part of model development and may take some time to optimize and run free of bugs. Figure 10. Computational mathematical programs which process information and generate results. Calibration and validation of the model After the model is formulated , it is necessary to calibrate and validate the model. This is achieved by adjusting the parameters so that the model’s outcome approximates to the observed A primer on Ecological Modelling in Limnology 19 data. (Figure 11). The calibration of the model may be achieved by try and error or by algorithms able to calibrate the parameters automatically utilizing objective functions that minimize the difference between the calculated and observed values. The validation of the model consists of testing the calibrated parameters in another period with the observed data. In case the model is not be considered valid, that is, if the model’s outcome was not close to the observed data, the modeler must reformulate hypothesis and simplifications and restarts the process. Observ Observated Calculated Calcula A Calibration period Validation period Figure 11. Process of model calibration and validation. The efficiency of the model estimative is measured through statistical techniques that evaluate particular characteristics from the calculated series. Examples of these techniques are presented in Table 1. The coefficient of determination Nash-Sutcliffe (R2) prioritises the comparison of values with the observed values mean; the root-mean-square error (RMSE) gives a higher weight to the values with a greater magnitude, and, the root-mean-squared-error inverted (RMSEI) prevails the adjustment to the small order values. A primer on Ecological Modelling in Limnology 20 These techniques of model efficiency analysis may demonstrate interesting aspects for the comprehension of restrictions, limitations and advantages of models. In general, due to the great number of differential equations used in ecological models (what leads to an increased quantity of parameters), the determination of a set of parameters that is better in agreement with the observed data may be a challenging task. In order to minimize this complexity, some abiotic processes and eco-physiological aspects of the aquatic organisms of the ecosystem could be adjusted separately in specific experiments, what would reduce the number of involved parameters in the calibration phase. This type of experimental calibration is denominated parameterization, which is guided to experimental adjustment of global abiotic and biological process coefficients within the aquatic ecosystem. That is, the parameterization refers to the adjustment of parameters through the variation estimative of such processes within established gradients. For example, in order to adjust the eco-physiological parameters related to state variables of phytoplankton or macrophytes (e.g. primary production, respiration, excretion), it is necessary to evaluate the variation of these processes within a controlled variation of the controlling abiotic variables (e.g. temperature, light, pH, etc). The necessity of parameterization is due to the large number of existent parameters in complex ecological models for representing, in a more approximate way, possible ecological, populational and eco-physiological processes and functions. Table 1. Coefficients used for describing the efficiency of the adjustments of the models. Coefficients Coefficient of determination by Nash-Sutcliffe (R2) Equation1 R2 1 YObs t YCal t 2 2 YObs t YObs t A primer on Ecological Modelling in Limnology Root-Mean-Square-Error (RMSE) Root-Mean-Square-Error (RMSEI) 21 RMSE Inverted RMSEI YObs t YCal t N 2 1 1 YObs t YCal t N 2 is the observed value, YCal is the value calculated by the model, YObs is the mean values observed and 1 YObs N is the total number of the values. Application of the model If the model has been considered valid, the same may be utilized in applications with diverse objectives, such as generating hypotheses, better understanding of a problem, explaining a phenomenon, analyzing the behavior of state variables, making forecasting and making decisions based on the outcome results. The last application option is the one that makes possible the management of situations associated with impacts on aquatic systems (i.e. study of scenarios). Considering the prey-predator model, proposed by Equations 2 and 3, the two organisms interact among themselves, where one of them serves as a primary food source to the other. In this application, the mathematical modeling was utilized for better understanding the related processes in the competition between these two organisms. For a specific set of parameters (ecosystem condition), phytoplankton works as prey and zooplankton as predators (Figure12). 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