Rozprawy doktorskie na temat „Ecosystem modelling”

At present, the viability of biodiversity in most of the remaining natural areas of the world is primarily threatened by human encroachment. This has led to an increased demand for active conservation. However, in order to devise and implement appropriate management strategies for a particular area, a specific understanding of ecosystem function is required. Creating a simulation model using available research data may provide a way to achieve this. In this thesis, the construction of a comprehensive model delineating the dynamics of the Serengeti-Mara ecosystem is initiated. Using the abundance of research data collected on this ecosystem over the last 40 years, the processes involved in setting-up such a model are investigated. First, a basic foundation, accommodating the spatial and temporal variation in climate and physiography across the Serengeti region, is established. The relationship between grass growth and rainfall is then incorporated, along with the mechanisms concerned with limiting grass availability, the subsequent survival and recruitment of grazing herbivores and finally, the influence of predation upon those herbivores. The model, even in these early stages of development, adequately depicted dynamics equivalent to those in the Serengeti-Mara ecosystem, indicating that the methods used were appropriate. It was found that grass availability was not the primary factor influencing the overall dynamics of grazing herbivores within the ecosystem, and only migratory wildebeest appeared to be strongly influenced by this factor throughout the time-scale of the model. It was suggested that other factors were responsible for regulating the majority of herbivore populations. By identifying where further research is required to increase our understanding of this particular ecosystem's function, the model demonstrates its effectiveness as an analytical tool. For the long-term conservation of the Serengeti-Mara ecosystem and other similar ecosystems, this reveals that the construction of such models is certainly beneficial, if not essential.

The potential for life to control its environment was first suggested by Lovelock (1972). Charlson et al (1987) proposed a role for marine planktonic ecosystems in global climate regulation via the production and ventilation to the atmosphere of dimethylsulphide (DMS), a by-product of phytoplankton metabolism. Once in the atmosphere DMS contributes to the formation of cloud condensation nuclei, and increases the amount and brightness of cloud. This affects the albedo of the planet, reflecting more incident sunlight back into space, and cooling the earth. In common with many other 'hypotheses' regarding complex adaptive systems, the hypothesis proposed by Charlson et al (1987) is not experimentally testable. The production and ventilation to the atmosphere of DMS is the result of complex interactions between biological, chemical and physical processes. Consequently, increasing use is being made of mathematical models that simulate these processes to advance understanding of it (Archer et al. 2002). This study examines one of the fundamental mechanisms proposed by the Charlson et al (1987) hypothesis, that increasing global temperatures will lead to increased ventilation of DMS from the ocean to the atmosphere. The study develops one-dimensional biogeochemical models of DMS production by upper ocean ecosystems, based on the model proposed by Gabric et al. (1993b). The models are examined to elucidate their fundamental mathematical properties, and are subjected to sensitivity analysis to identify important processes and parameters. These investigations identify a simpler model that can reproduce the predictions of the Gabric et al. (1993b) model. Predictions derived from model simulations forced by climatologies of measured physical data are compared to a global database of measurements of sea surface DMS concentrations, and to observed depth profiles of DMS in the upper ocean. These comparisons confirm that all models are in good qualitative agreement with measured data. The fifteen global climate prediction models currently in use around the globe all predict substantial warming effects from the ventilation of anthropogenic carbon dioxide to the atmosphere. A simplified DMS model is calibrated to climatologies of Antarctic chlorophyll and DMS data and reproduces the data with great precision. The calibrated model is applied in global warming scenarios to 'test' the efficacy of the mechanism proposed by the Charlson et al (1987) hypothesis. This simulation provides evidence that the response predicted by the hypothesis is indeed feasible, and that substantial increases (up to 45%) in the ventilation of DMS to the atmosphere could be possible in some circumstances. The results of the modelling study provide impetus for further examination of field data. If couplings between marine biota and atmosphere are feasible, then they may be operating contemporarily, and may be detectable. Atmospheric DMS is oxidised to form aerosols (Miller et al. 2002) that influence the aerosol optical depth of the atmosphere. Archives of remote sensed ocean chlorophyll a concentration and aerosol optical depth are examined for evidence of the biologically mediated couplings. A clear coupling between aeolian dust and marine phytoplankton is evident from this analysis, suggesting that the deposition of dust from the atmosphere is a major factor controlling phytoplankton growth in many parts of the ocean. A second coupling between marine phytoplankton and atmospheric aerosols is also detected. This coupling is apparently not related to dust and is symmetrical about the equator, despite the substantial differences in the atmospheres and oceans of each hemisphere. It is speculated that this coupling may reflect the influence of the ventilation of DMS produced by marine phytoplankton on the atmosphere. This thesis provides new evidence supporting the important role of marine ecosystems in global climate regulation by the production of DMS. This evidence is principally obtained from a biogeochemical modelling approach, but is supported by analyses of empirical data. The concordance of results obtained from different approaches suggests that the contribution of marine ecosystems to global climate regulation is real, important and currently active.

The potential for life to control its environment was first suggested by Lovelock (1972). Charlson et al (1987) proposed a role for marine planktonic ecosystems in global climate regulation via the production and ventilation to the atmosphere of dimethylsulphide (DMS), a by-product of phytoplankton metabolism. Once in the atmosphere DMS contributes to the formation of cloud condensation nuclei, and increases the amount and brightness of cloud. This affects the albedo of the planet, reflecting more incident sunlight back into space, and cooling the earth. In common with many other 'hypotheses' regarding complex adaptive systems, the hypothesis proposed by Charlson et al (1987) is not experimentally testable. The production and ventilation to the atmosphere of DMS is the result of complex interactions between biological, chemical and physical processes. Consequently, increasing use is being made of mathematical models that simulate these processes to advance understanding of it (Archer et al. 2002). This study examines one of the fundamental mechanisms proposed by the Charlson et al (1987) hypothesis, that increasing global temperatures will lead to increased ventilation of DMS from the ocean to the atmosphere. The study develops one-dimensional biogeochemical models of DMS production by upper ocean ecosystems, based on the model proposed by Gabric et al. (1993b). The models are examined to elucidate their fundamental mathematical properties, and are subjected to sensitivity analysis to identify important processes and parameters. These investigations identify a simpler model that can reproduce the predictions of the Gabric et al. (1993b) model. Predictions derived from model simulations forced by climatologies of measured physical data are compared to a global database of measurements of sea surface DMS concentrations, and to observed depth profiles of DMS in the upper ocean. These comparisons confirm that all models are in good qualitative agreement with measured data. The fifteen global climate prediction models currently in use around the globe all predict substantial warming effects from the ventilation of anthropogenic carbon dioxide to the atmosphere. A simplified DMS model is calibrated to climatologies of Antarctic chlorophyll and DMS data and reproduces the data with great precision. The calibrated model is applied in global warming scenarios to 'test' the efficacy of the mechanism proposed by the Charlson et al (1987) hypothesis. This simulation provides evidence that the response predicted by the hypothesis is indeed feasible, and that substantial increases (up to 45%) in the ventilation of DMS to the atmosphere could be possible in some circumstances. The results of the modelling study provide impetus for further examination of field data. If couplings between marine biota and atmosphere are feasible, then they may be operating contemporarily, and may be detectable. Atmospheric DMS is oxidised to form aerosols (Miller et al. 2002) that influence the aerosol optical depth of the atmosphere. Archives of remote sensed ocean chlorophyll a concentration and aerosol optical depth are examined for evidence of the biologically mediated couplings. A clear coupling between aeolian dust and marine phytoplankton is evident from this analysis, suggesting that the deposition of dust from the atmosphere is a major factor controlling phytoplankton growth in many parts of the ocean. A second coupling between marine phytoplankton and atmospheric aerosols is also detected. This coupling is apparently not related to dust and is symmetrical about the equator, despite the substantial differences in the atmospheres and oceans of each hemisphere. It is speculated that this coupling may reflect the influence of the ventilation of DMS produced by marine phytoplankton on the atmosphere. This thesis provides new evidence supporting the important role of marine ecosystems in global climate regulation by the production of DMS. This evidence is principally obtained from a biogeochemical modelling approach, but is supported by analyses of empirical data. The concordance of results obtained from different approaches suggests that the contribution of marine ecosystems to global climate regulation is real, important and currently active.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Australian School of Environmental Studies
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Production efficiency models (PEMs) have been developed to aid with the estimation of terrestrial ecosystems productivity where large spatial scales make direct measurement impractical. One of the key datasets used in these models is the fraction of photosynthetic active radiation absorbed by vegetation (FAPAR). FAPAR is the single variable that represents vegetation function and structure in these models and hence its accurate estimation is essential. This thesis focused on improving the estimation of FAPAR and developing a new PEM model that utilises the improved FAPAR data. Foremost, the accuracy of operational LAI/FAPAR products (i.e. MGVI, MODIS LAI/FAPAR, CYCLOPES LAI/FAPAR, GLOBCARBON LAI/FAPAR, and NN-MERIS LAI TOC algorithm) over a deciduous broadleaf forest was investigated. This analysis showed that the products varied in their prediction of in-situ FAPAR/LAI measurements mainly due to differences in their definition and derivation procedures. The performance of three PEMs (i.e. Carnegie-CASA, C-Fix and MOD17GPP) in simulating gross primary productivity (GPP) across various biomes was then analysed. It was shown that structural differences in these models influenced their accuracy. Next, the influence of two FAPAR products (MODIS and CYCLOPES) on ecosystem productivity modelling was analysed. Both products were found to result in overestimation of in-situ GPP measurements. This was attributed to the lack of correction for PAR absorbed by the non-photosynthetic components of the canopy by the two products. Only PAR absorbed by chlorophyll in the leaves (FAPAR chlorophyll) is used in photosynthesis and hence it was hypothesised that deriving and using this variable would improve GPP predictions. Therefore, various components of FAPAR (i.e. FAPAR canopy, FAPAR leaf and FAPAR chlorophyll) were estimated using data from a radiative transfer model (PROSAIL-2).The FAPAR components were then related to two sets of vegetation indices (i.e. broad-band: NDVI and EVI, and red-edge: MTCI and CIred-edge). The red-edge based indices were found to be more linearly related to FAPAR chlorophyll than the broad-band indices. These findings were also supported by data from two flux tower sites, where the FAPAR chlorophyll was estimated through inversion of net ecosystem exchange data and was found to be better related to a red-edge based index (i.e. MTCI).Based on these findings a new PEM (i.e. MTCIGPP) was developed to (i) use the MTCI as a surrogate of FAPAR chlorophyll and (ii) incorporate distinct quantum yield terms between the two key plant photosynthetic pathways (i.e. C3 and C4) rather than using species-specific light use efficiency. The GPP predictions from the MTCIGPP model had strong relationship with the in-situ GPP measurements. Furthermore, GPP from the MTCIGPP model were comparable to the MOD17GPP product and better in some biomes (e.g. croplands). The MTCIGPP model is simple and easy to implement, yet provides a reliable measure of terrestrial GPP and has the potential to estimate global terrestrial carbon flux.

Lough Neagh is the largest freshwater lake in the British Isles. The lough is an important multi-purpose resource for the province of Northern Ireland. Previous research on the lough was combined with data from this study to analyse trophic components of the Lough Neagh ecosystem. Analysis of the biomass and abundance of taxonomic groups indicated that size-structuring was important within the system. Macro-invertebrates showed strong evidence of size-structuring over a depth gradient with biomass, abundance and body-size all increasing with depth. Stable isotope analysis showed the lough to be a relatively simple system with strong bases in planktivory and detritivory. It also highlighted the need for further research into other possible base sources within the lake food web. A mass balance trophic model was constructed for the system using the user friendly software Ecopath with Ecosim (EwE). Twenty functional groups were used in the analysis and EwE was used to assess the trophic relationship, energy flow and interactions between them. The model showed the under-utilisation of phytoplankton and detritus by consumers in the system and hence the low transfer efficiency of 6.4% for the overall system. Summary statistics sensu Odum showed that the lough is its early stages of development and consequently may be prone to perturbations particularly anthropogenic events. The model allowed for key gaps in the present research on Lough Neagh to be pinpointed. It is recommended that any further studies on the Lough Neagh ecosystem should include components on the waterfowl populations surrounding the lough as well as incorporating a bacterial element into any future models. The Ecosim component to EwE was investigated as a management tool for the lake system. The Ecosim component was capable of predicting general trends but was not recommended for use as a sole management tool for the ecosystem but rather as part of an integrated management system.

Includes bibliographical references (p. 281-303).
The main objective of this thesis is to model the krill-predator dynamics of the Antarctic ecosystem so as to determine whether predator-prey interactions alone can broadly explain observed population trends of the species considered in the model without any appeal to systematic effects possibly caused by environmental change. The history of human harvesting in the Antarctic is summarized briefly, and the central role played by krill is emphasized. The background to the hypothesis of a krill surplus in the mid 20th Century is described, and the information, particularly regarding population trends, that has become available since the postulate was first advanced is discussed. By reviewing the consumption and abundance estimates for various species in the Antarctic, it is evident that among the baleen whales, blue, fin, humpback and minke whales feed mainly on krill, and could collectively be consuming up to 120 million tons of krill in this region for each of the years around 1990. Of the seals, the Antarctic fur seals and crab-eater seals also feed mainly on krill, and these two species could be consuming up to 70 million tons of krill each year. Consumption estimates for other krill predators (birds, fish and cephalopods) are relatively poorly determined by comparison. Of these four baleen whale species, minke whales currently make the greatest impact on krill due to their large number at present compared to the other larger whale populations which are still depleted. Trend information suggests that the large baleen whales that were heavily depleted during the commercial whaling period are now recovering at rates in the vicinity of 10% per year, but there are some indications of a recent decrease in minke whale numbers. Thus, the consumption of krill by these large baleen whales has probably been increasing over recent years, though decreasing for minke whales. Updated and refined catch-at-age analyses of minke whales for the International Whaling Commission (IWC) Management Areas IV and V suggest an increase in abundance of this species in the middle decades of the 20th Century to peak at about 1970, followed by a decline for the next three decades. Fitting the recruitment time trend obtained from these analyses to a stock-recruitment model suggests that minke whale carrying capacity first increased from about 1940 to 1960 followed by a 60% decrease from the 1960s to the present. General trends in the biological parameters of this species are consistent with such a decline. A predator-prey interaction model is developed including krill, four baleen whale (blue, fin, humpback and minke) and two seal (Antarctic fur and crab-eater) species. The model commences in 1780 (the onset of fur seal harvests) and distinguishes the Atlantic/Indian and Pacific sectors in view of the much larger past harvests in the former. A reference case and six sensitivities are fit to available data on predator abundances and trends, and the plausibility of the results and the assumptions on which they are based is discussed, together with suggested areas for future investigation. Amongst the key inferences of the study are that: i) species interaction effects alone can explain observed predator abundance trends, though not without some difficulty; ii) it is necessary to consider other species in addition to baleen whales and krill to explain observed trends, with crab-eater seals seemingly playing an important role and constituting a particular priority for improved abundance and trend information; iii the Atlantic/Indian region shows major changes in species abundances, in contrast to the Pacific which is much more stable; iv) baleen whales have to be able to achieve relatively high growth rates to explain observed trends; v) species interaction effects impact the dynamics of these predators in ways that differ from what might be anticipated in a conventional single-species harvesting context, and they need to be better understood and taken into account in management decisions, and vi) Laws' (1977) estimate of some 150 million tons for the krill surplus may be appreciably too high as a result of his calculations omitting consideration of density dependent effects in feeding rates. . A priority for future work is to obtain improved estimates of the amount of krill consumed by other species, such as birds, cephalopods and fish as well as to obtain consensus on current abundance estimates for crab-eater seals and baleen whales (especially minke whales and also the associated abundance trend). Once such information is improved, more thorough sensitivity tests to the assumptions of the model and uncertainties in the abundance estimates of the species considered need to be explored. With such further development, it is hoped that such a model may ultimately assist in providing scientific advice for appropriate sustainable harvesting strategies for the Antarctic marine ecosystem taking species interactions into account, as this is a matter of key importance for the IWC and for the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR).

Forest is a resource that is increasingly utilized for multiple purposes. The balance between energy demands and the long-term capacity of ecosystems to support biodiversity and other ecosystem services is crucial. The aim of this project was to increase the knowledge on and to develop methods and tools for trade-offs and synergies analysis among forest ecosystem services based on different forest management policies. Paper I provides an overview of existing models for integrated energy-environment assessment. A literature review was conducted on assessment models and their ability to integrate energy with environmental aspects. Missing environmental aspects concern land use, landscapes and biodiversity. In Paper II a modelling framework was set up to link a landscape simulator with a habitat network model for integrated assessment of bioenergy feedstock and biodiversity related impacts in Kronoberg County. In Paper III we continued with the same management scenarios, while the analysis was expanded to five ecosystem services by developing the Landscape simulation and Ecological Assessment (LEcA) tool: industrial wood, bioenergy, forest carbon stock, recreation areas and habitat networks. In Paper IV we present two heuristic methods for spatial optimization – simulated annealing (SA) and genetic algorithm (GA) – to find optimal solutions for allocating harvest activities, in order to minimize the impacts on habitat networks. In Paper V, as response to the findings in Paper I, we linked the energy model MESSAGE with our LEcA tool for forest bioenergy demand assessment while applying environmental and transport restrictions, in a study of Lithuania. We found trade-offs between industrial wood production and bioenergy on one side, and recreation values, biodiversity, and to some extent carbon storage on the other side. The LEcA tool integrated forest simulation and management with assessment of ecosystem services, which is promising for integrated sustainability assessment of forest management policies.

QC 20171023

Thesis submitted to the Faculty of Sciences and Technology, New University of Lisbon, for the degree of Doctor of Philosophy in Environmental Sciences
Over the past few decades, policy-makers have defined new instruments to address coastal ecosystem degradation. Emerging coastal management frameworks highlight the use of the best available knowledge about the ecosystem to manage coastal resources and maintain ecosystem’s services. Progress is required, however, in translating data into useful knowledge for environmental problem solving. This thesis aims to contribute to research assessing changes in coastal ecosystems and benefits generated due to management actions (or to the lack thereof). The overall objectives are to assess the ecological and economic impacts of existing management programmes, as well as future response scenarios and to translate the outcomes into useful information for managers. To address these objectives, three different approaches were developed: A multilayered ecosystem model A multilayered ecosystem model was developed to simulate management scenarios that account for the cumulative impacts of multiple uses of coastal zones. This modelling field is still at an early stage of development and is crucial, for instance, to simulate the impacts of aquaculture activities on the ecosystem, accounting for multiple farms and their interactions with other coastal activities. The multilayered ecosystem model is applied in this thesis to test scenarios designed to improve water quality and manage aquaculture. An ecological-economic assessment methodology (ΔDPSIR approach) The Differential Drivers-Pressure-State-Impact-Response (ΔDPSIR) approach further develops the integrated approach by providing an explicit link between ecological and economic information related to the use and management of coastal ecosystems. Furthermore, the ΔDPSIR approach provides a framework to synthesise scientific data into useful information for the evaluation of previously adopted policies and future response scenarios. The ΔDPSIR application is tested using different datasets and scales of analysis, including: (i)assessment of the ecological-economic impacts of the scenarios at the waterbody/watershed level, using the multilayered ecosystem model outputs, and (ii) evaluation of the ecologicaleconomic effects of aquaculture options at the individual aquaculture level, using data from an abalone farm. These are two important scale of analysis for the development of an ecosystem approach to aquaculture.A dynamic ecological-economic model (MARKET model) One of the missing links in ecosystem modelling is with economics. The MARKET model was developed to simulate the feedbacks between the ecological-economic components of aquaculture production. This model was applied to simulate shellfish production in a given ecosystem under different assumptions for price and income growth rates and the maximum available area for cultivation. Further application of the MARKET model at a wider scale might be useful for understanding the ecological and economic limitations on global aquaculture production. This integrated ecological-economic modelling and assessment approach can be further applied to address new coastal management issues, such as coastal vulnerability to natural catastrophes. It can also support implementation of current legislation and policies, such as the EU Integrated Coastal Zone Management recommendation or the development of River Basin Management Plans following the EU Water Framework Directive requirements. On the other hand, the approach can address recurring coastal management needs, such as the assessment of the outcomes of past or on-going coastal management plans worldwide, in order to detect symptoms of the overuse and misuse of coastal ecosystems.
Portuguese Foundation for Science and Technology(FCT) as a Ph.D. scholarship (SFRH/BD/25131/2005.European Union, Sixth Framework Programme FP6-2002-INCO-DEV-1 SPEAR (INCO-CT-2004-510706) project

An eastward shift in the West Coast rock lobster Jasus lalandii took place in the early 1990s along the south-west coast of South Africa in an area known as East of Cape Hangklip (EOCH). Given the predatory capabilities of J. lalandii, an intricate relationship between the urchin Parechinus angulosus and juvenile abalone Haliotis midae, and an already over-exploited ecosystem, the lobster âinvasionâ is assumed to have had serious consequences on the benthic community and associated fisheries. To investigate these effects, I used both empirical and modelling approaches. Based on field studies, I first analysed temporal changes in rock lobsters and the benthic community at two lobster-invaded sites EOCH. Prior to 1990, rock lobsters were rare EOCH, but from the mid 1990s onwards they achieved densities of 0.4- 0.8 m-2. The pre-invaded benthic community was significantly different from the postinvaded community at both sites. Three major changes followed the lobster invasion: (1) a decline or even a disappearance of herbivores (a direct effect), (2) macroalgal proliferation (an indirect effect) and (3) increases of a range of sessile taxa (unknown effect). This was followed by a detailed spatial analysis of J. lalandii densities and the benthic community EOCH, in which I surveyed six sites (three invaded and three noninvaded) at three different depth zones (< 5 m, 6-12 m and 13-20 m). At all three depth zones Jasus lalandii was significantly more abundant in invaded areas than in noninvaded areas, and invaded and non-invaded benthic communities were significantly different. Invaded sites were characterized by higher densities of rock lobsters, macroalgae and sessile species, whereas non-invaded sites had greater amounts of herbivores and encrusting corallines. Abalone abundance reflected their previouslyrecorded dependency on urchins and the effects of rampant poaching. Floral species diversity was on average greater at invaded sites and increased with depth, whereas faunal species diversity was greater at non-invaded sites but also increased with depth. The depths in which strongest effects of J. lalandii were felt coincided with the depth of maximum abundance of the urchin Parechinus angulosus, the abalone Haliotis midae, the kelp Ecklonia maxima and encrusting corallines. In line with an ecosystem approach to fisheries management and to better understand the ecosystem dynamics EOCH, a lobster-urchin-abalone Minimally Realistic Model was developed for a lobster-invaded area, and an adjacent nonvi invaded area. A key feature of the model is that its focus was restricted to the critical interactions of interest and was fitted to all available data. An existing abalone stockassessment model formed the foundation of this multispecies model, to which rock lobsters and urchins were added. Abalone and rock lobsters were modelled using agestructured production models and urchins were modelled using a simpler surplus production model because of data limitations. The model estimated a lobster starting biomass (in 1985) of 314 tonnes (MT) and a carrying capacity of 1511 MT. Speciesinteraction parameters, particularly the lobster-abalone interaction, were difficult to estimate and the model was unable to estimate the urchin intrinsic growth rate parameter because the data had insufficient contrast. Results from the model suggest that the lobster invasion was probably caused by an influx of adult lobsters as opposed to increased larval settlement. Future projections suggest that given the virtual disappearance of urchins, complete removal of rock lobsters would be needed to allow the urchin population to re-establish itself. Recovery of urchins could take up to 50 years and recovery of abalone would take even longer. The model-predicted differences in lobsters, abalone and urchins between invaded and non-invaded areas paralleled empirical data. Further model explorations included (1) a hypothetical lobster invasion into a currently non-invaded zone EOCH and (2) the addition of a top fish predator into a lobster-invaded zone. Various hypothetical lobster invasions into the non-invaded zone all resulted in the eventual disappearance of urchins and, consequently, juvenile abalone. Available catch and effort data for fish indicated that a major decline in linefish has taken place, but that this occurred prior to the 1980s and was thus not the direct cause of the rock-lobster invasion. This was supported by outputs of a model incorporating fish predation, which demonstrated that the presently over-exploited fish biomass has very little effect on the rock lobster population, but that at historical pristine levels, fish would have been capable of preventing the establishment of a dense rock-lobster population and the consequent disappearance of urchins and abalone. These results indicate that the over-fishing of top-predators would have had massive ramifications for the rest of the ecosystem. Through dual empirical and modelling approaches, my study highlights the complexity of ecosystem interactions and the need for multispecies models in developing an ecosystem approach to fisheries management, and adds to the understanding of the causes and implications of human- and environmentally-induced shifts in community structure.

Accurately estimating how much carbon is leaving the atmosphere and being taken up by plants, by processes such as photosynthesis, is critical in order to make accurate climate forecasts. There is a large uncertainty of this atmosphere-plant carbon flux, sometimes referred to as Net Ecosystem Exchange (NEE), therefore reducing this is essential. One way of doing this is through Data Assimilation (DA), the framework by which data and models are combined together in a statistically optimal way. A key aspect of DA is that the uncertainty on the estimate of interest, e.g. NEE, is less than either the uncertainty on using either the model or observations on their own. DA can also been used to estimate model parameters, which have traditionally been estimated from expert knowledge or from small scale studies. While DA has gained much interest as a powerful tool in estimating model parameters and quantities such as NEE, there are a number of issues surrounding its use, which are not yet properly understood. These include: (1) When using DA to estimate parameters using ground observations: (a) Understanding the limitations of DA and the conditions it performs best; (b) Determining likely factors that cause variations in parameter estimates. (2) Assessing the impact of assimilating satellite observations of leaf area index to improve the model states, and whether DA is robust against unrealistic features of the satellite data. The aim of this PhD was to address and learn more about these issues. This was done by using the evergreen and deciduous versions of the Data Assimilation Linked Ecosystem (DALEC) model. The main findings are summarised in the following four paragraphs: The Ensemble Kalman Filter (EnKF) is good at estimating parameters using synthetic NEE data. It was found that between 2 and 5 years of this data was required in order for the parameters and NEE forecasts to be close to the truth. There was for the most part very little difference to the EnKF parameter estimates and NEE forecasts whether very noisy or very non-noisy observations were used, or whether 20% or 100% of the daily observations were present in the dataset. For the Metropolis algorithm, most of the runs had to be discarded as it was found that the the algorithm was not converging for the global minimum for these runs; this caused some other problems, in particular residuals between the modelled and observed NEE were autocorrelated. For these discarded runs, the parameter estimates tended to be far from the truth and the 90% posterior intervals rarely included the truth. For the remaining runs, where the converse of the above was found to be true, as dataset length increased from 1 to 5 years, the posterior parameter distribution coincided with the truth to a greater extent. Using the Metropolis algorithm and assimilating three years daily NEE observations (with around 60% data coverage) and around 10 LAI observations during this period, it was found that parameter estimates were sensitive to the initial value of the labile carbon store. Moreover, the parameters were close to their true values if the true initial value of the labile C pool was used. It was also found that when these initial conditions were treated as parameters, although the modal value of the corresponding marginal posterior distributions were far from the truth, every other aspect of the model (parameters and trajectories of the model states) agreed well with the truth. This supported the common approach by many of the DA community that treating initial conditions as parameters is preferable than keeping them fixed (using site inventory data or from model spin-up). The novelty of this part of the thesis was for the first time an emulator was applied to a DA scheme. Finally, the EnKF was used to estimate the LAI and NEE model states, using a fixed parameter set and LAI data from the MODIS satellite sensor. It was found that processing the MODIS LAI in order to correct for unrealistic features of the dataset, such as excessive temporal variation and very small uncertainties, improved the fit of the modelled to observed NEE after assimilation. The improvement in the fit was significantly better for Gross Primary Production (GPP).

Earth's species are disappearing at a rate unprecedented in human history, yet whether this loss will make the ecosystem "services" that support our civilisation more vulnerable to environmental change is poorly understood. This thesis investigates two different aspects of land surface modelling. It firstly models the role of biodiversity in ecosystem resilience using the Lotka-Volterra and single resource models to model diversity using competition coeffcients, stochastic noise and evolution inspired trait diffusion and then examines if higher diversity makes these simple models more resistant to temperature increases. It secondly develops a theoretical plant demography model, based on the continuity equation, to robustly represent forest size diversity. This avoids both the complexity and maintainability issues seen in Forest Gap models and improves the representation of land use and land cover change and of regrowth time-scales after disturbance, which can be unrealistic in some of the previous generation of Dynamic Global Vegetation Models (DGVMs), such as TRIFFID (Cox et al., 2001). While the Lotka-Volterra with competition coeffcients and the single resource with stochastic noise approaches are found to be impractical, the single resource model with trait diffusion successfully shows that higher diversity requires a faster critical rate of temperature change before system net primary productivity (NPP) collapses. The continuity equation model of vegetation demography is solved analytically with the size dependence of the growth rate approximated first by a power law and then with a quadratic. The power law solution can be reduced to a "self-thinning" trajectory, and the quadratic solution gives either a rotated sigmoid or 'U-shape' distribution of plant sizes, depending on the ratio of mortality to maximum growth gradient. The model is then extended to produce the basis of a new Dynamic Global Vegetation Model (DGVM) called "Robust Ecosystem Demography" (RED), adapting the plant physiology from TRIFFID DGVM to generate a size-dependent growth function. A proportion of the NPP from this growth is used for reproduction and the shading is modelled simply by random overlap. The model is found to better represent regrowth time-scales compared to TRIFFID and is also found to demonstrate an optimum proportion of NPP to reproduction which decreases with plant lifetime.

A three-dimensional ocean model, ROMS, has been utilized to simulate the hydrodynamics and the ecosystem dynamics of the Northern Levantine Basin circulation. The model is one-way nested inside a coarser resolution Mediterranean Sea eco-hydrodynamics model, forced with realistically updated surface and lateral fluxes of momentum, mass, heat and nutrients. Scenario runs representing present and future time-slices of 5 years each have been used to investigate sensitivity to climate in the near future. Other sensitivity tests depending on model parameters and options have been performed. It is revealed that the Asia Minor Current, dominating the basin circulation, divides the basin into the two basic regions of coastal and open sea characteristics. Although satisfactory results are reached for the general behaviour of the ecosystem, the model tends to overestimate the surface chlorophyll concentration. Sea surface patterns of variables predicted by the model are compared with satellite data indicate general agreement in the seasonal patterns. Based on the selected climate change scenario for 30-40 year difference of the time slices, rises of 0.33

La mise en place de l’approche écosystémique des pêches (AEP) requiert une amélioration de nos connaissances sur la complexité des écosystèmes. Comprendre la réaction de l’écosystème à des mesures de gestion est essentiel pour atteindre les objectifs de conservation. La modélisation écosystémique a amélioré nos connaissances sur le fonctionnement des écosystèmes et leurs interactions avec les usages du domaine maritime; et est de plus en plus utilisée pour évaluer l’impact de mesures de gestion. Le comportement de pêche des flottilles démersales françaises en Manche Orientale a été analysé. Les résultats montrent que les pêcheurs conservent leurs habitudes de pêches et que le trafic maritime peut impacter leurs décisions. Une analyse globale des résultats d’études menées au cours des trente dernières années démontre l’influence des habitudes et des espèces ciblées sur le comportement de pêche. L’exploration de la dynamique de l’écosystème a nécessité l’utilisation du modèle Atlantis, en focalisant sur deux espèces commerciales, la sole (Solea solea) et la plie (Pleuronectes platessa). L’importance des zones estuariennes est révélée, ainsi que le rôle joué par les rejets et par deux espèces clés, la morue (Gadus morhua) et le merlan (Merlangius merlangius). La sole et la plie ont peu d’influence sur le réseau trophique excepté sur la dynamique des invertébrés benthiques. Nous évaluons les conséquences de l’application de fermeture de zones et d’une réduction d’effort sur le comportement de pêche et l’écosystème et mettons en évidence un bénéfice de l’application combinée de ces mesures sur la biomasse des espèces commerciales et sur la valeur débarquée par unité d’effort
The implementation of the ecosystem approach to fisheries management (EAFM) requires an enhancement of our knowledge of ecosystem complexity. Understanding the ecosystem reaction to management regulation is a key to achieve conservation objectives. Ecosystem modelling improves our knowledge on ecosystem functioning in interaction with human activities, and it is now widely used to evaluate management strategies. The fishers’ behaviour of the French demersal fisheries in the Eastern English Channel (EEC) has been investigated. Results showed that fishers tended to adhere to past annual fishing practices and maritime traffic may impact on fishing decision. A global analysis of the fisheries science literature during the last three decades evidenced the influence of tradition and species targeting in fishers’ behaviour. The exploration of ecosystem dynamics required the use of the ecosystem model Atlantis with a focus on two commercial flatfish species, sole (Solea solea) and plaice (Pleuronectes platessa). The importance of estuary areas and of nutrient inputs has been revealed as well as the role of discards and of two key species, cod (Gadus morhua) and whiting (Merlangius merlangius). Sole and plaice did not have a strong influence on the trophic network excepted on the benthic invertebrates’ dynamics. Finally, we investigated the consequences of area closure and effort reduction on fishers’ behaviour and the ecosystem impacted. We observed a noticeable benefit of combining area closure and effort reduction on the biomass of most commercial species and on the total value landed per unit effort

La mise en place de l’approche écosystémique des pêches (AEP) requiert une amélioration de nos connaissances sur la complexité des écosystèmes. Comprendre la réaction de l’écosystème à des mesures de gestion est essentiel pour atteindre les objectifs de conservation. La modélisation écosystémique a amélioré nos connaissances sur le fonctionnement des écosystèmes et leurs interactions avec les usages du domaine maritime; et est de plus en plus utilisée pour évaluer l’impact de mesures de gestion. Le comportement de pêche des flottilles démersales françaises en Manche Orientale a été analysé. Les résultats montrent que les pêcheurs conservent leurs habitudes de pêches et que le trafic maritime peut impacter leurs décisions. Une analyse globale des résultats d’études menées au cours des trente dernières années démontre l’influence des habitudes et des espèces ciblées sur le comportement de pêche. L’exploration de la dynamique de l’écosystème a nécessité l’utilisation du modèle Atlantis, en focalisant sur deux espèces commerciales, la sole (Solea solea) et la plie (Pleuronectes platessa). L’importance des zones estuariennes est révélée, ainsi que le rôle joué par les rejets et par deux espèces clés, la morue (Gadus morhua) et le merlan (Merlangius merlangius). La sole et la plie ont peu d’influence sur le réseau trophique excepté sur la dynamique des invertébrés benthiques. Nous évaluons les conséquences de l’application de fermeture de zones et d’une réduction d’effort sur le comportement de pêche et l’écosystème et mettons en évidence un bénéfice de l’application combinée de ces mesures sur la biomasse des espèces commerciales et sur la valeur débarquée par unité d’effort
The implementation of the ecosystem approach to fisheries management (EAFM) requires an enhancement of our knowledge of ecosystem complexity. Understanding the ecosystem reaction to management regulation is a key to achieve conservation objectives. Ecosystem modelling improves our knowledge on ecosystem functioning in interaction with human activities, and it is now widely used to evaluate management strategies. The fishers’ behaviour of the French demersal fisheries in the Eastern English Channel (EEC) has been investigated. Results showed that fishers tended to adhere to past annual fishing practices and maritime traffic may impact on fishing decision. A global analysis of the fisheries science literature during the last three decades evidenced the influence of tradition and species targeting in fishers’ behaviour. The exploration of ecosystem dynamics required the use of the ecosystem model Atlantis with a focus on two commercial flatfish species, sole (Solea solea) and plaice (Pleuronectes platessa). The importance of estuary areas and of nutrient inputs has been revealed as well as the role of discards and of two key species, cod (Gadus morhua) and whiting (Merlangius merlangius). Sole and plaice did not have a strong influence on the trophic network excepted on the benthic invertebrates’ dynamics. Finally, we investigated the consequences of area closure and effort reduction on fishers’ behaviour and the ecosystem impacted. We observed a noticeable benefit of combining area closure and effort reduction on the biomass of most commercial species and on the total value landed per unit effort

Baltic archipelago areas have high nature values despite being polluted from various antrophogenic activities within the Baltic Sea catchment area and from long-range transport of airborne substances. The discovery of environmental problems in the Baltic Sea in the 1960s led to countermeasures that gradually gave results in reducing the toxic pollution, e.g. from PCBs. Today, much of the environmental management is focused on reducing the effects of eutrophication. There is a demand from society on science to develop strategies that can direct remedial actions so that the cost-effectiveness is maximised. This work focuses on how mass-balance models can be used to understand how coastal ecosystems are controlled by abiotic processes and to predict the response to changes in loading of different substances. Advection, sedimentation and burial are examples of general transport processes that are regulated by morphometrical characteristics, e.g. size, form, effective fetch and topographical openness. This is why different coastal areas have different sensitivity to loading of pollutants. A comparison of six phosphorus and chlorophyll models of different complexity showed that the model performance was not improved with more state variables of total phosphorus (TP) than two water and two sediment compartments. Modelling chlorophyll as a separate state variable did not improve the results for individual values compared to a simple regression against total phosphorus in surface water. Field investigations of the phosphorus content in accumulation sediments along the coast of Svealand showed a distribution pattern that probably is related to differences in the redox status. The average content of mobile phosphorus was much higher than previously found in offshore Baltic sediments indicating that sediments may play an important role for the phosphorus turnover in Baltic archipelago areas. A one-year field study to measure the levels of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) in water, sediments and fish during different seasons was carried out in Kallrigafjärden Bay. The collected data set was used to test a mass-balance model for PCCD/F-turnover. It was possible to reproduce the concentrations of different PCDD/F-congeners with high accuracy using a general model approach, including one water compartment and two sediment compartments, indicating that the applied model has the necessary qualifications for successful predictions of PCDD/F-turnover in Baltic coastal areas.
Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 736

Unsustainable patterns of consumption by humankind have increased the rate of change in the natural ecosystems and consequently the levels of stress experienced within the environment. Access to sufficient good quality water is essential and a requirement to meet a number of the Millennium Development Goals (MDGs). However, poor land management and untenable agricultural practices have become the main drivers of the declining watershed services. Upstream farmers often have little or no incentives to take these impacts into account in their decision-making process. Therefore, without investment in ensuring proper land management, the trend in watersheds degradation will continue. Payment for Environmental Services (PES) has emerged as an incentive–based tool that is expected to motivate farmers to improve their agricultural practices. PES is set up to facilitate the process whereby the beneficiaries of environmental services pay compensation to providers of environmental services for conserving the ecosystem. This tool has received increasing attention as a means of creating incentive measures for managing the ecosystem, addressing livelihood issues for the rural poor, and providing sustainable financing for protected areas. The Government of Kenya, as part of its efforts to improve water resource management, is considering use of economic incentive. However, there is insufficient information to guide policy making in that direction. Little is known about the farmers’ preferences for management schemes that will affect land use patterns, their willingness to accept compensation and the willingness of potential buyers to pay for the services. This study evaluates the willingness to accept and the willingness to pay for environmental services with a view to assessing the viability of a PES scheme for the Kuywa Watershed in particular, as well as the Mt. Elgon Ecosystem and other areas with similar conditions. The objectives of the study are threefold (i) to examine respondents preferences for management options for the provision of environmental services in the watershed of River Kuywa of Mt. Elgon Ecosystem; (ii) to evaluate households’ willingness to pay (WTP) and willingness to accept (WTA) payment for improved environmental services from the River Kuywa watershed; and (iii) to propose viable PES approaches for the management of the natural resource of the Kuywa watershed and the Mt. Elgon ecosystem in general. Using six land management attributes relevant to the local situation, the study applied the conjoint method to evaluate farmers’ preferences for management options for the provision of environmental service and assess farmers’ willingness to pay and willingness to accept payment for environmental services. To enable assessment of viability, an analysis was done of the institutional and legal framework within which the PES scheme would operate. Data were collected using literature review and document analysis, questionnaires, focus group discussions and key informant interviews. Results indicate that poor water quality was the most acute problem, followed by deforestation. Results from the conjoint models show that the length of commitment period and land size that is 40% or more of the total land holding influence the farmers’ rating of the management scenarios. The study found that a management contract that requires use of 20% of land holding for a period of 5 years, combined with a cash incentive, harvesting partially permitted, administered by a local NGO and requiring contribution of free labour for two days had the highest likelihood of being selected. The conjoint valuation exercise also came up with a WTA by farmers upstream of KSh. 7,080/= per year. The corresponding value downstream was KSh. 43/= per month over and above their regular water bill. In terms of the institutional and regulatory framework, Kenya has a wide range of policies, laws and regulation on water and other natural resources which provide an enabling environment for PES. With the decentralized institutional setup implemented in both the water sector and the agricultural sector, the institutional setting also provides an enabling environment for PES. With a positive WTA and WTP coupled with an enabling legal and institutional environment, the study concludes that PES is a viable environmental management tool for the Kuywa water shed and similar watersheds.

Resource management is increasingly about the equitable distribution of benefits amongst a diversity of beneficiaries while ensuring the persistence of desirable social and ecological systems. Largely because of the complexity of social-ecological systems, models intended to support integrated resource management continue to suffer from poor treatment of uncertainty, and the challenges of defining appropriate model scope and benefit representation. I explored these challenges through the process of combining field data with population, habitat, and service models to build an integrated model of coastal ecosystem services on the West coast of Vancouver Island, British Columbia, Canada. I examined the tradeoffs between sea otter and invertebrate dominated systems under 3 spatial sea otter management plans. The model predicts that an otter-dominated system will produce, in aggregate, between 30 and 90 M$ / year more than one dominated by invertebrates. Disaggregation by benefits and by location provides insight into trade-offs and equity. For example, the value of increased finfish production from enhanced primary productivity is predicted to be almost double the losses incurred by the invertebrate fishery; while increased detail on the distribution of benefits supports the definition of novel, more equitable and legitimate indicators, allowing management alternatives to be more salient. Development of the model led to advances in the applied and theoretical aspects of integrated model development. Chapter 2 confirms that uncertainties and design assumptions are mostly ignored in the popular modelling literature, and includes a conceptual model to support more consistent model design decisions. In Chapter 3 I characterised key aspects of kelp ecology in Pacific Canadian waters, and showed how the trade-off between precision and accuracy depends on whether one is pursuing knowledge or application. Chapters 4 and 5 tell the story of the integrated model, respectively focusing on ecosystem service production, and the distribution of benefits. My results show how spatial resolution is key to identifying indicators of social and ecological value. All told, my dissertation offers applied, theoretical, and methodological advances in the use of ecosystem models for integrated management. Extending the model to include stakeholder objectives would complete the data-to-decision model, allowing formal decision analysis.
Science, Faculty of
Resources, Environment and Sustainability (IRES), Institute for
Graduate

Three trophic models of the Western English Channel were built using the Ecopath with Ecosim (EwE) software. A model for 1994 represented a warm period. Two models represented colder periods in 1973 and in 1985, the later coinciding with a considerable increase in fish and shellfish landings. One of the main observed differences among the models was an increase in primary production that seemed to be reflected in changes in fish biomass. Some parameters estimated indicate that (1) the ecosystem was relatively immature or disturbed, (2) despite the increase fishing effort since the 1970s, the system maturity increased in 1985 and (3) with the increased fishing mortalities operating in the system, this trend was reversed in the 1994 model. Ecosim simulations run from 1973 to 1999 indicated that a bottom-up mechanism plays an important role in the system production. By accounting for primary production changes and by estimating the so-called vulnerability parameters, it was possible to improve the goodness of fit of the model estimates to the available biomass data by about 62 to 68% compared to fitting using only the series of fishing mortalities. The 1994 model was used to explore the effects of the use of the EwE fishing optimization routine on profits, number of jobs and ecosystem structure. An "ideal" mixed policy configuration was found when ecosystem structure was weighted slightly higher than were profits and jobs. This scenario led to an overall reduction in effort but also to increased profits and biodiversity, with almost no lost in the number of jobs. The optimizations also showed that the average trophic level of the catches is quite conservative to changes in ecosystem structure, which contrasted with an estimated biodiversity index from Ecosim that showed huge changes as a function of the weights placed on the policy functions.

Firstly, I reviewed modelling approaches that were used to assess the impact of invasive alien species (IAS) in aquatic ecosystems. According to the review, multispecies/ecosystem mechanistic models dominated the applications, with dynamic and non-spatial models being the most prevalent. Most of the models included an additional human stressor, mainly fisheries, climate change and/or nutrient loading. I summarised the main features of these applications and analysed their capabilities and limitations. Based on my conclusions, I reflected on future directions of development and applications of suitable modelling tools. The review showed that the Ecopath with Ecosim (EwE) modelling approach was frequently used to assess the impacts of already established IAS and highlighted its capabilities to forecast existing, emerging and potential new IAS. As a second step, I developed two static Ecopath ecosystem models using the EwE approach and representing the food web of the Israeli Mediterranean coast in 1990s and 2010s. I characterized the structure and functioning of the ecosystem and assessed past and current impacts of IAS and fishing. I then used the time-dynamic Ecosim module of EwE to fit the 1990s model to available time series of observations between both periods and to explore the historical dynamics of the ecosystem considering the effects of IAS, fishing dynamics and sea warming. Finally, the time-dynamic ecosystem model was used to analyse alternative future simulations of ecosystem change. Particularly, and after interacting with key stakeholders, I assessed the future effects of a new set of fishing regulations currently being implemented in Israel, future changes in sea temperature following IPCC (Intergovernmental Panel on Climate Change) scenario projections and the potential increases in IAS biomass. I investigated the impacts of the stressors separately, and then I combined them to evaluate their cumulative effects. Results from the static Ecopath models highlighted that the Israeli marine ecosystem, despite productivity differences, shared some structural and functional traits with other Mediterranean ecosystems such as the dominance of the pelagic domain in term of flows, the important role of detritus through low trophic levels and the importance of the benthic-pelagic coupling. In both time periods investigated, the same keystone groups were identified with the exception of European hake in 2010s, which showed a decline in its keystone role. This may indicate that hake lost its ecological role due to population declines. Most of the functional groups identified as keystone species were previously identified as keystones in other Mediterranean ecosystems, such as dolphins, large pelagic fishes, sharks and squids. The temporal dynamic Ecosim model indicated that trophic interactions, ocean warming and fishing were important drivers of the ecosystem dynamics. In general, temporal biomass trends revealed that native demersal predators and native medium trophic level fishes largely declined over time, while an increase over time of alien species was observed. Results from ecological indicators suggested a degradation pattern of the ecosystem over time. Future scenarios using the temporal dynamic Ecosim model showed overall potential benefits of fishing effort reductions in the future, and detrimental impacts of increasing sea temperature and increasing biomass of alien species. Cumulative scenarios highlighted that the beneficial effects of fisheries reduction could be dampened by the impact of increasing sea temperature and alien species when acting together. These results support the need for reducing local and regional stressors, such as fishing and biological invasions, to retain marine ecosystems within a “safe operating space” and ensure ecosystem resilience in an ongoing warming and impacted sea.
Los ecosistemas marinos del Mediterráneo oriental han sufrido cambios ecológicos importantes debido a múltiples presiones antropogénicas, incluido el impacto de especies invasoras, la sobrepesca y el calentamiento del mar. En primer lugar, he revisado los modelos que se han utilizado para evaluar el impacto de las especies invasoras en los ecosistemas acuáticos. De acuerdo con esta revisión, predominan los modelos mecanísticos de carácter multiespecífico/ecosistémico, siendo los modelos dinámicos y no espaciales los más frecuentes. La mayoría de los modelos incluyen un impacto antropogénico adicional, principalmente la pesca, el cambio climático y el aporte de nutrientes. Además, he resumido las principales características de estos modelos y he analizado sus capacidades y limitaciones. En base a las conclusiones de esta revisión, se han mostrado posibles direcciones para futuros desarrollos de los modelos y la aplicación de modelos adecuados. En esta revisión, he observado que el modelo Ecopath with Ecosim (EwE) ha sido utilizado frecuentemente para evaluar los impactos de las especies invasoras ya establecidas. Además, la revisión ha destacado las capacidades de EwE de pronosticar los futuros impactos de las especies invasoras establecidas, emergentes y potenciales. Otras revisiones disponibles en la literatura han demostrado las capacidades de EwE para evaluar los impactos de la pesca y el cambio climático. Por lo tanto, he desarrollado dos modelos estáticos Ecopath que representan la red trófica de la costa Mediterránea de Israel en los años 1990 y 2010 para caracterizar la estructura y funcionamiento del ecosistema y evaluar los impactos de las especies invasoras y la pesca en el pasado y en el presente. Después he utilizado el módulo dinámico-temporal Ecosim para ajustar el modelo de 1990 a series temporales de datos disponibles entre ambos periodos y para explorar la dinámica histórica del ecosistema considerando el efecto de las especies invasoras, la dinámica de la flota pesquera y el calentamiento del mar. Finalmente, el módulo dinámico-temporal ha sido utilizado para realizar simulaciones futuras de cambios en el ecosistema. En particular, he evaluado los efectos de un nuevo conjunto de regulaciones de pesca que se están implementando actualmente en Israel, futuros cambios en la temperatura del mar siguiendo las proyecciones del Panel Intergubernamental sobre el Cambio Climático (IPCC por sus siglas en inglés) y posibles aumentos de la biomasa de las especies invasoras. Primero he investigado los diferentes impactos por separado y, luego, los he combinado para evaluar sus efectos acumulativos. Los resultados de los modelos estáticos Ecopath han destacado que el ecosistema marino israelí, a pesar de un patrón de productividad diferente, comparte algunas características estructurales y funcionales con otros ecosistemas mediterráneos como el dominio del hábitat pelágico en términos de flujos tróficos, el importante papel del detritus a través de niveles tróficos bajos y la importancia del acoplamiento bentónicopelágico. Los mismos grupos funcionales clave fueron identificados en ambos periodos investigados, a excepción de la merluza en 2010, lo que puede indicar que la merluza ha perdido su papel ecológico debido al declive de su población. La mayoría de los grupos funcionales identificados como especies clave ya han sido identificados previamente como tales en otros ecosistemas mediterráneos como por ejemplo los delfines, los grandes peces pelágicos, los tiburones y los calamares. El módulo dinámico-temporal Ecosim indicó que las interacciones tróficas, el aumento de la temperatura del mar y la pesca jugaron un papel clave en la dinámica del ecosistema. En general, las tendencias temporales de la biomasa revelaron que los depredadores demersales nativos (por ejemplo, la merluza) y los peces demersal nativos de nivel trófico medio (por ejemplo, los salmonetes) disminuyeron en gran medida con el tiempo, mientras que se observó un aumento de las especies invasoras con el tiempo. Los resultados de los indicadores ecológicos sugirieron un patrón de degradación del ecosistema con el tiempo. Los escenarios futuros utilizando el módulo dinámico-temporal Ecosim mostraron los beneficios potenciales generales de las reducciones del esfuerzo pesquero y los impactos negativos del aumento de la temperatura del mar y el aumento de la biomasa de las especies invasoras. Los escenarios acumulativos resaltaron que los efectos beneficiosos de la reducción de la pesca pueden verse disminuidos por el impacto del aumento de la temperatura del mar y las especies invasoras cuando actúan al mismo tiempo. Estos resultados respaldan la necesidad de reducir los impactos antropogénicos locales y regionales como la pesca y las especies invasoras, para mantener los ecosistemas marinos dentro de un “espacio operativo seguro (SOS por sus siglas en inglés)” y promover la resiliencia de los ecosistemas en un mar en continuo calentamiento y altamente impactado.
Els ecosistemes marins de la Mediterrànea oriental han patit canvis ecológics importants a causa de múltiples pressions antropogèniques, inclòs l’impacte d’especies invasores, la sobrepesca i el calentament del mar. En primer lloc, he revisat els models que s’han utilitzat per avaluar l’impacte de les espècies invasores en ecosistemes aquàtics. D’acord amb aquesta revisió, predominen els models mecanístics de caràcter multiespecífic/ecosistèmic, sent els models dinàmics i no espacials els més freqüents. La majoria dels models inclouen un impacte antropogènic adicional, principalment la pesca, el canvi climàtic i l’aport de nutrients. A més, he resumit les principals característiques d’aquest models i he analitzat les seves capacitats i limitacions. En base a les conclusions d’aquesta revisió, s’han exposat possibles direccions per futurs desenvolupaments dels models i l’aplicació de models adecuats. En aquesta revisió he observat que el model Ecopath with Ecosim (EwE) ha estat utilitzat freqüentment per avaluar els impactes de les espècies invasores ja establertes. A més, la revisió ha destacat les capacitats d’EwE de pronosticar els futurs impactes de les espècies establertes, emergents i potencials. Altres revisions disponibles a la literatura han demostrat les capacitats d’EwE per avaluar els impactes de la pesca i el canvi climàtic. Per tant, he desencolupat dos models estàtics Ecopath que representen la xarxa tròfica de la costa Mediterrànea d’Israel en els anys 1990 y 2010 per caracteritzar l’estructura i funcionament de l’ecosistema i avaluar els impactes de les espècies invasores i la pesca en el passat i el present. Després he utilitzat el mòdul dinàmic-temporal per ajustar el model de 1990 a sèries temporals de dades disponibles considerant l’efecte de les espècies invasores, la dinàmica de la flota pesquera i l’escalfament del mar. Finalment, el mòdul dinamic-temporal ha estat utilitzat per realitzar simulacions futures de canvis en l’ecosistema. En particular, he avaluat els efectes d’un nou conjunt de regulacions de pesca que s’estan implementant actualment a Israel, canvis en la temperatura del mar seguint les projeccions del panell intergovernamental sobre el Canvi Climàtic (IPCC per les seves sigles en anglès) i possibles augments de la biomass de les espècies invasores. Primer he investigat els diferents impactes per separat i, després, els he combinat per avaluar els seus efectes acumulatius. Els resultats dels models estàtics Ecopath han destacat que l’ecostema marí d’Israel, malgrat un patró de productivitat diferent, comparteix algunes característiques estructurals i de funcionals amd altres ecosistemes marins mediterrànis com el domini de l’hàbitat pelàgic en termes de fluxes tròfics, l’important paper del detritus a través de nivells tròfics baixos i la importància de l’acoplament bentònic-pelàgic. Els mateixos grups funcionals clau van ser identificats en els dos períodes investigats, a excepció del lluç en el 2010, que pot indicar que el lluç ha perdut el seus paper ecològic a causa del declivi de la seva població. La majoria del grups funcionals identificats com a espècies claus ja han estat identificats com a tals en altres ecosistemes mediterranis com ara els dofins, els gran peixos pelàgics, els taurons i els calamars. El mòdul dinàmic-temporal Ecosim ha indicat que les interaccions tròfiques, l’augment de la temperatura del mar i la pesca van jugar un paper clau en la dinàmic de l’ecosistema. En general, les tendències temporals de la biomasa van revelar que els depredadors demersals natius (per exemple, el lluç) i els peixos dersals natius de nivell tròfic mitjà (per exemple, els rogers) van disminuir en gran mesura amb el temps, mentre que es va observar un augment de les espècies invasores amb el temps. Els resultats dels indicadors ecològics van suggerir un patrò de degradació de l’ecosistema amb el temps. Els escenaris futurs van mostrar els beneficis potencials generals de les reduccions de l’esforç pesquer i els impactes negatius de l’augment de la temperatura del mar i ’augment de la biomasa de les espècies invasores. Els escenaris acumulatius van ressaltar que els efectes beneficiosos de la reducció de la pesca poden ser reduïts per l’impacte de l’augment de la temperatura del mar i les espècies invasores quan actuen al mateix temps. Aquests resultats recolzen la necessitat de reduir els impactes antropogènics locals i regionals com la pesca i les espècies invasores, per mantenir els ecosistems marins dins d’un “espai operatiu segur (SOS per les seves sigles en anglès)” i promoure la resiliència dels ecosistemes en un mar en continu escalfament i altament impactat.

Human activities such as urban settlement, farming, forestry and recreation, have caused deterioration of water quality in many freshwater lakes worldwide. Apart from anthropogenic impacts, it is also recognized that climate has a direct influence on lake water temperature, nutrient loads, phytoplankton abundance and chemistry. However, little is known about the potential effects of future climate change on lake water quality. Understanding the dynamics, abundance and availability of nutrient pools in lake bottom sediments is fundamentally important for predicting how, and over what time-scales, lake ecosystems will respond to future scenarios such as climate change, in-lake restoration or altered external nutrient loading. Through a sediment field study on 14 different lakes, and applications of complex lake ecosystem models to three New Zealand lakes, this study examined the spatial and temporal dynamics of sediment nutrient concentrations, and made considerations of the effects of restoration measures and future climate change on lake water quality. To gain insight into processes influencing the dynamics of horizontal and vertical gradients of sediment nutrient concentrations, intact sediment cores were collected from twelve lakes within the Bay of Plenty province, North Island of New Zealand. In addition, intact sediment cores were collected from shallow Lake Te Waihora (Ellesmere) in the Canterbury province, South Island of New Zealand and shallow Lake Taihu in the Jaingsu province, China. The observed vertical concentration profiles of total phosphorus (TP) in the sediments revealed that the shape of these profiles can be similar across gradients of widely differing trophic status. Empirical and mechanistic steady state profile models were derived to describe the vertical distribution of total carbon (TC), total nitrogen (TN) and TP concentrations in the sediments. These models revealed that density-driven burial and biodiffusive mixing, which in the models also includes effects of redox-driven gradients, are strongly correlated with vertical gradients of sediment TC, TN and TP content, whereas lake trophic status was not. Despite enhancing knowledge of the processes influencing vertical gradients of sediment nutrient concentrations, little is known about the rates at which sediment nutrient concentrations may change as a response to changes in external loading or climate. Studies into the composition of bottom sediments have been undertaken intermittently over the past three decades for the 12 lakes in the Bay of Plenty. These studies, together with the data collected in this study, were used to quantify temporal changes in sediment chemistry across the lakes. Comparison of the data collected in this study with results from a survey in 1995 showed that surficial sediment (0-2 cm) TP concentrations have increased in three of the 12 lakes, at rates ranging from 27.5 to 114.4 mg P kg-1 dry wt yr-1. TN concentrations in surficial sediments have increased in nine of the 12 lakes at rates ranging from 51.8 to 869.2 mg N kg-1 dry wt yr-1. A correlation analysis revealed that temporal changes in sediment TP and TN concentrations were not significantly linearly related (pgt0.05) to catchment area or temporal changes of different water column indices considered to reflect lake trophic state, including annual mean water column concentrations of TP, TN or chlorophyll a (Chl a). While vertical profiles of sediment nutrient concentrations can be used to provide information about historical changes of trophic status in lakes, little is known about horizontal variability of sediment nutrient concentrations, including possibly relationships with horizontal variations in water column variables. In the large, shallow and eutrophic Lake Taihu, China, there are distinct horizontal water column concentration gradients of nutrients and Chl a. Concentrations are generally high in the north, where some of the major polluted tributaries enter the lake, and relatively low in the south, where macrophytes generally are abundant. To test whether these water column concentration gradients are similarly reflected in spatial heterogeneity of nutrient concentrations within the bottom sediments of Lake Taihu, I examined correlations between concentrations of TP and TN in surficial sediments (0-2 cm) and TP, TN and Chl a concentrations in water column samples determined for 32 sites in 2005. Linear correlation analysis revealed that surficial sediment TP concentrations across the 32 stations were related significantly, though weakly, to annual mean water column concentrations of TP and TN as well as Chl a. Correlations of surficial sediment TN with water column variables were, however, not significant (p gt 0.05). To better understand the effects of future climate change on lakes of different trophic status, I applied the one-dimensional lake ecosystem model, DYRESM-CAEDYM, to oligo-mesotrophic Lake Okareka, eutrophic Lake Rotoehu and highly eutrophic Lake Te Waihora. All three models were calibrated based on a three-year period (July 2002 - June 2005) and validated on a separate two-year period (July 2005 - June 2007). The model simulations generally showed good agreement with observed data for temperature, dissolved oxygen (DO), and total nutrient and Chl a concentrations. To represent a possible future climate of 2100, temperature predictions were derived from the regional climate model, DARLAM, based on the Intergovernmental Panel on Climate Change (IPCC) A2 scenario, which suggests that air temperatures by the year 2100 will increase by an average of 2.5 'C and 2.7 'C for the Bay of Plenty and the Canterbury province, respectively, relative to the base scenario (years 2002-2007). Model simulations of the future climate scenarios indicate that climatic changes generally will lead to a degradation of lake water quality in all three lakes, especially during summer months, and further suggest that the effects on annual mean surface concentrations of TP, TN and Chl a will be equivalent to an increase in external TN and TP loading by 25-50%. Simulations for Lake Rotoehu, where diatoms and cyanophytes were represented in the conceptual model, further suggest that cyanophytes will be more abundant in the future, increasing by gt15% in annual mean biomass. Although the effects of climate change may be delayed or slightly mediated by the chemical resilience of the sediment nutrient pools, the effects of climate change on lake water quality in the New Zealand lakes will be of a magnitude that should be considered as management strategies are planned and implemented, thus increasing the probability of successful preservation or improvement in water quality in future decades.

The human gut microbiota is considered to be a highly specialized organ providing nourishment, regulating epithelial cell development, modulating innate immune responses and colonization resistances, and it significantly impacts human health and disease. Dispite of being extensively studied for several decades, the functionality of the microbiota colonization in the human gastrointestinal tract and the mechanisms of the interactions between the host and bacteria are still poorly understood. This research follows a novel and unique approach, which combines the complementary strengths of in vitro experiment, in vivo study and mathematical modelling. The work undertaken has three emphases: 1) probiotic strains and their impact on human health; 2) the development of gut microbiota in infants; 3) quantification of human gut microbial ecosystem at both the species level and the system level. In the first part of this research, a versatile anaerobic continuous culture platform was implemented following a novel and unique design, which allows easy and continuous sampling and monitoring of microbial growth. A number of carefully planned in vitro experiments have been conducted to investigate the growth and competition of probiotic strains under different culture conditions. These in vitro experiments improve the understanding for the growth behaviour of the specific probiotic strains. The second part of this project analyzed 50 faecal samples collected from 9 healthy infants with administration of probiotic strains and placebo. The analysis is based on the 454-pyrosequencing technology, which reveals the complete profiles of gut microbiota in these infants and confirmed the modulation effect of the specific probiotic strains. The last part of this research focused on the development of mathematical and computational models of human gut microbial ecosystem. The outcome from this part of the research includes: a) a new bacterial growth model that overcomes the parodox of competitative exclusion caused by previous models; b) a versatile computational framework to simulate in vitro fermentation experiments; and c) a comprehensive mathematical model for human gut and gut microbiota that is the first model for its nature.

O interesse em valorizar os serviços ecossistêmicos fornecidos pela vegetação natural aumentou em um esforço para mitigar os efeitos da mudança do uso da terra. Nesta linha de pensamento, desenvolvemos um índice para valorar as comunidades de árvores - do ponto de vista antropocêntrico - da savana brasileira (Cerrado). O índice e a cartografia produzida servirão como ferramenta para a priorização da conservação, bem como para revelar como a colonização e a expansão da agricultura tem ocorrido. Para desenvolver o índice, foram produzidas novas camadas ambientais com resolução de 90m; A distribuição das 93 espécies mais comuns foi modelada; e a cartografia da distribuição de cada uso humano das árvores (alimentos, aromáticos, fibras, cosméticos, cortiça, etc., totalizando 20 usos) e um índice de valor total fo desenvolvido. O novo índice de valor, nomenado a Soma de Usos (SoU, Sum of Uses), representa o número esperado de usos para a montagem de espécies potenciais que poderia estar ocorrendo no lugar em condições ideais. O impacto da agricultura foi avaliado pela contabilização da área que foi convertida em lavouras. Nossos resultados indicam fortemente que a colonização humana e a expansão de terras cultivadas eliminaram as árvores de áreas que antes eram melhores prestadores de serviços ambientais. Por outro lado, observamos também que as áreas protegidas no Cerrado estão localizadas onde esperamos encontrar valor marginal para as espécies ótimas. Esses resultados nos levam a pensar que a estratégia de conservação pode estar longe de ser ideal para o maior remanescente arável do mundo.
The interest in valuing the ecosystem services provided by the natural vegetation has increased in an effort to mitigate the effects of land use change. In this line of thinking, we developed an index to value the tree communities -from an anthropocentric point of view- of the Brazilian savannah (Cerrado). The index and the cartography produced will serve as a tool for prioritization of conservation, has well as to unveil how colonization and agriculture expansion has taken place. In order to develop the index: new environmental layers at 90m resolution were produced; the most common 93 species’ distribution was modelled; and cartography for each use humans derive from the trees (food, aromatic, fiber, cosmetic, cork, etc., totaling 20 uses) and a total value index were developed. The new index of value, namely the Sum of Uses (SoU), represent the expected number of uses for the potential species assemblage that could be taking place under optimal conditions. The impact of agriculture was assessed by accounting for the area that has been converted to croplands. Our results strongly indicate that human settlement and cropland expansion have cleared the trees of areas that once were better than average ecosystem service providers. On the other hand, we also observe that protected areas in the Cerrado are located where we expect to find marginal value for the optimal communities. These results lead us to think that the conservation strategy might be far from optimal for the largest remaining arable patch in the world.

En els últims anys, s'han dut a terme diversos projectes de recerca importants en el marc de les iniciatives de Single European Sky Air Traffic Management (ATM) Research i Next Generation Air Transportation System, que s'ocupen de l'automatització en caixers automàtics. Aquestes iniciatives han previst l'automatització com un procés impulsat pel rendiment general de l'ATM, centrat en els objectius i limitacions del sistema. En un àmbit més ampli, els objectius es defineixen com una disposició de la separació necessària entre aeronaus per assolir els nivells objectiu de seguretat, mentre que la competitivitat del trànsit es manté mitjançant un sistema eficient, respectuós amb el medi ambient i socialment valuós. Una major densitat operativa, juntament amb la manca de capacitat de control del trànsit aeri (ATC), en el maneig d'una major complexitat del trànsit, imposa bàsicament una disposició de separació que s'ha d'implementar com a cooperativa i distribuïda, a més d'utilitzar usuaris d'espai aeri (AU). En aquest context, cal passar d'un model d'intervenció tàctica purament centralitzada cap a una planificació estratègica més eficient i operacions tàctiques proactives, que assumeixen canvis significatius dels rols i responsabilitats de tots els grups d'interès implicats. Això anticipa una integració operativa i fluida dels mecanismes i mecanismes de la xarxa de seguretat de tal manera que qualsevol parell d'avions implicats en un conflicte, juntament amb els avions de trànsit que l'envolten, es comporten com un sistema de trànsit aeri estable i eficient i sense conflictes. El treball d'investigació d'aquesta tesi explica un nou marc de seguretat que es basa en el concepte d'ecosistemes aeris per transformar els objectius no coordinats entre la gestió de la separació a nivell tàctic i l'evitació de col·lisions a nivell operatiu, en una cooperativa i eficient, sense conflictes sistema. Els ecosistemes aèries es poden entendre com un paradigma dels sistemes adaptatius complexos, en què les trajectòries aeronàutiques canvien i evolucionen amb el pas del temps a causa de les interaccions entre els avions implicats i el seu entorn canviant. La tesi comprèn pocs resultats analítics utilitzats pels mètodes quantitatius per a la identificació de les interdependències espaciotemporals i el càlcul de les solucions totals de nivell de l'ecosistema i el punt mort en el temps de l'ecosistema disponible. Els mètodes analítics són orientats a les aplicacions en comptes d'un basat en la teoria, desenvolupat amb un enfocament de modelització quantitatiu i discret, i personalitzat a les demandes de trànsit actuals i a l'entorn operatiu. Com a resultat, el marc de l'ecosistema té la capacitat d'explorar encara més la possible capacitat de resolució en un espai de cerca de les solucions del sistema. Un percentatge decreixent dels recursos disponibles de l'ecosistema i un temps transcorregut descriuen un camí potencial en una determinació explícita de la dinàmica de resolució, el que significa que cada moment perdut en la realització d'un acord de resolució podria repercutir en un nombre menor de maniobres lliures de conflictes, però també mantenir o augmentar-les en algunes circumstàncies. L'enfocament ha mostrat una importància en proporcionar la capacitat de temps d'un conjunt de certes maniobres a nivell operatiu, quan la gravetat de la situació del conflicte es produeix molt ràpidament. Amb un increment causal en diversos avions d'ecosistemes i diverses geometries de trajectòria, l'estructura de les interdependències espaciotemporals es fa més gran que pot produir menys capacitat de resolució i un menor temps de presa de decisions. La metodologia de modelatge es pot implementar com a eina de suport a la decisió a l'aire i en terra. Les investigacions de seguiment es formalitzaran en múltiples direccions a través de l'avanç conceptual de les regions de resolució, la integració dels models d'actuació de l'avió, el desenvolupament d'un model de modelatge de la complexitat del trànsit circumdant i la implementació dels ecosistemes cooperatius i competitius per a vehicles aeris no tripulats.
En los últimos años, se han llevado a cabo varios proyectos de investigación importantes en el marco de las iniciativas de Single European Sky Air Traffic Management (ATM) Research y Next Generation Air Transportation System, que abordan la automatización en ATM. Esas iniciativas han previsto la automatización como un proceso impulsado por el rendimiento global de ATM, centrado en los objetivos y limitaciones del sistema. En un ámbito más amplio, los objetivos se definen como una disposición de la separación requerida entre las aeronaves para alcanzar los niveles de seguridad objetivo, mientras que la competitividad del tráfico se mantiene mediante un sistema eficiente, respetuoso con el medio ambiente y socialmente valioso. Una mayor densidad operativa junto con la falta de capacidad de control de tráfico aéreo (ATC), al manejar una mayor complejidad de tráfico, impone esencialmente una disposición de separación que se implementará como cooperativa y distribuida, incorporando también a los usuarios del espacio aéreo (AU). En este contexto, es necesario pasar de un modelo de intervención táctica puramente centralizado a una planificación estratégica más eficiente y operaciones tácticas proactivas, que supongan cambios significativos en los roles y responsabilidades de todas las partes interesadas. Eso anticipa una integración operacionalmente fluida de los mecanismos y procedimientos de la red de seguridad de tal manera que cualquier par de aeronaves involucradas en un conflicto, junto con la aeronave de tráfico circundante, se comporten como un sistema de tráfico aéreo estable, eficiente y libre de conflictos. El trabajo de investigación en esta tesis elabora un nuevo marco de red de seguridad que se basa en el concepto de ecosistemas aéreos para transformar los objetivos no coordinados entre la gestión de la separación a nivel táctico y la prevención de colisiones en el nivel operacional, en una cooperativa y eficiente, libre de conflictos sistema. Los ecosistemas aéreos se pueden entender como un paradigma de los complejos sistemas adaptativos, en los que las trayectorias de los aviones cambian y evolucionan con el tiempo debido a las interacciones entre las aeronaves involucradas y su entorno en constante cambio. La tesis comprende pocos resultados analíticos utilizados por medio de métodos cuantitativos para la identificación de las interdependencias espaciotemporales y el cálculo de las soluciones totales del nivel del ecosistema y el punto muerto dentro del tiempo del ecosistema disponible. Los métodos analíticos están más orientados a las aplicaciones que a la teoría, desarrollados con un enfoque de modelado discreto y cuantitativo, y personalizados según las demandas actuales de tráfico y el entorno operativo. Como resultado, el marco del ecosistema tiene la capacidad de seguir explorando la capacidad de resolución potencial en un espacio de búsqueda de las soluciones del sistema. Una tasa decreciente de los recursos del ecosistema disponibles y un tiempo transcurrido describen un camino potencial en una determinación explícita de la dinámica de resolución, lo que significa que cada momento perdido al hacer un acuerdo de resolución podría repercutir en un menor número de maniobras libres de conflicto, pero también mantenerlos o aumentarlos en algunas circunstancias. El enfoque ha demostrado la importancia de proporcionar la capacidad de tiempo para un conjunto de ciertas maniobras a nivel operacional, cuando la gravedad de la situación de conflicto ocurre muy rápidamente. Con un incremento causal en una serie de aeronaves de ecosistema y diversas geometrías de trayectoria, la estructura de las interdependencias espaciotemporales se hace más grande, lo que puede producir una menor capacidad de resolución y un tiempo de toma de decisiones más corto. La metodología de modelado se puede implementar como herramienta de apoyo a la decisión tanto en el aire como en tierra. La investigación de seguimiento se formalizará multidireccionalmente a través del avance conceptual de las regiones de resolución, la integración de los modelos de performance de la aeronave, el desarrollo de un modelo de aprendizaje automático para la complejidad del tránsito circundante y la implementación de ecosistemas cooperativos y competitivos para vehículos aéreos no tripulados.
In recent years, several important research projects under the Single European Sky Air Traffic Management (ATM) Research and the Next Generation Air Transportation System initiatives, addressing the automation in ATM have been conducted. Those initiatives have envisaged the automation as a process driven by the overall ATM performance, focused on the system objectives and limitations. In a broader scope, the objectives are defined as a provision of the required separation between aircraft to meet the safety target levels, while the traffic competitiveness is maintained by means of an efficient system, environmentally friendly and socially valuable. An increased operational density together with a lack of the air traffic control (ATC) capacity, in handling a higher traffic complexity, essentially imposes a separation provision to be implemented as cooperative and distributed, engaging also the airspace users (AUs). In this context, it is necessary to shift from a purely centralized tactical intervention model towards a more efficient strategic planning and proactive tactical operations, which assume significant changes of the roles and responsibilities of all involved stakeholders. That anticipates an operationally seamless integration of the safety net mechanisms and procedures in such a way that any pair of aircraft involved in a conflict, together with the surrounding traffic aircraft, behave as a stable and efficient, conflict-free air traffic system. The research work in this thesis elaborates a novel safety net framework relying on the concept of aerial ecosystems to transform the non-coordinated targets between separation management at the tactical level and collision avoidance at the operational level, into a cooperative and efficient, conflict-free system. The aerial ecosystems can be understood as a paradigm of the complex adaptive systems, in which aircraft trajectories change and evolve over time because of interactions among involved aircraft and its ever-changing environment. The thesis comprises few analytical outcomes utilized by the means of quantitative methods for identification of the spatiotemporal interdependencies and computation of the total ecosystem-level solutions and deadlock within available ecosystem time. The analytical methods are applications-oriented rather than a theory-based, developed with a quantitative and discrete modelling approach, and customized to the current traffic demands and the operational environment. As a result, the ecosystem framework has an ability to further explore the potential resolution capacity in a search space of the system solutions. A decreasing rate of the available ecosystem resources and an elapsed time describe a potential path in an explicit determination of the resolution dynamics, meaning that each missed moment in making a resolution agreement might reprobate in a less number of the conflict-free maneuvers, but also maintain or increase them in some circumstances. The approach has shown a significance in providing the time capacity for a set of certain maneuvers at the operational level, when a severity of the conflict situation occurs very rapidly. With a causal increment in a number of ecosystem aircraft and diverse trajectory geometries, the structure of spatiotemporal interdependencies becomes larger which can produce less resolution capacity and a shorter decision-making time. The modeling methodology can be deployed as both the airborne and ground-based decision support tool. Follow-up research will be multi-directionally formalized throughout conceptual advancement of the resolution regions, integration of the aircraft performance models, development of a machine learning model for the surrounding traffic complexity, and implementation of the cooperative and competitive ecosystems for unmanned aerial vehicles.

Doutoramento em Engenharia do Ambiente - Instituto Superior de Agronomia
In freshwater ecosystems associated with agricultural areas, organisms are exposed to a multitude of toxicologically and structurally distinct pesticides in concentrations that may fluctuate over time. However, the environmental risks of chemicals are traditionally evaluated and regulated on the basis of single substance. Understanding and improving the link between effects and exposure assessment is an important step in the current challenges of risk assessment in order to increase its ecological relevance. To this end, integrated approaches of different hierarchical levels of complexity and ecological realism have been developed and applied, including: exposure modelling, laboratory testing with individual organisms, species sensitivity distribution, ecosystem models and assessment of aquatic community interactions to evaluate the effects of realistic pesticide combinations on water bodies associated with rice, tomato and maize typical agroecosystems of Mediterranean conditions. Contributing to the overall knowledge of the adequacy of the prospective risk assessment and demonstrating that pesticide risk may be underestimated during the actual registration procedure. The data generated in the present study contributed to the derivation of optimized programs of measures under the scope of European legislation; the identification of sites with the highest expected impacts of pesticide mixtures; the evaluation of the major pesticide compounds that contributed mostly to the identified aquatic risks. Furthermore contribute to a deeper knowledge and unravel the effects of co-occurring chemicals, environmental and biological stressors in aquatic ecosystems considering the effects of biotic and abiotic interactions at community and ecosystem levels. The results contribute to reducing the risks of pesticides in freshwater
N/A

Radionuclides are widely used in energy production and medical, military and industrial applications. Thus, understanding the behaviour of radionuclides which have been or may be released into ecosystems is important for human and environmental risk assessment. Modelling of radionuclides or their stable element analogues is the only tool that can predict the consequences of accidental release. In this thesis, two dynamic stochastic compartment models for radionuclide/element transfer in a marine coastal ecosystem and a freshwater lake were developed and implemented (Paper I and III), in order to model a hypothetical future release of multiple radionuclides from a nuclear waste disposal site. Element-specific mechanisms such as element uptake via diet and adsorption of elements to organic surfaces were connected to ecosystem carbon models. Element transport in two specific coastal and lake ecosystems were simulated for 26 and 13 elements, respectively (Papers I and III). Using the models, the concentration ratios (CR: the ratio of the element or radionuclide concentration in an organism to the concentration in water) were estimated for different groups of aquatic organisms. The coastal model was also compared with a 3D hydrodynamic spatial model (Paper II) for Cs, Ni and Th, and estimated confidence limits for their modelled CRs. In the absence of site-specific CR data, being able to estimate a range of CR values with such models is an alternative to relying on literature CR values that are not always relevant to the site of interest. Water chemistry was also found to influence uptake of contaminants by aquatic organisms. Empirical inverse relationships were derived between CRs of fish for stable Sr (CRSr) and Cs (CRCs) and water concentrations of their biochemical analogues Ca and K, respectively (Paper IV), illustrating how such relationships could be used in the prediction of more site-specific CRCs and CRSr in fish simply from water chemistry measurements.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.

Finding a common language in describing and interpreting multivariate data associated with rehabilitation and disturbance ecology, has became a major challenge. The main objective of this study is to find and evaluate mathematical models to describe ecosystem change based on selected indicators of change. Existing data from a previous rehabilitation project on Hendrina Power Station (Mpumalanga, South Africa) was used as a database for this study and this study aims to report on the development of models concentrating on radar graphs and a model based on matrix mathematics. The main groups of organisms selected for the construction of models, were vegetation, soil mesofauna and ant species. The datasets were limited to some indicative species and their mean abundances were determined. The grids that were used were randomly chosen and the models were constructed. Radar graphs were constructed to model the suite of species identified, through a sensitivity analysis, to indicate possible rehabilitation success over time and was applied to the different rehabilitation ages. The surface areas under the radar graphs were determined and compared for the different rehabilitation ages in the same year of survey. Correlation graphs were drawn between the surface area and the rehabilitation ages. These graphs did not indicate much relevance in indicating rehabilitation success, but the radar graphs proved to be good indicators of change in abundance of the selected species over time. iv The vegetation species, Eragrostis curvula, was the only species that showed a strong significant positive relationship with rehabilitation age and could be considered a good rehabilitation species and indicator of rehabilitation success. After the evaluation of this model, Eragrostis curvula, and two additional ant species, Tetramorium setigerum and Lepisiota laevis, were added. These species that were added, showed an increase in abundance over time, as found in a previous study. These radar graphs also did not indicate much relevance and it can be concluded that the radar graphs can only be used for a visual representation of the changes in abundance of the relevant species over time. This study also refers to a matrix model. This model focused on the interactions between the different variables selected. The percentage carbon in the soil were also added to the list of species. Model fitting graphs were constructed and correlations were drawn between the species that had significant values in the interaction table. This model could be useful for future studies, but more data and replication is necessary, over a longer period of time. This will serve to eliminate possible shortcomings of the model.
Thesis (M. Environmental Science (Biodiversity and Conservation Biology))--North-West University, Potchefstroom Campus, 2007.

The world is undoubtedly being threatened by the negative impacts of climate change. The degradation of the ecosystem, the loss of species and the endangerment of human health, livelihood and wellbeing are the main consequences of this ever-growing pressure. Coastal communities, particularly Small Island Developing States (SIDS), require extra attention due to their increased vulnerability and dependency on ecosystem services. Services provide by coral reefs are among the most fragile ecosystems that provide essential services to local SIDS communities. Adaptation is a commonly accepted method by both international and local governments and authorities to tackle this phenomenon; adaptation refers to moderating the adverse effects of climate change through a wide range of actions to protect, accommodate or retreat. However, some adaptation actions and policies are not being adopted in a comprehensive approach, causing negative impacts on each other or possibly resulting in the failure of the desired and designed effectiveness. Thus, it is essential to use a holistic approach to identify adaptation solutions that are economically and practically feasible and realistic without compounding additional pressures on natural systems. The ecosystem-based approach is the key to dealing with common adaptation challenges and to addressing the needs of SIDS local communities. However, planning for SIDS communities under rapidly changing, uncertain non-climatic and climatic conditions requires following a practical approach capable of fulfilling the general adaptation planning requirements as well as specific characteristics of SIDS traditional communities. Thus, the needs and features of successful adaptation planning were studied through a systematic literature review to create a practical and effective planning approach. A total of 650 relevant papers were initially nominated and reviewed; however, this number was reduced to 116 papers for thorough revision and detailed analysis. First, it was found that an integrative stepwise planning approach is required to integrate the results of multidisciplinary analyses and assessments and stakeholders' knowledge and opinions. Next, three crucial dimensions of a fully integrated climate change adaptation planning process—integration in assessment, modelling and adaptive responses—were identified. Adopting this novel approach, the multi-layered integrative climate change adaptation planning approach, is more likely to yield better climate change adaptation planning outcomes over the long-term. In accordance with the proposed multi-layered integrative climate change adaptation planning approach, a hybrid dynamic modelling framework was developed to assess the health and resilience of coral reefs under different climate change scenarios and their consequential impacts on human wellbeing in Port Resolution, Tanna Island, Vanuatu. This framework follows a structured process and employs suitable techniques capable of dealing with different challenges, including the complexity and dynamicity of socioeconomic and environmental systems and impacts of trans-discipline variables. This multi-layered integrative approach employed structural analysis, fuzzy cognitive mapping (FCM), Bayesian networks (BN) and system dynamics (SD) techniques. Each of these techniques features its own benefits and limitations, and integrating these modelling tools can maximise their respective advantages by compensating for another's limitations. First, the principal influential factors in coral reef health and ecosystem services were identified, and their causal relationships were subsequently mapped using the participatory FCM technique. As a result of structural and FCM analyses, the following outcomes were achieved: (i) system variables were identified and grouped under different categories including marine ecology, climatic, community and socioeconomic variables; (ii) all variables were assessed based on their level of influence on other variables; (iii) the interrelationships of all variables were mapped based on expert knowledge; and (iv) a preliminary scenario-based analysis was performed, and the role and significance of the factors in the time horizon of the study were determined. Next, the long-term perspective of the future health and resilience condition of coral reefs under different sets of management interventions was explored using the BN technique. The BN model was conceptualised using the results of the previously completed step (i.e., FCM). The BN technique was used to incorporate existing data and experts' knowledge and to predict the future conditions of coral reefs under different scenario settings. Finally, the SD modelling step investigated the nexus between environmental and economic values under different combinations of management or adaptation strategies over a long-term period, which is 50 years or by 2070. As an innovative approach, the SD model was parameterised from the outcome of the BN modellings, in which the existing data and information were insufficient to quantify the model. Furthermore, comparing the results of modelling outcomes and their respective sensitivity analyses supported the model behaviour testing process of the final SD model. While each research stage has its own specific practical, methodological and scientific contribution, the main findings of this PhD research are: (1) sustainable management or adaptation planning of coastal coral reefs should be studied from a multidisciplinary socio-ecological lens; (2) identifying, assessing and prioritising all potential adaptive responses, including engineering, social and regulatory, through an integrated vulnerability assessment and decision-making process with all of their subsets is the key to success; (3) immediate actions to preserve coral reef health and resilience are required to protect the current flow of ecosystem services; (4) local management interventions are not likely to protect coral reefs under the worst-case climate change scenario; and (5) the steady and integrated implementation of management strategies alongside global mitigation efforts to minimise the impacts of climate change could protect the long-term flow of economic benefits and maintain functional coral cover despite economic loss over a short-term period. The predominant output of this study is a novel hybrid BN-SD modelling framework to support ecosystem-based climate change adaptation planning.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Eng & Built Env
Science, Environment, Engineering and Technology
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Adaptation is necessary to cope with, or take advantage of, the effects of climate change on socio-ecological systems. This is especially important in the forestry sector, which is sensitive to the ecological and economic impacts of climate change, and where the adaptive decisions of owners play out over long periods of time. These decisions are subject to experienced and expected impacts, and depend upon the temporal interactions of a range of individual and institutional actors. Knowledge of, and responses to, climate change are therefore very important if forestry is to cope with, or take advantage of, the effects of climate change over longer timescales. It is important to understand the role of human behaviour and decision-making processes in the study of complex socio-ecological systems and modelling is a method that can support experiments to advance this understanding. This study is based on the development of CRAFTY-Sweden; an agent-based model that allows the exploration of Swedish land-use dynamics and adaptation to climate change through scenario analysis. In CRAFTY-Sweden, forest and farmland owners make land use and management decisions according to their objectives, management preferences and capabilities. As a result of their management and location characteristics they are able to provide ecosystem services. To explore future change, quantitative scenarios were used that considered both socio-economic development pathways and climatic change. Simulations were run under the different scenarios for the period 2010-2100, for the whole of Sweden. Furthermore, because institutions (i.e. organisations) also influence socio-ecological systems through their actions and interactions between them and with land owners and the environment, a conceptual model of institutional actions applied to socio-ecological systems was developed. The application of this conceptual model was explored through a model of institutions that can act, interact and adapt to environmental change in attempting to affect ecosystem service provision within a simple forestry governance system. I found that forestry in the future will likely be unable to meet societal demands for forest services solely on the basis of autonomous adaptation. A northward expansion of agriculture and especially of forestry proved positive for both sectors to adapt to changing conditions, under several scenarios, given the substantial land availability and the improved environmental conditions for plant growth. Legacy effects of past land-use change can have a great impact on future land-use change and adaptation processes, especially in forestry. Also, greater competition for land may lead to shorter forest rotation times. Socio-economic change and land owner behavioural differences may have a larger impact on owner competitiveness, land-use change and ecosystem service provision than climate-driven changes in land productivity. Different owner objectives and behaviour resulted in different levels of ecosystem service provision. Also, particular forest types were differently suitable for adaptation depending on the sets of objectives under which they were managed. Owners implementing particular management strategies can be differently competitive under different future scenarios, and the suitability of such strategies for adaptation is not a static, inherent characteristic of a system. Instead, it evolves in response to changing contexts that include both the external global change drivers and the internal dynamics of agent interactions. Additionally, institutional conceptual models as presented here can support better understanding of the key institutional decision-making dynamics and their consequences, endogenously, flexibly across different socio-ecological systems. Finally, study limitations, future research and the policy relevance of findings are discussed.

The Tonle Sap is the largest and most important natural wetland in Southeast Asia. It covers an area of more than 15,000 km2 with a unique mosaic of natural and agricultural floodplain habitats that coexist with the largest fishery in the Mekong Basin. Accelerating hydropower development and climate change, however, are altering the Mekong’s hydrology, which could negatively affect downstream ecosystems. The Tonle Sap is facing a two-fold problem. First, the link between its hydrology and ecosystem properties is not well understood. Second, potential ecological changes caused by future hydrological disruptions related to hydropower and climate change are unknown. Thus, the main objective of this thesis was to quantify how alterations to the Mekong hydrology could affect the Tonle Sap ecosystem. The following studies were performed to addressed the objective: (1) an assessment of landscape patterns using geographical information and remote sensing tools; (2) an assessment of habitat patterns based on field surveys of water, vegetation, and soils; (3) ecosystem function modelling to simulate net primary production (NPP) as a function of water quantity, sediments, and habitat type; and (4) fauna habitat modelling linking the results from the assessment of landscape patterns to fauna species. The assessment of landscape patterns revealed a distinct relationship between inundation and vegetation. Habitats in the Tonle Sap were divided into five groups based on annual flood duration, as well as physiognomic factors and human activity: (1) open water, (2) gallery forest, (3) seasonally flooded habitats, (4) transitional habitats, and (5) rainfed habitats. Large habitat shifts could occur as a result of hydropower development scenarios by the 2030s; areas optimal for gallery forest could decrease by 82% from baseline conditions, whereas areas of rainfed habitats could increase by 10-13 % (813-1061 km2). The assessment of habitat patterns demonstrated that despite the complexity and intense human use of this ecosystem, the flood-pulse is the underlying driver of habitat characteristics by (1) determining inundation depth and duration; (2) creating the main soils gradient; (3) limiting the area cleared for agriculture; (4) influencing vegetation structure and water quality; and (5) shaping the composition of plant species. The ecosystem function model was used to estimate a reduction of 9-39% in annual NPP caused by different scenarios of hydropower development and/or climate change during 2032-2042. Cumulative impacts from hydropower would disrupt NPP to a greater extent than climate change. The fauna habitat model revealed that species richness was greatest in the gallery forests and seasonally flooded habitats. Animals that permanently reside in or that rely on these habitats to complete essential life-history stages would be the most affected by future changes. This thesis provides the first quantitative formulation that directly links fundamental components of the Tonle Sap ecosystem to its flood-pulse hydrology. It also provides a comprehensive assessment of the impacts of expected hydrological alterations. Hydropower is expected to bring more abrupt and distinct ecological alterations than climate change in future decades. Relative aerial changes to the gallery forests are expected to be greater than in other habitats. A decline of the Tonle Sap’s ecosystem services will occur if appropriate measures are not implemented. These measures include mitigating hydropower alterations, conserving natural habitats in areas that are likely to remain hydrologically undisturbed, restoring natural habitats in projected areas for optimal growth, and optimizing agricultural practices in the floodplain. Research findings from this thesis focused on the Tonle Sap, but given the fundamental commonalities between this system and other large floodplains, the information presented is highly informative to other large flood-pulse driven systems around the globe.

Yield losses due to wild species are relevant for a variety of cropping systems worldwide, e.g., in the case of rice weeds they can reach 60%. However, in the broader sense, wild species may also have positive effects on cropping systems for their capability to provide environmental benefits. In fact, they are fundamental to maintain high levels of biodiversity and, in the context of grassland communities, they are crucial for the provision of ecosystem services like those involved with pollination and recreational experiences. A quantitative understanding of the complex and dynamic interactions among species within agro-environmental systems is thus crucial to better analyze, for instance, the possible effects of climate change on community dynamics and to timely define effective adaptation strategies. In this context, the aim of this thesis was the development of new models for the simulation of the interaction between cultivated and wild species. Biophysical models are powerful tools to analyze the interactions between plants and environmental variables as well as to optimize crop management. However, one of their main weakness is the lack of algorithms for simulating the interactions between cultivated and wild species. The few examples available that consider these interactions are mainly related to fungal pathogens, whereas approaches considering weeds, insects and multi-species plant communities are extremely rare and insufficiently validated. To fill this gap, this PhD Thesis focused on the modelling of three categories of communities of increasing complexity: crop-weed (two plant species), grasslands (multi-species plant communities) and crop-insect-insect predators (different kingdoms). For the three categories, agroecosystems of worldwide importance were identified as case studies: paddy rice (chapter 2), grasslands (chapter 3 and 4) and olive trees (chapter 5). In particular, in chapter 2 a new model was developed for simulating the interaction between rice and two weeds (barnyardgrass and red rice); chapter 3 and 4 are focused on the extension of a model for the simulation of plant community dynamics in the context of mountain grassland systems, with case studies in temporary grasslands in the Apennine and in natural pastures in the Alps. The third chapter, in particular, focuses on the definition of strategies for adapting 9 grasslands management to climate change by explicitly considering their floristic composition, whereas the fourth chapter presents initial results on the effects of grazing and climate change on the productivity and floristic composition of pasture communities. Chapter 5 shows a new model of interactions among olive trees, the olive fruit fly (Bactrocera oleae (Rossi, 1790)) and its predators, whereas chapter 6 refers to the general conclusions of the researches carried out in this PhD Thesis. Although the new models developed in this work are process-based to reflect the complexity of interactions occurring in agroecosystems, they assume simplified descriptions of biophysical processes through a limited number of parameters to make them usable in operational contexts.

Dissolved Organic Carbon accounts for many different functions in the boreal forest ecosystem. It is the main vehicle for organic carbon transport from the litterfall to the forest soil profile and together with water drainage it can be transported to streams. In boreal forests, the DOC transport have gain attention because of recently documented rise in concentration. Several models have been proposed, first to gain understanding in the main cauces of this increase in concentration, and then to simulate the transport of DOC in the landscape. An exploratory work was made to identify the extent of physical control and hydrological pathways for DOC discharge and the long-term biological control over DOC production, transport in the soil profile and discharge in 2 different situations. A 22-year dataset from the Krycklan Catchment site was used. Meteorological data was used as driving variables to calibrate DOC concentration and runoff in a small catchment (Site C7). The CoupModel was set up to represent the described vegetation and documented soil characterization and then calibrated to fit the measured variables. A stepwise calibration process was preferred to promote the understanding of the different components of the landscape in the organic carbon cycle. Results point to soil heat and water transfer processes as the most relevant group to explain both water runnof and DOC discharge, with increasing relevance in the deeper layers, explaining up to 97% of short-term variability in DOC discharge for the 27-35 cm layer. Soil organic carbon pools showed to have relevance in organic carbon stock balance along the soil profile. Conclusions state that, In concordance with other authors, there is a hydrological primary control over DOC discharge, but that soil organics and especially vegetation perform a relevant role in long-term balance of the organic carbon cycle. Further studies with this model could include time-series of atmospheric deposition of Sulphur and nitrogen and running the model in cascade.

Land degradation is a widespread problem that affects about 1.5 billion people globally. It can be defined as the decline in the productive capacity of the land, and the loss of functionality of ecosystems. Overall, land degradation leads to ecosystem services degradation, because it affects and causes the depletion of several soil functions (e.g. sediment retention, nutrient cycling, carbon stocks, and water retention). Therefore, it is also a constraint in securing food production and it could cause food insecurity. Hence, land degradation represents a considerable problem especially in developing countries, where people strongly rely on the ecosystems and natural resources for their livelihoods. The principal aim of this study was to assess land degradation by integrating different sources of knowledges and data, to derive a synthesis relevant to inform decision-making processes, and to target priority areas for conservation and restoration interventions. In this study, three ecosystem services (ESS) were modelled to infer land degradation in a small area, in the Halaba special woreda, located in the Ethiopian Great Rift Valley. In particular, sediment erosion and retention, nutrient retention and export, and carbon storage and sequestration were modelled. Data from a local soil survey, from global coverage datasets, and from a supervised land use cover classification were used for the ESS modelling. Remote Sensing data were used during the parametrisation phase of the ESS modelling. Local knowledges and perspectives were gathered using an extensive participatory approach that targeted the communities of three kebeles in the study area, and the experts of the Halaba woreda Agricultural Office. 33 focus group discussions and 32 semi-structured interviews were conducted in the summer 2016. The information acquired through the ESS modelling and during the participatory approach was then integrated in a Bayesian Belief Network (BBN), a probabilistic graphical model, to derive a spatial explicit land degradation risk assessment. The results showed that assessing land degradation through the lens of key ecosystem services represents a valid approach. The ESS modelling results showed that the study area is characterised by high soil erosion rates, low carbon storage and sequestration, and low nitrogen retention. Moreover, the ESS modelling also showed that using data from global coverage datasets could affect the reliability of the ESS assessment. Furthermore, the qualitative study, derived from the participatory approach, highlighted the presence of complex linkages between environmental and socio-economic factors, which exacerbate land degradation. The integration of ESS modelling results, participatory approach and literature data in the BBN proved to be an efficient approach to derive a synthesis of the several knowledges acquired during the several steps of this PhD project. Overall, this study demonstrated that a transdisciplinary and interdisciplinary approach is an effective means to address land degradation risks, taking into consideration people needs and priorities. In order to reverse land degradation trends, there is the need to adopt intense restoration and sustainable land management programs. However, there is also the need to couple conservation interventions with development strategies, such as market access and development, land tenure system improvements, off-farm job opportunities generation, and livelihoods diversification. This could foster land conservation and restoration, and could support sustainable economic growth and inclusive development.

Climate change and habitat fragmentation are altering the structure and functioning of plant communities world-wide. Understanding how, why and with what consequences are major challenges of ecology today. Trait-based approaches focus on functional rather than taxonomic identity to facilitate process-based explanation and prediction. This thesis develops new ways of operationalising traits to understand plant community responses to the environment and community effects on ecosystem functioning and services. Wetlands, distinct in nature and patchy in their distribution, serve as a natural laboratory to extend plant trait theory and as inspiration for metacommunity modelling. The first part of the thesis (Papers 1 and 2) focuses on wetland plant traits in relation to current and future environmental conditions, ecosystem functioning and ecosystem services. Paper 1 surveys the state of knowledge regarding (i) ultimate and proximate drivers of wetland plant community functional composition, trait covariation and responses of individual traits along gradients, as well as (ii) trait effects on the sets of ecosystem properties and processes that underlie the generation of three key wetland ecosystem services (regulation of water flow, water quality, and climate). Paper 2 modifies species distribution modelling to predict future changes in plant community trait distributions due to climate change in central Sweden, which allows a qualitative estimate of changes in ecosystem service potential. Climate change induced functional changes may benefit water quality and flow regulation provided by fens and riparian wetlands, but compromise carbon sequestration capacity in bogs. The second part of the thesis (Papers 3 and 4) develops trait-based metacommunity models to study the interplay of local and regional dynamics on species, community and whole-metacommunity responses to climate change. Paper 3 finds model assumptions about species dispersal capacity to strongly influence predictions of diversity loss following climate change. While differences in species dispersal capacity drastically increase predicted extinction risk, more realistic models based on an empirically derived seed mass – seed number trade-off strongly moderate these predictions. Without considering fitness effects of covarying traits, models that include variable dispersal capacities thus might overestimate extinction risk from climate change. Paper 4 studies the development and recovery of the regional average trait-lag of response trait distributions, as a direct measure of the instantaneous realised metacommunity response to temperature change with implications for levels of ecosystem functioning. The dynamical response jointly depended on local response capacity and regional adaptive re-organisation via species range shifts. Where habitat was scarce, connectivity network properties mediated response capacity and may guide conservation priorities. This thesis makes contributions to plant trait ecology, wetland functional ecology, ecosystem service science and metacommunity theory. As a whole it furthers progress towards a predictive ecology that can bridge scales from individual physiology to ecosystem dynamics and anticipate global change effects on biodiversity and ecosystem functioning.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript.

 

The terrestrial CO2 exchange in the Arctic plays an important role in the global carbon (C) cycle. The Arctic ecosystems, containing a large amount of organic carbon (C), are experiencing ongoing warming in recent decades, which is affecting the C cycling and the feedback interactions between its different components. To improve our understanding of the atmosphere-ecosystem interactions, the Greenland Ecosystem Monitoring (GEM) program measures ecosystem CO2 exchange and links it to biogeochemical processes. However, this task remains challenging in northern latitudes due to an insufficient number of measurement sites, particularly covering full annual cycles, but also the frequent gaps in data affected by extreme conditions and remoteness. Combining ecosystem models and field observations we are able to study the underlying processes of Arctic CO2 exchange in changing environments. The overall aim of the research is to use data-model approaches to analyse the patterns of C exchange and their links to biological processes in Arctic ecosystems, studied in detail both from a measurement and a modelling perspective, but also from a local to a pan-arctic scale. In Paper I we found a compensatory response of photosynthesis (GPP) and ecosystem respiration (Reco), both highly sensitive to the meteorological drivers (i.e. temperatures and radiation) in Kobbefjord, West Greenland tundra. This tight relationship led to a relatively insensitive net ecosystem exchange (NEE) to the meteorology, despite the large variability in temperature and precipitations across growing seasons. This tundra ecosystem acted as a consistent sink of C (-30 g C m-2), except in 2011 (41 g C m-2), which was associated with a major pest outbreak. In Paper II we estimated this decrease of C sink strength of 118-144 g C m-2 in the anomalous year (2011), corresponding to 1210-1470 tonnes C at the Kobbefjord catchment scale. We concluded that the meteorological sensitivity of photosynthesis and respiration were similar, and hence compensatory, but we could not explain the causes. Therefore, in Paper III we used a calibrated and validated version of the Soil-Plant-Atmosphere model to explore full annual C cycles and detail the coupling between GPP and Reco. From this study we found two key results. First, similar metrological buffering to growing season reduced the full annual C sink strength by 60%. Second, plant traits control the compensatory effect observed (and estimated) between gross primary production and ecosystem respiration. Because a site-specific location is not representative of the entire Arctic, we further evaluated the pan-Arctic terrestrial C cycling using the CARDAMOM data assimilation system in Paper IV. Our estimates of C fluxes, pools and transit times are in good agreement with different sources of assimilated and independent data, both at pan-Arctic and local scale. Our benchmarking analysis with extensively used Global Vegetation Models (GVM) highlights that GVM modellers need to focus on the vegetation C dynamics, but also the respiratory losses, to improve our understanding of internal C cycle dynamics in the Arctic. Data-model approaches generate novel outputs, allowing us to explore C cycling mechanisms and controls that otherwise would not have been possible to address individually. Also, discrepancies between data and models can provide information about knowledge gaps and ecological indicators not previously detected from field observations, emphasizing the unique synergy that models and data are capable of bringing together.

Includes bibliographical references (p. 177-194)
Hypotheses regarding the spawning strategy and recruitment of sardine (Sardinops sagax) in the southern Benguela ecosystem are tested using an individual-based Lagrangian particle tracking model linked with a 3-D hydrodynamic model of the region. Experiments focus on the dispersion of eggs and larvae among possible spawning and nursery areas. The two main areas of interest were the west coast upwelling region and the south coast shelf region (Agulhas Bank). A stage-based temperature-dependent development model is incorporated and vertical positioning schemes are tested. The spatial distribution and size structure of the sardine spawning stock for the period 1991-1999 are presented and a simple size-based fecundity model, combined with modelled recruitment, is used to determine the relative importance of each spawning and nursery area. The area of spawning plays a fundamental role in determining the destination of spawned eggs, and recruitment of sardine in the southern Benguela ecosystem appears to be divided into three recruitment systems by the circulation of the region: eggs spawned west of Cape Agulhas recruiting on the west coast (the WAB/WC-WC system), eggs spawned east of Cape Agulhas recruiting on the west coast (the CAB-WC system), and eggs spawned east of Cape Agulhas recruiting to the south coast (the SC-SC system). There is a slight increase in retention in the two nursery areas during winter, but the transport of eggs and larvae from the Agulhas Bank to the west coast is optimal during spring to early summer. Slow development arising from cold temperatures on the west coast could negatively impact recruitment by increasing offshore loss of individuals before they develop to a stage when they are able to actively avoid offshore currents and through its effect on mortality rate. This could explain the spatial separation of spawning and nursery areas in this system. The vertical position of individuals has an effect on the level of modelled recruitment and mortality rate, but observed vertical distributions of sardine egg and larvae do not significantly increase the level of modelled recruitment to optimal nursery areas. This suggests that efficient transport and retention are traded-off against other factors such as predator avoidance or prey abundance. Observed size structure and spatial distribution of the sardine spawning stock for 1991-1999 fluctuated greatly with most spawning centred on the western Agulhas Bank. When spawning was centred east of Cape Agulhas, recruitment was poor. No significant relationship could be established between potential reproductive output reaching the west coast and estimated recruitment, but positive recruitment anomalies required good transport to, and retention on, the west coast. A conceptual model of the early life history of sardine is proposed in light of limitations imposed by transport and retention of individuals. Lower primary production and the possibility of higher predation on the Agulhas Bank suggest that the south coast supports less recruitment than the west coast. The hypotheses tested using available data and model results could improve the understanding of recruitment of sardine in this complex ecosystem. These need to be validated by field observations. Additionally, further avenues for research that could help in developing a better understanding of the sardine life history in the southern Benguela ecosystem are suggested.

L'objectif de cette thèse était d'anticiper les effets de l'Obligation de Débarquement (OD) mise en place en UE depuis début 2015 en Manche Orientale (MO). Pour accomplir ces objectifs, il a été prévu de : i) mieux comprendre la distribution spatiale saisonnière d'espèces commerciales à l'aide d'observations embarquées sur des navires commerciaux, ii) les comparer avec la distribution de l'effort de pêche à fine échelle des chalutiers de fonds (OTB), et iii) développer un modèle individu-centré de dynamique des flotilles, DSVM, à intégrer avec le modèle écosystémique OSMOSE pour simuler l'OD. L'utilité des données d'observations embarquées a été prouvée pour une majeure partie des espèces échantillonnées, en utilisant une validation par la bibliographie et un indicateur géostatique. Ensuite la comparaison de l'effort de pêche à fine échelle a fourni une amélioration de la quantification de l'effort de pêche effectif et mis en valeur l'importance de la seiche et du rouget barbet pour la distribution des OTB en MO. De plus, l'intensité de ciblage des OTB a été quantifiée en octobre à l'aide d'un nouvel indicateur, et démontré l'intérêt pour les mêmes espèces, mais aussi la contrainte d'un faible quota de cabillaud pour les pêcheurs. Les résultats du couplage OSMOSE-DSVM montrent que k'OD aurait des effets négatifs à court terme pour le revenu des pêcheurs, induits par le déplacement de l'effort de pêche afin d'éviter les dépassements de quota, mais serait profitable à moyen terme. Cependant, l'OD provoquerait une hausse de la pression de prédation produite par le cabillaud et le merlan sur les autres espèces, ce qui n'améliorerait pas l'état global de l'écosystème
The objective of this thesis was to anticipate the effects if the EU Landing Obligation (LO) implemented since the beginning of 2015 in the Eastern English Channel (EEC). To achieve these objectives, it was planned to : i) better understand seasonal spatial distribution of commercial species using on-board commercial vessels observation data, ii) compare them with the final scale fishing effort distribution of EEC bottom otter trawlers (OTB), and iii) develop an individual-based model of fleet-dynamics, DSVM, to be integrated within the ecosystem model OSMOSE to simulate a LO. The usefulness of on-board observation data was proved for a main part of a species sample, using validation from the literature and a geostatistical indicator. Then the comparison of fine scale fishing effort provided an improvement of the quantification of effective fishing effort and emphasized the importance of cuttlefish and red mullet for the global distribution of EEC OTB. In addition, the targeting intensity of OTB was quantified in October using a newly-developed indicator, and demonstrated the attractiveness of the same species, but also the constraint of low cod quota for fishers. Results of the OSMOSE-DSVM coupling show that the LO would have short-term negative effects on fishers' revenue, induced by a large reallocation of their fishing effort to avoid quota over-shooting, but would be profitable in the medium-term. However, the LO would induce an increase of the predatory pressure operated by cod and withing on the other species, which would not improve the overall ecosystem health

Collective intelligence (CI) emerges from local coordination, collaboration and competition among the individuals within a social group. CI mainly results in a global intelligent behavior. One of the fundamental interactional channels within a CI system is energy flow. Each agent within an artificial or physical ecosystem must absorb energy in order to survive, evolve, breed, and reshape its local environment. In addition because the energy resources are limited in the environment, each agent has to compete with other agents to reach the required level of energy. Understanding the internal energy flow can potentially provide a deep insight into internal activities and external emergent behaviors of a given complex system. This study proposes a stochastic scheme for modeling a multi-species prey-predator artificial ecosystem with two levels of food chain. This will enable us to investigate the influence of energy flow on the ecosystem’s lifetime. The proposed model consists of a stationary hosting environment with dynamic weather condition and fruit trees. The inhabitants of this ecosystem are herbivore and carnivore birds each consisting of species. In our model, the collective behavior emerges in terms of flocking with more added rules consist of breeding, competing, resting, hunting, escaping, seeking and foraging behaviors. Using multi-species scheme, we define the ecosystem as a combination of prey and predator species with inter-competition among species within same level of food chain and intra-competition among those belonging to different levels of food chain. Furthermore, in order to model the energy within the ecosystem, some energy variables as functions of behaviors are incorporated in to the model. Finally, a simulation and visualization structure for implementing the proposed model is developed in this study. The experimental results of 11,000 simulations analyzed by Cox univariate analysis and hazard function suggest that only five out of eight behaviors can statistically significant influence the ecosystem’s lifetime. Furthermore, the results of survival analysis show that out of all possible interactions among energy factors, only two of them, interaction between flocking and seeking energies, and interaction between flocking and hunting energies, have statistically significant impact on the system’s lifetime. In addition, software implementation of the proposed framework validates the stability of simulation and visualization architecture. At last regression results using Nelson-Aalen cumulative hazard function and Cox-Snell variable and scaled Schoenfeld residuals test strongly validate our experimental results. To the best of our knowledge, there are three contributions in this research: First, the high level of complexity in the structure of the proposed model in comparison with the other systems which mostly contains only one species of prey, one species of predator and a kind of resource. While this study introduces two species of prey, capability of competition among species, dynamic weather condition with two element of wind and rain and dynamic resources, various behavioral rules such as escaping, breeding, hunting, resting, etc. Energy flow analysis within an artificial ecosystem is the second contribution. To the best of author’s knowledge there is no similar comprehensive model in the previous literature that investigates the life span of a stochastic multi-species predator-prey artificial ecosystem based on energy flow using Survival Analysis method. Lastly, the simulation results show that the flocking and seeking energy and flocking and hunting energy interactions are the most significant interactions which match with the Thompson iii et al. [ 65] observations in the real life. Their findings indicate that in the real life, birds use flocking behavior for better movement, more efficient food searching and social learning. Flocking motion also decrease predation risk as much as the flock size increases.

Recent shifts towards ecosystem based fisheries management (EBFM) around the world have necessitated consideration of effects of fishing on a larger range of species than previously. Non-selective multispecies fisheries are particularly problematic for EBFM, as they can contribute to erosion of ecosystem structure. The trade-off between catch of productive commercial species and abundance of low-productivity species is unavoidable in most multispecies fisheries. A first step in evaluation of this trade-off is estimation of productivity of different species but this is often hampered by poor data. This thesis develops techniques for estimating productivity for data-limited species and aims to help clarify EBFM policy objectives for the fisheries of New South Wales (NSW), Australia. It begins with development of an age-structured model parameterised in terms of optimal harvest rate, UMSY. UMSY is a measure of productivity, comparable among species and easily communicated to managers. It also represents a valid threshold for prevention of overfishing. The model is used to derive UMSY for 54 Atlantic fish stocks for which recruitment parameters had previously been estimated. In most cases, UMSY was strongly limited by the age at which fish were first caught. However, for some species, UMSY was more strongly constrained by life history attributes. The model was then applied to twelve species of Australian deepwater dogshark (Order Squaliformes), known to have been severely depleted by fishing. Results showed that the range of possible values of UMSY for these species is very low indeed. These findings enabled a preliminary stock assessment for three dogsharks (Centrophorus spp.) currently being considered for threatened species listing. Preliminary results suggest they have been overfished and that overfishing continues. Finally, an Ecopath with Ecosim ecosystem model, representing the 1976 NSW continental slope, is used to illustrate trade-offs in implementation of fishing policies under alternative policy objectives. Results are compared with those of a biogeochemical ecosystem model (Atlantis) of the same system, built by scientists from CSIRO. While there were large differences in model predictions for individual species, they gave similar results when ranking alternative fishing policies, suggesting that ecosystem models may be useful for exploring broad-scale strategic management options.

In urban environments, the breakdown of chemicals and pollutants, especially ions and metal compounds, can be favoured by Green Water Infrastructures (GWIs). If a better picture of chemicals and pollutants input and an improved understanding of hydrological and biogeochemical processes affecting these pollutants were known, GWIs could be designed to efficiently retain these pollutants for site-specific meteorological patterns and pollutant load. To fill in these gaps, the existing literature was surveyed to retrieve a comprehensive dataset of anions and heavy metal pollutants incoming to urban environments. The existing literature was then surveyed to review the metal retention efficiency, and hydrological- and metal biogeochemical- models of GWIs. Next, biogeochemical processes related to inorganic metal compounds were proposed to be integrated in biogeochemical models of GWIs. A deterministic model has been developed to describe the bulk breakdown rate, accumulation and leaching of Cu, Pb, and Zn in GWIs. The model describes aqueous complexation, mineral adsorption and kinetic methylation of those metals, and has been tested against experimental hydrographs and pollutographs of a GWI (a stormwater biofilter in Monash University) over a period of 100 days. Parameter calibration resulted in R2  98% and in NRMSE < 12% against cumulative effluent water and metal mass. The concentration of Cu and Pb was linearly correlated to the hydraulic conductivity, and equilibrium and kinetic rate constants, whereas Zn concentration was exponentially correlated to them; it was found that ± 20% change in these parameter values returned changes in Cu, Pb and Zn concentrations within about ± 52%, ± 45% and ± 96%, respectively. The maximum annual metal load in the outflow from the biofilter was observed for the rainfall combination with lowest frequency and highest intensity. This model can be effectively used to assist in designing biofilters and assessing their long-term performance.