Dissertations / Theses on the topic 'Dynamic ecosystem modelling'

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.

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.

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.<br>Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 736

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.<br>Thesis (PhD Doctorate)<br>Doctor of Philosophy (PhD)<br>School of Eng & Built Env<br>Science, Environment, Engineering and Technology<br>Full Text

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<br>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

<p>This thesis presents models applicable for aquatic ecosystems. Geographical Information Systems (GIS) form an important part of the thesis. The dynamic mass balance models focus on nutrient fluxes, biotic/abiotic interactions and operate on different temporal and spatial scales (site, local, regional and international). The relevance and role of scale in mass balance modelling is a focal point of the thesis.</p><p>A mesocosm experiment was used to construct a model to estimate the nutrient load of phosphorus and nitrogen from net cage fish farming (i.e., the site scale). The model was used to estimate what feeding conditions that are required for a sustainable aquaculture scenario, i.e., a zero nutrient load situation (a linkage between the site scale and the regional scale). </p><p>A dynamic model was constructed for suspended particulate matter (SPM) and sedimentation in coastal areas (i.e., the local scale) with different morphometric characteristics and distances to the Sea. The results demonstrate that the conditions in the Sea (the regional and international scale) are of fundamental importance, also for the most enclosed coastal areas.</p><p>A foodweb model for lakes was transformed and recalibrated for Baltic Sea conditions (i.e., the international scale). The model also includes a mass balance model for phosphorus and accounts for key environmental factors that regulate the presuppositions for production and biomasses of key functional groups of organisms. The potential use of the new model for setting fish quotas of cod was examined.</p><p>For the intermittent (i.e., regional) scale, topographically complex areas can be difficult to define and model. Therefore, an attempt was made to construct a waterscape subbasin identification program (WASUBI). The method was tested for the Finnish Archipelago Sea and the Okavango Delta in Botswana. A comparison to results from a semi-random delineation method showed that more enclosed basins was created with the WASUBI method.</p>

Sustainable land management (SLM) practices, as conservation agriculture (CA) and conventional tillage with cover crops (CC), aimed at balancing competitive agricultural production and environmental protection, have been encouraged throughout the EU through policy and subsidisation. Adoption of SLM practices that regulate biogeochemical cycles, however, requires further study, especially given the effects of local pedo-climatic variability and because middle and long-term effects are not fully understood and may differ from short-term outcomes. For these reasons, in this work, field experiments were conducted in three farms in the low-lying venetian plain, characterized by loamy soils, where CA and CC were compared to conventional intensive tillage system (CV) on trials established since 2010. The first objective of the thesis was to evaluate, by integrating experimental field results with model predictions, the potential ecosystem services provided by CA and CC practices on SOC dynamic, air quality and climate regulation, nutrition biomass and regulating of water conditions. In this experiment, CA and CC results contrasted according to the soil functions, the ecosystem service category and evaluation time span. The former was more effective in providing regulating services in the short term, and less consistent in the long term, at least for GHG mitigation. GHG control is only one of the numerous ecosystem services provided by conservation practices (e.g. reduction of erosion and P particulate loss). Many of these depend on the C content which are strongly affected by the C stratification processes. Cover crop adoption, on the contrary, showed promise in the long term, whereas short-term outcomes (two-year experiment) were negatively affected by poor cover crop growth. The second objective aimed to assess the SOC stock variation due to the adoption of CA and CC in comparison to CV within a large sample (i.e., 240) of 0-50-cm soil profiles, comparing two expansive soil sampling operations conducted in 2011 and 2017. The study showed that CA enhances SOC stratification rather than SOC accumulation, with high topsoil SOC that may have partly counteracted soil surface compaction. However, a comparison with previous SOC stock quantifications between CA and CV after three years of the experiment suggests that some SOC stock increase occurred, even at 50 cm, despite being not significant. The burial of fresh biomass-C with cover crops in arable systems (CC) enhanced SOC stock depletion most likely due to priming effects, suggesting that C input management is pivotal for its accumulation in agroecosystems with low soil fertility and low SOC protection capacity.

Changing environmental conditions often impose stressful growing conditions in plant communities. Until now, morphological plasticity, i.e. polymorphic growth physiognomies of plants, has not been sufficiently studied as a pivotal strategy for the whole ecosystem adaptation to environmental stress. We consider mangrove ecosystems as suitable models to provide insights on this subject. In the thesis, I investigate the ecological significance of tree morphological plasticity in the structural development and the dynamics of mangrove forests. I conducted field experiments in two regions located on both sides of the Amazon River mouths i.e. in French Guiana and North Brazil. Forest inventories were carried out in contrasting mangrove stands in both regions. The thesis combines empirical analysis of field data, terrestrial laser scanning (TLS), and mechanistic, individual-based computer simulations. We published results that proved the TLS-based analysis of individual tree structure useful for a better knowledge on biomass allocation between trunk and branches in tall and large Avicennia germinans mangrove trees reaching 45 m high and 125 cm of trunk diameter. Combining structural descriptions of A. germinans trees found in both sites, I highlighted the site-specific differences in tree allometries. The study suggests that regional differences in mangrove tree structure and function could be captured through better description of crown metrics, and that selected indicators of local morphological plasticity and consequent stand structure could generate a plus-value in the understanding of mangrove stand dynamics across contrasting coastal environments. Beyond the extension of allometric models to large Avicennia trees, we proposed new biomass equations with improved predictive power when crown metrics is taken into account. Additionally, we developed a novel software tool, named Lollymangrove, based on the AMAPStudio suite of software, with the objective of maximizing the potential of further field descriptions and modeling works. Lollymangrove allows standardized forest data capture, 3D visualization of structural data, aboveground biomass computations from a configurable module and export formats for forest dynamics and remote sensing models. Simulation experiments were conducted by means of the spatially explicit, individual-based stand model BETTINA_IBM. This model describes the important mechanism of water uptake limited by salt stress, and revealed insights into the relation between environmental conditions, allometric variations and biomass partitioning of mangrove trees, and stand characteristics. The simulation results suggest close matches with observed ecological patterns (e.g., tree allometries, mortality distributions, and self-thinning trajectories) under higher salinity. In low salinity conditions, however, the current parameterization underestimates the maximum tree height and diameter, and consequently, aboveground biomass and self-thinning trajectories of forest stands. This suggests that the morphology of trees under low levels of salinity are explained by further regulation mechanism(s) that still need to be addressed in a subsequent model improvement. Overall, this work has essentially pointed out the need to elucidate how morphological plasticity relates with structural development of forest stands. It establishes that TLS measurements and structural data analysis associated to efforts for integrative software and mechanistic modelling works could link mangrove dynamics to fast-changing coastal processes.

The research conducted explored the dynamics of the historical water-management system that was in use at Engaruka, Tanzania, between the 15th to 18th centuries CE, the aim being to model the primary human and environmental factors and their interactions, and to assess how these influenced the development of the system at several spatial and temporal scales. The ABMs developed in this research represent first steps in the integration of archaeological evidence with ABM techniques in order to understand the Engaruka site. This research shows how the integration of data from different sources and disciplines can help in our understanding of how the system could have developed by integrating a multitude of factors and showing how these interactions influenced the development of the system.

There is significant worldwide environmental concern related to the transportation of Invasive Aquatic Species (IAS) by ships ballast water into non-native environments. This has given rise to the development of a vast array of technological ballast water treatment systems. The complex environmental challenges and tight operational characteristics of marine vessels limits the scope of the technologies used for Ballast Water Treatment (BWT). As a result few technologies have progressed beyond the research and development stage; however one of the most promising technologies for ship board use is the cyclonic separator, or hydrocyclone. Despite the use of hydrocyclones in a wide variety of engineering applications they have yet to be successfully adapted towards the removal of suspended sediment and marine organisms from large volumes of ballast water. The following primary objectives of this study have been met: • Via critical review identify the technological solutions for treating ballast water best suited to onboard use. • Define the critical flow regimes evident within hydrocyclonic separators. • Establish a series of Computational Fluid Dynamics (CFD) simulations, evaluating standard turbulence models in order to determine the capacity for commercial CFD to model hydrocyclonic flow. This study has detailed the operational characteristics of ballast water hydrocyclones with the aim of enabling hydrocyclones to be optimised for individual ship configurations. Flow simulations have been conducted using CFD, and in particular the Detached Eddy Simulation (DES) turbulence model. Finally the DES model is shown to be a legitimate turbulence model for hydrocyclonic flow regimes, validated against empirical and experimental data.

Interacting particle systems are a particular class of stochastic processes where single degrees of freedom interact through probabilistic rules defined over a graph which reflects the spatial topology of the model. From the statistical mechanics point of view these models are of particular interest since they are genuinely out-of-equilibrium processes and introduce new universality classes and dynamical phase transitions. Among these processes, systems with absorbing states are characterized by points in the state-space in which the dynamics becomes trivial and, once reached, cannot be leaved. Because of the several possible interpretations, these models have found many applications in different areas of science: from condensed matter Physics to Biology, from Ecology to Sociology and Finance and also, in their quantum versions, to quantum control theory. Despite their importance for possible applications, though, a unified understanding of these systems is still lacking. In theoretical ecology, many open fundamental questions about the dynamics of ecosystems provide the cue for a further development of the theory of interacting particle systems. In particular, in this thesis we will address three main topics: i) Spontaneous neutral symmetry breaking. A central problem in ecology is the elucidation of the mechanisms responsible for biodiversity and stability. Neutral theory provides gross patterns in accord with empirical observations, but its validity is still highly debated. In particular, it is not clear how this theory can originate the observed non-neutral dynamics. Within a completely species-symmetric theory, we demonstrate that nonlinear dynamics can lead to a stationary state characterized by both stability and biodiversity by spontaneously breaking the neutral symmetry. ii) Habitat heterogeneities. It is known that habitat can have a great impact on the dynamics of species. In its most basic level of abstraction, its effects can be mimicked by an interacting particle system in a quenched random external field that locally breaks the species symmetry. We propose here an effective solution of the model in the long-times limit. iii) Role of boundary conditions. For non-equilibrium systems near a critical point, little is known about the role of the boundary conditions to the global phase diagram of the system. We analyze here a paradigmatic non-equilibrium critical model with mixed symmetry-preserving boundary conditions.<br>I sistemi di particelle interagenti sono una particolare classe di processi stocastici in cui singoli gradi di libertà interagiscono secondo leggi probabilistiche su di un grafo che definisce la particolare topologia spaziale del modello. Dal punto di vista meccanico - statistico questi modelli sono particolarmente interessanti in quanto sono genuinamente fuori equilibrio ed introducono nuove classi di universalità e transizioni di fase dinamiche. Tra questi processi, i sistemi con stati assorbenti sono caratterizzati da punti nello spazio delle fasi in cui la dinamica diventa banale e che una volta visitati non possono essere abbandonati. Date le numerose possibili interpretazioni, questi modelli hanno trovato numerose applicazioni in aree differenti: dalla Fisica alla Biologia, dall'Ecologia alla Sociologia e la Finanza, fino, nelle loro versioni quantistiche, alla teoria del controllo quantistico. Tuttavia, nonostante la loro importanza per le loro possibili applicazioni, è ancora carente una comprensione teorica unificata di questi sistemi. In Ecologia teorica, molte domande fondamentali sulla dinamica degli ecosistemi forniscono lo spunto per uno sviluppo ulteriore della teoria dei sistemi di particelle interagenti. In particolare, in questa tesi affronteremo i seguenti argomenti: i) Rottura spontanea della simmetria neutrale. Un problema centrale in ecologia è la spiegazione dei meccanismi responsabili della biodiversità e della stabilità. La teoria neutrale fornisce risultati in accordo con le osservazioni sperimentali, ma la sua validità è ancora fortemente dibattuta. In particolare, non è chiaro come essa possa produrre gli effetti non neutrali osservati. In una teoria completamente specie-simmetrica, dimostriamo che dinamiche non lineari posso produrre uno stato stazionario caratterizzato da stabilità ed una ricca biodiversità tramite la rottura spontanea della simmetria neutrale. ii) Habitat eterogeneo. E' noto che l'habitat può influenzare grandemente la dinamica di un ecosistema. In prima approssimazione, questi effetti possono essere mimati introducendo un campo esterno aleatorio di tipo <<quenched>> che rompe localmente la simmetria tra specie. Proponiamo qui una soluzione efficace di questo problema nel limite di tempi lunghi. iii) Ruolo delle condizioni al contorno. Per i sistemi fuori dall'equilibrio vicino a punti critici si conosce poco sul ruolo delle condizioni al contorno sul diagramma di fase del sistema. Noi studiamo un importante modello critico fuori dall'equilibrio con condizioni miste al contorno che preservano la simmetria globale del sistema.

The recognition of nature in the resolution of societal challenges has been growing in relevance. This recognition has been associated with the development of new concepts from science and policy such as natural capital, ecosystem services, green infrastructure, and more recently Nature-Based Solutions (NBS). NBS intends to address societal challenges in an effective and adaptive form providing economic, social, and environmental benefits. The overall aim of this PhD thesis is to develop an environmental and economic assessment of NBS for highly urbanised territories based on rationales and models underpinning ecosystem services, urban/landscape ecology, and life cycle thinking approaches. This combined evaluation approach would help to better understand if NBS are cost-effective or not. The aim is developed according to four specific objectives. The first objective corresponds to the characterisation of NBS in relation to urban contexts and the problematics that they can help to address or mitigate. To achieve this objective a critical review on the study of the relationship between NBS, ecosystem services (ES) and urban challenges (UC) was developed. As a main output, a graph of plausible cause-effect relationships between NBS, ES and UC is obtained. The graph represents a first step to support sustainable urban planning, moving from problems (i.e. urban challenges) to actions (i.e. NBS) to resolutions (i.e. ES). The second objective corresponds to the definition of an adequate set of biophysical and monetary assessment methods and indicators to evaluate the value of NBS in urbanised contexts. To achieve this objective, a review of existing methods on ecosystem services valuation, life cycle cost analysis and life-cycle assessment are developed. The review takes into account specific constraints such as easiness to use and availability of data. At the end, potential methods and indicators were selected, which will be later integrated in the combined assessment framework. The third objective corresponds to the design of a combined assessment framework integrating methods from life cycle assessment, landscape/urban ecology and ecosystem services that quantifies the environmental and economic value of NBS informing about the cost-effectiveness of its entire life cycle. To achieve this objective, a conceptual framework is developed. From it, a system dynamics model of ecosystem (dis)services is developed and coupled with a life cycle assessment method. The combined evaluation is tested with a relevant NBS type (i.e. urban forest) in a case study in the metropolitan area of Madrid. The fourth objective is the development of a decision support (DSS) tool that integrates the assessment framework as part of iterative design processes in urban planning and landscape design. The DSS intends to enhance the interrelation between science, policy and planning/design. To achieve this objective a user-friendly web-based prototype DSS on NBS, called NBenefit$®, is developed. The prototype DSS provides the user a simple form of quantifying the provision of multiple ES and costs over the entire life cycle (implementation, operational life, and end-of-life) of NBS. This thesis contributed to the characterisation of NBS and its environmental and economic assessment to inform urban planning and landscape design processes, allowing decisions that are more informed.<br>Il riconoscimento della natura nella risoluzione delle sfide sociali è diventato sempre più importante. Questo riconoscimento è stato associato allo sviluppo di nuovi concetti provenienti dalla scienza e dalla politica, come il capitale naturale, i servizi ecosistemici, le infrastrutture verdi e, più recentemente, le soluzioni basate sulla natura (NBS). NBS intende affrontare le sfide della società in una forma efficace e adattabile fornendo benefici economici, sociali e ambientali. Lo scopo di ricerca di questa tesi di dottorato è quello di sviluppare una valutazione ambientale ed economica delle NBS per territori altamente urbanizzati basata su logiche e modelli che hanno alla base i servizi ecosistemici, l'ecologia urbana e paesaggistica e degli approcci di approcio life cycle. Questo quadro di valutazione combinato aiuterebbe a capire meglio se le NBS sono costo effetive e se contribuiscono a uno sviluppo resiliente e sostenibile. Questo scopo di ricerca è sviluppato secondo quattro obiettivi specifici. Il primo obiettivo corrisponde alla caratterizzazione delle NBS in relazione ai contesti urbani e alle problematiche che possono aiutare ad affrontare o mitigare. Per raggiungere questo obiettivo è stata sviluppata una revisione critica dell letteratura sullo studio della relazione tra NBS, servizi ecosistemici (ES) e sfide urbane (UC). Come risultato principale, si ottiene un grafico delle relazioni causa-effetto plausibili tra NBS, ES ed UC. Il grafico rappresenta un primo passo per supportare la pianificazione urbana sostenibile, passando dai problemi (es. UC) alle azioni (es. NBS) alle risoluzioni (es. ES). Il secondo obiettivo corrisponde alla definizione di un set di metodi e indicatori di valutazione biofisica e monetaria adeguate per valutare il valore della NBS in contesti urbanizzati. Per raggiungere questo obiettivo, viene sviluppata una revisione dei metodi esistenti sulla valutazione dei servizi ecosistemici, l'analisi dei costi del ciclo di vita e la valutazione del ciclo di vita. La revisione tiene conto di vincoli specifici come la facilità d'uso e la disponibilità dei dati. Alla fine, sono stati selezionati potenziali metodi e indicatori, che saranno successivamente integrati nel quadro di valutazione combinato. Il terzo obiettivo corrisponde alla progettazione del quadro di valutazione combinato, integrando metodi di valutazione del ciclo di vita, ecologia paesaggistica / urbana e servizi ecosistemici che quantifica il valore ambientale ed economico della NBS informando sull'efficacia in termini di costi del suo intero ciclo di vita. Per raggiungere questo obiettivo, prima viene sviluppato un quadro concettuale. Da esso, viene sviluppato un modello di dinamica di sistemi per calcolare i servizi (e disservici) ecosistemici, il quale è interrelazionato con un metodo di valutazione life cycle. Questa valutazione combinata viene testata con un tipo di NBS pertinente (foresta urbana) in un caso di studio nell'area metropolitana di Madrid. Il quarto obiettivo è lo sviluppo di uno strumento di supporto decisionale (DSS) che integri il quadro di valutazione come parte dei processi di progettazione iterativa nella pianificazione urbana e nella progettazione del paesaggio. Il DSS intende migliorare l'interrelazione tra scienza, politica e pianificazione / progettazione. Per raggiungere questo obiettivo è stato sviluppato Nbenefit$® un prototipo di DSS online per la valutazzione NBS di facile uso. Il prototipo DSS fornisce all'utente una forma semplice per quantificare multipli ES e costi (internalizatti o no) durante l'intero ciclo di vita (implementazione, vita operativa e fine vita) del NBS. In conclusione, questa tesi ha contribuito alla caratterizzazione di NBS e alla sua valutazione ambientale ed economica per informare i processi di pianificazione urbana e progettazione del paesaggio, consentendo decisioni più informate.

L’organisation des territoires ruraux d’Afrique de l’Ouest a été bouleversée ces vingt dernières années par des changements rapides, dus à un accroissement démographique sans précédent, à des politiques favorisant les cultures d’exportation et à l’introduction de nouvelles techniques culturales. On assiste aujourd’hui à une mutation des structures d’exploitation, une pression sur les ressources forestières, un épuisement des sols et une saturation de l’espace cultivé. Les tensions pour l’accès aux ressources se multiplient, faisant souvent ressurgir d’anciens conflits ethniques, et la question de la sécurité alimentaire se pose. Dans ce contexte, des systèmes d’alerte précoce ont été mis en place dans le but d’anticiper et d’endiguer l’insécurité alimentaire par l’analyse des risques de catastrophe.La thèse s’inscrit dans le cadre de ces systèmes d’alerte précoce et traite de l’étude des changements agraires et de leurs mécanismes. Elle se propose d’explorer de nouvelles pistes méthodologiques, basées à la fois sur la modélisation et la télédétection, pour réaliser une analyse rétrospective et prospective des dynamiques agraires de la province du Tuy, située à l’ouest du Burkina Faso.Nous abordons tout d’abord la question du croisement d’échelles dans les modèles de dynamiques des agroécosystèmes en développant un modèle multiscalaire des évolutions passées. Le modèle utilise les graphes d’interaction pour simuler des processus allant de l’échelle de la parcelle à l’échelle régionale (évolution des rendements, évolution des assolements, déforestation). Nous montrons ainsi qu’il est possible d’effectuer un croisement d’échelles dans un modèle sans avoir recours aux méthodes d’agrégation ou de désagrégation habituellement employées pour ce type d’étude.Le modèle est ensuite utilisé pour analyser deux aspects des dynamiques agraires de la province du Tuy. Le premier aborde les dynamiques de défriche, d’abord analysées à la lumière du débat Malthus-Boserup qui porte sur l’impact de la croissance démographique sur les ressources naturelles. Des scénarios prospectifs sont simulés et leurs conséquences sur les surfaces en végétation naturelle sont évaluées : ces scénarios simulent l’émigration d’une partie de la population vers d’autres régions, la création de zones protégées, la mise en place de politiques démographiques et la conversion progressive des systèmes de production à l’agro-écologie.Le second aspect concerne les processus décisionnels des agriculteurs pour constituer leurs assolements. L’étude consiste plus précisément à comprendre les importantes variations des surfaces allouées aux différentes cultures, observées au cours de la période étudiée, via l’analyse de l’évolution simulée du poids des différents facteurs intervenant dans la prise de décision.Dans une dernière partie, nous montrons qu’il est possible de détecter explicitement des empreintes de processus anthropiques dans les images de télédétection en utilisant les simulations multiscalaires du modèle développé. Nous réalisons ensuite une assimilation de l’information satellitaire dans le modèle, pour le ré-étalonner et ainsi renforcer ses capacités à reproduire les dynamiques ayant eu lieu. Cette dernière partie ouvre d’importantes perspectives concernant l’utilisation conjointe de l’information satellitaire et des modèles de dynamiques des agroécosystèmes<br>Rural areas of West Africa have seen notable transformations these last two decades, mainly due to high population growth, development policies in favor of export crops and introduction of new cropping practices. The results of these developments are a pressure on forestry resources, an evolution of farming systems, a depletion of soils and a saturation of cultivated areas. The number of conflicts for resources access increases, reviving buried ethnical tensions, and the question of food security is raised. In that context, early warning systems have been developed in order to foresee and curb food insecurity by the mean of hazard analyses.The present work deals with agrarian changes and their mechanisms, in the context of early warning systems development. New methodological approaches are explored, based on modeling and remote sensing in order to create a retrospective and prospective analysis of agrarian dynamics of the Tuy province, located in West Burkina Faso.We first focus on the issue of cross-scaling in agro-ecosystems dynamics models, by building a multi-scalar model of past developments. The model uses interaction graphs to simulate processes occurring from the plot scale to the regional scale (crop production, crop rotation and crop area expansion). We show that modelling across scales is achievable without resorting to methods of aggregation or disaggregation, usually applied for this type of study.The model is then used to analyze two aspects of agrarian dynamics of Tuy province. The first one deals with clearances dynamics in the context of Malthus vs Boserup debate, concerning the impacts of demographic growth on natural resources. Prospective scenarios are simulated and their consequences on natural vegetation surfaces are assessed: these scenarios simulate emigrations of a part of the population towards other areas, the implementation of protected areas, a demographic regulation and an ecological intensification of farming systems.The second aspect concerns decisional processes of farmers in order to constitute their crops rotations. The study consists in understanding the important variations of cultivated species, observed during the studied period, by analyzing the simulated weight evolution of different determining factors involved in the decisional processes.Finally, we show that anthropic processes footprints are explicitly detectable in remote sensing images, by using multi-scalar simulations of the model developed. Then, we create an assimilation of satellite data in the model in order to re-calibrate it and reinforce its abilities to reproduce past dynamics. This last part opens important perspectives concerning the joint use of remote sensing data and agro-ecosystems dynamics

Une alternative prometteuse à la lutte chimique pour la régulation des ravageurs de culture consiste à favoriser les populations de leurs prédateurs en jouant sur la structure du paysage agricole. L'identification de structures spatio-temporelles favorables aux ennemis naturels peut se faire par l'exploration de scénarios paysagers via une modélisation couplée de paysages et de dynamiques de population. Dans cette approche, les dynamiques de populations sont simulées sur des paysages virtuels aux propriétés structurales contrôlées, et l'observation des motifs de populations associés permet l'identification de structures favorables. La modélisation des dynamiques de populations repose cependant sur une connaissance fine des processus écologiques et de leur variabilité entre les différentes unités du paysage. L'état actuel des connaissances sur les mécanismes écologiques régissant les dynamiques des ennemis naturels de la famille des carabidés demeure l'obstacle majeur à la recherche in silico de scénarios paysagers favorables. La littérature sur les liens entre motifs de population de carabes et variables paysagères permet de formuler un ensemble d'hypothèses en compétition sur ces mécanismes. Réduire le nombre de ces hypothèses en analysant les convergences entre les motifs de population qui leur sont associés, et étudier la stabilité de ces convergences le long d'un gradient paysager apparaît comme une première étape nécessaire vers l'amélioration de la connaissance sur les processus écologiques. Dans une première partie, nous proposons une heuristique méthodologique basée sur la simulation de modèles de réaction-diffusion porteurs de ces hypothèses en compétition. L'étude des motifs de population a permis d'effectuer une typologie des modèles en fonction de leur réponse à une variable paysagère, via un algorithme de classification, réduisant ainsi le nombre d’hypothèses en compétition. La sélection de l'hypothèse la plus plausible parmi cet ensemble irréductible doit s'effectuer sur la base d'une observation des motifs de population sur le terrain. Cela implique que ces derniers soient caractérisés à des résolutions spatiales et temporelles suffisantes pour sélectionner une unique hypothèse parmi celles en compétition. Dans la deuxième partie, nous proposons une heuristique méthodologique permettant de déterminer a priori des stratégies d'échantillonnage maximisant la robustesse de la sélection d'hypothèses écologiques. Dans un premier temps, la simulation de modèles de réaction-diffusion représentatifs des hypothèses écologiques en compétition permet de générer des données biologiques virtuelles en tout point de l'espace et du temps. Ces données biologiques sont ensuite échantillonnées suivant des protocoles différant dans l'effort total d'échantillonnage, le nombre de dates, le nombre de points par unité d'espace et le nombre de réplicats de paysages. Les motifs des populations sont caractérisés à partir de ces échantillons. Le potentiel des stratégies d'échantillonnage est évalué via un algorithme de classification qui classe les modèles biologiques selon les motifs de population associés. L'analyse des performances de classification, i.e. la capacité de l'algorithme à discriminer les processus écologiques, permet de sélectionner un protocole d'échantillonnage optimal. Nous montrons également que la manière de distribuer l'effort d'échantillonnage entre ses composantes spatiales et temporelles est un levier majeur sur l'inférence des processus écologiques. La réduction du nombre d'hypothèses en compétition et l'aide à l'échantillonnage pour la sélection de modèles répondent à un besoin fort dans le processus d'acquisition de connaissances écologiques pour l'exploration in silico de scénarios paysagers favorisant des services écosystémiques. Nous discutons dans une dernière partie des implications de nos travaux et de leurs perspectives d'amélioration<br>A promising alternative to the chemical control of pests consists in favoring their natural enemies populations by managing the agricultural landscape structure. Identifying favorable spatio-temporal structures can be performed through the exploration of landscape scenarios using coupled models of landscapes and population dynamics. In this approach, population dynamics are simulated on virtual landscapes with controlled properties, and the observation of population patterns allows for the identification of favorable structures. Population modeling however relies on a good knowledge about the ecological processes and their variability within the landscape elements. Current state of knowledge about the ecological mechanisms underlying natural enemies’ of the carabid family population dynamics remains a major obstacle to in silico investigation of favorable landscape scenarios. Literature about the relationship between carabid population and landscape properties allows the formulation of competing hypotheses about these processes. Reducing the number of these hypotheses by analyzing the convergence between their associated population patterns and investigating the stability of their convergence along a landscape gradient appears to be a necessary tep towards a better knowledge about ecological processes. In a first step, we propose a heuristic method based on the simulation of reaction-diffusion models carrying these competing hypotheses. Comparing the population patterns allowed to set a model typology according to their response to the landscape variable, through a classification algorithm, thus reducing the initial number of competing hypotheses. The selection of the most likely hypothesis from this irreducible set must rely on the observation of population patterns on the field. This implies that population patterns are described with spatial and temporal resolutions that are fine enough to select a unique hypothesis among the ones in competition. In the second part, we propose a heuristic method that allows determining a priori sampling strategies that maximize the robustness of ecological hypotheses selection. The simulation of reaction-diffusion models carrying the ecological hypotheses allows to generate virtual population data in space and time. These data are then sampled using strategies differing in the total effort, number of sampling locations, dates and landscape replicates. Population patterns are described from these samples. The sampling strategies are assessed through a classification algorithm that classifies the models according to the associated patterns. The analysis of classification performances, i.e. the ability of the algorithm to discriminate the ecological processes, allows the selection of optimal sampling designs. We also show that the way the sampling effort is distributed between its spatial and temporal components is strongly impacting the ecological processes inference. Reducing the number of competing ecological hypotheses, along with the selection of sampling strategies for optimal model inference both meet a strong need in the process of knowledge improvement about the ecological processes for the exploration of landscape scenarios favoring ecosystem services. In the last chapter, we discuss the implications and future prospects of our work

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg. in fulfilment of the requirements tor the degree of Master of Science<br>This thesis develops the theoretical basis of the qualitative frame based modelling technique, a paradigm recently proposed by Starfield for the modelling of ecosystems with a multiplicity of stable states. This technique is a refinement of the State-and- Transition conceptual model of Westoby et al which involves the division of the ecosystem dynamics into a catelog of stable 'states' and a suite of transitions between these states. The frame models of Starfield associate with each stable configuration of the ecosystem a qualitative rule based model for the key processes in that stable configuration. The aims of this thesis are the following, 1. A rigorous definition of frame modelling of dynamic ecosystems is proposed, and this theoretical foundation is used to demonstrate that qualitative frame models may be used to mode! dynamic ecosystems to an arbitrary accuracy. 2. The development of implementation software. A qualitative rule based frame modelling environment is presented. and a specification for an improved environment is proposed based on the theoretical work.<br>Andrew Chakane 2019

Fire is used in the management of ecosystems worldwide because it is a relatively inexpensive means of manipulating thousands of hectares of vegetation. Deciding how, where and when to apply fire depends primarily on the management objectives of the area concerned. The decision to ignite vegetation is generally subjective and depends on the experience of the fire manager. To facilitate this process, ancillary tools, forming a decision support system, need to be constructed. In this study a spatial model has been developed that is capable of simulating fire dynamics in savanna ecosystems. The fire growth model integrates spatial fuel and topographic data with temporal weather, wind settings and fuel moistures to produce a time-evolving fire front. Spatial information required to operate the model was obtained through remote sensing techniques, using Landsat Thematic Mapper (TM) satellite imagery, and existing Geographic Information Systems (GIS) coverage's. Implementation of the simulation model to hypothetical landscapes under various scenarios of fuel, weather and topography produced fire fronts that were found to be in good agreement with experience of observed fires. The model was applied actual fire events using information for prescribed burning operations conducted in Mkuze Game Reserve during 1997. Predicted fire fronts were found to accurately resemble the observed fire boundaries in all simulations.<br>Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 1999.

Human impacts on natural systems are driving rapid ecological and evolutionary changes. In the ocean, we know that fishing and climate change are affecting the functional traits of species and restructuring ecosystems. However, the extent to which evolutionary adaptations can buffer ecosystems against these impacts is not well understood. This information is needed to improve knowledge of how ecosystem function and biodiversity are being affected by a rapidly changing ocean. This thesis is centred around the introduction of evolutionary dynamics into trait-based models. Trait-based models capture functional biodiversity of ecosystems by resolving traits within and across multiple species. However, current trait-based models do not allow for traits to change through adaptation and natural selection on the same time scales as ecological processes. Yet there is growing recognition that evolution can act on the same time scales as ecology. The key aim of the thesis is to extend trait-based size spectrum models, widely used to assess impacts of fishing and climate change on fish communities, by exploring how species adaptation can alter population and ecosystem responses to environmental and human-induced change. I develop an eco-evolutionary simulation model that introduces new phenotypes into a dynamic trait- and size-based community model. I then apply the model to three theoretical case-studies, each focusing on the adaptation of a key trait thought to be under strong selection from external drivers. Firstly, I explore the case of fisheries induced evolution or how fishing drives the adaptation of maturation size in fish. Here, the study confirms previous empirical findings and single-species based predictions that size selective fishing will generally drive a reduction in maturation size for large fish species. However, due to interacting forces of predation and competition, this effect was not found for small species and was sometimes reversed for medium-sized species. Secondly, I examine species’ thermal performance as an adaptative trait under a warming climate. This study shows that in the short-term (~50 years), under a projected ‘high emissions’ climate scenario, marine species’ phenotypic diversity helps to buffer against warming temperature by species slowly adapting towards more generalist thermal strategies. However, at the projected rate of warming of 3.5° per 100 years over 200 years of simulation, phenotypic diversity eventually collapsed as as adaptation could not keep up with rapid change and specialised phenotypes disappeared. Thirdly, I investigate the driver of food limitation to explore how feedbacks between predation and competition might lead to species-specific differences in the relative prey size preferences of fish. This chapter asks why some large marine fish (e.g. large planktivores) feed on much smaller prey relative to their own body size compared to others (e.g. predatory sharks). The model predicts that low resource availability drives an adaptation towards smaller relative prey size and that apex carnivores, who feed on relatively larger prey, only emerges as an alternative strategy if enough energy is available to transfer up the food webs. In summary, the model developed in this thesis has been used to show that there is significant scope for adaptations in size-structured multispecies systems. Some of the general patterns predicted by the model were consistent with macroecological patterns for fish. Future work would be needed to develop and test the model to support biodiversity policy and ecosystem-based management.

Humanity has not yet been able to contain its influence on global average temperatures nor on the carry-over effects of that to the biosphere, namely climate change initiated by our carbon emissions, and positive feedback on temperature is likely to increase. The contribution played by our land use change (LUC) is millennia-old and annually it is currently comparable to that of fossil fuel usage, but it is less precisely known. The key aim of this thesis is to improve the knowledge about carbon emissions from LUC to the atmosphere so that we can control them better (‘climate change mitigation’), and in order to facilitate better climate change modelling. Extremes of intensity and expanse of change in carbon, accompanying LUC, were studied using carbon-dense forests and rangelands respectively. The dynamics were reviewed and re-assessed, and previously discounted carbon pools were quantified. Tools used in the analysis included conceptualisation of carbon dynamics, standard forest mensuration, remote sensing and GIS, soil data collection and carbon assay, terrestrial photogrammetry using innovative software, formulae development, and mathematical modelling including forecasting of carbon flux. Most data were from Australia but the concepts applied, theories developed and thematic results are applicable globally. For intense LUC the focus was on the more carbon-dense forests, especially those in Tasmania which were the major feedstock of the Pacific rim’s hardwood pulpwood market until 2012. For expansive areas the Australian commercially grazed rangeland was studied and two case studies were the States of Queensland and New South Wales. In those, LUC had recently been more intensive, with accompanying greater public scrutiny and consequently more data availability. The findings will contribute towards more precise estimates of carbon fluxes for emission trading schemes, national reports and for climate change modelling from several millennia in the past to two in the future. There were several main areas of knowledge enhancement: 1) increased quantification of anthropogenic influence on C flux in woodyecosystems accompanying logging and rangeland grazing, past and future 2) revealing that the half-lives of wood products need to be increased by nearly an order of magnitude to not lose nearly half the carbon of primary forests when they are converted to secondary forests on harvesting cycles; 3) increased formulaic relations between natural phenomena for use in modelling carbon dynamics; 4) showed how a comprehensive time-space (4D) context of carbon dynamics in woody ecosystems can reveal both higher carbon emissions and higher carbon sequestration for LUC or ecosystem recovery respectively, and how it provides an overarching explanation to relieve points of contention by (e.g. for woody-thickening, deforestation; and forest logging); 5) increased understanding of SOC distribution and change (e.g. development of a robust method to calculate cumulative SOC down a diverse soil profile; finding associated with large trees ~6% more SOC than earlier tallied, the same trees targeted for logging; 6) improved experimental methods, e.g.: use of Photoscan software to quantify large trees, and remote sensing/GIS to locate carbon stock benchmarks in degraded rangeland; 7) discovery of a new natural substance (cunnite) constituting a novel but small carbon pool; and 8) informative, diagrammatic portrayal of a sequence of relationships between land-use, woody ecosystems, and climate, in the carbon cycle. To help increase knowledge it is imperative, for carbon accounting of both forest logging and rangeland commercial grazing, that greater data transfer occurs between industry, government departments and the scientific community.

Equitable water allocation in the context of local-scale water conflicts can be very challenging. This study aimed at providing new perspectives to the analysis of local water conflict with a special focus on two issues. First, the most vulnerable communities, who face the largest risk from unbalanced water management decisions, are often devoid of any technical and scientific support. And second, ecosystem services are hardly took into account when it comes to water allocation decision-making. We present a holistic framework for the analysis of small-scale water disputes, contributing an integrated approach to the analysis of water conflicts, by providing technical solutions combined with an in-depth analysis of social dynamics. The analysis focuses on an ongoing water conflict in El Carracillo region (Spain), related to an artificial aquifer recharge project. This case study involves two competing water users: on the one hand horticultural farmers; and, on the other hand, ecosystem services provided by Cega river, from which water is diverted in order to recharge the aquifer. Based on a stakeholder analysis, a tool was built to support participatory processes by facilitating mediation procedures. The optimization showed that solutions exist that account for ecosystem needs without causing major negative impacts on El Carracillo agriculture, and suggested that a re-negotiation of the rules that govern water diversion from Cega river is needed.

In a changing climate, it is increasingly important to be able to model environmental effects on food webs, and to do that, one must have appropriate dynamic models. I present a shallow lake ecosystem model where producers, grazers, carnivores, piscivores, and detritivores are coupled through resource (light, nutrients and detritus) fluxes between the benthic and pelagic habitats and through carnivore life history events (ontogenetic habitat and diet shifts). The two habitats each contain primary producers, grazers, carnivores and detritivores. Within the habitats, there is strong top-down regulation, but across habitat boundaries, bottom-up interactions drive production. In the absence of piscivores, stage-structured carnivores cause intriguing patters of alternative stable states. Notably, the model predicts a lesser dependence on benthic production with detritus presence. Model predictions are largely in agreement with empirical studies. The results have implications for management of freshwater, and for the interpretation of previous models.

The land-sea interface provides some of the world’s most valuable and biodiverse habitats, despite being exposed to anthropogenic pressures. Marine predators which cross this interface are particularly vulnerable, with human activities in coastal zones diminishing both the quality and availability of suitable breeding and foraging areas. These predators are constrained to forage in smaller oceanic regions while rearing young on-land, therefore their reproductive success is intrinsically linked to the productivity of nearshore waters. Changing environmental conditions, as a direct and indirect consequence of climate change, can alter the structure, distribution and community composition of lower-trophic level prey. In order to predict the response of ecosystems to this change, and to changes as a result of extreme events such as marine heatwaves (MHW), an in depth understanding of the links between environmental factors, prey-field dynamics and predator behaviour is needed. The continental shelf to the south-east of Tasmania is a hotspot of biodiversity, where seasonal productivity supports a large and diverse array of marine birds and mammals. However, this region is also subject to rapid environmental change, being situated within the south-east Australian climatic-hotspot. Due to the intensification and increasing southward penetration of the East Australian Current (EAC), a major western boundary current running from the sub-tropical Coral Sea to the south-east coast of Australia, warming is occurring at an accelerated rate. Quantifying how prey-field dynamics respond to these changing environmental conditions, and the flow-on effects to the behaviour of apex predators, formed the main objective of this study. Surveys were conducted over a three-year period (2015-2018), during which a prolonged marine heatwave (MHW) event occurred that increased water temperatures of the entire western Tasman Sea by a mean of 2.9°C above climatology for 251 days. To develop an integrated understanding of ecosystem dynamics through a period of high environmental variability, zooplankton prey-field dynamics, fish school presence, little penguin (Eudyptula minor) foraging behaviour, and the distribution and abundance of key bird species were analysed in relation to local environmental factors. Zooplankton community composition and abundance were examined in relation to environmental drivers. Generalised additive models (GAMs) indicated a significant decrease in community abundance during the MHW, with a shift in species assemblages away from temperate species and towards EAC-associated species. The size structure of the zooplankton community was also analysed using the normalised biomass size spectra (NBSS). The NBSS is an effective way to demonstrate the variability present in a community, in terms of gains and loss of energy through respiration, predation and mortality. It can also be indicative of changes to the equilibrium of a community. Strong seasonality was detected in the results, with temperature, current velocity and mixed-layer depth being significant drivers of variability in the NBSS. These lower trophic level dynamics were linked to the behaviour of top predators through a detailed case study of the at-sea habitat preference of little penguins breeding in south-east Tasmania (n=13). Tracking was conducted over two summer periods, in 2016 during the MHW, and in 2018 under cooler and more stable environmental conditions. Habitat models (species distribution models) were developed to asses spatial distribution patterns and examine the bio-physical factors influencing foraging trips at fine-scale. Regions of higher sea-surface temperature gradients and cooler than average temperatures were found to increase the probability of penguin presence. The predictability of little penguin habitat-use according to prey-type was also assessed by including covariates for the general distribution of resources in the region; e.g. total zooplankton abundance, and the abundance of Australian krill (Nyctiphanes australis), which forms part of little penguin diet. Little penguin foraging areas were more influenced by the distribution of Australian krill than by general zooplankton abundance. The response of local predators to changes in bio-physical parameters were measured by modelling the distribution of 10 species of seabirds using boosted regression trees. Key species ranged from small planktivores, such as the common diving petrel (Pelecanoides urinatrix), to albatross (family Diomedeidae). Therefore, to encompass the range of prey that underpins the distribution of these species, biological covariates included zooplankton biomass, and the presence (and absence) of fish schools (determined using hydro-acoustics during surveys). Seabird species were separated into feeding groups using multivariate analysis and modelled separately to reveal potential drivers for each group. Despite different biological predictors influencing the distribution of different groups, sea surface temperature was found to explain the greatest amount of variation across all feeding groups. This influence is thought to be prey-mediated, as both biological covariates tested exhibited negative correlations with increasing SST. Through considering the complex links which exist between predators, their prey and the physical environment, this study produces new insights into the potential effects of extreme events. Further, it improves our understanding of how general warming trends affect prey structure and the possible flow-on effects for predators. Modelling the distribution of apex predators enables the identification of important foraging regions with favourable bio-physical characteristics. We highlight how detailed assessments of ecosystem and environmental interactions can be pivotal to informing the effective management of these vulnerable and biodiverse ecosystems into the future.

Terrestrial environments are highly complex and dynamic. It consists of various types of soils which are constantly exposed to fluctuating conditions affecting their physical and biological properties. Moreover, soils are delivering several ecosystem services with high relevance for the human well-being such as water purification, nutrient cycling, or biodegradation. For many of those ecosystem services, microorganisms are the main drivers. In consequence, it is important to understand the functional response of microbial ecosystems to disturbances. Thus, identifying key factors for the functional stability of microbial ecosystems in terrestrial environments is of high interest. A powerful tool for analysing dynamics and underlying mechanisms of ecosystems are computational simulation models. Within this doctoral thesis, a spatiotemporally explicit bacterial simulation model was developed for assessing dynamics of biodegradation as a typical microbial ecosystem function under the influence of disturbances. Disturbances were introduced as lethal events for the bacteria within a certain, randomly picked disturbance area. The disturbance characteristics vary in the spatial configuration and frequency of the disturbance events. Functional stability was analysed in terms of the ability to recover the function after a single disturbance event, i.e. functional resilience, and the ability to maintain the function during recurrent disturbance events, i.e. functional resistance. Key factors for functional stability were assessed by systematically varying properties and processes of the microbial ecosystem and characteristics of the disturbance regime. Simulation results show a high influence of the disturbance characteristics, especially its spatial distribution pattern, on the stability of biodegradation. Functional resistance and resilience increase with fragmentation of the spatial pattern of the disturbances. The frequency of recurrent disturbance events proved also essential for the functional resistance: if the disturbances occur too often, the emergence of a functional collapse may not be preventable. However, if the fragmentation of the applied disturbance patterns increases, the function is also maintained under more frequent disturbances without a functional collapse. Ecological processes such as bacterial dispersal and growth are shown to enhance the biodegradation performance, but only under specific disturbance regimes, again depending on frequency and fragmentation of the disturbances. Dispersal networks are shown to increase the functional stability in many scenarios and, thus, may serve as a buffer mechanism against disturbances. Therefore, strategies facilitating these ecological processes, for instance stimulating fungi that act as dispersal networks for bacteria, or modulating the physical soil structure to alter the spatial configuration of disturbances are proposed to increase the functional stability of microbial ecosystems.

Worldwide, ecosystems have demonstrated the potential for dramatic shifts to an alternative persistent state under gradual long-term environmental changes or following sudden short-term perturbations. Such shifts are documented for numerous marine examples from coral reef to pelagic communities and may become more common as ecological dynamics adjust to climate-driven changes. These shifts are often sudden, challenging to predict and can have disastrous and unpredictable consequences on both ecosystem functioning and the human activities that rely on the associated natural resources. They often result in irreversible dramatic changes in community structure and productivity and represent a growing concern for managers of natural systems. In ecosystems where the presence of an alternative persistent state is well documented, the drivers of these shifts (e.g. anthropogenic stressors or changes in environmental conditions) can be analysed retrospectively so as to address key management questions, as has occurred in several applications on coral reefs. However, phase shifts are often swift and observed a posteriori, i.e. after the ecosystem has shifted to the alternative state. Thus, thresholds in ecosystem dynamics are difficult to identify empirically despite that this is crucial for sound management of marine resources. Additionally, controlled experimental assessment of the effects of alternative management scenarios on community state is hardly ever achievable in marine ecosystems. When they occur, phase shifts are unique to each ecosystem, hence case-specific simulation models present a valuable tool to explore ecological dynamics with alternative persistent community states, test the effects of management scenarios and inform decision-making. On the east coast of Tasmania, shallow rocky reef communities on the exposed coast mainly occur in two alternative persistent states: (1) the seaweed bed state characterised by a dense productive canopy of macroalgae; or, (2) the sea urchin ‘barren’ state characterised by a poorly productive rocky habitat largely bare of seaweeds as a result of destructive grazing by the long-spined sea urchin (Centrostephanus rodgersii ). The establishment of these widespread sea urchin barrens result from a combination of both: (1) the climate driven range extension of the long-spined sea urchin C. rodgersii from Australia’s mainland to Tasmania; and (2) depletion of key reef predators by fishing. Large southern rock lobster (Jasus edwardsii ) individuals constitute the main predator of the long-spined sea urchin in Tasmania. Relative to the seaweed bed state, C. rodgersii barrens represent dramatic losses of habitat, species diversity and productivity, including commercial species such as blacklip abalone (Haliotis rubra) and southern rock lobster, the two most valuable fisheries in Tasmania. Thus, the spread of sea urchin barrens presents a major and pressing threat for the lobster and abalone fishing industries. This thesis presents a suite of models specifically developed to better understand the dynamics of Tasmanian rocky reef communities and inform management interventions to mitigate destructive grazing of seaweed beds by the invasive long-spined sea urchin. Chapter 2 investigates the causal relationships between positive feedback and the occurrence of alternative states in community dynamics. Modelling of community feedback informed by available qualitative knowledge about ecosystem structure constitutes a valuable framework to detect the potential for alternative states in ecological dynamics as illustrated with some examples from Tasmanian rocky reef communities. Qualitative modelling assists to understand the essential features of temperate reef dynamics around Tasmania, and provides a useful first step towards quantitative modelling of rocky reef dynamics. The approach provides an ideal framework to (i) collate all available information about rocky reef ecology, (ii) test model structure uncertainty, and (iii) identify key drivers of alternative states in ecosystem dynamics. The quantitative model presented in the subsequent chapters captures the dynamics of the three key groups or species (i.e. the rock lobster, sea urchin, and seaweed assemblage) directly involved in the positive feedback that drives the shift between alternative states on Tasmanian rocky reef. Chapter 3 describes the development, parameterisation and calibration of a mean field model of the local dynamics (reef area of 100 m2 - 10 ha) of a reef community. The model’s ability to capture the potential for phase shifts, from dense seaweed bed to sea urchin barrens habitat and back, is validated against largescale patterns observed on rocky reefs where C. rodgersii occurs. In the simulations, the time for extensive sea urchin barrens to form is of the order of two decades, while restoration of seaweed cover from the sea urchin barrens habitat takes about three decades if relying on management interventions that cannot effectively reduce urchin density to zero. Thus, restoration of seaweed beds seems unrealistic to implement within the current timeframe of management plans. Comprehensive model-independent sensitivity analysis of model behaviour to parameter estimates also suggests that, in addition to lobster fishing mortality, recruitment rates of sea urchins and rock lobsters, which are strongly influenced by large scale oceanographic features and highly variable in eastern Tasmania, are key factors in determining the potential for sea urchin barren formation in the model. In Chapter 4, sets of Monte-Carlo simulations with this model are used to address three sets of questions related to management for mitigation of sea urchin destructive grazing of Tasmanian seaweed beds. Model behaviour suggests that thresholds in shifting from seaweed bed to sea urchin barren and restoration of seaweed cover reveal the existence of a hysteresis in model dynamics. The hysteresis implies that the establishment of sea urchin barrens cannot be reversed easily. These thresholds provide valuable ecological reference points to prevent the establishment of sea urchin barrens. The model indicates that culling of sea urchins appears as the most effective management strategy to minimise the ecological impact of C. rodgersii on Tasmanian reef communities. Indirect interventions relying solely on the rebuilding of rock lobster population (through reduction in fishing or implementation of a maximum legal catch size) perform poorly but, when combined with direct control of the sea urchin population, they can provide optimal outcomes both in terms of minimising barren formation and fishery performance. Finally, the model shows that to allow lobsters to play their critical ecological ‘service’ role in preventing sea urchin barrens formation, a reduction in lobster fishing mortality from current levels is required. A maximum sustainable yield as estimated from the single species stock assessment model does not account for the ecosystem service delivered by larger lobsters, and the models emphasise the need for an ecosystem-based fishery management approach. This suite of models contributes to the general understanding of mechanisms and drivers that can facilitate shift between alternative states in ecological dynamics. The quantitative simulation model provides specific information to managers about the drivers of shifts between the seaweed bed and the sea urchin barren state in the dynamics of Tasmanian rocky reefs. In particular, the presence of a hysteresis in reef community dynamics means that effort to prevent barrens formation constitutes a more viable and cost effective management strategy than the restoration of seaweed beds once extensive barrens habitat has developed. The commercially-fished rock lobster is an essential reef predator delivering key ecosystem services to Tasmanian rocky reefs and model simulations highlight the necessity for fisheries management to move away from a single species focus and account for the ecological role of targeted commercial species. The tools implemented here to inform an ecosystem-based management of Tasmanian rocky reefs are generic and ‘transportable’ to other ecosystems with alternative states. While C. rodgersii barrens currently constitute a pressing concern for managers of reef communities and fisheries in Tasmania, the longspined sea urchin is only one example of a species that is dramatically restructuring Tasmanian reef communities. There are many other ‘natural’ invaders, whose ecosystem roles and impacts are unknown, currently extending their distribution from Australia’s mainland to the warming Tasmanian waters. In the coming decades, climate-driven changes are likely to bring more surprises to Tasmanian rocky reefs, and just as many challenges for the associated fisheries and their managers.

The affect on leaf area index (LAI) and net ecosystem production (NEP) of the mountain pine beetle (Dendroctonus ponderosae) (MPB) outbreak in British Columbia affecting lodgepole pine (Pinus contorta var. latifolia) forests was examined from 1999 to 2008. The process-based carbon (C) cycle model – Boreal Ecosystem Productivity Simulator (BEPS) with remotely sensed LAI inputs was used to produce annual NEP maps, which were validated using field measurements. The annual NEP ranged from 2.43 to -8.03 MtC between 1999 and 2008, with sink to source conversion in 2000. The inter-annual variability for both LAI and NEP displayed initial decreases followed by a steadily increasing trend from 2006 to 2008 with NEP returning to near C neutrality in 2008 (-1.84 MtC). The resistance of LAI and NEP to MPB attack was attributed to ecosystem resilience in the form of secondary overstory growth and increased production of non-attacked host trees.

Changing environmental conditions often impose stressful growing conditions in plant communities. Until now, morphological plasticity, i.e. polymorphic growth physiognomies of plants, has not been sufficiently studied as a pivotal strategy for the whole ecosystem adaptation to environmental stress. We consider mangrove ecosystems as suitable models to provide insights on this subject. In the thesis, I investigate the ecological significance of tree morphological plasticity in the structural development and the dynamics of mangrove forests. I conducted field experiments in two regions located on both sides of the Amazon River mouths i.e. in French Guiana and North Brazil. Forest inventories were carried out in contrasting mangrove stands in both regions. The thesis combines empirical analysis of field data, terrestrial laser scanning (TLS), and mechanistic, individual-based computer simulations. We published results that proved the TLS-based analysis of individual tree structure useful for a better knowledge on biomass allocation between trunk and branches in tall and large Avicennia germinans mangrove trees reaching 45 m high and 125 cm of trunk diameter. Combining structural descriptions of A. germinans trees found in both sites, I highlighted the site-specific differences in tree allometries. The study suggests that regional differences in mangrove tree structure and function could be captured through better description of crown metrics, and that selected indicators of local morphological plasticity and consequent stand structure could generate a plus-value in the understanding of mangrove stand dynamics across contrasting coastal environments. Beyond the extension of allometric models to large Avicennia trees, we proposed new biomass equations with improved predictive power when crown metrics is taken into account. Additionally, we developed a novel software tool, named Lollymangrove, based on the AMAPStudio suite of software, with the objective of maximizing the potential of further field descriptions and modeling works. Lollymangrove allows standardized forest data capture, 3D visualization of structural data, aboveground biomass computations from a configurable module and export formats for forest dynamics and remote sensing models. Simulation experiments were conducted by means of the spatially explicit, individual-based stand model BETTINA_IBM. This model describes the important mechanism of water uptake limited by salt stress, and revealed insights into the relation between environmental conditions, allometric variations and biomass partitioning of mangrove trees, and stand characteristics. The simulation results suggest close matches with observed ecological patterns (e.g., tree allometries, mortality distributions, and self-thinning trajectories) under higher salinity. In low salinity conditions, however, the current parameterization underestimates the maximum tree height and diameter, and consequently, aboveground biomass and self-thinning trajectories of forest stands. This suggests that the morphology of trees under low levels of salinity are explained by further regulation mechanism(s) that still need to be addressed in a subsequent model improvement. Overall, this work has essentially pointed out the need to elucidate how morphological plasticity relates with structural development of forest stands. It establishes that TLS measurements and structural data analysis associated to efforts for integrative software and mechanistic modelling works could link mangrove dynamics to fast-changing coastal processes.