During the 1990s a large-scale study of Port Phillip Bay, Australia, was undertaken by the CSIRO (the Commonwealth Scientific and Industrial Research Organisation, Australia's national research body). A major outcome of the study was a complex ecosystem model intended to provide scientific input into management decisions concerning the nutrient load to the bay. However, its development was costly and time-consuming. Given this effort, it is natural to seek smaller models (reduced models) that reproduce the performance measures of the large model (the full model) that are of interest to decision makers. This thesis is concerned with identifying such models. More generally, this thesis is concerned with developing methods for identifying these smaller models. Several methods are developed for this purpose, each simplifying the full model in different ways. In particular, methods are proposed for aggregating state variables, setting state variables to constants, simplifying links in the ecological network, and eliminating rates from the full model. Moreover, the methods can be implemented automatically, so that they are transferable to other ecological modelling situations, and so that the reduced models are obtained objectively. In the case of the Port Phillip Bay model, significant reduction in model complexity is possible even when estimates of all the performance measures are of interest. Thus, this model is unnecessarily complex. Furthermore, the most significant reductions in complexity occur when the methods are combined. With this in mind, a procedure for combining the methods is proposed that can be implemented for any ecological model with a large number of components. Aside from generating reduced models, the process of applying the methods reveals insights into the mechanisms built into the system. Such insights highlight the extent to which the model simplification process can be applied. Given the effectiveness of the model simplification process developed here, it is concluded that this process should be more routinely applied to large ecosystem models. In some cases, the full sequence of methods might prove too computationally expensive to justify its purpose. However, it is shown that even the application of a subset of the methods can yield both simpler models and insight into the structure and behaviour of the system being modelled.

The soil organic carbon (C) pool is estimated to contain at least three times as much organic C as is stored in vegetation. However, the processes controlling below-ground C dynamics are poorly understood, representing a key uncertainty in ecosystem models. Soil respiration rate (Rs) is a large component of the forest carbon cycle, however the factors that control it are still poorly understood, and those affecting autotrophic (Ra) and heterotrophic (Rh) respiration rates differ and vary in space and time. A variety of direct (i.e. soil and ingrowth cores) and indirect (i.e. rhizotron and minirhizotron) methods exist for obtaining estimates of fine root (< 2 mm diameter) production, with the consequence that there is a high variability in root biomass estimates between root studies. In this thesis I aim to contribute towards a better understanding of processes governing below-ground C dynamics. In particular I focus on: 1) the spatial and seasonal variability of Rs and drivers; 2) the uncertainty on fine root C pool measurement methods; 3) comparing novel datasets of Rs, fine root biomass and girth increment, with outputs from the SPA v2 model. To determine the dominant controls and spatial heterogeneity of Rs, I measured Rs and key biotic and abiotic drivers seasonally, in a Quercus robur forest in southern England. Measurements were made quarterly in three plots, each with measurement points arranged according to a spatial sampling design, enabling any spatial autocorrelation to be detected. Rs drivers were categorised into plant (i.e. leaf area index, weighted tree proximity (i.e. mean dbh within 4 m of a point), and fine root biomass), physical (i.e. soil moisture, soil temperature and soil bulk density) and substrate (i.e. litter depth and organic layer depth) factors. I explore: 1) what the dominant controls of Rs are and whether they change during the growing season; 2) whether micro-topography and stand structure are correlated with drivers, and influence the spatial variability of Rs, thereby simplifying up-scaling processes; 3) if physical drivers of Rs are spatially more homogeneous than plant drivers and the availability of substrate. I found no clear seasonal difference in drivers, with Rs consistently responding to litter depth, bulk density and soil moisture. The only significant response of Rs to micro-topography and tree factor was in August and September respectively and physical factors were found to be the most spatially homogeneous. Rs measurements were non-normally distributed, with ‘hotspots’ of particularly high fluxes found that remained stable throughout the measurement campaign. These findings suggest that the seasonal and spatial variability and distribution of Rs and its main drivers should be considered at the sampling design stage, to avoid bias for up-scaling non-linear processes. To address the uncertainties associated with determining fine root biomass change, we compared the measurement error for five methodologies (four indirect and one direct) in a Pinus contorta and Quercus robur forest during 2010. Rhizotron and ingrowth measurements were taken during 2010 and fine root standing crop was measured in 2009. Root length against the rhizotron screens was measured using novel software (ORIDIS), developed as part of a collaboration here in Edinburgh. The software was developed to increase precision and reduce the cost and processing time of rhizotron measurements. Differences in final cumulative root ingrowth for each conversion method ranged between 20.7g-2 - 245.0 g m-2 in the oak forest and 89.7 g m-2 - 273.0 g m-2 in the pine forest. The study found that indirect measurements of root length had less operator error than indirect measurements of root diameter. Direct methods of determining root growth using ingrowth cores also showed a seasonal trend; however artefacts may have been introduced into the method, from the affect of severing roots and changing soil conditions. To test the representation of below-ground processes in an ecosystem model, I validate modelled dynamics using default SPA v2 parameters, against independent CO2 flux and C pool datasets. The flux data were of eddy covariance and automatic chamber measurements, partitioned into root (Rroot), mycorhizal (Rmyc) and microbial heterotrophic (Rh) components. The biometric measurements were of foliage, fine root biomass and woody biomass increment. The key findings of this study were that: 1) SPA outputs compare well to ecosystem scale measurements of NEE and GPP. However, model-data mismatch occurs for fine root and wood C allocation; 2) the timing of fine root C allocation is 53 days too late and the turnover rate of fine roots 17 times too high; 3) the timing of modelled below-ground Rh and Ra could be improved by separating above and below-ground Ra and including individual root, mychorrizae and microbial C pools. The thesis concludes by discussing the implications of each chapter for our understanding and capability to model below-ground C dynamics. I find that the key challenge for measuring individual below-ground C pools and fluxes is ensuring that the measurements are spatially representative and avoid bias. The key challenge for modelling below-ground C dynamics is ensuring processes sufficiently reflect reality, when the sparse data that exist for corroboration, capture multiple processes. I explore the possibilities of further research that could be conducted, as a result of this work.

Connectivity is a major contributor to the overall dynamics of marine populations. However, it still remains challenging to describe connectivity on ecologically meaningful scales of time and space. This is a major impediment to evaluating the impacts of marine protected area with respect to fisheries management objectives. This dissertation brings together a wide array of spatial and connectivity information in the Gulf of Mexico (GOM) with the goal of 1) understanding the spatial distribution of fish populations and source-sink dynamics and 2) evaluating whether this information can be integrated, through a modeling framework, to identify closed areas that could be beneficial to fisheries management in the Gulf of Mexico. First, a generalized additive modelling (GAM) approach is used to describe the distribution of a large number of species groups (i.e. functional groups) across the Gulf of Mexico (GOM) using a large fisheries independent data set (SEAMAP) and climate scale (decades) oceanographic conditions. Next a numerical Lagrangian particle transport model was developed that incorporates two major connectivity processes; site specific larval production and oceanographic transport for an entire large marine ecosystem and over multiple years. The two components are then combined to develop larval dispersal patterns for the entire GOM and identify areas operating as larval sources and sinks. Last, this information is integrated into an end-to-end ecosystem model to evaluate effectiveness of closing source and sink areas for the management of reef fish fisheries. Closed area managemeny simlautions for reef fish indicated closing reef fish source areas, as opposed to sinks, in the GOM is most efficient method of increasing total biomass and yield. However, the impacts across individual functional groups were site specific. Ultimately, these simulations demonstrate the inclusion of connectivity information could improve fishery management objectives in an ecosystem context.

Made available in DSpace on 2015-04-11T13:56:26Z (GMT). No. of bitstreams: 1 Sandrelly Inomata.pdf: 1831508 bytes, checksum: 70e18c38fe0ec673ca26c307400231aa (MD5) Previous issue date: 2013-06-21 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Studies on fishing activities in the Amazon region are facing trough the Solimões-Amazonas, however little is known about commercial fishing in black water rivers. Thus, considering the lack of data in the region of the Middle Negro River this study was to assess the sustainability of commercial fishing in the municipality of Barcelos, by characterizing the fleet landing analysis and modeling ecosystem of fishing activity. Information on the physical, operational and economic features were collected through structured questionnaires from February 2012 to January 2013, with the fishermen of fishing boats and motorized canoes. Overall, commercial fishing is the main economic activity, but they also participate in other activities, mainly related to sport and ornamental fishing. The physical characteristics of the vessels are similar to those of other regions studied in the Amazon. The fishing boats are the primary storage facilities for fish landings. Gillnets were the main gear used by fishermen. Fuel was the greatest expense associated with fishing. 56.0 tons of fish were landed, with the average values of landing 3.6 (± 2.2 t/month) and 1.1 (± 0.7 t/month) tons per month for the larger-boats and the small boats with outboard motors respectively. Pacu (Subfamily Myleinae), aracu (Family Anastomidae) and tucunaré (Cichla spp.) were the main species caught, responsible for approximately 50% of the landings. The Demeni River, Anauali Lake and Zamula stream fishing sites were more exploited. It was evident that the boats exploited the lakes in dry and flood seasons, while the rivers were explored in all seasons of the hydrological cycle, with a slight predominance of outflow season. The streams were also exploited in all seasons, with the exception of the flood. In regards to small motor boats, lakes remained the preferred environments in the dry season. While the rivers were explored throughout the year. The streams were operated mainly in the outflow and flow seasons. The vessels showed a decrease in fishing effort in the flood and dry season increased, with average CPUE of 21.9 and 23.9 kg/fisherman*day for boats and canoes respectively. Four scenarios were simulated to verify the behavior of the stock front to drastic changes in the system, which comprised the following variations: a) Scenario I: increased rates of fishing mortality of Characiformes, Siluriformes and Perciformes (b) Scenario II: reduction in the rate of replenishment of stock, (c) Scenario III: 50% reduction in fishing mortality rates, and (d) Scenario IV: analyzed the effect of the combination of the scenarios I, II and increased total costs and price per kilogram of fish. The planning horizon utilized was 70 years. Scenario III proved to be the most sustainable use of fishery resources as the conditions used in this simulation the stock remained in place for well over 70 years. Given this optimistic scenario, it would be interesting as a management measure for the region, had effective control of fishing access. Where users can be aware and take into account that these natural resources, even though renewable, are also liable to exhaustion. Key words: commercial fishing, Barcelos, costs, system dynamics, sustainability, ecosystem models / Estudos sobre a atividade pesqueira na região Amazônica são voltados para a calha do Solimões-Amazonas, entretanto pouco se sabe sobre a pesca comercial em rios de água preta. Deste modo, considerando à carência de dados na região do Médio rio Negro este estudo se propôs avaliar a sustentabilidade da pesca comercial do município de Barcelos, através da caracterização da frota, análise do desembarque e modelagem ecossistêmica da atividade pesqueira. As informações sobre as características físicas, operacionais e econômicas foram coletadas por intermédio de questionários estruturados no período de fevereiro de 2012 a janeiro de 2013, junto aos pescadores de barcos de pesca e de canoas motorizadas. No geral, a pesca comercial era a principal atividade econômica dos entrevistados, porém estes também desenvolviam outras atividades, principalmente relacionadas à pesca esportiva e ornamental. As características físicas das embarcações foram similares às de outras regiões estudadas na Amazônia. Os barcos de pesca atuaram principalmente como armazenadores de pescado. A malhadeira foi o apetrecho mais utilizado. O combustível foi o principal item dos custos a encarecer as expedições de pesca. Foram desembarcadas 56,0 toneladas de pescado, tendo como valores médios de desembarque 3,6 (± 2,2 t/mês) e 1,1 (± 0,7 t/mês) toneladas por mês para barcos e canoas, respectivamente. O pacu (Subfamília Myleinae), aracu (Família Anastomidae) e tucunaré (Cichla spp.) foram as principais espécies capturadas, responsáveis por aproximadamente 50% da frequência de ocorrência no desembarque. O rio Demeni, o lago Anauali e o igarapé Zamula foram os locais de pesca mais explotados. Ficou evidenciado que os barcos exploraram os lagos na seca e na cheia, enquanto os rios foram explorados em todos os períodos do ciclo hidrológico, com leve predominância do período de vazante. Os igarapés também foram explorados em vários períodos, com exceção da enchente. Em relação as canoas motorizadas, os lagos continuaram sendo os ambientes preferenciais no período de seca. Enquanto os rios foram explorados durante o ano todo. Os igarapés foram explorados principalmente na vazante e cheia. As embarcações apresentaram diminuição no esforço de pesca no período de cheia e aumento na estação seca, com valores médios de CPUE de 21,9 e 23,9 kg/pescador*dia, para barcos e canoas, respectivamente. Foram simulados quatro cenários para verificar o comportamento do estoque frente às alterações nas características do sistema, que compreenderam as seguintes variações de mudanças: (a) Cenário I: aumento nas taxas de mortalidade por pesca de Characiformes, Perciformes e Siluriformes; (b) Cenário II: redução na taxa de reposição do estoque; (c) Cenário III: redução de 50% nas taxas de mortalidade por pesca, e; (d) Cenário IV: foi analisado o efeito da combinação dos cenários I, II e o aumento dos custos totais e preço por quilo de pescado. Como horizonte de planejamento foi escolhido um período de 70 anos. O cenário III mostrou-se o mais adequado ao uso dos recursos pesqueiros de forma sustentável, pois com as condições usadas nesta simulação o estoque se manteria por bem mais de 70 anos. Diante a este cenário otimista, seria interessante que como medida de manejo para a região, houvesse um efetivo controle do acesso à pesca. Onde os usuários pudessem se conscientizar e levar em conta que esses recursos naturais, mesmo sendo renováveis, também são passíveis de exaustão