With the rapid development of the coastal environment and advances in fishing technology, marine biodiversity and fishery resources are decreasing dramatically. Therefore, each state is now focusing on conserving the marine environment. Planning Marine Protected Areas is one of the simplest and most efficient ways to do this. In recent years, researches have been conducted on Marine Protected Areas around the world. The government and academic fields in Taiwan also has started to value its surrounding marine environment. However, literature on the Marine Protected Areas in Taiwan has focused on policy and management, not so much on planning and zoning strategies. Therefore, this study uses the Geographic Information System (GIS) to simulate the planning and zoning process. This research set principles and zoning framework for Marine Protected Areas in Taiwan based on case studies and spatial analysis techniques. This study uses Gueishan Island in Yilan County as case study since the unique geographical environment of Gueishan Island provides potentiality to set Marine Protected Areas. In this study, it is suggested that "hot spring resources", "cetacean resources", and "fisheries resources" are the main protected objectives. The zoning strategies, management guidelines and recommendations are provided in this study based on these three protected objectives. According to the GIS simulation process, using the spatial analysis techniques is one of the possible efficient methodologies to plan and zone the Marine Protected Areas. With supplementary data and information, the results can be discussed more specifically in the further study. In addition, techniques of visualization during the MPAs zoning process can be a easier way for various stakeholders to understand, and to strengthen mutual communication, thereby reducing disputes to create successful Marine Protected Areas.

It is an internationally acknowledged that marine protected area (MPA) is an important measure for maintaining biodiversity and rescuing endangered species. MPA can also effectively inhibit human interferences such as development and pollution discharge. The establishment of MPA is possible to fulfill the goal of sustainable management, which is to conserve marine habitat for an integrative ecosystem and a higher biodiversity. However, how to design an effective MPA remains an important research issue to be explored. In order to grasp the spatial distribution of the ecological data in the study area, the current research uses spatial interpolation tool, Kriging, provided by the Geographic information system (GIS) software. Then three spatial analytical models have been developed based on integer programming techniques. It is guarantee that all three models can find the global optimal solutions for the best protective area partitions. This quantitative approach is more efficient and effective compared to the qualitative methods in many aspects. The models are able to preserve the maximum ecological resources under the limited spatial area. Besides, the model formulation can be adjusted from different environmental impact factors to fulfill the requirements of users. The case study of the research is to design a MPA for Kaomei wetland. However the spatial analytical models developed in this research can also be applied to protected area design in land area.

Intégrer les connaissances sur la connectivité écologique dans la gestion des écosystèmes marins est essentiel, surtout dans un contexte d'appauvrissement des ressources marines et de dégradation des habitats côtiers à l'échelle mondiale. Des outils environnementaux, tels que les Aires Marines Protégées ont été mises en œuvre pour protéger la biodiversité, restaurer les écosystèmes endommagés, soutenir les pêcheries et reconstituer les stocks surexploités. Leur efficacité dépend en partie du maintien de la connectivité entre les populations marines, assurée à travers divers processus écologiques dont la dispersion larvaire. Dans le cadre de ce travail de thèse, un modèle biophysique intégrant des données de courants, issues de mesures d'altimétrie par satellite, a été utilisé pour évaluer la connectivité entre les récifs de l'océan Indien d'une part, et à travers le réseau d'AMP de Méditerranée d'autre part. Différentes méthodes d'analyse ont été utilisées, telles que la théorie des graphes et le clustering. Dans l'océan Indien occidental, l'analyse des connectivités marines montre que le nombre de connexions entre les récifs augmente avec la durée de vie larvaire des poissons. Elle met également en évidence une faible connectivité à l'échelle de la région, mais une forte inter-connectivité au sein de plusieurs sous-régions (Canal du Mozambique, Mascareignes). En Méditerranée, la connectance est globalement faible à l'échelle régionale, bien que plus importante dans le bassin occidental que le bassin oriental. L'analyse des connectivités marines montre également un taux de connectivité élevé à l'échelle d'un même pays. Selon le cas d'étude, une liste de récifs ou de sites prioritaires dans la mise en œuvre des AMP a été proposée. Enfin, les implications de ces résultats en termes de politiques transfrontalières et de coopération régionale sont discutées. / Integrating ecological connectivity into marine ecosystem management and planning is important, especially in a global context of severe fish stocks depletion and growing habitat degradation. Environmental tools such as Marine Protected Areas have been proposed to protect biodiversity, restore damaged ecosystems, sustain fisheries, and rebuild overexploited stocks. The effectiveness of marine protected areas depends in part on the maintenance of connectivity between marine populations, linked by ecological processes such as larval dispersal. In this thesis, we applied a biophysical model driven by ocean currents derived from satellite altimetry to evaluate connectivity between Western Indian Ocean reefs and across the current MPA system in the Mediterranean Sea. We applied different methods of analysis such as graph-theoretic and clustering. In the Western Indian Ocean, marine connectivity analyses show that the number of connections between reefs increases with fish pelagic larval duration. It also highlights a low connectivity across the region and a high interconnectivity within several regions (Mozambique Channel, Mascarene archipelago). In the Mediterranean Sea, connectance is globally low at the regional scale. This connectance is more important in Western than Eastern Mediterranean. Moreover, the marine connectivity analyses revealed high domestic connectivity rates. Depending on the study area, priority reefs or sites for MPA implementation are proposed. Finally, implications for transboundary marine policies and regional cooperation are discussed.

A growing number of scientists are investigating applications of landscape ecology principles to marine studies, yet few coral reef scientists have examined spatial patterns across entire reefscapes with a holistic ecosystem-based view. This study was an effort to better understand reefscape ecology by quantitatively assessing spatial structures and habitat arrangements using remote sensing and geographic information systems (GIS). Quantifying recurring patterns in reef systems has implications for improving the efficiency of mapping efforts and lowering costs associated with collecting field data and acquiring satellite imagery. If a representative example of a reef is mapped with high accuracy, the data derived from habitat configurations could be extrapolated over a larger region to aid management decisions and focus conservation efforts. The aim of this project was to measure repeating spatial patterns at multiple scales (10s m2 to 10s km2) and to explain the environmental mechanisms which have formed the observed patterns. Because power laws have been recognized in size-frequency distributions of reef habitat patches, this study further investigated whether the property exists for expansive reefs with diverse geologic histories. Intra- and inter-reef patch relationships were studied at three sites: Andavadoaka (Madagascar), Vieques (Puerto Rico), and Saipan (Commonwealth of the Northern Mariana Islands). In situ ecological information, including benthic species composition and abundance, as well as substrate type, was collected with georeferenced video transects. LiDAR (Light Detection and Ranging) surveys were assembled into digital elevation models (DEMs), while vessel-based acoustic surveys were utilized to empirically tune bathymetry models where LiDAR data were unavailable. A GIS for each site was compiled by overlying groundtruth data, classifications, DEMs, and satellite images. Benthic cover classes were then digitized and analyzed based on a suite of metrics (e.g. patch complexity, principle axes ratio, and neighborhood transitions). Results from metric analyses were extremely comparable between sites suggesting that spatial prediction of habitat arrangements is very plausible. Further implications discussed include developing an automated habitat mapping technique and improving conservation planning and delimitation of marine protected areas.