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In spite of the growing attention towards the overall quality of Marine Protected Areas (MPAs), most empirical studies so far have narrowly focused their assessments on specific natural or social features and governing structures. In response, this study analyzed multi-use MPAs in the eelgrass restoration site in Hinase, Okayama, Japan in their environmental, economic and social dimensions. Considering changes in time and space as well as internal and external influences, the study faced many difficulties in dealing with the dynamics of MPA environments. At the same time, it showed clearly the control over development and fishery activities by several MPA relevant regulations, improvements of the ecological function by the regrowth of eelgrass, an increase in some fish species due to the same regrowth, and expansion of social networks deriving from the restoration activity. The study also revealed convincing evidence that self-motivated MPA management practice by fishers under the Territorial Use Rights for Fisheries (TURFs), in conjunction with other mixed management systems such as Satoumi, could lead to flexible and long-term efforts for improving food security, livelihoods, and the marine environment. This study highlights the importance of comprehensive research to deepen the understanding of the structure and functions of complex and diverse marine ecosystems and social systems.

This paper focuses on a collection of methods that can be used to analyze the water-energy-food (WEF) nexus. We classify these methods as qualitative or quantitative for interdisciplinary and transdisciplinary research approaches. The methods for interdisciplinary research approaches can be used to unify a collection of related variables, visualize the research problem, evaluate the issue, and simulate the system of interest. Qualitative methods are generally used to describe the nexus in the region of interest, and include primary research methods such as Questionnaire Surveys, as well as secondary research methods such as Ontology Engineering and Integrated Maps. Quantitative methods for examining the nexus include Physical Models, Benefit-Cost Analysis (BCA), Integrated Indices, and Optimization Management Models. The authors discuss each of these methods in the following sections, along with accompanying case studies from research sites in Japan and the Philippines. Although the case studies are specific to two regions, these methods could be applicable to other areas, with appropriate calibration.