Coral reef cryptofauna (coelobites) are metazoans that occupy the hidden recesses formed by structural taxa such as corals. While cryptic communities are thought to account for the majority of reef biodiversity and play important roles in reef trophodynamics, little empirical evidence exists supporting these claims. Quantitative sampling of coelobites has been thus far limited due to highly heterogeneous reef topographies as well as difficulties associated with identification of large numbers of species. In the eastern Pacific, monogeneric stands of Pocillopora form reef structures that are homogeneous across a horizontal plane and support a relatively depauperate fauna, thereby permitting detailed multispecies analysis. Sampling of motile cryptofauna associated with live coral and dead coral frameworks typifying four levels of degradation, was conducted at Playa Larga Reef on Contadora Island in the eastern Pacific, Gulf of Panamá. Communities associated with live coral colonies were less diverse than those associated with dead corals and the species richness of cryptofauna living on dead coral substrates was higher in more degraded habitats. Living coral colonies, however, support significantly greater densities of cryptofauna and more biomass per volume substrate than their dead coral counterparts. On dead coral frameworks, numbers of individuals and biomass were significantly greater per volume in areas of intermediate degradation. A field experiment was conducted to test the effects of flow, porosity and coral cover on cryptic communities associated with artificial reef frameworks (ARFs). Coral cover (live vs. dead) was not observed to affect the structure of communities occupying underlying frameworks, however, lower porosity substrates sheltered greater abundances of individuals per volume substrate and low flow environments supported elevated biomass. Additionally, porosity and flow were both found to significantly affect relative species abundances as well as overall community diversity. Data from quantitative sampling of natural reef environments and experimental manipulation of cryptic reef habitats suggest novel and unexplored responses to mass coral mortality and reef habitat degradation. Coral death is considered to be vital to the maintenance of reef ecosystem habitat and biotic diversity. Contrary to the popular paradigm that a healthy reef ecosystem has high coral cover, the most diverse reef ecosystems are those which have experienced intermediate levels of degradation. Furthermore, while living corals support elevated cryptofauna abundances and biomass, the magnitude of communities associated with dead framework materials suggest that abundant cryptofauna populations persist in highly degraded reef environments.

To achieve a sustainable development, impacts onbiodiversity of urbanisation, infrastructure, land use changesand other developments must be considered on a landscape andregional scale. Landscape ecology can provide a conceptualframework for the assessment of consequences of long-termdevelopment processes like urbanisation on biodiversity on alandscape scale, and for evaluating the impacts of alternativeplanning scenarios. The aim of this study was to explore theeffects of habitat quality, quantity and connectivity on forestbird diversity in an urban-rural gradient. The purpose of theanalyses was to develop knowledge and methods for integratingbiodiversity issues in planning and assessments in anurbanising environment, on landscape and regional scales. The study area was situated in and around Stockholm, thecapital of Sweden, covering the city centre, suburbs andperi-urban areas. Data on breeding forest birds were collectedthrough bird censuses in an urban-suburban gradient. In orderto embrace also the peri-urban areas for a more completeurban-rural gradient, data on two fragmentation-sensitiveforest grouse species were obtained through a questionnaire tohunters in the whole study area. Response variables in theanalyses were forest bird species richness and diversity,relative species richness and occurrence of single sensitivespecies like selected sedentary forest birds, including theforest grouse species, and red list species. Habitat quality,quantity and connectivity were analysed using available data onabiotic conditions, including urban disturbances, andvegetation in geographical information systems. In addition, afield study on vegetation structure and composition wasperformed in a subset of the smaller sample sites.Relationships between the response variables and habitatquality, quantity and connectivity were explored usingstatistical methods like multivariate statistics and regressionmodelling. Further, for some models, spatial dependencies werequantified and accounted for. When habitat models wereretrieved, they were used for spatial predictions of habitatsuitability. They were also applied on future planningscenarios in order to predict and assess the impacts onsensitive species. In the urban-rural gradient, the foreststructure and composition changed, so that in more urban areas,coniferous forest on rich soils, wet forests and wetlandsbecame less abundant and more scattered. Sensitive birdspecies, tied to these habitat types, were shown to besensitive to habitat fragmentation caused by urbanisation.Large, well-connected habitat patches and aggregations ofsuitable habitat in the landscape had a higher probability ofoccupancy when compared to other patches. For the forest grousespecies, effects of car traffic added to the explanation oftheir distribution. By contrast, deciduous forest was stillquite common in predominantly urban areas, due to both latechanges in land use and a history of human preferences. Certainred listed bird species tied to deciduous forest did not seemto be affected by isolation, and also occurred in suitablehabitats in some highly urbanised areas. Furthermore, relativespecies richness in the urban-suburban gradient was related tomulti-layered deciduous forest habitats with a large amount ofdead wood. Such habitats were associated with natural shorelineand with old pastures and parks. From the derived statisticalmodels, describing the relationships between sensitive speciesand environmental variables, predictive habitat maps could becreated for the present situation and for planning scenarios.The predictions of the impacts on habitats of sensitive speciesmade it possible to quantify, integrate and visualise theeffects of urbanisation scenarios on aspects of biodiversity ona landscape scale.

A total of 840 fish species names (belonging to 143 families) were gathered from the Taiwan coastal area-economic geographical database. [http://fishdb.sinica.edu. tw/ 2001new/main1.asp] The near-shore area of Taiwan were divided into eight areas for studies of geographical distribution and biodiversity pattern. Biological data for individual species was gathered from ICLARM (Fishbase) including trophic level and VBGF growth parameters. The temporal and spatial difference between different areas were studied using traditional statistical methods and S-P chart analysis. The results show that Eastern area has higher trophic level , asymptotic length (L¡Û) , maturity length (Lm) , age at maturity (Tm) and Maximum age (Tmax) than the West. Also the Eastern has relatively lower food items on plant , M value and K values. Presence and absence of fish species were organized and presented into the so-called S-P chart for demonstrating the interaction between species or family diversity and habit. Results on family level show that the West has greatest species richness (96 families) in contrast to the North-West and South-East (69 families).A total of 29 families distributed at all areas, whereas fishes belonging to the other 22 families can only be found on one single area. Results on species level show that the West has greatest species richness (538 species) in contrast to the North-West (207 species).Result from the S-P chart also serves for statistical testing in identifying the significance difference on species-habit interactions among different area of fish populations. Cluster analysis show that North-East , East and South-East can be grouped into one group. The other individual groups were North-West , West , South-West , North and South.

The North Mountain of the Annapolis Valley, NS, in eastern Canada, is a ~200 km basalt ridge drained by many small first or second order streams in independent catchments. The area is fairly uniform geologically, presenting an opportunity to compare streams of similar chemistry, slope and aspect, that vary in other respects, such as invertebrate community structure. In this thesis, I examine two macroinvertebrate functional groups to determine key factors influencing their abundance, composition and diversity across catchments. Chapters 2 and 3 are concerned with the predatory invertebrate guild in eight of the streams, in two groups separated by ~65 km. In Chapter 2, I assessed factors influencing composition of the predator guild using similarity matrices. Similarity in predator composition declined with distance, and streams that were more similar in disturbance (spates) were more similar in predator composition. Similarity within one family, Rhyacophilidae, was related to similarity in fish population. Chapter 3 reports the results of laboratory experiments involving two widespread species. Field data suggested an asymmetric interaction between Sweltsa onkos (Plecoptera: Chloroperlidae) and Rhyacophila vibox (Trichoptera: Rhyacophilidae); behavioural observations in artificial streams supported this. In the presence of R. vibox, S. onkos had higher mortality and injury rates, and grew less. The results of these chapters suggest that, although disturbance is important in shaping community structure, the results of interspecific interactions can be detected at large scales. S. onkos can only attain high numbers in streams where fish predation reduces the abundance of R. vibox. Chapter 4 examines biodiversity patterns in the macroinvertebrate detritivore guild in 25 streams encompassing ~80 km of the ridge. Using density and richness of the detritivore community, detrital resource quantity, and top predator abundance, I looked for evidence in support of several mechanisms that can lead to positive species-energy relationships. Patterns conformed to expectations of the More Individuals Hypothesis. It appears that taxonomic richness of the detritivore guild increases with detrital resource availability because more taxa can attain their minimum viable population size where more resources are available.

Esta investigación está motivada por dos observaciones. En primer lugar, la constatación de que, a pesar de la multiplicación de directivas, leyes e iniciativas, la biodiversidad continúa disminuyendo. En segundo lugar, el reconocimiento de que la biodiversidad articula consideraciones sociales, políticas y científicas. En este marco, la pérdida de biodiversidad requiere de un análisis teórico en tres dimensiones, teniendo en cuenta las cuestiones sociales y éticas (¿cuál es el valor de la biodiversidad?), políticas (¿cuáles son los mecanismos legítimos para proteger la biodiversidad?) y epistemológicas (¿cómo podemos entender la biodiversidad?). Esta tesis presenta una conceptualización de la biodiversidad teniendo en cuenta estos tres niveles. Se discute cómo podemos mejorar la gobernanza de la biodiversidad desde estas tres perspectivas, poniendo así en relieve las bases sociales, políticas y científicas que la humanidad necesita entender y apoyar si quiere tratar de forma efectiva la cuestión de la protección de la biodiversidad. Para responder a esta pregunta, he enfocado mi investigación en las interfaces entre los actores clave de la investigación europea en biodiversidad. Adopto un punto de vista normativo según el cual las investigaciones que incluyen a las partes interesadas son por definición más ‘sociales’. En este contexto, los objectivos de esta tesis son: (i) pasar de un enfoque antropocéntrico basado en las necesidades humanas hacia otro más global y ecosistémico, (ii) poner de relieve las perspectivas que reconocen los procesos politicos de gobernanza de abajo a arriba, (iii) avanzar hacia procesos poliédricos y multidireccionales de producción y transferencia de conocimientos, y (iv) convertir las tensiones y desafios relacionados con la investigación intercultural e interdisciplinaria en oportunidades. Para cumplir estos objetivos, la tesis se apoya en cuatro estudios que valoran críticamente (i) la extensión del Modelo de Desarrollo de Escala Humana hacia lo no-humano como parte del análisis de los conflictos ambientales en el sur de Europa, (ii) dos mecanismos de gobernanza: la participación de los actores no gubernamentales y la producción de escenarios para la planificación ambiental en Europa occidental, (iii) los niveles y formas de involucramiento de los participantes en los proyectos europeos de investigación en biodiversidad (FP6) y el impacto de un enfoque más participativo, y (iv) los retos y oportunidades que surgen cuando nueve estudiantes de Doctorado escriben sus tesis a partir de sus proyectos de investigación interdisciplinarios (GoverNat). Para mejorar la gobernanza de la biodiversidad, propongo una visión holistica de las necesidades humanas y no humanas, reconociendo el valor intrínseco del mundo de los seres vivos (la dimensión social del concepto de biodiversidad, capítulo 1); fortalecer la vida comunitaria presente y futura promoviendo los procesos de toma de decisión colectivos de abajo a arriba (dimensión política del concepto de biodiversidad, capítulo 2); involucrar y compartir las experiencias de las partes interesadas claves, creando redes locales para la co-construcción de un conocimiento común (dimensión científica del concepto de biodiversidad, capítulo 3); y generar las condiciones para permitir la comunicación interdisciplinaria (capitulo 4). Esta tesis ofrece argumentos y herramientas para justificar la protección de la biodiversidad en sus dimensiones social, política y científicas, en un contexto interdisciplinario. Tambièn alimenta el debate sobre el diseño de las políticas públicas. A partir de ahora, necesitamos apoyar un enfoque integrador de la gobernanza basado en las necesidades fundamentales y en el cual el público esté involucrado. Esto permetirá una reflexión inclusiva, permanente pero dinámica sobre las propuestas futuras de políticas ambientales. / This research is underpinned by two observations: despite man-made directives, laws and initiatives, biodiversity is still shrinking; and the very concept of biodiversity combines societal, political and scientific considerations. The challenge of biodiversity loss therefore requires us to consider a three-layered theoretical framework that contains social and ethical (what are the values of biodiversity?), political (what are the legitimate mechanisms by which biodiversity can be protected?) and epistemological questions (how can we understand biodiversity?). In this thesis I develop this three-layered understanding of biodiversity and of the general issue of how we may best improve biodiversity governance from these three viewpoints in order to highlight the social, political and scientific foundations that humanity must understand and support if it is to address the issue of biodiversity protection in an effective way. To respond to this question, I focus on science-stakeholders interfaces in the field of European biodiversity research. I adopt a normative standpoint in which research that includes stakeholders was by definition more ‘social’, integrating human needs and the impact of human activity as fundamentals that should be considered if we are to meet the environmental challenges of the present and the future. In this context, the objectives of this thesis are (i) to shift from an anthropocentric human needs-based approach to a more global and ecosystemic one, (ii) to highlight perspectives that acknowledge the redistribution of state functions towards non-state, and bottom up environmental governance process, (iii) to shift toward multi-faceted, multi-directional process of knowledge production and transfer, and (iv) to turn the tensions and challenges related to interdisciplinary and intercultural research for sustainable development into opportunities. To reach these objectives, the thesis builds on four case studies that cover a critical assessment of (i) the extension of the Human-scale Development model to non-humans in analysing environmental conflict in South Europe, (ii) two mechanisms of governance: the participation of non-state actors and scenario-building for environmental planning in Western Europe, (iii) the level and modalities of stakeholder engagement in EU-funded FP6 biodiversity research projects and the impact of a more participatory approach, and (iv) the challenges and opportunities that arise when nine PhD students set out to write a doctoral dissertation within an interdisciplinary research project (GoverNat). To improve biodiversity governance, I therefore propose a holistic view of human and non-human needs, recognizing the intrinsic value of the living world (i.e. the social dimension of the concept of biodiversity, chapter 1); strengthen community life present and future, encouraging bottom-to-top collective decision-making (i.e. political dimension of the concept of biodiversity, chapter 2); involve and share experiences of key stakeholders, creating local networks for the co-construction of common knowledge (i.e. scientific dimension of the concept of biodiversity, chapter 3); and enable interdisciplinary communication and networks that require time and patience (chapter 4). This thesis offers arguments and tools to justify the protection of biodiversity in its social, political and scientific dimensions, and therefore also in an interdisciplinary context. It also feeds the debate on sustainable public policy-making. From now on, we need to support an integrative approach to governance in which the public are involved based on fundamental needs. This would enable an inclusive, permanent but dynamic reflexion on future environmental policy proposals.

Coral reefs have high biodiversity among the many marine ecosystems. Many hypotheses explain marine biodiversity, e.g., the Intermediate Disturbance Hypothesis, the Lottery hypothesis and the Resource Allocation Hypothesis, but there is no mention of the possible role of seasonal effects. Here, we propose the Seasonal Recruitment Hypothesis to explain the possible role of seasonal recruitment and succession in a disturbed ecosystem. In this investigation, we tested several prediction of the hypothesis: a. Does recruitment have seasonal variation? b. Does variable recruiting communities diverge in succession? c. Are high biodiversities of coral reefs contributed by different communities originating from patches created in different seasons? In this study, we used plastic plates as proxy of empty space generated after disturbance to survey the seasonal patterns of settling benthos. Recruitment plates were placed and retrieved at two-month intervals for two consecutive years. Then, the composition and densities of settled taxa were estimated. The PRIMER software was used to compare the community similarities. We looked for possible seasonal patterns in each benthic populations but found few not real examples of such. Although there is difference between communities started in different seasons, no cyclic pattern in similarity was found by MDS plots in two years of recruitment communities. There are variations of recruitment community between different year and month, and the community structures converged after succession. These results do not support the prediction of the Seasoanl Recruitment Hypothesis.

In the wake of the Diamond Action Plan for Biotech Takeoff, the government's drafting of the Biotech and New Pharmaceutical Development Statute and signing of the Economic Cooperation Framework Agreement (ECFA) and Cross-strait Cooperation Agreement on Medicine and Public Health Affairs with China will expand collaboration opportunities for the biotech industries in Taiwan and China, bring future market opportunities, and induce domestic and foreign firms to sharply increase their investment in the biotech industry.Furthermore, as demographic aging continues worldwide, healthcare reform in numerous countries and the continued growth of emergency markets will increase demand for pharmaceuticals and medical products,creating more opportunities for the biotech industry. In view of this background, the Diamond Action Plan for Biotech Takeoff will enable industry to take advantage of upstream R&D results and technologies at an early date, promote the establishment and development of R&D-oriented pharmaceutical and medical devices companies, attract investment by international capital, and transform Taiwan into a major biotech hub providing foreign firms with convenient access to the Asian market.

Benthic community structure was studied by sample quadrates on transects at depths of 5 to 10 m in four sites, including Wanlitong, Leidashih, Siangjiao Bay, and Longkun, in coral reefs of southern Taiwan from 2003 to 2005. Totally 154 species in 45 genera of hard coral and 45 species in 10 genera of soft coral, representing 67% of known coral species were recorded. Covers of benthic organisms and hard coral growth forms were similar among years, but were significantly different among sites. Mean cover of all corals was high in Siangjiao Bay (56.88%) and Leidashih (65.69%), but hard coral (65.43%) was dominanted in Siangjiao Bay while soft coral (39.00%) was dominanted in Leidashih. Mean cover of all coral and benthic algae was similar in Wanlitong and Longkun. For hard coral growth forms, massive and encrusting corals were dominanted in three of four sites. This may be resulted from the strong wave. Cover of bare substrate was high (21.39%) in Longkun which was the most exposed to wind and wave stress. Foliaceous coral was abundant with the dominated species, Montipora aequituberculata (20.59%) in Siangjiao Bay which was a more protected site. However, foliaceous coral was more susceptibe to typhoon. Coral diversity was higher in Leidashih. This was related to both hard and soft corals were common and no dominant species. Comparing to previous studies, the long term change of coral abundance shows stable and/or increasing trends. It may be related to the dominance of massive and encrusting coral communities in southern Taiwan.

The distribution of benthic polychaetes in the Mississippi Canyon was examined to evaluate impacts of environmental variables on species assemblages. Environmental variables considered included depth, bathymetric slope, hydrographic features, sediment grain size, food availability and sediment contamination. Samples were collected using GOMEX boxcorer. Density decreased with increasing depth exponentially. Diversity exhibited a unimodal pattern with depth with a maximum value in the intermediate depth range (about 1269 m). Deposit feeders were the most abundant feeding guild. Both the feeding guilds and faunal composition could be divided into three groups along the depth gradient: shallow (300 – 800 m), intermediate (800 – 1500 m) and deep (> 1500 m). Results of statistical analyses revealed that depth was the most important determinant in organizing polychaete assemblages in the study area. The Mississippi Canyon and the Central Transect (a non-canyon area) were found not contaminated by trace metals or Polynuclear Aromatic Hydrocarbons (PAHs) in sediments, although the highest PAHs concentration occurred at the head of the Canyon, MT1. The mean density was higher in the Mississippi Canyon (1668 N/m2) than in the Central Transect (979 N/m2), while the mean diversity in the Canyon (ES(100) = 26.9 ) was lower than the Central Transect (ES(100) = 33.1). Large amounts of terrigenous input from the Mississippi River to the Canyon could enhance polychaete density and accelerate competitive exclusion, and thus lead to lower diversity. The faunal composition was significantly different between the two transects, with higher species richness in the Mississippi Canyon (301 species). This could be attributed to structure complexity in the Mississippi Canyon. The distribution of feeding guilds was similar between two transects. The differences observed in polychaete assemblages between two transects may be largely due to high terrigenous sediment and organic matter input to the Mississippi Canyon by the Mississippi River.

<p>To achieve a sustainable development, impacts onbiodiversity of urbanisation, infrastructure, land use changesand other developments must be considered on a landscape andregional scale. Landscape ecology can provide a conceptualframework for the assessment of consequences of long-termdevelopment processes like urbanisation on biodiversity on alandscape scale, and for evaluating the impacts of alternativeplanning scenarios. The aim of this study was to explore theeffects of habitat quality, quantity and connectivity on forestbird diversity in an urban-rural gradient. The purpose of theanalyses was to develop knowledge and methods for integratingbiodiversity issues in planning and assessments in anurbanising environment, on landscape and regional scales.</p><p>The study area was situated in and around Stockholm, thecapital of Sweden, covering the city centre, suburbs andperi-urban areas. Data on breeding forest birds were collectedthrough bird censuses in an urban-suburban gradient. In orderto embrace also the peri-urban areas for a more completeurban-rural gradient, data on two fragmentation-sensitiveforest grouse species were obtained through a questionnaire tohunters in the whole study area. Response variables in theanalyses were forest bird species richness and diversity,relative species richness and occurrence of single sensitivespecies like selected sedentary forest birds, including theforest grouse species, and red list species. Habitat quality,quantity and connectivity were analysed using available data onabiotic conditions, including urban disturbances, andvegetation in geographical information systems. In addition, afield study on vegetation structure and composition wasperformed in a subset of the smaller sample sites.Relationships between the response variables and habitatquality, quantity and connectivity were explored usingstatistical methods like multivariate statistics and regressionmodelling. Further, for some models, spatial dependencies werequantified and accounted for. When habitat models wereretrieved, they were used for spatial predictions of habitatsuitability. They were also applied on future planningscenarios in order to predict and assess the impacts onsensitive species. In the urban-rural gradient, the foreststructure and composition changed, so that in more urban areas,coniferous forest on rich soils, wet forests and wetlandsbecame less abundant and more scattered. Sensitive birdspecies, tied to these habitat types, were shown to besensitive to habitat fragmentation caused by urbanisation.Large, well-connected habitat patches and aggregations ofsuitable habitat in the landscape had a higher probability ofoccupancy when compared to other patches. For the forest grousespecies, effects of car traffic added to the explanation oftheir distribution. By contrast, deciduous forest was stillquite common in predominantly urban areas, due to both latechanges in land use and a history of human preferences. Certainred listed bird species tied to deciduous forest did not seemto be affected by isolation, and also occurred in suitablehabitats in some highly urbanised areas. Furthermore, relativespecies richness in the urban-suburban gradient was related tomulti-layered deciduous forest habitats with a large amount ofdead wood. Such habitats were associated with natural shorelineand with old pastures and parks. From the derived statisticalmodels, describing the relationships between sensitive speciesand environmental variables, predictive habitat maps could becreated for the present situation and for planning scenarios.The predictions of the impacts on habitats of sensitive speciesmade it possible to quantify, integrate and visualise theeffects of urbanisation scenarios on aspects of biodiversity ona landscape scale.</p>