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The variety of life forms within a given species, ecosystem, biome or planet is known as biodiversity. Biodiversity can also be referred as species diversity and species richness. Understanding the drivers of biodiversity requires an understanding of intertwined biotic and abiotic factors, including climate patterns over the earth, primary productivity processes, e.g. photosynthetic pathways which change with climate and latitude; latitude, geology, soil science, ecology and behavioural science. Diversity of living organisms is not evenly distributed; instead it differs significantly across the globe as well as within regions. The aim of my study is to try to understand the diversity patterns of aquatic plants, using both information derived from previous studies and by collecting new data across the globe, allowing me to examine the underlying mechanisms driving biodiversity at regional and local scales. Both geographical location and local environmental factors were found to contribute to variation in macrophyte assemblage and alpha diversity (i.e. number of species in a locality), with important roles being played by local biotic interactions and abiotic environmental factors. Overall aquatic plants, or macrophytes, play a significant role in the ecology of large numbers of freshwater ecosystems worldwide. For the purpose of my study only calcareous steams, located in both temperate and tropical/subtropical regions were included. Such streams are common in catchments throughout the world because approximately one fifth of the earth’s surface is underlain by carbonate-containing rock. Overall my findings in Chapter 3 provide evidence that there is a high variation in macrophyte assemblages of calcareous rivers across the different countries included in my study, broadly agreeing with information from the literature. I found two large groups based on species assemblages across the different countries included, i.e. a subtropical/tropical and a temperate group. As demonstrated in different parts of Chapter 4, it is possible to identify different 4 diversity responses of macrophyte functional groups to environmental conditions, at local scale, in hardwater rivers. Width and flow were found to be significantly affecting the distribution patterns of diversity of free-floating and floating-leaved rooted species, whereas diversity of marginal species was significantly related to alkalinity and width, and floating-leaved rooted diversity was significantly related to alkalinity. Last but not least submerged species were related to shading. Chapter 5 shows that variation in richness and community structure for hardwater river macrophytes can be partly explained by environmental variation relative to spatial processes in the British Isles (temperate scenario) and in Zambia (tropical scenario). Among the environmental variables, climatic ones explained a great part of species richness and composition distribution for the British Isles. Conversely in Zambia spatial processes made the greatest contribution to variation in hardwater river macrophyte species richness and community structure. Moreover Chapter 6 illustrates how macrophyte species richness, measured as alpha-diversity in calcareous rivers, was at best only very weakly attributed to latitudinal gradient. This is most likely due to the effect of other physical, chemical and biotic variables overriding broader-scale influences on species richness, at more local scales.

Biomineralisation is the process by which living things produce hard mineral tissues with unique physical properties. The study of this process can help us produce biomimetic materials, reproducing such properties, with the study of nucleation and crystallisation of the materials being particularly important. I have used molecular simulation techniques to help gain a greater understanding of these processes, focussing particularly on identifying the conformations and solid phases available to nanoparticles of two biomineral compounds. The bones and teeth of mammals are made largely of calcium phosphates. I have used metadynamics to study nanoparticles of tricalcium phosphate (TCP) and have identified high and lower order configurations. To facilitate this work I reviewed the extant empirical potentials for calcium phosphate systems, selecting the most appropriate for TCP. Calcium carbonate, found in examples throughout the animal kingdom, has three crystalline polymorphs relevant to biomineralisation: calcite, aragonite and vaterite. While nanoparticles of calcite have been extensively studied the other polymorphs have been neglected to date. In this work I present a technique for predicting crystalline morphologies for all three polymorphs across a range of sizes, and compare the energetic ordering. In water the energetic ordering of the nanoparticles is heavily dependent on nanoparticle size. Furthermore, I present work calculating the surface enthalpies of a variety of calcium carbonate surfaces, many of which are negative. It appears that entropic penalty of ordered water is key to understanding the stability of nanocrystals. Also presented is an application of the nudged elastic band method to study transitions between nanoparticle crystal conformations. Between all three crystal polymorphs the nanoparticles passed through an amorphous region of phase space. These results have also been used to evaluate order parameters for use in metadynamics simulations.

This thesis examines the colony size structure and taxonomic composition of coral communities from eight regions of the Indian Ocean approximately 10 years after thermal stress-induced mass mortality events. Coral community composition and population structure differed widely within and between regions, reflecting the different climatic and anthropogenic impacts experienced by each over the past decade. Coral communities in most areas started from a similarly depleted condition but after 1998 their recovery trajectories varied significantly, reflecting different surviving adult communities and continuing, different local stressors; some have remained highly depleted, while others have shown marked recovery. Profound differences between coral communities at intra and inter-regional spatial scales are identified and related to diversity and taxonomic composition, colony abundance, surface area, size frequency distributions, and population demographic parameters within taxa. These are analysed through multivariate techniques and univariate graphical representations to illustrate the significantly different size frequency distributions, taxonomic composition, taxonomic richness and dominance patterns at different spatial scales. A novel technique is assessed for surveying juvenile coral communities, using ultraviolet light, which causes new, growing tissue to fluoresce. This method significantly increases detected juveniles, with important consequences to size frequency patterns and to some previously published views on juvenile densities. The surveying methodologies used are far more revealing than most commonly-used conventional benthic assessments such as intercept surveys, cover values and diversity, which rarely capture discriminatory information on overall composition of coral communities, let alone the structure of populations within them. These colony size-based studies of individual genera are extremely sensitive for interpreting spatial and temporal variations in reefs and greatly enhance understanding of coral reef condition and complexity. The spatial differences demonstrate the applicability of the methods for advising reef management, specifically in identifying areas where ecological resilience is impeded by recruitment failure. Long-term consequences of changes in coral communities may include reduced ecological functional redundancy, reduced structural complexity, reduced carbonate accretion and reef growth, and impaired recovery potential.

There has been growing concern by policy and other decision makers that timber extraction by local communities is the main threat to achieving sustainable management of mangrove systems in Unguja Island, Zanzibar, Tanzania. However, this concern, and responses to the perceived threat to date, do not appear to be informed by a clear understanding of the complexity and capacity of mangrove Social-Ecological Systems (SES) at different scales to adapt to this and other disturbances. The aim of this study was to assess the resilience of mangroves to the increased demand for provisioning ecosystem services and other drivers with a view to identifying options for sustainable mangrove management on Unguja Island. This study was guided by broad resilience concepts and specific approaches, particularly the components-relationship-innovation-continuity framework developed by Cumming et al. (2005). Data relating to both social and ecological components of the mangrove system was collected. A total of 185 plots were surveyed within mangrove forests from three case study sites of Pete- Jozani, Charawe and Michamvi Shehia (lowest administrative unit) on Unguja Island in which mangrove tree species, diameter and height of trees, the numbers of seedlings and stumps were collected to assess the ecological condition of the forests. Key informant interviews (with government officials and village stakeholders), semi-structured household interviews, village meetings and focus group discussions (with beekeepers, mangrove harvesters, village elders and village conservation organisations) were used to collect social-economic data from the three case study sites. The results showed that between the 1920s and 1970s at each case study site local communities reported that they were able to obtain diverse ecosystem services while the key variables that defined the identities of the mangrove SES were maintained. The mangrove SES from each case study site was found to have changed over the past three decades in temporal and spatial scales and currently reside at different phases of change. The current mangrove ecological systems of Pete, Charawe and Kinani (part of Michamvi) were found to have been degraded compared to the past. This was evidenced by the quality and quantity of trees present, with a relatively high density of small-sized mature trees with correspondingly small basal areas and volumes, together with significant numbers of tree stumps in the ecosystems. The areas covered by mangrove vegetation in the study sites were also found to have declined. The decline in quality and quantity of trees was found to correspond with a reduction in desirable ecosystem services as reported by communities. The levels of dependence on mangrove wood provisioning ecosystem services and management approaches have changed across the case study sites. Excessive rates of harvesting of mangrove wood were identified as the key direct driver on mangrove ecological systems, which was fuelled by several underlying drivers including poverty, population change, limited livelihood activities, inappropriate management regimes, and markets for trading mangrove wood ecosystem services. Vijichuni mangrove (another part of Michamvi) was found to be an exceptional case whereby the quality and quantity of mangrove ecological variables had improved. Availability of reliable alternative income sources by the majority of villagers and effective management institutions had contributed to these changes. The drivers identified were used to develop three alternative future scenarios to explore whether projected changes will result in the mangrove SES maintaining their identities in the future. The findings suggest that the Non-inclusive State Control scenario strictly conserves the mangroves, but does not provide alternative livelihood opportunities to improve the well-being of local communities and so is not desirable. Coastal Boom scenario, characterised by unregulated economic growth, particularly in the tourism sector and community forest management with limited benefits for local communities, results in complete degradation of mangrove and reduced wellbeing of local people. However, the Techno-green scenario which includes green growth, access to low-cost cooking energy and co-managed mangrove forests with benefits for local communities, provides decision makers and other stakeholders with an alternative pathway towards more resilient mangrove SES in Unguja.

Anopheles gambiae is a major vector of malaria in sub-Saharan Africa. Given the widespread emergence of pesticide resistance in Anopheles gambiae populations, vector control programs involving the release of sterile males or genetically-modified male mosquitoes designed to diminish malaria transmission are eliciting renewed interest. The success of such mosquito release projects depends on the ability of released males to effectively mate and transfer sperm to wild females. Here, firstly we investigated the interactive effect of the environmental factor hydric stress and adult mosquito phenotypic quality on male and female reproductive success. Secondly, we studied the impact of colonization and genetic modification on potential correlates of reproductive success by comparing sperm quality and sexual organs in the wild strains with transgenic and colonized strains. We then experimentally tested for the potential effects of inbreeding depression on reproductive traits by creating hybrid males from inbred colonized strains. The quality of these 'Super males' was assessed by comparing sperm quality, testes and accessory gland sizes, and estimating the quantity of Plugin and Transglutaminase proteins in their accessory glands. Finally, we assessed the reproductive performance of Super males by estimating the amount of accessory gland protein transferred to females after overnight mating and estimating female fecundity and number of larvae produced. The results underline the importance of female phenotypic quality as determinant of mosquito reproductive success. Inbreeding associated with the colonization and/or genetic modification processes strongly affects sperm length. In contrast, offspring of field-collected females strain have smaller testes and larger accessory glands than older colonized strains. Super males had a good sperm quality. Importantly, the present study suggests that Super males could represent a way to improve male’s reproductive quality under laboratory conditions.

The aim of this thesis is to critically assess the implementation of Integrated Coastal Zone Management (ICZM) in the wider context of coastal planning regimes in order to develop a more effective model of collaboration for coastal governance. This research is set within the context of a complex system of rights and responsibilities which dominate governance of the UK coastline. Within this system of governance, ICZM stands out as a means of adopting a joined-up approach towards the many different interests in coastal areas – both on the land and at sea. However the implementation of ICZM has traditionally been weak - without statutory powers ICZM has suffered from a voluntary approach to implementation, being delivered through bodies collectively known as coastal or estuary partnerships. Coastal partnerships are highly participatory in nature, but can only deliver limited outcomes due to the lack of national coastal policies, and deficits in financial and human resources. In addition, as the Marine and Coastal Access Act and Water Framework Directive come into full legal force, with overlapping jurisdictions in the coastal zone, this raises questions for the future role of non-statutory coastal and estuary partnerships. The research therefore addresses the problems of ICZM in two ways. First, considering ICZM in the wider context of coastal planning regimes, attention is given to the way that the problems of the coast are socially constructed. This is achieved by comparing the social construction of coastal, marine and river catchment problems using the prerequisites outlined by John Hannigan for the social construction of an environmental problem. Whilst identifying limitations in Hannigan’s model regarding the influence of certain conditions in constructing a problem, and the model’s inability to explain progress from problem definition to implementation of a solution, most significantly, it has been found organisations which are able to define a problem also dominate in the proposal and implementation of solutions. Therefore, as the “coastal problem” is subject to ambiguous definitions in which issues of the land and sea are not considered together, this has resulted in weaknesses in addressing coastal problems at the national level. Secondly, in addressing the ways that ICZM implementation could be improved, the communicative planning approach outlined by Patsy Healey and the model of inter-organisational collaboration developed by Barbara Gray are identified as providing conditions that would enable greater integration of stakeholders within coastal partnerships, through for example open dialogue, joint learning and consensus building, and more importantly, facilitating the integration of ICZM and other coastal governance regimes. Using case studies from ICZM, Marine Planning and River Basin Management, it has been shown that by adapting Hannigan and Gray’s models into a cycle of collaborative policy making, building consensus on the nature of the problem at an early stage in decision making fosters a greater sense of ownership and willingness to participate amongst stakeholders in collaborative arrangements. Finally, it is recommended that in trying to improve the implementation of ICZM, greater attention is given to the communication of scientific evidence in simpler, more engaging terms to build greater consensus on the nature of coastal problems, and that the model of collaborative policy making is used to help stakeholders understand the benefits of collaborative working and ensure that the right conditions are in place to aid collaboration and consensus at each stage of decision making.

Due to forest degradation and loss, the use of ecological restoration techniques has become of particular interest in recent years. One such method is the Framework Species Approach (FSA), which was developed in Queensland, Australia. The Framework Species Approach involves a single planting (approximately 30 species) of both early and late successional species. Species planted must survive in the harsh conditions of an open site as well as fulfilling the functions of; (a) fast growth of a broad dense canopy to shade out weeds and reduce the chance of forest fire, (b) early production of flowers or fleshy fruits to attract seed dispersers and kick start animal-mediated seed distribution to the degraded site. The Framework Species Approach has recently been used as part of a restoration project in Doi Suthep-Pui National Park in northern Thailand by the Forest Restoration Research Unit (FORRU) of Chiang Mai University. FORRU have undertaken a number of trials on species performance in the nursery and the field to select appropriate species. However, this has been time-consuming and labourintensive. It has been suggested that the need for such trials may be reduced by the pre-selection of species using their functional traits as predictors of future performance. Here, seed, leaf and wood functional traits were analysed against predictions from ecological models such as the CSR Triangle and the pioneer concept to assess the extent to which such models described the ecological strategies exhibited by woody species in the seasonally-dry tropical forests of northern Thailand. It was found that seed storage behaviour (orthodox and recalcitrant) was strongly linked to other functional traits and that this was the basis of observed differences in performance based on seed size. There was evidence for the existence of a leaf economic spectrum in these forests and for differing positions of deciduous and evergreen species on this spectrum. It was further found that wood hydraulic capacity and safety was more strongly linked to leaf traits than wood mechanical strength; reflecting the importance of the seasonal drought in this type of forest. Selected functional traits were then used to predict the performance of species within the FORRU project. It was found that a combination of wood and leaf traits that encompassed mechanical strength, hydraulic capacity and water storage best described species growth rates in most years and that survival may be linked to a combination of both drought and pathogen load that differs by year due to environmental conditions. In conclusion, functional traits were found to be valuable indicators of performance in forest restoration projects.

To address global biodiversity loss, national and subnational actions are imperative. Malaysia is a biodiversity hotspot with a federal system of government. The literature points to gaps in governance of biodiversity. The aim of this Ph.D. was to understand issues on biodiversity governance in Peninsular Malaysia, with the following objectives: (i) identify conservation priorities; (ii) review and assess the effect of federalism; and (iii) review and analyse the governance of protected areas (PA). This research identified conservation priorities defined by multi stakeholder participation, deploying a workshop and snowball survey approach. This generated a ranked list of 35 priority issues under seven themes, with high degree of agreement among stakeholders. The prioritisation exercise and the literature revealed current federal system of governance posed biodiversity governance challenges. Building on postcolonial and political ecology frameworks, theoretical and empirical qualitative research was carried out on the impact of federalism on biodiversity governance; and the governance of protected areas. I concluded that that states did not want to give up their land for conservation as it is their source of revenue in the absence of incentives for conservation from federal government due to the dichotomy in the federal constitution. Governance of PAs is compromised with different laws operating at both state and federal level, shortage of manpower and funds. This study provides a menu of recommendation options which highlights constitutional, institutional, financial and legal reforms to strengthen governance of biodiversity. In terms of contribution, this study took an innovative approach to identify conservation priorities in Peninsular Malaysia while applying postcolonial and political ecology theory to examine biodiversity governance in a federalised developing country. I highlight the potential of this study to influence policy space and if the proposed reforms are implemented, Peninsular Malaysia has all the ingredients in terms of economic capability, sizeable forest cover and low population density for the effective conservation of biodiversity.

Clathrin-mediated endocytosis is the major route of internalisation of a wide range of cargo at the plasma membrane. Despite the high frequency of endocytic events, it is difficult to predict when and where a clathrin-coated pit will form, complicating any analysis of initiation mechanisms. This thesis describes the development of an inducible model of endocytosis that provides spatiotemporal control over initiation. This is achieved through chemical- or light-induced dimerisation of a clathrin-binding protein (hook) to a plasma membrane cargo (anchor), bypassing any preparation steps prior to clathrin recruitment. It was found that this rapidly induced clathrin-mediated endocytosis that could function independently of AP‑2 and without detriment to endogenous CME. This synthetic endocytosis was found to be a useful measure of functional interaction between clathrin and its adaptors, for example β3 adaptin hinge + appendage was non-functional for CME despite previous reports of in vitro clathrin binding. Also, these clathrin hooks can be easily mutated to pinpoint interaction sites. Mutagenesis of a β2 hinge + appendage hook revealed that a low level of endocytic activity could be maintained when either the hinge or appendage site was disrupted, but mutation of both sites or removal of the entire appendage inhibited synthetic endocytosis. Additionally, the ability of clathrin alone to promote clathrin-coated vesicle formation was shown by the success of a GTSE1 hook, a protein not known to interact with endocytic accessory proteins. This technique offers great potential for further examination of molecular level clathrin/adaptor interactions as well as CME mechanics on a cell-wide scale. In particular, the localised initiation of endocytosis demonstrated here using optogenetics is ideally suited to manipulate cells displaying polarised endocytosis.