Tsitsikamma National Park (TNP) possesses the oldest (established 1954), and one of the largest (350 km2) ‘no-take’ marine protected areas (MPA) in South Africa. A long-term monitoring (LTM) programme to observe the subtidal reef fishes in the TNP MPA was established in 2007. To date, 243 angling replicates have been completed, and a total of 2,751 fish belonging to 41 different species have been caught and released. In an era of unprecedented global biodiversity loss, data that can be used to monitor ecosystems and gauge changes in biodiversity through time are essential. This thesis aims to improve the methodological and statistical processes currently available for LTM of subtidal reef fish by providing an evaluation of the TNP MPA LTM programme. Angling data revealed definitive spatial structuring, in the form of spatial autocorrelation, and a shift in viewing spatial dependency as a statistical obstacle to a source of ecological information created a new avenue of data inference. Species-specific distribution maps identified localized habitat as the main predictor variable for species abundance, emphasizing the need for accurate a priori bathymetric information for subtidal monitoring. ‘Random forest’ analyses confirmed spatial variables are more important than temporal variables in predicting species abundance. The effectiveness of Generalized Linear Mixed Models (GAMMs) to account for spatial autocorrelation was highlighted, and evidence that disregarding spatial dependencies in temporal analyses can produce erroneous results was illustrated in the case of dageraad (Chrysoblephus cristiceps). Correlograms indicated that the current sampling strategy produced spatially redundant data and the sampling unit size (150 m2) could be doubled to optimize sampling. Temporal analyses demonstrated that after 50 years of ‘no take’ protection the TNP MPA ichthyofauna exhibits a high level of stability. Species-specific size structure was also found to be highly stable. Dageraad was the only species to exhibit a definitive temporal trend in their size structure, which was attributed to recruitment variation and the possibility that large individuals may migrate out of the study area. The inadequacy of angling as a method for monitoring a broad spectrum of the fish species was highlighted, particularly due to its selectivity towards large predators. As a result, a new sampling technique known as Stereo Baited Remote Underwater Videos (stereo-BRUVs) was introduced to the LTM programme in 2013. Stereo-BRUVs enabled sampling of 2640 fish belonging to 52 different species, from 57 samples collected in less than two years. A comparison of the sampling methods concluded that, compared to angling, stereo-BRUVs provide a superior technique that can survey a significantly larger proportion of the ichthyofauna with minimal length-selectivity biases. In addition, stereo-BRUVs possess a higher statistical power to detect changes in population abundance. However, a potential bias in the form of ‘hyperstability’ in sites with unusually high fish densities was identified as a possible flaw when using stereo-BRUVs. In an attempt to provide a more rigorous method evaluation, simulation testing was employed to assess the ability of angling and stereo-BRUVs to accurately describe a decreasing population. The advantage of this approach is that the simulated population abundances are known, so that each sampling method can be tested in terms of how well it tracks known abundance trends. The study established that stereo- BRUVs provided more accurate data when describing a distinct population decline of roman (Chrysoblephus laticeps) over 10- and 20-year periods. In addition, spawner-biomass was found to be a more accurate population estimate than relative abundance estimates (CPUE and MaxN) due to the inclusion of population size structure information, highlighting the importance of length-frequency data. The study illustrated that an evaluation framework that utilizes simulation testing has the potential to optimize LTM sampling procedures by addressing a number of methodological questions. This includes developing a procedure that aligns data collected from different sampling methods by applying correction factors, thus ensuring LTM programmes are able to adapt sampling strategies without losing data continuity.

Coral reefs and the ecological, social, and economic benefits that they provide are seriously endangered by a colossal number of threats. This study was conducted in marine protected area (MPA) in the Mexican Caribbean. The purpose of this study was to provide results that can be directly applied by MPA managers to improve coral reef conservation and management. Characterization of four coral reef sites and stressors described in a proxy map were integrated into a comparative resilience assessment. Sites ranged from 16.5% to 3.5% coral cover and 47.5% to 12% macroalgal cover. Stressor distribution and intensity was highest near the Puerto Morelos town center and followed general water current patterns. Fishing, tourism, and pollution were identified as major stressors on which management can positively influence. The results of this study provide managers throughout the Caribbean a managerial tool chest to improve management efficacy and bolster conservation initiatives.

The coastal ocean is a marginal region of the global ocean, but is home to metabolically intense ecosystems which increase the structural complexity of the benthos. These ecosystems have the ability to alter the carbon chemistry of surrounding waters through their metabolism, mainly through processes which directly release or consume carbon dioxide. In this way, coastal habitats can engineer their environment by acting as sources or sinks of carbon dioxide and altering their environmental chemistry from the regional norm. In most coastal water masses, it is difficult to resolve the ecosystem effect on coastal carbon biogeochemistry due to the mixing of multiple offshore end members, complex geography or the influence of variable freshwater inputs. The Red Sea provides a simple environment for the study of ecosystem processes at a coastal scale as it contains only one offshore end-member and negligible freshwater inputs due to the arid climate of adjacent land. This work explores the ability of three Red Sea benthic coastal habitats (coral reefs, seagrass meadows and mangrove forests) to create characteristic ecosystem end-members, which deviate from the biogeochemistry of offshore source waters. This is done by both calculating non-conservative deviations in carbonate stocks collected over each ecosystem, and by quantifying net carbonate fluxes (in seagrass meadows and mangrove forests only) using 24 hour incubations. Results illustrate that carbonate stocks over ecosystems conform to broad ecosystem trends, which are different to the offshore end-member, and are influenced by inherited properties from surrounding ecosystems. Carbonate fluxes also show ecosystem dependent trends and further illustrate the importance of sediment processes in influencing CaCO3 fluxes in blue carbon benthic habitats, which warrants further attention. These findings show the respective advantages of studying both carbonate stocks and fluxes of coastal benthic ecosystems in order to understand the spatial, temporal and net effects of their metabolism on the coastal ocean.

As a region renowned for high biodiversity, endemism and extreme temperature and salinity levels, the Red Sea is of high ecological interest. Despite this, there is relatively little literature on basic broad scale characteristics of the biodiversity or overall reef fish communities and how they change across latitude. We conducted visual transects recording the abundance of over 200 species of fish from 45 reefs spanning over 1000 km of Saudi Arabian coastline and used hierarchical cluster analysis to find that for combined depths from 0m-10m across this geographical range, the reef fish communities are relatively similar. However we find some interesting patterns both at the community level across depth and latitude as well as in endemic community distributions. We find that the communities, much like the environmental factors, shift gradually along latitude but do not show distinct clusters within the range we surveyed (from Al-Wajh in the north to the Farasan Banks in the south). Numbers of endemic species tend to be higher in the Thuwal region and further south. This type of baseline data on reef fish distribution and possible factors that may influence their ranges in the Red Sea are critical for future scientific studies as well as effective monitoring and in the face of the persistent anthropogenic influences such as coastal development, overfishing and climate change.

The Red Sea is one of the warmest, saltiest, and most oligotrophic seas in the world that supports a healthy and extremely diverse coral reef ecosystem. Increasing development along the Saudi Arabian coast may increase eutrophication due to impacts of human population and also oil pollution from increased shipping traffic and refinery activity. The risk of oil pollution combined with increased eutrophication due to coastal development provides a clear stressor interaction which is vastly understudied. Individually, these stressors are known to negatively impact coral reproduction, recruitment, and growth. This study focuses on reef settlement and recovery following experimentally-simulated disturbance scenarios. Carbonate recruitment tiles were placed on the reef and exposed to four treatments: control, nutrient enrichment with slow-release fertilizer, tiles soaked in crude oil, and a combination treatment of nutrient enrichment and oil-coated tiles. At periods of 3, 6, 9, 14, and 17 weeks, tiles were collected to classify the settled community and measure oxygen production. Oil, nitrate, and phosphate were the biggest determining factors predicting settlement and oxygen production of the different treatments. The oil treatment had the least overall settlement and oxygen production, whereas the nutrient treatment had the most turf algal recruitment and oxygen production. The combination treatment had an antagonistic effect on algal growth: the nutrients facilitated growth on the otherwise toxic oiled tiles.

In this research, I explore the changes in the functional diversity of herbivorous fishes in zones of coral reefs with different benthic composition: a zone dominated by corals, a zone dominated by algae and a transition zone in between the previous two. I choose to use functional traits which explain the feeding mechanics of this group of fish, as well their feeding rates and their previously established functional groups to understand how different assemblages of this fishes could affect their environment in different ways. I found clear differences in the functional diversity by calculating five indexes, functional dispersion (FDis), functional richness (FRic), functional divergence (FDiv), functional evenness (FEve) and functional specialization (FSpe). Each zone showed different species composition with different abundances; both parameters contribute to obtaining different values of the indexes. The coral-dominated zone showed the biggest multidimensional functional trait space (MFTS) with a value of FRic equals to 1 which means that its assemblage occupies 100% of the MFTS, while the transition zone assemblage occupied 83% and the algae-dominated zone occupied 16% of it. Thanks to this index I identified three functionally redundant species in the coral-dominated and the transition zones. The algae-dominated zone showed the lower FDis explained by the high abundance of grazers individuals. FDiv did not vary significantly between the three zones. FEve was higher in the algae-dominated zone; the index value decreased in the transition and coral-dominated zones, a similar tendency was shown by FSpe. Finally, to explore the importance of including functional diversity I made a comparison between the taxonomic and functional β-diversity. This research showed close relations of herbivorous fishes with their environment, but I could not establish if the benthic composition shapes the herbivorous fish assemblage or the other way around. This research can be a baseline to start working in functional diversity in the Red Sea coral reefs, can help to understand what to expect in the evaluation of reefs in different health state and to identify which herbivorous fish species or groups are more vulnerable and more important according to their function for coral reefs.

Coral reefs are priority habitats which are vulnerable to natural and anthropogenic disturbances. These can cause phase shifts from coral habitat to degraded algal-dominated states – and consequent changes in the distribution, abundance and activity of associated fish species. In the eastern Red Sea, human-induced reef degradation is likely to increase with planned development of the Saudi Arabian coast and the changing climate. The present study therefore investigates the ecological effects of coral-algal phase shifts in reef-associated fish communities, using naturally occurring within-reef benthic zones as proxies for levels of habitat health - with a focus on how these responses differ temporally. These zones were dominated by: hard coral (coral zone), coral and turf algae (transition zone), and macroalgal canopies (algal zone). Six inshore reef areas, were studied in periods with low and high densities of Sargassum in the algal zones (May and November respectively). Community composition was assessed via visual census and predation activity predicted using two proxies: in situ experiments and biomass of carnivores. In both periods, we observed distinct fish communities in each zone - with reduced species richness, Shannon-Wiener diversity and predation intensity, from the coral to the algal zones. Decreases in the abundance and biomass of fish also occurred from the coral to algal zones in May but a spike, as well as a shift in community composition, occurred in the algal zone in November. This shift is attributed to the vast increases in grazer biomass, predominantly Siganus luridus, associated with the November bloom of Sargassum canopies. The present study established, the composition and functioning of Red Sea fish communities is spatially and temporally affected by increased macroalgal dominance. This finding supports the need for herbivorous fish to be made a conservation priority in the management and conservation of reef systems in order to prevent phase shifts to algal dominated states. We conclude that if Red Sea reefs are allowed to shift to alternate states, depending on the density of macroalgal canopies, reefs may support high biomass and abundance of fish but the functioning of the fish community will be altered and the diversity lost.

The wide variety of strata, structural features, and landscapes of Capitol Reef National Park result from its complex, yet discoverable history. Our task was to write and design an informative book on this complexity while making it engaging for the public. We approached the design of this book using Stufflebeam's (2007) CIPP model. The CIPP model uses both summative and formative evaluations in the categories of context, input, process, and product. It provides the framework to methodically investigate the value of a product and identify and correct less effective pedagogical and design elements during its development. We demonstrated the use of the CIPP model as we wrote and illustrated pages of our book. Beginning with context, we identified our target audience, decided how we would provide a book that would serve this cohort, and made a plan for what we would accomplish with Exploring the Diverse Geology of Capitol Reef National Park. The input step involved understanding how to make our goals reality, especially concerning the design of the final book. We researched how the brain learns most effectively and incorporated those ideas into our book. We used principles developed by Clark and Mayer (2011) to reduce extraneous cognitive load. Research by James Hartley (1994) guided the instructional design and typography techniques. The process step helped us stay organized and follow our original plans. Finally, the product step enabled us and others to evaluate our product both formatively and summatively to make necessary alterations and plans for possibly future editions.

Despite high temperature and salinity conditions that challenge reef growth in other oceans, the Red Sea maintains amongst the most biodiverse and productive coral reefs worldwide. It is therefore an important region for the exploration of coral reef functioning, and expected to contribute valuable insights towards the understanding of coral reefs in challenging environments. This dissertation assessed the baseline variability of in situ abiotic conditions (temperature, dissolved oxygen, pH, and total alkalinity, among others) in the central Red Sea and highlights these environmental regimes in a global context. Further, focus was directed on biotic factors (biofilm community dynamics, calcification and bioerosion), which underlie reef growth processes and are crucial for maintaining coral reef functioning and ecosystem services. Using full-year data from an environmental cross-shelf gradient, the dynamic interplay of abiotic and biotic factors was investigated. In situ observations demonstrate that central Red Sea coral reefs were highly variable on spatial, seasonal, and diel scales, and exhibited comparably high temperature, high salinity, and low dissolved oxygen levels, which on the one hand reflect future ocean predictions. Under these conditions epilithic bacterial and algal assemblages were mainly driven by variables (i.e., temperature, salinity, dissolved oxygen) which are predicted to change strongly in the progression of global climate change, implying an influential bottom up effect on reef-building communities. On the other hand, measured alkalinity and other carbonate chemistry value were close to the estimates of preindustrial global ocean surface water and thus in favor of reef growth processes. Despite this beneficial carbonate chemistry, calcification and carbonate budgets in the reefs were not higher than in other coral reef regions. In this regard, seasonal calcification patterns suggest that summer temperatures may be exceeding the optima of calcifiers. As a possible interpretation of the here observed environmental regimes, it can be concluded that the central Red Sea may be less sensitive to ocean acidification, but is already impacted by ocean warming. Importantly, this dissertation provides valuable present-day baseline data of the natural variability of relevant abiotic drivers together with benthic community and reef growth dynamics. These data will be important for future comparative studies and efforts to quantify the impact of future environmental change in the region.

The exceptional environment of the Red Sea has lead to high rates of endemism and biodiversity. Located at the periphery of the world’s coral reefs distribution, its relatively young reefs offer an ideal opportunity to study biogeography and underlying evolutionary and ecological triggers. Here, I provide baseline information on putative seasonal recruitment patterns of reef fishes along a cross shelf gradient at an inshore, mid-shelf, and shelf-edge reef in the central Saudi Arabian Red Sea. I propose a basic comparative model to resolve biogeographic patterns in endemic and cosmopolitan reef fishes. Therefore, I chose the genetically, biologically, and ecologically similar coral-dwelling damselfishes Dascyllus aruanus and D. marginatus as a model species-group. As a first step, basic information on the distribution, population structure, and genetic diversity is evaluated within and outside the Red Sea along most of their global distribution. Second, pelagic larval durations (PLDs) within the Red Sea environmental gradient are explored. For the aforementioned, PLDs of the only other Red Sea Dascyllus, D. trimaculatus, are included for a more comprehensive comparison. Third, to further assess ongoing pathways of connectivity and geneflow related to larval behavior and dispersal in Red Sea reef fishes, the genetic composition and kinship of a single recruitment cohort of D. aruanus arriving together at one single reef is quantified using single nuclear polymorphisms (SNPs). Genetic diversity and relatedness of the recruits are compared to that of the standing population at the settlement reef, providing insight into putative dispersal strategies and behavior of coral reef fish larvae. As a fourth component to study traits shaping biogeography, the ecology and adaptive potential of the cosmopolitan D. aruanus is described by studying morphometric-geometrics of the body structure in relation to the stomach content and prey type from specimen along the cross-shelf of the central Red Sea and at a site outside the Red Sea, in Madagascar, and approach whether foraging strategies change depending on geographic location and environment, and if differences in diet are followed by phenotypic plasticity. Jointly, results suggest that biological responses and putative adaptive strategies are correlated with different biogeographic ranges and habitat preferences.