Coral reefs around the world are threatened by a variety of sources, from localized impacts, including overfishing and coastal development, to global temperature increases and ocean acidification. Conserving these marine biodiversity havens requires both global and local action informed by scientific research. In this thesis, I use data collected from the coral reefs around Kiritimati atoll (Republic of Kiribati) in the central equatorial Pacific, first to assess the applicability of two common metrics used in passive underwater acoustic research, and second to examine the effects of a marine heatwave and local human disturbance on an assemblage of corallivorous fish. Using acoustic data recorded in 2017 and 2018 on reefs around Kiritimati, I assess how sound pressure level (SPL) and the acoustic complexity index (ACI) respond to changes in fish sounds in a low frequency band (160 Hz – 1 kHz) and snapping shrimp snaps in a high frequency band (1 kHz – 22 kHz). I found that while SPL was positively correlated with increases in fish sounds and snap density, changes in ACI were dependent upon the settings chosen for its calculation, with the density of snaps negatively correlated with ACI across all settings. These findings provide evidence that despite its quick and prolific adoption, acoustic metrics like ACI should be thoroughly field-tested and standardized before they are applied to new ecosystems like coral reefs. Next, using underwater visual censuses (UVCs) of reef fish assemblages, I quantified how two functional groups of corallivores, obligate and facultative, responded to a mass coral mortality event created by the 2015-2016 El Niño. Declines in abundance of both groups were largely driven by the response of coral-associated damselfishes, Plectroglyphidodon johnstonianus in the obligate group and Plectroglyphidodon dickii in the facultative group, to heat stress and subsequent coral mortality. I also observed a significant decline in the species richness of obligate corallivores, and a continued decline in the abundance of obligate corallivores three years after the mass coral mortality event. Additionally, facultative corallivore abundance increased with disturbance, although the effect was modulated by year, likely due to their more adaptable diets. Corallivore assemblage structure was also influenced by the heat stress event, recovery, and local human disturbance. These results detail how an entire corallivorous assemblage is impacted by a coral mortality event and incidentally provide a timeline for corallivore decline. Together, these results provide information about new ways of monitoring coral reefs, and the ways in which two components of the reef fish community, obligate and facultative corallivores, respond to a mass coral mortality event. / Graduate / 2022-01-15

A new geologic map of the Twin Rocks 7.5 minute quadrangle primarily located within Capitol Reef National Park, south-central Utah, provides stratigraphic and structural detail not previously available. This map has also been instrumental in understanding the evolution and development of fluvial terraces associated with Sulfur Creek and the structural geology of the backlimb of the Miners Mountain uplift. Nine bedrock stratigraphic formations and eight types of Quaternary deposits were mapped throughout the quadrangle. Bedrock stratigraphy ranges in age from Permian to Jurassic. New details absent on previous geologic maps include members of the Chinle and Moenkopi Formations and the Jurassic Page Sandstone, a stratigraphic unit herein separated from the Navajo Sandstone. Terraces associated with Sulfur Creek record the central pathway of ancient streams rather than the lateral extent of the floodplain. Volcanic boulder-rich terrace deposits were likely created as stream channels were clogged with volcanic boulders and subsequently abandoned. The boulder-fill effectively armored the underlying softer bedrock. As the stream moved away from the abandoned, boulder-filled channel, it eroded and downcut into the adjacent softer mudstone bedrock, rather than eroding through the more resistant boulder alluvium. Thus, the abandoned boulder-filled channel becomes elevated relative to the stream. This inverted topography is preserved as elevated fluvial terrace deposits. This style of preservation of linear terraces developed over a broad area is in contrast to nearby terraces along the Fremont River which are preserved as "steps" cut into the resistant sandstones of the Glen Canyon Group along the Waterpocket Fold. These terraces have been used to identify changes in the location of Sulfur Creek through time. Kinematic analysis of structures in the backlimb of the uplift show a principle compressive stress orientation nearly perpendicular to the uplift axis and rotated 30° counter clockwise from the stress indicated by deformation bands measured in the forelimb. These data suggest that stress transmitted through the basement is partitioned and rotated in the backlimb, likely due to decoupling and differential slip in strata with low shear strength. Such decoupling would allow the stress to be rotated perpendicular to the resisting fold axis, rather than parallel to the far-field stress transmitted through the basement. Sandbox models produced in this study display boundary perpendicular structures similar to those measured in the backlimb of the Miners Mountain uplift.

No description available.

Thesis (MScEng (Civil Engineering))--University of Stellenbosch, 2009. / Multi purpose reefs are a relatively new concept that incorporate functionalities of beach stabilization, breakwater/seawall protection, biological enhancement and recreational amenity. Economic benefits increase their attractiveness. There is, however, some degree of uncertainty in design guidelines as to the predictability of each of these aspects. With regards to recreational amenity enhancement, one such uncertainty exists in the ability to predict the reef configuration required to give a certain degree of surfability of a reef, and more specifically, to predict the shape of a plunging wave. An extensive survey of the relevant literature has been conducted to provide a background on multi purpose reefs and the uncertainties in predicting the success of multi purpose reefs in achieving their design objectives. A study of wave breaking has been done, along with an analysis of existing breaker height and breaker depth formulae. The effects of bottom friction, refraction, shoaling, winds currents and varying water level on wave breaking has been addressed. Surfability aspects were reviewed including a definition of breaking intensity which is defined by the wave profile in terms of vortex shape parameters, and other surfability parameters that influence the surfability of a reef. Background on numerical modelling methods has been given, along with a description and some trial runs of a new and promising method, Smooth Particle Hydrodynamics. Numerical models were run using the open source SPHysics package in order to assess the applicability of the package in measuring vortex shape parameters. The SPHysics package is, however, still in a stage of development, and is not yet suitable for reef studies with very long domains and with high numbers of particles (required for sufficient resolution in the plunging vortex). A theoretical examination was done on the relevant literature in order to gain an insight into the dynamics affecting the development of the plunging vortex shape. A case study of a natural surf reef was carried out in order to give qualitative estimation of the wave dynamics and reef structure required to give good quality surfing waves and high breaking intensity. The West- Cowell surfing reef factor was used as a tool in predicting wave focusing effects of a naturally occurring reef. Extensive two dimensional physical model laboratory studies were conducted in order to quantify the effects of the reef configuration and wave parameters on breaking intensity. Design guidelines were developed in order to assist in the prediction of breaking intensity for reefs constructed with surfing amenity enhancement as one of their design objectives. The results show that large underwater topographic features can significantly affect the shape and size of incoming waves. Refraction, focusing and shoaling can transform ordinary waves into waves deemed suitable for surfing. The West-Cowell surfing reef factor gives reasonable results outside its applicable range. The 2D physical model laboratory tests show significant variations in vortex shape parameters due to interactions between broken and unbroken waves in a wave train and also to the reflections developed in the flume. Results show that the predicted trends agree with the observations. The results also show that the junction between the seaward reef slope and the horizontal crest may have an effect on the wave shape in the form of a secondary crest between the primary crests. Design guidelines based on the results are presented, and show that breaker height formulae for smooth planar slopes show good agreement with the values of breaker heights measured in the physical model tests, and that existing breaker depth formulae show average agreement. The design guidelines could assist with more effective design of artificial reefs for surfing purposes.

Thesis (MEng)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: In recent years, breakwater design has been governed not only by structural stability, but by cost effectiveness as well. Breakwater designers are constantly trying to find the perfect balance between low-risk design and low-cost design. The combination of a main rubble mound breakwater and a submerged offshore reef, that are designed to function together, is known as a tandem breakwater. The reef structure is responsible for dissipating some of the energy by causing wave breaking. Thereafter, the area between the reef and the main structure - the tranquillity zone - allows for natural energy dissipation. The combination of the effects of the reef and tranquillity zone results in reduced significant wave heights at the main rubble mound structure, which allows it to be designed with lighter armour units. This study investigates the application of a tandem breakwater, based on the conditions at the port of Mossel Bay, by achieving the following set of objectives: (1) to determine the influence of the tandem breakwater‟s submerged reef crest elevation on the damage level of the main rubble mound structure, (2) to determine the relationship between the relative wave attenuation distance and the percentage wave attenuation, and (3) to compare the abovementioned parameters for rock and geotube reefs. A physical model test series was conducted to gain the data required for achieving the objectives. A rubble mound structure that makes use of dolos armour units, resembling the one at Mossel Bay, was constructed inside a concrete flume equipped with a single-paddle wavemaker. Two reef structure types (rock and geotube) were tested at three crest elevations (below-LAT, LAT and ML), against combinations of two significant wave heights (2.5 m and 3 m) and two peak periods (8 s and 12 s), at one water level (ML) and one offshore reef distance (50 m). From the model test results, it is evident that the presence of a reef structure significantly affects the wave conditions that reach the main structure. When comparing significant wave heights measured at a prototype distance of 20 m in front of the main breakwater, a reduction of as high as 42% can be observed for a reef structure made from rocks and 54% for a geotube structure. In all cases, the geotube structure causes more wave attenuation due to its lower permeability, which enables it to reflect more wave energy. However, it should be noted that the stability of the geotube reef was not considered during testing. Generic graphs are presented, that aim to provide guidance in the design process of such a tandem breakwater system. The graphs are produced for a case where dolos armour units are used and might not be exactly the same when a different type of armour unit is used. One graph shows the relationship between the damage reduction at the main breakwater and the relative reef submergence. The other shows the relationship between wave attenuation and the relative wave attenuation distance. Unfortunately, the implementation of geotube reefs of the nature described in this investigation is not likely in the South African context at present. This, however, does not eliminate the possibility of future applications. As geotextile technology develops and greater operational experience and equipment is gained, tandem breakwaters that incorporate geotube reefs could provide an alternative that is both cost-effective and more environmentally friendly with regards to transport emissions. Until then, tandem breakwaters that incorporate rock reefs may be able to provide a desired alternative design for certain scenarios. / AFRIKAANSE OPSOMMING: In die afgelope jare, word breekwater ontwerp nie net beheer deur strukturele stabiliteit nie, maar ook koste effektiwiteit. Ontwerpers poog alewig om die perfekte balans tussen lae-risiko ontwerp en lae-koste ontwerp na te streef. Die kombinasie van 'n hoof ruklipgolfbreker en 'n sekondêre onderwater rif breekwater, wat ontwerp is om as 'n eenheid te funksioneer, staan bekend as „n tandem breekwater. Die rif struktuur is verantwoordelik vir die verlies van 'n gedeelte van die golf energie deur golf breking te veroorsaak. Daarna veroorsaak die area tussen die rif en die hoof struktuur – die kalmeringsone – verdere natuurlike energie verlies. Die gekombineerde effek van die rif en kalmeringsone veroorsaak dat kleiner branders die hoof breekwater bereik, wat toelaat dat dit ontwerp kan word met kleiner pantser eenhede. Dié studie ondersoek die toepassing van 'n tandem breekwater, gebaseer op die kondisies by die Mosselbaai hawe, deur die volgende doelwitte te bewerkstellig: (1) om die invloed van die onderwater rif kruinhoogte op die vlak van skade aan die hoof breekwater te bepaal, (2) om die verhouding tussen die relatiewe golfhoogte-verminderings-afstand en die golfhoogte vermindering te bepaal, en (3) om die bogenoemde parameters vir rots en geo-buis riwwe te vergelyk. 'n Fisiese model toets reeks is uitgevoer sodat die benodigde data ingesamel kan word om die doelwitte te bereik. „n Rotsvul breekwater wat gebruik maak van dolos pantser eenhede, soortgelyk aan dié by Mosselbaai, is gebou in 'n beton kanaal wat toegerus is met 'n enkel-spaan golfmasjien. Twee tipes riwwe (rots en geo-buis) is getoets met drie kruin hoogtes (onder-LAG, LAG en GV), teen kombinasies van twee beduidende golfhoogtes (2.5 m en 3 m) en twee spitsperiodes (8 s en 12 s), by een watervlak (GV) en een sekondêre breekwater afstand (50 m). Uit die model toets resultate is dit duidelik dat die teenwoordigheid van 'n rif struktuur, die golfkondisies wat die hoof breekwater bereik, beduidend beïnvloed. Wanneer beduidende golfhoogtes, gemeet op 'n prototipe afstand van 20 m voor die hoof breekwater, vergelyk word, word 'n vermindering van so hoog as 42% waargeneem vir 'n rif bestaande uit rots en 54% vir 'n rif bestaande uit geo-buise. In alle gevalle veroorsaak die geo-buis struktuur meer golfhoogte vermindering, as gevolg van sy laer deurlaatbaarheid, wat dit in staat stel om meer golfenergie te reflekteer. Die stabiliteit van die geo-buis struktuur is egter nie in ag geneem tydens die toetse nie. Generiese grafieke word weergegee, met die doel om leiding te gee tydens die ontwerpsproses van só 'n tandem breekwater struktuur. Die grafieke hou verband met die geval waar dolos pantser eenhede gebruik word, en mag verskil vir ander tipes pantser eenhede. Een van die grafieke dui die verhouding tussen skadevermindering aan die hoof breekwater en die relatiewe posisie van die onderwater rif se kruinhoogte aan. Die ander grafiek dui die verhouding tussen die golfhoogte vermindering en die relatiewe golfhoogte-verminderings-afstand aan. Huidiglik is die toepassing van die tipe geo-buis riwwe soos beskryf in hierdie ondersoek, ongelukkig onwaarskynlik in die Suid-Afrikaanse konteks. Dit skakel egter nie die moontlikheid van toekomstige toepassings van dié aard uit nie. Soos geo-tekstiel tegnologie ontwikkel en meer operasionele ervaring en toerusting bekom word, kan die effektiewe implementasie van geo-buis riwwe 'n alternatief bied wat beide koste effektief en omgewingsvriendelik is met betrekking tot die vrystelling van uitlaatgasse tydens die vervoer van materiale. Tot dan, kan tandem breekwaters wat van rots riwwe gebruik maak, moontlik die gewenste alternatiewe ontwerp bied vir sekere situasies.

published_or_final_version / Biological Sciences / Master / Master of Philosophy

Longline fishing is the most common elasmobranch capture method in the world, both for commercial fishing, and to a lesser extent for scientific surveys. The capture of an animal on a longline initiates a series of physiological responses designed to promote survivorship in the short term, but if unchecked, can cause reduced individual fitness and/or mortality in the long term. Given widespread declines in shark populations, an improved understanding of the physiological costs of longline capture is needed. The aim of this thesis was to investigate the physiological response of sharks to capture and restraint, to assess novel, non-invasive alternatives to scientific longline surveys, and to generate scientific insight into poorly understood elasmobranch populations in The Bahamas. The results presented herein suggest that some species of shark are able to recover from the physiological stress of capture despite the presence of persistent negative stimuli. Tonic immobility was assessed as a means of generating baseline blood chemistry data, but was found to be inappropriate given that it increases the magnitude of physiological perturbation in the short term. To avoid the stress of capture altogether, Baited Remote Underwater Video Surveys (BRUVS) were considered as a non-invasive alternative to capture based surveys, however, it was concluded that they lack the resolution necessary to answer fine scale demographic questions. For the Caribbean reef shark, longline surveys yielded high resolution data allowing the identification of fine scale spatiotemporal shifts in demographic population structure with minimal cost (mortality). Nevertheless, the ethics of using capture based surveys on sensitive species are questionable when alternative techniques are available. Deep water sharks caught on longline surveys exhibited high mortality rates, however, for these very poorly understood species moribund specimens have great scientific value which in some cases can offset the high ecological costs of the surveys. The results presented in this thesis highlight the on-going need for improved biological and ecological research into the majority of elasmobranch populations, particularly with regards to anthropogenic interactions such as capture. Given the tenuous conservation status of many species, the acquisition of applied, management focused data should remain the priority of elasmobranch scientists.

Caribbean coral reefs are in crisis. Degradation of living coral and fish assemblages has accelerated during the past half century, with a suite of anthropogenic drivers –from local fishing pressure to unprecedented global scale climate change– implicated. Accompanying these losses is the physical disintegration of the three-dimensional calcium carbonate reef structure. Flattening of reefs, synonymous with loss of ecosystem function and provision of services, is caused by an imbalance in the carbonate budget: a trade-off between carbonate production and consolidation by calcifying organisms (principally coral-algal symbioses) and framework breakdown by bioeroding organisms and storms. This thesis focuses on expanding our understanding of two functionally critical issues that strongly influence Caribbean coral reef community composition and dynamics, and which look likely to have a key bearing on the future state of reefs in the region: coral photosynthetic endosymbionts, and carbonate budgets. The former exert an important role in the production of the coral carbonate framework, whilst the latter reflect the dynamics of reef carbonate production and erosion. In the first part of the thesis, existing information on rates of carbonate production and erosion on Caribbean reefs is utilised to construct a detailed theoretical carbonate budget model. The model is used to chart historic changes in Caribbean carbonate budgets, tracking reef flattening across time and identifying key ecological drivers of these changes. This “eco-geomorphic” model is then coupled with state-of-the-art climate and ecological models, to project reef processes to the end of the century, asking the question ‘at what point will Caribbean reefs shift to net erosional regimes?’. The models are also used to explore the efficacy of local management and climate mitigation in altering the negative trajectory of reefs under projected warming and ocean acidification. In the second part of the thesis, 632 corals from across the wider Caribbean are screened, to construct the largest recorded baseline of symbiont biogeography for the region’s key remaining reef framework builder, Montastraea annularis. Spatial patterns of symbiont diversity are explored in terms of environmental, geographic and genetic factors, contributing to the growing body of work currently in the early stages of cataloguing symbiont diversity and its ecological significance. Although carbonate budget models forecast a bleak outlook for the Caribbean, detection of widespread low-level prevalence of thermally-tolerant endosymbionts in M. annularis provides a weak ‘nugget of hope’ for potential coral acclimation. Combined local management and aggressive mitigative action on carbon emissions are pre-requisites for maintenance of functioning reefs into the next century. Coral reef conservation efforts can be improved if we fully appreciate the contributions of all reef components –not just the enigmatic ones– to healthy reef functioning.

The present thesis deals with the related themes of mortality and growth in coral reef fishes. In the first chapter, a nine-year dataset from Bermuda is used to quantify how reef fish populations respond to the introduction of a trap-fishing ban, finding that herbivores exhibit extremely strong recovery, but that stock-recruitment relationships may be decoupled by a numerical response in a meso-predator. In the second chapter, a dataset from Bonaire is used to test the efficacy of the widely-used coefficient of natural mortality, M, in modelling a population of stoplight parrotfish (Sparisoma viride). As determined from simulation models, this statistical coefficient performs considerably less well than a novel mechanistic function that partitions mortality into size- and age-based processes and achieves extremely good fits to the field data. The third chapter presents a new approach to estimating growth parameters of reef fish from tagging data that exploits the disproportionate response of certain parameters to misestimates in the true age of the tagged individuals. The method works considerably better than the most widely used method when sample sizes are small, as is commonly the case in reef fish tagging studies where recapture rates tend to be low. The fourth and final chapter uses non-lethal stable isotope techniques to tease apart the invasion dynamics of Indo Pacific lionfish (Pterois spp.) that are currently colonising the wider Caribbean. The results show that lionfish exhibit habitat-specific ontogenetic shifts in prey selection, inflicting elevated mortality on small, bommie-dwelling fishes on forereefs but switching to seagrass-foraging invertivores as they grow. Lionfish also display ontogenetically shifting competition with native Nassau grouper (Epinephelus striatus), which may provide a greater barrier to invasion success on patch reefs than on fore reefs, where competitive overlap is diminished. The thesis concludes with a discussion of some lines of enquiry that could not be undertaken owing to time or data limitations, but which may hold as much interest for the reader as they do for the author.

Artificial reefs may enhance the biological production of reef-associated flora and fauna, but their trophic structure relative to that of natural reefs remains understudied. We assessed trophic dynamics by comparing δ13C and δ15N in 43 fish species from artificial and natural reef tracts of Broward County, Florida. We tested the effect of sampling location (artificial, first, and second reef), general feeding strategy (herbivore, omnivore, planktivore, invertivore, and carnivore), phylogeny, and standard length. For all samples, δ13C and δ15N ranged from -19.5 to -13.1‰ and 6.7 to 13.3‰, respectively. Lower trophic level feeding behavior resulted in more depleted δ13C and δ15N and higher trophic level feeding behavior resulted in more enriched δ13C and δ15N. We detected significant effects of both general feeding strategy and phylogeny. We also detected significant differences in δ13C and δ15N profiles between artificial and natural reefs; however, these differences were not great enough to suggest changes in the feeding strategy or trophic dynamics of individual fish taxa.