Thesis (Ph.D.) - University of Queensland, 2005. / Includes bibliography.

Thesis (M.S.)--Universidad de Puerto Rico, Recinto Universitario de Mayagüez, 2005. / Tables. Printout. Includes bibliographical references (leaves 45-51).

Herbivory is a key process that mediates the abundance of primary producers and community composition in both terrestrial and aquatic ecosystems. On tropical coral reefs, changes in herbivory are often related to phase shifts between coral-dominance and dominance by seaweeds, or foliose macroalgae. Resilience or capacity to resist and reverse such phase shifts is, therefore, viewed as a critical function on coral reefs. This thesis used grazer exclusion and assay experiments at six sites within three different fisheries management regimes in Kenya to identify the impacts of herbivores (sea urchins and fishes) on algal dynamics in the context of coral reef resilience. First, I examined the grazing rates necessary to prevent phase shifts by quantifying consumption and algal production. Here, I found that, over a 390-day experiment, at least 50 percent of algal production must be consumed to avoid accumulation of algal biomass. Using video observations, I also showed that scraping parrotfishes remove more algae (per unit of fish biomass) than previously assumed, and that sea urchins, if released from predation, have similar impacts to fishes. Then I focused on algal succession, and found that sea urchins and fishes have different effects that are mediated by their abundances and species composition. Where sea urchins were less abundant and parrotfishes absent (e.g. young fisheries closures), progression of algae from turfs to early and then late successional macroalgae occurred rapidly and within 100 days. I then turned my focus to the removal of already established macroalgae (grown for > 1 yr in the absence of herbivores) and showed that sea urchins and browsing fishes were able to remove significant amounts of macroalgae where either herbivore was abundant. However, using multiple-choice selectivity assays and in situ video recordings, I found that browsing fishes fed very selectively with low overlap in diet among species, leading to low functional redundancy within a high diversity system. Finally, using long-term survey data (from 28 sites) to build a 43-year chronosequence, I showed that it is possible that the effects of herbivory will not be constant across transitions from open fishing to fishery closures through non-linear grazing intensity. Therefore, increases in herbivory within fisheries closures may not be immediate and may allow a window of opportunity for algae to go from turf to unpalatable macroalgae until scraping and browsing fishes fully recover from fishing (~ 20 years). The findings in this thesis are novel and raise concern over the potential implications of the slow recovery of parrotfishes or, given lower than expected functional redundancy in grazing effects, the absence of even one browsing fish species in fisheries closures. Overall, this thesis highlights the importance of herbivore community dynamics in mediating interactions among algae, and provides new insights for conservation and management actions that attempt to bolster the resilience of coral reefs.

The reefs off Broward County exist as three shore-parallel, sequentially deeper terraces named the "inner", "middle", and "outer" reefs and also a shallower, nearshore ridge complex. These structures span the continental coast of southeast Florida from Palm Beach County to southern Miami-Dade County and were characterized as relict, early Holocene shelf-edge and mid-shelf reefs along with limestone ridges. Presently, the reefs are colonized by a fauna characteristic of West Atlantic/Caribbean reef systems. Scleractinian coral cover is low except for a few dense patches of Acropora cervicornis, while Acropora palmata is absent except for a few individual living colonies. Coral reef core-drilling is a useful analytical tool to extract observable and datable geological samples from within reefs. This technique was employed to retrieve 4 cores from the inner reef off Broward County to better understand its age, composition, and Holocene growth history. Sub-samples from corals in cores provided 7 new radiocarbon ages ranging from 7,860-5,560 cal BP, and reef accumulation rates of l.7-2.45 m/1,000 yrs were calculated from these ages. In addition, coral species composition and taphonomic characteristics were analyzed to identify former reef environments/reef zonation, and signals for inner reef termination. Reef zonation was detectable but no clear taphonomic signal for inner reef termination was evident. Current data and radiocarbon ages from all three Broward County reefs suggest that the outer reef accumulated from ~10.6-8 ka cal BP, the middle reef from at least ~5.8-3.7 ka cal BP, and the inner reef from ~7.8-5.5 ka cal BP. A lack of significant age overlaps between the three reefs has led to the assertion that they represent backstepping reefs in response to Holocene sea-level rise. This study has provided the oldest and youngest ages from the inner reef thus far, and confirms that reef backstepping from the outer reef to the inner reef occurred within just a few hundred years after the termination of the outer reef. The middle reef remains poorly understood and thus a definitive Holocene growth history and ultimately an understanding of their formation are still largely unknown.

Carpenter, Argyrozona argyrozona (Valenciennes, 1830), is an endemic South African sparid fish. They form an important component of the commercial linefishery on the South African east coast, where they are the third most important species landed. Recent investigations revealed that the catch per unit effort (cpue) of this species has declined markedly since the early 1900’s. Despite these declines and the importance of this resource, remarkably little biological information on this species exists for providing management advice. This thesis investigates the life history of carpenter, particularly those aspects that are used for management. This includes an investigation into the stock distribution and identification of nursery areas, and an assessment of age, growth, reproduction and movement patterns. Age and growth was assessed using methods based on both otoliths and mark-recapture. Transverse sagittal sections from the Tsitsikamma National Park showed clear opaque and translucent growth increments. Marginal growth zone analysis and mark-recapture of chemically tagged fish (Oxytetracycline) revealed that these were deposited on an annual basis: opaque in summer and translucent in winter. A. argyrozona were found to be long lived (up to 27 years) and slow growing. Within reader (between counts) and between readers average percent error (APE) was 5.3 and 1.8, respectively, showing that readability of carpenter otoliths is high. Comparison between whole and sectioned otoliths showed that the former significantly under-estimated the age of fish older than 10 years (p<0.01). A large proportion (68%) of the individual growth rates derived from mark-recapture data were below those predicted by the otolith based von Bertalanffy growth model (p<0.01). This was attributed to the negative influence of external tags, as hydroids, frequently occurring on the tags of recaptured fish, were observed to cause severe lesions and in some cases, extensive fin damage. This brings into question the use of mark-recapture studies to calculate growth of some species. The effects of sampling design and sample size on age and growth estimation were assessed. The minimum sample size required to accurately estimate growth and mortality, and the effects of using either random or stratified sampling procedures were tested. Decimal and integer ageing both produced similar estimates of von Bertalanffy growth parameters, growth curves, spawner biomass-per-recruit (SB/R) and fishing mortality (F) estimates. Sampling monthly throughout the year and collecting data in a single large sample provided similar growth curves, von Bertalanffy, F and SB/R estimates. The data showed that estimates based on less than 300 random samples were unreliable. However, accurate growth parameter estimates were achievable with less than 200 samples if the sample was stratified with 10 or more samples per 2 cm size class. An investigation into the reproductive biology of A. argyrozona within the Tsitsikamma National Park revealed that they were serial spawning late gonochorists. The size at 50% maturity (L₅₀) was estimated at 292 and 297 mm FL for females and males, respectively. Both monthly gonadosomatic indices and macroscopically determined ovarian stages strongly suggest that A. argyrozona within the Tsitsikamma National Park spawn in the austral summer between November and April. The presence of post-ovulatory follicles (POF's) confirmed the six month spawning season, while monthly proportions of early (0-6 hour old) POF's showed that spawning frequency was highest (once every 1-2 days) from December to March. Although spawning season was more highly correlated to photoperiod (r = 0.859) than temperature (r = -0.161), the daily proportion of spawning fish was strongly correlated (r = 0.93) to ambient temperature over the range 9-22⁰C. Both spawning frequency and season increased with fish length. As a result of the allometric relationship between annual fecundity and fish mass a 3 kg fish was calculated to produce 5 fold more eggs per kilogram of body weight than a fish of 1 kg. In addition to producing more eggs per unit weight each year, larger fish also produce significantly larger eggs. Adult emigration and larval dispersal of A. argyrozona from the Tsitsikamma National Park (TNP), South Africa, were investigated using mark-recapture data and Acoustic Doppler Current Profiler measurements of currents. Tagging data showed that adult carpenter were mainly resident, with a small proportion (7%) leaving the TNP in both easterly and westerly directions. No relationship was found between fish movement patterns and fish size or time-at-liberty. Current patterns suggest that eggs and larvae spawned within the TNP are mainly transported eastwards towards established nursery grounds; the median estimated distance moved was 299 km (range 42-561 km) in 30 days (time to flexion). Given this pattern of ichthyoplankton dispersal together with the fact that adult carpenter within the TNP display a high degree of residency and that they are much more abundant than in adjacent fishing grounds (cpue = 23 times greater), it appears that the TNP protects a viable carpenter spawner population capable of seeding adjacent fishing grounds. Fishery independent biomass surveys and commercial linefish catch returns were used to elucidate the spatial patterns of A. argyrozona distributed along the South African continental shelf. Two distinct areas of abundance were determined, one on the central and the other on the eastern Agulhas Bank. Tagging studies revealed little exchange between them. Two distinct nursery areas were identified. These data suggest that in each area juvenile A. argyrozona settle and move inshore, and then move offshore as they grow. Otolith readability and growth rates varied between regions, with fish from the Eastern Cape having the lowest average percentage error and the slowest growth rates, readability decreased westward. L₅₀ varied between the central and eastern Agulhas Bank as did mass at length. Based on the distribution of carpenter, variability in otolith readability, mass at length, variation in growth and size at maturity, it is concluded that carpenter exist as two separate stocks, one on the central Agulhas Bank and the other on the eastern Agulhas Bank. SB/R, fecundity-per-recruit (Egg/R) and yield-per-recruit (Y/R) models were used to model both South African carpenter stocks. Owing to the allometric relationship between annual fecundity and individual size, Egg/R ratios were between 40 and 74% of SB/R at equivalent F. Egg/R ratios account for allometric increases in fecundity with size/age, and are therefore regarded as more accurate estimates of reproductive potential, and biological reference points for per-recruit analysis should wherever possible be based on this quantum. It is shown that the current length at first capture (lc) (250 mm TL) and F (at M = 0.1) will reduce Egg/R to 6.41% of the pristine value in the Eastern Cape and between 6.06 and 14.15% on the central Agulhas Bank, indicating that both stocks are heavily over exploited. An increase in lc from 250 to 350 mm TL and a 70% reduction in commercial fishing effort is recommended to attain a target reference point of 40% Egg/RF=0. Bag frequency analysis indicates that a reduction in daily bag limit from 10 to 4 fish.person¹.day⁻¹ would effect an equivalent reduction in recreational F. The trawl bycatch of carpenter is only 3% of the reported line catch, consequently restrictions to this fishery are not recommended.

The Vaal Reef placer is situated on the unconformable junction of the Strathmore and Stilfontein formations of the Johannesburg Subgroup. Within the South Division of the Vaal Reefs Exploration and Mining company lease, the Vaal Reef Placer is shown to be composed of several different units. Each unit exhibits its own specific characteristics and trend direction which can be used to establish distinct "Reef packages". These packages can be mapped in such a way as to provide a preliminary lithofacies map for the Vaal Reef Placer. The delineation of such geologically homogenous zones, and the development of a suitable depositional model, can be utilised in several ways. The characteristics of a particular zone are shown to influence the control of stoping width, evaluation of remnant pillars and the geostatistical methodology of evaluating current and future ore reserve blocks.

Borehole radar is a short-range, high-resolution geophysical technique that can be used to delineate the position of the Merensky platinum reef in underground mines situated in the Western Bushveld Complex. In this study, borehole radar is used in reflection mode from four boreholes drilled sub-parallel to the expected position of the Merensky Reef within an underground mining block bounded by two cross-cuts and a haulage. This study relates the stratigraphic column at Amandelbult Section to borehole radar reflectivity. The radar illumination line coordinates produced along the Merensky Reef surface are used to construct a three-dimensional surface of the reef within the defined mining block. The geophysical interpretation presented here shows how a slump in the Merensky Reef, called a pothole, is imaged using borehole radar. This study analyses the increase in geological confidence related to the improved delineation of the elevation of the Merensky Reef. The financial impact of using borehole radar to delineate this pothole is analysed at the various mining steps, namely: orebody definition, mine planning, mine development, ore extraction and ore processing. The information gained by conducting borehole radar is compared with the information acquired using only standard geological drilling. This study concludes that the application of borehole radar significantly increases the confidence in the geological model prior to mining. Conducting borehole radar prior to mining improves mine planning and development, ensures that less waste is mined, facilitates the effective deployment of labour crews, prevents waste being sent to the processing plant and avoids deferring income until a later date. Recommendations are made on how to plan for and include borehole radar in the mining process. / Dissertation (MSc)--University of Pretoria, 2009. / Geology / unrestricted

abstract: A novel underwater, open source, and configurable vehicle that mimics and leverages advances in quad-copter controls and dynamics, called the uDrone, was designed, built and tested. This vehicle was developed to aid coral reef researchers in collecting underwater spectroscopic data for the purpose of monitoring coral reef health. It is designed with an on-board integrated sensor system to support both automated navigation in close proximity to reefs and environmental observation. Additionally, the vehicle can serve as a testbed for future research in the realm of programming for autonomous underwater navigation and data collection, given the open-source simulation and software environment in which it was developed. This thesis presents the motivation for and design components of the new vehicle, a model governing vehicle dynamics, and the results of two proof-of-concept simulation for automated control. / Dissertation/Thesis / Masters Thesis Computer Science 2020

Boat noise has been shown to distract and cause harm to many marine organisms. Most of the study effort has been focused on fish & marine mammals, even though invertebrates represent 99% of all living organisms, both terrestrial and aquatic. The small amount of studies conducted on invertebrates have demonstrated a clear negative correlation between anthropogenic noise pollution and invertebrate well-being. The small giant clam Tridacna maxima and the spider conch Lambis lambis are two invertebrate species which play key roles in coral reef ecosystems, and are little studied for the effects of noise disturbance. If their behaviour is significantly affected by boat noise, this could cause a knock on effect on the rest of the reef ecosystem. T. maxima functions as prey to many fish species, contributing up to 9% of the reef’s calcium carbonate budget, as well as playing a role in nutrient cycling. L. lambis is essential prey for molluscivore snails and certain elasmobranchs, and through its herbivorous feeding, helps to keep filamentous algae levels low. Moreover, coral reefs are reliant on the biological sound primarily created by invertebrates, such as snapping shrimp, to attract larvae from the pelagic environment for settlement. During experiments conducted in February 2020 in the Red Sea, Daily Diary Monitoring (DDMT) smart tags were used to measure the reactions of T. maxima and L. lambis respectively during underwater playback of boat noise compared with ambient reef sound. It was found that both T. maxima and L. lambis exhibited behavioral changes during the boat noise treatment. The implications of this study is that individuals of L. lambis and T. maxima may spend energy averting the invisible "threat" of boat noise, rather than feeding and/or photosynthesizing, in the case of T. maxima. If this hinders the acquisition of food/production, the whole reef ecosystem may be compromised in a knock-on effect from these producers and primary consumers. As boat noise is prevalent on inshore Red Sea reefs, shown by a 24-hour acoustic analysis of a patch reef sound pressure levels (SPL), invertebrates might be affected on a large scale in the Red Sea.

Marine ecosystems are already threatened by the effects of climate change through increases in ocean temperatures and pCO2 levels due to increasing atmospheric CO2. Marine fish living close to their thermal maximum have been shown to be especially vulnerable to temperatures exceeding that threshold, and even relatively small increases in elevated pCO2 levels have led to behavioral impairments with amplified predation risks. These ongoing threats highlight the need for further understanding of how these changes will impact fish and if any potential for adaptation or acclimation exists. The coral reef fish, Acanthochromis polyacanthus, has been well studied in response to singular environmental changes both through its phenotype and molecular expression profiles within and across generations. However, key questions regarding transgenerational heritability and molecular responses to multiple environmental changes have not been addressed. To further understand A. polyacanthus I examined the mechanisms behind heritability of behavioral tolerance to elevated pCO2 in an attempt to determine the maternal and paternal contributions to this phenotype. There was a strong impact of parental phenotype on the expression profiles of their offspring regardless of environmental exposure. Offspring from both parental pairs expressed mechanisms involved in tolerance to ocean acidification suggesting this phenotype is reliant on input from both parents. Creation of a new proteomic resource, a SWATH spectral library, delivered a closer examination of the link between phenotypic and expression changes. Analysis on different constructed libraries led to the use of an organism whole library combined with study specific data to analyze proteomic changes in A. polyacanthus under the combined environmental changes of ocean acidification and warming. With direct comparisons to transcriptomic changes in the same individuals I identified an additive effect of elevated pCO2 and temperature associated with decreases in growth and development. However, a strong role of parental identity on the expression profiles of offspring reinforced the high genetic variability of this species. This thesis provides novel insights into the heritability of phenotypic traits and the molecular responses to combined stressors in A. polyacanthus, as well as presenting a new resource for proteomic studies in this fish and other non-model species.