Coral reefs are arguably the most threatened marine habitat because of multiple anthropogenic stressors degrading the health and resilience of these systems. In the past 20 years there have been increasing observations of mass coral bleaching and mortality associated with increasing water temperatures in the tropics. Reefs provide ecosystem services worth billions of dollars to people living in tropical coastal areas and are the architects of one of the most beautiful structures found on earth. Conserving these habitats is paramount, and conservation planning must contend with climate change along with local and regional stressors. In this thesis Watamu Marine National Park in Kenya is used as a case study of the current challenges facing the conservation of reefs in a warming world. The Western Indian Ocean suffered dramatic bleaching during 1998, which caused the mortality of 70% of Watamu's corals. Using datasets from the 1980s to present the historical trajectory of Watamu's reef community is presented. The current ecosystem resilience is assessed to suggest how this reef will respond to future climate stress. It appears that Watamu's coral community has remained in an altered state post-1998, which, based on its past thermal stress and current coral community, should be resistant to future bleaching. Watamu's resilience and reef health is compared with other locations in the Indian Ocean, including reefs in Kenya and the Maldives that bleached in 1998 and examples from Mozambique and Sumatra of reefs with little evidence of historical thermal stress. Resilience is a multi-faceted process with different major components and numerous interacting factors, which act synergistically on the reef community. Conservation options and opportunities are discussed for the 6 locations examined, using current resilience models and theory as a framework for identifying priority actions. Local and regional-scale human impacts on shallow marine habitats during the last 50 years has been dramatic, and with global-scale climate change as an additional major threat, the next 50 years will be critical for the future of reefs. The locations visited during this study showed encouraging signs of resilience to past thermal stress, with evidence to suggest that corals are acclimatising and/or adapting to increasing water temperatures. The future of reefs in locations like Watamu is uncertain. Better understanding of reef ecology, appropriate conservation techniques and ultimately greater public concern for reefs is required to ensure that there is a future for these ecosystems in the Indian Ocean.

Novel environments and biological communities created by the large-scale deployment of Marine Renewable Energy Devices (MREDs) have the potential to promote the spread of non-native species (NNS). Knowledge of how community composition resident on MREDs is shaped by geography, local hydrodynamics and the duration of deployment, will clarify how these technologies will interact with natural habitats, including the provision of suitable habitat for NNS. A network of navigation buoys was used to study biofouling communities in areas proposed for MRED deployment. Significant differences in community structure were observed in different geographic areas. A significant reduction in number of taxa present and community wet-weight was observed where buoys were deployed in greater tidal flow rates. However, overall community composition was not significantly different between ‘high’ (>1 ms-1) and ‘low’ (<1 ms-1) flow areas and for buoys deployed for different time durations (1-7 years). These finding have important implications for the longevity of devices and their interaction with natural habitats, including proposed ‘artificial reef’ effects. In total five non-native species were identified on the buoys sampled, supporting the need to monitor MREDs as the industry grows. Hydrodynamic and biotic features of the epibenthic communities were used to predict the presence of the most prevalent NNS, the amphipod Caprella mutica, in addition to other native amphipod species. Caprella mutica presence was found to be significantly affected by increasing flow speed compared with the native amphipod Jassa herdmani. Behavioural flume studies investigating flow-related processes governing the presence of non-native amphipods supported these findings. This study details how the hydrodynamic and biological environments created by MREDs determine their suitability for the establishment of self-sustaining populations, and therefore their dispersal potential for NNS. These findings inform design criteria and management options to minimise the biosecurity risk that these structures will pose as the industry expands.

Habitat fragmentation is a fundamental process that determines trends and patterns of distribution and density of organisms. These patterns and trends have been the focus of numerous terrestrial and marine studies and have led to the development of several explanatory hypotheses. Systems and organisms are dynamic and no single hypothesis has adequately accounted for these observed trends. It is therefore important to understand the interaction of these processes and patterns to explain the mechanisms controlling population dynamics. The main aim of this thesis was to test the effect of patch size and isolation on organisms with different modes of dispersal. Mode of dispersal has previously been examined as a factor influencing the effects that habitat fragmentation has on organisms. Very few studies have, however, examined the mode of dispersal of marine organisms because it has long been assumed that marine animals are not directly influenced by habitat fragmentation because of large-scale dispersal. I used two co-occurring species of siphonariid limpets with different modes of dispersal to highlight that not only are marine organisms affected by habitat fragmentation but that they are affected in different ways. The two species of limpet, Siphonaria serrata and Siphonaria concinna, are found within the same habitat and have the same geographic range along the South African coastline, however, they have different modes of dispersal and development. The effect of patch size on organism density has been examined to a great extent with varied results. This study investigated whether habitat patch size played a key role in determining population density and limpet body sizes. The two species are found on the eastern and southern coasts of South Africa were examined across this entire biogeographic range. Patch size was found to have a significant effect on population density of the pelagic developer, S. concinna, but not the direct developing S. serrata. Patch size did play a role in determining limpet body size for both species. S. concinna body size was proposed to be effected directly by patch size whilst S. serrata body size was proposed to be affected indirectly by the effects of the S. concinna densities. The same patterns and trends were observed at five of the seven examined regions across the biogeographic range. The trends observed for S. concinna with respect to patch size conform to the source-sink hypothesis with large habitat patches acting as the source populations whilst the small habitat patches acted as the sink populations. Many previous studies have focused on the effects of habitat patch size at one point in time or over one season. I tested the influence of habitat patch size on the two species of limpets over a period of twelve months to determine whether the trends observed were consistent over time or whether populations varied with time. S. concinna showed a consistently significant difference between small and large patches; whilst S. serrata did not follow a consistent pattern. The mode of dispersal for the two limpets was used to explain the different trends shown by the two species. This examination allowed for the determining of source and sink populations for S. concinna through the examination of fluctuations in limpet body sizes and population densities at small and large habitat patches over twelve months. The direct developing S. serrata trends could not be explained using source-sink theory, as populations were independent from one another. S. serrata demonstrated body size differences at small and large patches which, may be explained by interspecific and intraspecific competition. Habitat isolation is known to play an important role in determining the structure of assemblages and the densities of populations. In this study the population density of the pelagic developing S. concinna showed a weak influence of degree of isolation whilst that of the direct developing S. serrata did not, which may be because of habitat patches along the South African coastline not having great enough degrees of isolation. The population size-structure was influenced directly influenced by isolation for S. concinna, whilst the different population size structure for S. serrata may be explained by assemblage co-dependence. The mode of dispersal showed effects on the relationship of population density and population size-structure with habitat size and isolation. This study indicates the importance of investigating patterns and processes across a range of spatial and temporal scales to gain a comprehensive understanding of factors effecting intertidal organisms.

Orientador: Fosca Pedini Pereira Leite / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-09T22:39:00Z (GMT). No. of bitstreams: 1 Siqueira_SilvanaGomesLeite_M.pdf: 3457727 bytes, checksum: 6c473d589145fe72fa976a3a068adb64 (MD5) Previous issue date: 2007 / Resumo: Este estudo teve como objetivo caracterizar a biologia populacional e a fecundidade do gamarídeo Leucothoe sp. associado à ascídia Phallusia nigra no Canal de São Sebastião, Litoral Norte do Estado de São Paulo. A estrutura populacional, crescimento, razão sexual, fecundidade, dimorfismo sexual e mortalidade deste anfípode foram observadas bimestralmente em oito costões do infralitoral e relacionados com a temperatura da água e a biomassa das ascídias. Em cada período e local foram coletadas três ascídias. Indivíduos de todos os estágios de desenvolvimento de Leucothoe sp. foram encontrados associados a P. nigra, caracterizando o ambiente como estável e propício para a sua reprodução e alimentação. A associação não variou no período de estudo, não foi influenciada pela biomassa da ascídia e nem pela temperatura da água. A maior parte da população de Leucothoe sp. foi composta de jovens. O menor número de indivíduos adultos pode estar relacionado a fatores como mortalidade e à busca dos jovens por novos hospedeiros. Os dados referentes à estrutura de tamanho e crescimento indicam que Leucothoe sp. pode viver entre 7,2 e 11 meses caracterizando um ciclo de vida semi-anual. A razão sexual de Leucothoe sp. foi desviada a favor das fêmeas, fato provavelmente relacionado com migração e mortalidade diferencial dos machos. A reprodução de Leucothoe sp. é contínua e a fecundidade está positivamente relacionada com o tamanho do corpo, como é freqüente entre os gamarídeos. Machos e fêmeas de Leucothoe sp. apresentam diferenças morfológicas nos segundos gnatópodo indicando a presença de dimorfismo sexual / Abstract: The aim of this study was to characterize the population biology and the fecundity of the gammaridean amphipod Leucothoe sp. associated to the ascidia Phallusia nigra on the Channel of São Sebastião, situated in the north coast of Estado de São Paulo, analyzing aspects such as population structure, growth, sex-ratio, fecundity, sexual dimorphism and mortality of this amphipod. Every two months, three ascidians had been collected in the sub littoral of eight rocky coasts of the Channel. The results were related with the temperature of the water and the biomass of the ascidian. Individuals of all development stages of Leucothoe sp. had been found associated with the P. nigra, characterizing this host as a steady and propitious environment for its reproduction and feeding. The association did not vary with the study period and wasn¿t influenced by the biomass of the ascidians or by the water temperature. Most of the population of Leucothoe sp. inside P. nigra was composed by juveniles. The reduced number of adults can be related to the increase of mortality and to the exit of the juveniles for searching new hosts. The data related to the population, size structure and growth indicate that Leucothoe sp. can live from 7.2 to 11 months characterizing an semi-annual life cycle. The sex-ratio of Leucothoe sp. was deviated in favor of the females, fact probably related with migration and differential mortality of the males. The reproduction of Leucothoe sp. is continuous and the fecundity is positively related with body size, an usual pattern for gammarideans. Males and females of Leucothoe sp. present sexual dimorphism with morphologic differences in the second gnathopods / Mestrado / Mestre em Ecologia

Ocean acidification is a phenomenon associated with global change and anthropogenic CO2 emissions that is changing the chemistry of seawater. These changes result in elevated pCO2 and reduced pH in seawater and this is impacting marine organisms in various ways. Marine fishes are considered generally tolerant to conditions of ocean acidification; however, these assumptions are based on juvenile and adult fish tolerance and the larval stages have not been frequently assessed. Furthermore, it has been suggested that temperate species, particularly those with an estuarine association, may be tolerant to variable CO2 and pH. This study used an eco-physiological approach to understand how the early life stages of Argyrosomus japonicus, an estuarine dependent marine fisheries species found in warm-temperate regions, may be impacted by ocean acidification. The metabolic response of early stage larvae (hatching to early juvenile stage) was assessed under conditions of elevated pCO2 and reduced pH in a controlled laboratory setting. Small volume static respirometry was used to determine the oxygen consumption rate of larvae raised in three pCO2 treatments including a low (pCO2 = 327.50 ± 80.07 µatm at pH 8.15), moderate (pCO2 477.40 ± 59.46 µatm at pH 8.03) and high treatment (PCO2 910.20 ± 136.45 µatm at pH 7.78). These treatment levels were relevant to the present (low) and projected conditions of ocean acidification for the years 2050 (moderate) and 2100 (high). Prior to experimentation with ocean acidification treatments, baseline metabolic rates and diurnal variation in oxygen consumption rates in early stage A. japonicus was determined. Distinct ontogenetic structuring of metabolic rates was observed in early stage A. japonicus, with no cyclical fluctuations in metabolic rate occurring during the 24 hour photoperiodic cycle. Pre-flexion larvae showed no metabolic response to ocean acidification treatments; however post-flexion stage larvae showed metabolic depression of standard metabolic rate in the moderate (32.5%) and high (9.5%) pCO2 treatments (P = 0.02). Larvae raised in the high pCO2 treatment also showed high levels of mortality with no individuals surviving past the post-flexion stage. Larvae raised in the moderate pCO2 treatment were unaffected. This study concluded that ocean acidification conditions expected for the end of the century will have significant impacts on the metabolism of early stage A. japonicus, which may result in reduced growth, retardation of skeletal development and ultimately survival as a result of increased mortality. Furthermore, the timing of reduced metabolic scope will significantly impact the recruitment ability of A. japonicus larvae into estuarine habitats. This could ultimately impact the sustainability of A. japonicus populations. Most importantly, this study highlighted the need to consider the combined effect of ontogeny and life-history strategy when assessing the vulnerability of species to ocean acidification.

The aim of this study was to investigate various aspects of the life history of white sharks Carcharodon carcharias at Dyer Island, South Africa, between August 1999 and January 2001. Inter-specific predatory interactions between the white shark and various potential prey species such as the Cape fur seal (Arctocephalus pusillus pusillus), African penguin (Spheniscus demersus), Cape cormorant (Phalacrocorax capensis), bank cormorant (P. neglectus), crown cormorant (P. coronatus) and white-breasted cormorant. (P. carbo) were observed. White sharks were attracted daily to a research vessel positioned at various anchorages in the vicinity of Dyer Island. Spatial and temporal abundance, and population composition of white sharks were recorded throughout the year and revealed seasonal trends in habitat utilisation. White sharks occupied inshore waters, away from the Geyser Rock seal colony in the summer. Sharks became abundant in the near vicinity of Geyser Rock in the winter period. The summer inshore population was characterised by the increased total length of sharks and the exclusive presence of female sharks. Prey resembling decoys were used to investigate trends in the 'predatory motivation' of white sharks in relation to various independent variables. White sharks displayed greatest predatory motivation in close proximity to a seal colony, in overcast conditions, and when water clarity was low. White sharks evidently elevate their motivation to hunt large prey, which are difficult to catch, in situations where the likelihood of encountering valued prey and completing a successful attack is greatest. Ontogenetic difference in predatory motivation towards the decoys existed, with sharks above 325 cm TL displaying greater predatory motivation than smaller sharks. Various choice tests were conducted to determine the visual discriminatory ability and prey preference of white sharks at Dyer Island. The results suggested that white sharks preferred a biologically familiar shape (pinniped) over an inanimate shape (rectangle), smaller (75 mm TL pinniped) over larger (1800 mm TL pinniped) prey, and a pinniped decoy over a penguin decoy of similar size. Selectivity in larger white sharks (>375 cm TL) was most noticeable in the prey shape (pinniped vs. rectangle) experiment, which suggests they may readily utilise a speculative hunting strategy based on rough similarities between detected potential prey and recognised prey. In this situation mistaken identification of prey is more possible. Smaller white sharks (a majority of the sample) displayed most selectivity in the prey size experiment, with strong preference for the smaller seal decoy over the large one. This pattern indicates that prey size may be a partial limiting factor in the feeding of smaller white sharks. Negative impacts (such as conditioning or distraction) of cage-diving on white sharks were assessed by the measurement of white shark contact time and visit time in relation to the chumming vessel. These results revealed that smaller sharks had longest visit times, and that sharks in the vicinity of Geyser Rock displayed visitation patterns indicative of hunting sharks. Particular vigilance should be kept by operators not to allow small sharks to take bait (reward). The channel area appears to be an important hunting ground and white shark cage-diving should perhaps be restricted in this area. White sharks also showed greater activity around the chumming vessel on cloudy days and operators must be particularly vigilant to deny sharks any rewards (bait) under these conditions. Both the white sharks and Cape fur seals predate and/or attack seabirds and predatory interactions were quantified and qualified by the routine collection and inspection of seabird carcasses and injured birds, as well as opportunistic observations of live attacks throughout this study. White sharks are infrequent predators of seabirds in this ecosystem, perhaps due to an abundance of Cape fur seals (a preferred prey), anti¬predator behaviour by penguins, and seabirds not being a sought after prey type. Cape fur seals were a more conspicuous seabird predator, annually attacking a significant percentage of the adult penguin (1.99-2.52%), white-breasted cormorant (5.21-5.72%), and crowned cormorant (3.13%) populations. A minimum estimate of 1.09% of the fledgling Cape cormorant population also succumbed to Cape fur seal predation. / Dissertation (MSc(Zoology))--University of Pretoria, 2006. / Zoology and Entomology / unrestricted

Studying the diet of marine top predators is important for understanding the trophic ecology of the predators but also the distribution, abundance and seasonal variation of prey species. Dietary studies on subantarctic fur seals (Arctocephalus tropicalis) and Antarctic fur seals (A. gazella) is important for assessing their role as predators in the Southern Ocean. Seven hundred and sixty four scats were collected from an A. tropicalis colony at Cape Davis while 659 scats were collected from an A. gazella colony at Watertunnel stream from April 2006 to March 2010. Hard remains such as fish otoliths and cephalopod beaks were used for identification and quantification of prey. A. tropicalis diet comprised of three animal groups (fish, cephalopod and crustaceans) while A. gazella diet was made up of four animal groups (fish, cephalopods, crustaceans and seabirds). Fish contributed substantially more than other prey items in the diet of both fur seal species over the study period. Both species fed predominantly on fish of the family Myctophidae which constituted a numerical abundance of 98.9 percent in scats for both species combined. A. tropicalis fed on fish prey species from eight families, namely: Myctophidae, Notosudidae, Paralepididae, Nototheniidae, Bathylagidae, Chlorophthalmidae, Sternoptychidae and Photichthyidae while A. gazella fed on fish from six of these families, with Chlorophthalmidae and Photichthyidae not represented in its diet. Cephalopods and crustaceans were found in low numbers in the diet of both seal species and seabird remains were only found in the diet of A. gazella. Numerically, the most dominant species were from the genus Gymnoscopelus followed by Protomyctophum and then Electrona. In the diet of A. tropicalis, Gymnoscopelus contributed 66 percent, Protomyctophum 18 percent and Electrona 5.9 percent while in the diet of A. gazella Gymnoscopelus, Protomyctophum and Electrona contributed 59.43 percent, 20.24 percent and 14.24 percent respectively. Gymnoscopelus species comprised G. piabilis, G. bolini, G. braueri, G. fraseri, and G. nicholsi; Protomyctophum comprised Protomyctophum bolini, P. choriodon and P. tenisoni while Electrona comprised Electrona antarctica, E. carlsbergi and E. subaspera. Gymnoscopelus piabilis was the most dominant species from this genus while Electrona carlsbergi and Protomyctophum tenisoni dominated the genus Electrona and Protomyctophum respectively. The total number of fish species utilised by A. tropicalis was twenty four while twenty three fish species were identified in A. gazella diet. Bathysauropsis gracilis only featured in the diet of A. tropicalis while Lampanyctus ater and Lepidonotothen larseni were only found in the diet of A. gazella. To compare the diet of the seal species between seasons, a year was divided into three seasons, early summer, late summer and winter. Their diet was also compared between years from 2006 to 2010. Myctophid fish species showed substantial seasonal and annual fluctuations in the diet of the two fur seal species. E. carlsbergi, G. nicholsi and G. piabilis increased in numerical abundance in winter while Melectrona ventralis increased in late summer. The numerical abundance of G. fraseri and P. tenisoni increased in early summer. Generally, the two fur seal species fed on the same prey species. However, there was a significant difference when the diet of both fur seals was compared seasonally. There was no significant difference when the diet of A. gazella was compared annually, although such a difference was apparent for A. tropicalis.

Primary production was studied in Fram Sound, part of the Hell Gate-Cardigan Strait polynya, from June to August, 1982. Primary production rates, phytoplankton biomass (chlorophyll α), and water transparency were measured and used in conjunction with modelled solar radiation values to numerically model primary production during this time. The major phytoplankton nutrients were also measured. Early season chlorophyll α concentrations were low, and the increased light availability due to reduced ice cover in this area did not appear to enhance early season production. Chlorophyll concentrations peaked twice; the first peak occured on 20 July and the second on 14 August. The mean primary production rate and phytoplankton biomass were 998 mg C.m⁻² .d⁻¹ and 72 mg chl.m⁻² . This production rate is higher than that measured in other High Arctic areas. Nitrogen, phosphorus and silica were essentially homogeneously distributed during the sampling period and these concentrations varied little from June to August except during 5 days in late August, when they decreased by half then returned to previous levels. / Applied Science, Faculty of / Civil Engineering, Department of / Graduate

This study examines seasonal changes in the relationship between a test organism and changes in the hydrographic and chemical properties of Indian Arm, a coastal fjord. There is a close relationship between changes in the hydrographic properties of the water and changes in the metal complexing ability of water in the inlet, as determined with the test organism. The relationship between the organism and the availability of metals changes with time; the complexing ability of natural water increases at the time of the major intrusion of water from the Strait of Georgia into Indian Arm, and then decreases. The addition of a variety of metals under experimental conditions affects the relationship between the organism and the complexing ability of the water. Additional studies examine the effect of material extracted from sediment samples on the toxic effect of copper enrichment. The ability of the extracted material to reduce the toxic effect changes and is related to the seasonal productivity in the surface waters of the inlet. / Science, Faculty of / Zoology, Department of / Graduate

M.Sc. / Richards Bay Harbour is notably one of the fastest growing, economically important harbours in South Africa. However, this economic growth has lead to increased anthropogenic activities surrounding the harbour, which may result in higher contaminant, including metal, concentrations within the harbour. These contaminants may negatively influence the natural ecosystem functioning within the harbour. Consequently, assessment of the extent and effect of contamination, through continuous biomonitoring of Richards Bay Harbour, is essential. In the present study, the main aim was to assess the marine health in Richards Bay Harbour by studying spatial and temporal variation of bioaccumulation and biological responses within the mussel, Perna perna, using an active biomonitoring (ABM) approach. The ABM approach was preferred over the traditional passive biomonitoring of resident mussels since it eliminates several inherent factors that may mask the mussels’ true responses to the ambient environment. This approach entailed the transplantation of reference mussels from a relatively uncontaminated environment into Richards Bay Harbour, which is known to be contaminated by metals. In order to identify the reference mussel population for transplantation purposes, a study was undertaken to assess metal levels in two other P. perna populations within the same ecoregion as Richards Bay Harbour, namely Dawson’s Rocks and Sheffield Beach. The results showed that most metal concentrations were lower at Sheffield Beach, which consequently lead to the selection of this population as a reference. The effect of size differences on metal bioaccumulation was also assessed using the three latter mentioned mussel populations, which showed that, although local conditions strongly influence the relationship between metal bioaccumulation and size, utilisation of a narrow size range would minimise the size effect on bioaccumulation and should be used for ABM studies. / Prof. V. Wepener