Dusky kob Argyrosomus japonicus is a wide-ranging estuarine-dependent Sciaenid and an important fishery species throughout most of its distribution. It is one of South Africa’s most valuable coastal fishery species. High levels of juvenile exploitation in estuaries and ineffective management regulations have led to stock collapse, highlighting the need to better understand the spatial and temporal aspects of estuarine-dependency and multiple habitat use. Habitat connectivity is a critical property of estuarine-associated fishes and it therefore follows that knowledge of this link is fundamental in understanding population dynamics and the nursery role of estuarine and/or marine habitats. While dusky kob occur in both estuaries and nearshore coastal zones, limited information on connectivity among these habitats exists. The aim of this study is to assess the role of estuarine nursery habitats in the life cycle of the dusky kob by examining multiple habitat connectivity and determining the drivers associated with estuarine use. A total of 96 dusky kob (237–1280 mm total length) were tagged with acoustic transmitters in both the estuarine and marine environments of Algoa Bay, Eastern Cape, South Africa between May 2008 and September 2010. Their movements were monitored using a network of automated data-logging acoustic receivers deployed in the Sundays Estuary, seven neighbouring estuarine habitats, two commercial harbours and various sites within Algoa Bay. And more...

Recruitment of planktonic larvae into sedentary benthic populations regulates the population dynamics of marine invertebrates. The processes controlling recruitment, however, are poorly understood, and recruitment remains largely unpredictable, which complicates management of exploited shellfish resources. The mussels Perna perna, Choromytilus meridionalis and Mytilus galloprovincialis, found on the south coast of southern Africa, have planktonic larvae and sedentary adult stages. This thesis examines dispersal, settlement and early post-settlement growth and mortality, and their effect on recruitment and demography of intertidal mussel populations in the region of Algoa Bay on the south coast of southern Africa. Temporal and spatial variation in the body mass, density and size structure of mussels, the distribution of bivalve larvae on plankton grids in the nearshore zone and the distribution of a recently introduced invasive mussel, Mytilus galloprovincialis, were examined between 1989 and 1992. Furthermore, data on hourly or daily changes in wind strength and direction, air and sea surface temperatures and low and high tide levels in the study region, were obtained. There were 3-4 peaks in spawning (characterised by an abrupt decline in weight) and settlement activity annually. These peaks varied in exact timing, intensity and duration between sites and over time. However, at a site, spawning was followed by settlement 4-8 weeks later, and there was a significant (P < 0.05) direct correlation between spawning intensity prior to the appearance of a new cohort and the cohort density (settlement intensity). The stochastic spatial and temporal variation in breeding activity was superimposed on a more general pattern of a higher intensity of spawning and settlement in Algoa Bay than on the open coast, and a higher settlement intensity on coastal sandstone shores than on dune rock shores. Spawning was more frequent in winter and spring, and the probability of spawning and settlement peaked around the spring and autumn equinox, if temperature and wind conditions were suitable. Larval behaviour had little effect on their dispersal in the well-mixed nearshore region. Larvae were passively dispersed by currents, and their dispersal range and direction depended on prevailing winds and local topography. The sharp decline in density of recruit and adult M. galloprovincialis with increasing distance from the point of introduction, showed that some larvae were carried by wind generated currents over moderately long distances (-100 km). However, since most (76 %) M. galloprovincialis recruited within 4 km of the parent population, it is possible that larvae become trapped in small gullies and crevices around rocky shores, and have a limited dispersal range. This could explain the link between local patterns of spawning and settlement. The distribution and abundance of settlers on the shore was influenced by larval behaviour and the availability of settlement, substrata. Larvae preferred to settle primarily on foliose coralline algae and migrate to the adult mussel bed when they were larger (0.60-7 mm), but larvae also settled directly on adult mussels, possibly because the amount of coralline algae was limited. Both direct and secondary settlement were considered to be important in maintaining mussel populations since the rate of settlement was low(generally < 60 000.m-2). Cohort analyses showed that prior to maturity post-settlement growth (- 30 mm in 10 months) and mortality rates (60-100%) were high, but varied. When settlement intensity was low this variability uncoupled the relationship between spawning and recruitment intensity. Multiple regression analysis showed that together reproductive effort (gamete output), settlement intensity, growth and mortality prior to maturity, accounted for 76 % of the variance in recruitment into mature adult populations. The low settlement rate coupled with the short life span of mussels « 3 years), meant that populations underwent marked spatial and temporal variations in structure and abundance as settlement intensity varied, but there were consistent general differences between mussel populations on dune rock and sandstone shores in Algoa Bay and on the open coast. It was concluded from these results that, spawning intensity and post-settlement growth and mortality, rather than dispersal, regulated recruitment and the structure and abundance of intertidal P. perna and C. meridionalis populations along the south coast of southern Africa. On the basis of these results it is recommended that species with limited dispersal, variable recruitment and high natural mortality, such as P. perna, should be conserved by protecting a small part of the population in reserves, and controlling utilisation outside reserves to minimize disturbance to local brood stocks. Furthermore, since the potential for reseeding adjacent exploited areas is limited, several small reserves placed at regular intervals along the coast would be more effective than a single large reserve.

Algoa Bay Latrunculid sponges are well known for their production of cytotoxic pyrroloiminoquinones with speculation that these secondary metabolites may have a microbial origin. This study describes a thorough investigation into the bacterial community associated with Tsitsikamma favus, Tsitsikamma scurra a newly described Latrunculia sp. and a yellow encrusting sponge associated with T. scurra. Molecular and chemical characterisation were used in conjunction with traditional taxonomy in identification of the sponge specimens. The 28S rRNA and COX1 analysis confirmed the traditional taxonomy with T. favus and T. scurra being very closely related. Chemical analysis revealed that T. favus and T. scurra shared the discorhabdins 2,4-debromo-3-dihydrodiscorhabdin C, 7,8-dehydro-3-dihydrodiscorhabdin C and 14-bromo-1-hydroxy-discorhabdin V in common with each other and Tsitsikamma pedunculata indicating that these pyrroloiminoquinones are common to Tsitsikamma sponges in general. The bacterial community associated with T. favus was explored using 16S rRNA molecular techniques including DGGE, clonal libraries of full length 16S rRNA genes, as well as 454 pyrosequencing. DGGE analysis revealed that the bacterial community associated with T. favus appeared to be highly conserved, which was confirmed by both the clone library and 454 pyrosequencing, with the Betaproteobacteria as the most dominant class. Further exploration into T. favus, as well as T. scurra, Latrunculia sp. and the yellow encrusting sponge indicated that the bacterial populations associated with each of these sponge species were conserved and species specific. OTU analysis to the species level revealed that T. favus and T. scurra shared an abundant Spirochaete species in common while the most abundant species in the Latrunculia sp. and the yellow encrusting sponge belonged to the class Betaproteobacteria. The exclusivity of the tsitsikammamines to T. favus precipitated attempts to culture the T. favus associated bacteria, with a focus on the dominant betaproteobacterium as indicated by the 16S rRNA clone library. Actinobacteria associated with the Algoa Bay sponge specimens were also cultured and the actinobacterial isolates were sent for screening against Mycobacterium aurum with two Kocuria kristinae isolates and a Streptomyces albdioflavus isolate showing good antimycobacterial activity.

The site fidelity of humpback and southern right whales in Algoa Bay was investigated as a baseline study to examine the importance of this area for the future conservation of these species. An absence of whales since the 1980’s from Algoa Bay and more frequent sightings of southern right and humpback whales during a survey conducted between 2008 and 2011 in Algoa Bay led to the present photo-identification study. Data were collected from boat-based surveys along the coastline in 2015 and 2016 and data from a previous boat-based study during 2008-2011 assessing the occurrence of all cetaceans in Algoa Bay were added. A cumulative number of 96 individual southern right whales and 184 individual humpback whales were identified from callosity patterns and dorsal fins, respectively, over this period in Algoa Bay. A low resighting rate for both species was observed within (6.25 for southern right whales & 6.98% for humpback whales) and between years (1.04% for southern right whales & 9.24% for humpback whales) with mainly individual adult humpback whales being resighted. In contrast, all southern right whale resightings were confirmed to be mother-calf pair individuals. The timing of monthly sightings and resightings of mother-calf pair individuals in the bay may suggest that this area may serve as a fairly new nursery area for southern right whales and as a possible migratory corridor for humpback whales during their migrations to and from their breeding grounds. The sighting distribution within the bay suggest that mother-calf pairs are located closer inshore and further away from the shipping activities on the eastern side of the bay in the proximity of two operational ports. This forms an important baseline for future monitoring to assess the effect of increased shipping activity in the bay on the breeding behaviour of the whales. The site fidelity of humpback and southern right whales in Algoa Bay was investigated as a baseline study to examine the importance of this area for the future conservation of these species. An absence of whales since the 1980’s from Algoa Bay and more frequent sightings of southern right and humpback whales during a survey conducted between 2008 and 2011 in Algoa Bay led to the present photo-identification study. Data were collected from boat-based surveys along the coastline in 2015 and 2016 and data from a previous boat-based study during 2008-2011 assessing the occurrence of all cetaceans in Algoa Bay were added. A cumulative number of 96 individual southern right whales and 184 individual humpback whales were identified from callosity patterns and dorsal fins, respectively, over this period in Algoa Bay. A low resighting rate for both species was observed within (6.25 for southern right whales & 6.98% for humpback whales) and between years (1.04% for southern right whales & 9.24% for humpback whales) with mainly individual adult humpback whales being resighted. In contrast, all southern right whale resightings were confirmed to be mother-calf pair individuals. The timing of monthly sightings and resightings of mother-calf pair individuals in the bay may suggest that this area may serve as a fairly new nursery area for southern right whales and as a possible migratory corridor for humpback whales during their migrations to and from their breeding grounds. The sighting distribution within the bay suggest that mother-calf pairs are located closer inshore and further away from the shipping activities on the eastern side of the bay in the proximity of two operational ports. This forms an important baseline for future monitoring to assess the effect of increased shipping activity in the bay on the breeding behaviour of the whales.

Huge populations of sardine and anchovy exist in the four major upwelling systems around the world. These fish are both important ecologically and economically. Pelagic fish dominate the mid trophic level and can exert both a top-down control of zooplankton and a bottom-up control on predatory fish and marine top predators. They also make up a substantial contribution of the world catches in seas around the world where they co-exist in upwelling areas. The fluctuations of sardine and anchovy are largely influenced by recruitment from the larval stage and by the physical environmental forces that determine the planktonic compositions upon which they feed. In southern Africa, the biology and behaviour of two threatened seabird species, African penguins (Spheniscus demersus) and Cape gannets (Morus capensis), are directly influenced by the availability of sardine (Sardinops sagax) and anchovy (Engraulis encrasicolus). This study aimed to provide further insight into the fluctuations of sardine and anchovy in relation to the variability of environmental factors such as wind, sea surface temperature, rainfall and plankton abundance, focusing specifically on Algoa Bay in the Eastern Cape, South Africa. Algoa Bay is particularly important as it is home to the world’s largest African penguin colony and the world’s largest gannetry. Therefore, to further investigate the populations of these two seabird species, the fluctuations of their food source were studied.

Cape St Francis, Eastern Cape, has been identified as one of four potential sites for establishing a mainland-based African penguin (Spheniscus demersus) colony. This thesis comprises three main components: a verification of a preparation method for stable isotope samples from penguin feathers; a dietary analysis of the penguins on Bird Island, Algoa Bay, though stable isotope analysis of whole blood and feathers (2012 and 2013); and an estimation of available fish surplus that could potentially support a colony of penguins at Cape St Francis. Each component contributes towards the next, all building towards answering the main research question: Will there be enough food around St Francis Bay to support a colony of penguins and sustain the already established fisheries industry within the bay? Stable isotope analysis of whole blood and feathers from breeding adults and whole blood from juveniles provided insight into the variability of African penguins’ diets at different stages in their life history. Stable isotope mixing models indicated that the predicted proportions that each prey species could potentially contribute to diet conflicted with published stomach sample data. This might arise from inaccurate trophic enrichment factors used in the model, or from systematic biases in the published stomach sampling techniques, or both. Dietary sexual dimorphism was not demonstrated by the isotope signatures of breeding penguins. Based on official catch data, the fisheries activity on the south coast, and especially around the potential colony site at St Francis, is much lower than around the west coast’s penguin colonies. The model provided a first-order estimate for fish supply around the potential colony site at St Francis both at a large coastal scale and a local small scale. At both scales the estimate indicated an ample availability of fish at current fishing levels. The model in Chapter 4 can also be applied to refining the assessments of other potential colony sites on the south coast. In conclusion, the south coast is a promising area for a new colony of penguins in terms of food availability. There is relatively low fishing activity in the area and, as suggested by the large-scale model in Chapter 4, an ample fish resource. The final chapter briefly discusses factors that need to be considered before attempting to establish a mainland-based colony of African penguins.

This thesis investigates the chemistry of 25 ascidian species collected from Algoa Bay, South Africa with a concerted focus on metal accumulation by these ascidians and the possible interaction of these metals with ascidian metabolites. Chapter 2 details the screening techniques employed to establish the presence of nitrogenous metabolites (1H- 15N HMBC), hyper-accumulated metal ions (ICP-MS) and potential metal ion/ ascidian metabolite complexes (LC-ICP-MS/ESI-MS). Unfortunately, exhaustive attempts to detect intact metal ion/ascidian metabolite complexes through the use of liquid chromatography with parallel inductively coupled plasma mass spectrometry/electrospray mass spectrometry (LC-ICPMS/ ESI-MS) were unsuccessful. However, the LC-ICP-MS/ESI-MS data obtained for the crude organic extracts of six of the Algoa Bay ascidian species, Distaplia skoogi, Aplidium monile, Aplidium sp., Didemnum sp., Leptoclindines sp. and Polycitor sp. enabled identification of a number of ten halogenated metabolites, namely the indoles 2.28-2.30, and the tyramine and tyrosine derivatives (2.31-2.33, 2.41, 2.43, 2.44 and 2.46), within the ascidian extracts. This study confirmed that LC-ICP-MS/ESI-MS is a powerful tool for the dereplication of halogenated metabolites in complex mixtures especially where these compounds are present in very small amounts. This study is also the first report of these compounds (eight of which are known) in African ascidians. Compounds 2.32 and 2.46 have not been reported before from a marine source. Compounds 2.28-2.30 and 2.33 were present in sufficient amounts in the respective ascidian extracts to allow their isolation and structure elucidation using standard spectroscopic techniques Chapter 3 explores the ability of ascidians to accumulate a wide range of metal ions at concentrations which are often orders of magnitude higher than those of the surrounding sea water. Inductively coupled plasma mass spectrometry (ICP-MS) was used to determine the total ion concentrations of 24 metals in 25 Algoa Bay ascidian species. To the best of our knowledge this is the largest and most extensive investigation of metal concentrations in a group of different ascidians occurring in the same area. Hypotheisizing that the metal ion concentrations for each ascidian specimen screened may represent a unique fingerprint for each specimen principal component analysis (PCA) was used in an attempt to establish whether there were spatial, temporal or phylogenetic relationships associated with the metal concentration fingerprints of the ascidians that formed part of this study. The PCA results showed that there were no statistically significant relationships between ascidian metal ion concentrations and either the collection year or the collection site of the ascidians. However, species from the family Didemnidae provided the clearest statistical evidence supporting a phylogenetic relationship between these ascidians and their hyperaccumulated metal ion profiles. Furthermore, these results suggested that ascidian species are indeed actively concentrating metal ions from the surrounding sea water and are not simply sinks for passively accumulated metal ions. Interestingly, the concentration of vanadium in the set of ascidians studied did not appear to correlate with any of the other metals accumulated by these ascidians suggesting that there is possibly a unique method employed for the accumulation of vanadium by ascidians. Chapter 4 investigated this possibility further after the nucleosides 4.10, 4.11, 4.13, 4.15, 4.17 and 4.40 were isolated from the vanadium accumulating ascidian Aplidium monile. Studies into the interactions between nucleosides and vanadyl are unfortunately rare and usually qualitative in nature with limited information provided about the stability or structures of the complexes formed. The vanadyl accumulating aplousobranch ascidians e.g. Aplidium monile dominated our study of Algoa Bay ascidians therefore providing us with the rationale to investigate the relatively little studied binding ability and stability of vandyl-nucleoside complexes. Potentiometric studies were conducted to determine the stability constants of complexes formed between the oxovanadium ion vanadyl (VO2+) and the commercially available nucleosides 4.10-4.14. The data afforded by this analysis clearly confirmed the complexity of the vanadyl/nucleoside complexation and suggested that guanosine (4.12) formed the most stable complex with oxovanadium ions. We were also able to establish a third protonation constant for the hydroxyl moiety in 4.12 with a logK 8.87 which has not been previously reported. Finally, Chapter 5 revisited the cytoxicity two Algoa Bay ascidians, Clavelina sp. and Atriolum marinense the extracts from which produced promising bioactivity results in previous studies against oesophageal cancer cells. The HP-20 fractionated extracts of Clavelina sp. and Atriolum marinense proved to be similalrly cytotoxic to breast cancer cells. With the exception for the 100% acetone(aq)fractions the NMR data for both species suggested that most active non polar fractions were dominated by what appeared to be structurally unremarkable fatty acid glycerides and as such were not pursued further. Purification of the 100% acetone(aq)fraction of A. marinense resulted in the isolation of a styrene trimer, 5.1, common to both ascidian extracts. The NMR simulation software WIN-DAISY was employed to confirm the structure of 5.1. Attempts to establish if 5.1 was an isolation artefact or a product of marine pollution were inconclusive

Thesis (MScEng (Civil Engineering))--University of Stellenbosch, 2002. / 198 leaves double sided printed, preliminary pages i-xx and numberd pages 1-1-12-6.Includes bibliography. List of tables, figures and appendices and acronyms. Scanned with a HP Scanjet 8250 Scanner to pdf format (OCR). / ENGLISH ABSTRACT: In this study the numerical short wave model SWAN is evaluated for application to a selected coastal region in South Africa. The aim of this study was to evaluate the degree of accuracy with which SWAN can simulate prototype nearshore wave spectra and wave parameters (e.g. wave height, mean wave direction and mean wave period) for an Algoa Bay field case. Algoa Bay represents a typical deep, sheltered embayment on the South African south coast, which is exposed to high-energy swell. Sensitivity analyses on various wave-related processes were also done, with the aim of establishing the dominant physical processes and appropriate model setup for the Algoa Bay field case. With the dominant wave-related processes and appropriate model setup for the Algoa Bay field case established, selected final runs were performed to determine the degree of accuracy with which SWAN can simulate prototype conditions, by comparing its results with available field recordings. This study comprises a review of the SWAN evaluation work conducted to date by others, an overview of South African coastal conditions, and numerical model simulations. The model simulations, which represent the main focus of this study, were conducted for a selection of available offshore wave conditions (at 85 m water depth) observed during the Algoa Bay field case and were compared to available nearshore observations (at 17 m water depth). Environmental conditions of waves, wind and currents were included in these simulations. The study focuses on model application and sensitivity analysis, rather than model development, and includes evaluation of all relevant processes, without focussing on any specific model aspect. The results of this study show that SWAN simulations correlated well with observations at the nearshore station in Algoa Bay, both in wave spectral shape and its associated parameters. Dominant processes identified for the field case were depth-induced refraction, bottom friction and directional spreading. This finding agrees with those of previous evaluations of SWAN and previous modelling experience by others. It is shown that high-energy swell is relatively more sensitive to the choices of model setup than wind sea. Based on the simulation results of high-energy swell, it is concluded that the calculation of depth-induced refraction in SWAN seem to contain a degree of inaccuracy. It is also concluded that the findings of this study could be used as a guideline to SWAN modelling studies along the South African south coast. / AFRIKAANSE OPSOMMING: In hierdie studie word die toepassingsmoontlikhede van die numeriese kortgolf model SWAN vir 'n geselekteerde gedeelde van die Suid-Afrikaanse kuslyn beoordeel. Die doel van hierdie studie is om die vlak van akkuraatheid waarmee SWAN prototipe golfspektra en golfparameters (bv. golfhoogte, gemiddelde golfrigting en gemiddelde golfperiode) in die vlakwater kan simuleer te beoordeel, vir 'n Algoabaai gevallestudie. Algoabaai verteenwoordig 'n tipiese diep, beskermde baai aan die Suid-Afrikaanse kuslyn, wat blootgestel is aan hoe-energie deining. Sensitiwiteitstoetse is ook uitgevoer vir verskillende golfprosesse, met die doel om die dominante fisiese prosesse en gepaste modelopstelling vir die Algoabaai gevallestudie te vind. Nadat die dominante golfprosesse geidentifiseer is, en die toepaslike modelopstelling gevind is, is finale simulasies uitgevoer vir geselekteerde gevalle om die mate van akkuraatheid te bepaal waarmee SWAN prototipe kondisies kan simuleer, deur simulasie resultate met beskikbare veldmetings te vergelyk. Hierdie studie bestaan uit 'n samevatting van die evaluasiewerk verrig op SWAN deur andere, 'n samevatting van golf-, wind- en stroomtoestande aan die Suid-Afrikaanse kus en numeriese modelsimulasies. Die modelsimulasies, wat die hooffokus van hierdie studie is, is uitgevoer vir 'n seleksie van beskikbare diepsee golftoestande (in 85 m waterdiepte) uit die Algoabaai gevallestudie en is vergelyk met beskikbare vlakwater metings (in 17 m waterdiepte). Omgewingstoestande van golwe, wind en seestrome is ingesluit in hierdie simulasies. Die studie fokus op modeltoepassing en sensitiwiteits-analise, eerder as modelontwikkeling, en behels die beoordeeling van alle toepaslike modelprosesse, sonder om te fokus op enige spesifieke model aspek. Die resultate van hierdie studie toon aan dat die SWAN simulasies goed korrileer met vlakwater meetings in Algoabaai, vir beide golfspektraalvorm en verwante golfparameters. Bodemrefraksie, bodemwrywing en rigtingsspreiding is geidentifiseer as dominante modelprosesse. Hierdie resultaat kom ooreen met bevindings van vroeere beoordeling van SWAN en modelleer-ervaring deur andere. Dit word aangetoon dat hoe-energie deining relatief meer sensitief is vir modelopstelling as wind-see. Gebasseer op resultate van simulasie met hoe-energie deining, word die gevolgtrekking gemaak dat die berekening van bodemrefraksie in SWAN 'n mate van onakkuraatheid toon. Die gevolgtrekking word ook gemaak dat die resultate van hierdie studie as riglyn gebruik kan word vir modelleerwerk met SWAN aan die Suid-Afrikaanse suidkus.

[For the Abstract, please see the PDF files below, namely "front.pdf"] CONTENTS. Chapter 1 Introduction. Chapter 2 Gross and microscopic visceral anatomy of the male Cape fur seal with reference to organ size and growth. Chapter 3 Age determination and growth in the male Cape fur seal: part one, external body. Chapter 4 Age determination and growth in the male Cape fur seal: part two, skull. Chapter 5 Age determination and growth in the male Cape fur seal: part three, baculum. Chapter 6 Suture age as an indicator of physiological age in the male Cape fur seal. Chapter 7 Sexual dimorphism in the adult Cape fur seal: standard body length and skull morphology. Chapter 8 Reproduction in the male Cape fur seal: age at puberty and annual cycle of the testis. Chapter 9 Diet and foraging behaviour of the Cape fur seal. Chapter 10(a) The Impact of the fur seal industry on the distribution and abundance of Cape fur seals. Chapter 10(b) South African Airforce wildlife rescue: Cape fur seal pups washed from Black Rocks, Algoa Bay, during heavy seas, December 1976. Chapter 11(a) Operational interactions between Cape fur seals and fisheries: part one, trawl fishing. Chapter 11(b) Operational interactions between Cape fur seals and fisheries: part two, squid jigging and line fishing. Chapter 11(c) Operational interactions between Cape fur seals and fisheries: part three, entanglement in man-made debris. Chapter 12 Concentrations of heavy metals (Cd, Cu, Pb, Ni & Zn) and organochlorine contaminants (PCBs, DDT, DDE & DDD) in the blubber of Cape fur seals. Chapter 13 Endoparasites of the Cape fur seal. Chapter 14(a) Preliminary investigations of shark predation on Cape fur seals. Chapter 14(b) Aggressive behaviour of an adult male Cape fur seal towards a great white shark Carcharodon carcharias. Chapter 15 Conclusions and future directions.