Includes bibliographical references (leaves 27-32). / The accuracy of using CUFES (continuous underway fish egg sampler) as an alternative method to vertical bongo nets for sampling zooplankton abundance and distribution is assessed. Analysis is based on 14 taxonomic groups representing a wide variety of organism sizes. Samples were collected in March 2004 in the southern Benguela, South Africa. In total, 64 CUFES samples were collected while the ship was underway and 32 CUFES and vertical bongo net on-station samples were collected along four inshore-offshore transects. The frequencies of obtaining the taxa using the CUFES and vertical bongo net samples were the same for small copepods, amphipod adults and juveniles, and Nannocalanus.

Southern Africa is home to highly diverse marine environments along its coasts. The main reason for the contrasting environments is the two major boundary currents, the Benguela and Agulhas currents, and their interaction around the tip of South Africa. Algal blooms are known to proliferate predominantly off the nutrient - rich west coast, however, sporadic inshore upwelling on the east coast can also illicit these events. In addition, solar salt - pans located on the coast that draw their water from the bay area are affected by bloom events. Algal viruses play a key role in regulating phytoplankton communities and modulate the dynamics of these bloom events. Identifying the viruses associated with algal blooms is the first step in determining the role they play in the bloom dynamics. Here I chose to focus on phycodnaviruses, known agents of bloom termination. Samples were taken from two specific algal blooms that occurred in 2013 in different bioregions namely Elands Bay (west coast) and Algoa Bay (east coast). Additionally the Cerebos solar salt pans located along the west coast were selected as sample sites to investigate viral composition. DNA polymerase (pol) gene fragments were amplified from environmental samples using algal - virus specific PCR primers AVS1 and POL. Amplified fragments were then sequenced. Viral sequences were identified and mapped to existing virus families. Amplicon specific primers were designed for select dominant virus group identified for both bloom events. These were used to screen across all samples to determine viral prevalence. Phylogenetic analysis of viral sequences revealed new clades of Phycodnaviridae in the Elands Bay and Algoa Bay regions. A bloom terminating virus, EB1, is proposed for the Elands Bay bloom event. The Cerebos salt pans showed the greatest diversity of all samples analysed and novel halophilic algal viruses were identified in regions with the highest salinity.

Mark-recapture is used to investigate the abundance, survival and social relationships and even individual-specific habitat use of a number of species. Several studies suggest that individually distinctive acoustic signals could be used in a mark-recapture framework. We investigated the potential of using individually distinctive signature whistles of bottlenose dolphins, Tursiops truncatus. Acoustic and photo identification data were collected simultaneously from a small population of common bottlenose dolphins in Walvis Bay, Namibia, between 2009 and 2015. Visual classification and bout analysis was used to identify signature whistle types. Photos were graded for quality and fins for distinctiveness and matched to a pre-existing catalogue of individuals. Whistle data was graded on signal to noise ratio. Abundance was calculated for both signature whistles and photographic data for the years 2011, 2012 and 2015 separately using Huggins closed models. Since not all animals were used in the photographic mark-recapture and the signature whistles of all animals were not recorded in all encounters, it was necessary to extrapolate mark-recapture estimates up to total population size. Two methods of calculating theta (the proportion detected or 'marked') for acoustic data were investigated, one calculated from the field group size and another based solely on acoustic data. An attempt to match individuals with their signature whistle type was also conducted through a process of encounter matrices and elimination. Assuming that photographic mark-recapture data provides the most accurate measure of population size (2011=65, 2012=82, 2015=83 animals estimated), the acoustic abundance estimate extrapolated using a theta calculated from field group size overestimated the population (2011=131, 2012=243, 2015=133), while the acoustic abundance extrapolated using solely acoustic data gave an underestimation (2011=44, 2012=63, 2015=78). Differences between the acoustic estimates and photo identification estimates were between a 25% decrease and 121% increase. Seventeen signature whistle types were used in the matching process, 3 out of which were confidently matched with individuals and a further 3 were matched through the process of elimination. Overall, this study shows that acoustic abundance estimates using signature whistle data has the potential to provide a conservative estimate of abundance compared to photographic methods. However, estimates were effected by how theta was estimated and further studies to better estimate theta are required to improve abundance estimates from signature whistle data.

Includes bibliographical references. / The aims of this study were to observe changes in ectoparasite abundance and diversity on fish in relation to salinity gradients in the Berg Estuary. The host species studied was the commercially important, euryhaline southern mullet Liza richardsonii that is superabundant in estuaries of the Western Cape. A total of 210 fishes were sampled by using a single haul with a beach seine net at each of seven localities along a salinity gradient from the mouth to the upper reaches. Seven species of parasite were found. These included five species of Copepoda; a member of the family Caligidae, an Ergasilus species, a Dermoergasilus species, a Brachiella species and an unidentified caudal fin parasite. Two representatives of the Monogenea were found, one from the family Microcotylidae and another that was not identified.

Includes bibliographical references (leaves 47-55). / This thesis has investigated changes in the frequency of extreme cold and hot tails in the probability distributions (percentile indices) of minimum and maximum temperature events over the Western Cape and Eastern Cape for the period 1960-2005. The focus was to determine whether the changes in hot and cold tails (extreme tails) showed any trends or variability. The data used in this thesis are from 12 high quality observing weather stations over the two regions.

Includes abstract. / Includes bibliographical references (leaves 59-65). / Stomach contents of sardine (Sardinops sagax), anchovy (Engraulis encrasicolus), west coast redeye (Etrameus whiteheadi) and east coast redeye (E. teres) were collected from presumed mixed shoals off South Africa's east coast. The stomach contents were analysed to 1) determine the diet composition of each species in terms of dietary carbon, 2) assess whether resource partitioning by prey type and/or prey size occurs amont the four species, 3) compare results with what is known about the diet of these species on the west and south coasts of South Africa and 4) characterize diet of east coast redeye.

Includes abstract. / Includes bibliographical references (leaves 81-94). / In this dissertation, the variability in the East African coastal ocean (Somali basin) due to the monsoon transition is investigated. The monsoon is characterized by wind reversals and seasonality in the precipitation of a region. The surface circulation of the western Indian Ocean during the summer (JAS) and winter (JFM) monsoon winds is investigated using the Regional Ocean Modelling System (ROMS) ROMS is forced with the Comprehensive Ocean Atmosphere Data Sets (COADS) while the initial and lateral boundary conditions are derived from the World Ocean Atlas The domain area of the model study is constrained by 10•S to 15'N and 3S"E to 55"E, An overview of the surface circulation of the Somali basin is given. discussing the Somali Current East African Coastal Current, South Equatorial Counter Current Southern Gyre, and the Great Whirl The motivation of this dissertation is to improve the understanding of the circulation patterns within the Somali Basin from intra seasonal to seasonal timescales, using the ROMS model The model results suggest a seasonally reversing Somali current with a sub-surface counter current, consistent with observations_ Other prominent features such as the Great Whirl, which occurs during the Southwest monsoon and the Southern Gyre, are also apparent in the simulation The East African Coastal Current (EACC) and the South Equatorial Counter Current (SECCI are also major features of the Somali basin circulation that are equally apparent from the model simulation The model equally reproduces the equatorial jets as expected during the transition period of April/May and October/November with the net result of mass transport from the western end of the basin towards the east.

Although mesopelagic fishes are an important component of marine food webs, the adaptive features used to facilitate niche partitioning among co-existing and presumably competing mesopelagic species is unclear. This study examined the trophic ecology of the two principal mesopelagic fishes off the west coast of South Africa (lanternfish Lampanyctodes hectoris and lightfish Maurolicus walvisensis) sampled during the spring 2014 and autumn 2015 cruises, using stable isotope and stomach content analyses. Stable isotope values were extracted from the white muscle tissue of fishes, but due to the high lipid content of both species, samples were processed in duplicate: δ13C was measured from lipid-extracted samples and δ15N from non-extracted samples. To validate the stable isotope results, stomach contents were examined and the relative importance of prey items was assessed using three measures: frequency occurrence (%F), numerical abundance (%N), and dietary carbon (%C). Both mesopelagic species occupied different isotopic niches that were separated by their δ15N values across a similar δ13C range. Furthermore, the relationship found between trophic position and standard length emphasizes the structuring effect of size within the assemblage, with the larger species (L. hectoris) occupying a higher trophic position than the smaller species (M. walvisensis). Although copepods dominated the diet of L. hectoris in terms of numerical abundance (42%), macro-zooplankton was by far the most important dietary component, with euphausiids contributing 53% of dietary carbon. Conversely, copepods - particularly Calanus sp. - were the most important component of the diet for M. walvisensis in terms of their occurrence (84%), numerical abundance (64%), and dietary carbon (67%). Though some dietary overlap exists between L. hectoris and M. walvisensis, the results of this study suggest resource partitioning within the mesopelagic assemblage, likely facilitated by differences in alimentary morphology (i.e. trophodynamically mediated), and possibly by differences in their respective foraging strategies. Similarly, ontogenetic shifts in trophic position were detected, which suggests that these adaptive features may also be used to mitigate intra-specific competition within populations. Furthermore, the trophic positions of both L. hectoris and M. walvisensis inferred from dietary and isotopic data signify that mesopelagic fishes (in the context of this study) are secondary and tertiary consumers in the marine ecosystem of the southern Benguela. Nevertheless, samples covering a larger area of the southern Benguela and multiple years would be needed for a more complete understanding of the trophic ecology of these two species.

Remotely sensed weekly MODIS data of chlorophyll α (Chl-α) concentration, sea surface temperature (SST) and satellite altimetry data of Absolute Dynamic Topography (ADT) and geostrophic velocities are used to examine the seasonal and interannual patterns in the Chl-α concentration and SST over three pilot study areas of the southwest Indian Ocean, namely Northeast Madagascar, Southeast Madagascar and Mascarene Islands. The weekly and monthly climatology and the weekly means of each variables are assessed using image displays and time series from 2003 to 2014. It is found that there is a seasonal cycle of phytoplankton blooms occurring twice a year across northeast and southeast Madagascar. The two blooms occur during the summer monsoon and during the winter monsoon, respectively. Unlike these two areas, the Mascarene Islands area has only one bloom during the summer monsoon. There is a negative correlation between SST and Chl-α concentration across all three areas; when SST is high, Chl-α concentration is low and vice versa. Also, the current patterns showed that the two Madagascar study areas, are more physically dynamic than the Mascarene Islands region. Unlike the Masacarene region, the Madagascar regions are more affected by the forcing of the South Equatorial Current that splits into the Southeast Madagascar Current and Northeast Madagascar Current, thus causing displacement of surface water. New outcomes of this study are that the north Indian Ocean (north of 100S) is not the only area that is affected by the summer and winter monsoons but the areas south of 100S may also be indirectly affected by the monsoons. Across Northeast Madgascar region, the summer monsoon bloom is well spread over the area while the winter monsoon bloom is mostly coastal. Across the Southest Madagascar region, the summer monsoon bloom spreads from east to west while, the winter monsoon bloom spreads from west to east. The Mascarene region is less productive with higher sea surface height and weaker eddies compared to the other areas and the mixed layer depth is greater across the Mascarene region, thus less nutrients are injected to the euphotic zone and the weaker eddies result in less mixing and consequently in weak Chl-α production. This study should improve our understanding of the seasonal and interannual variability of the SST and Chl-α and the dynamics of the ADT and geostrophic velocities in these regions for improved management of fishery resources using an ecosystem approach to fisheries.

Includes bibliographical references (leaves 56-67). / Knowledge of the vertical distribution of phytoplankton in the upper ocean is essential for accurate estimates of primary production. Satellite remote sensing has given scientists an unprecedented view of near-surface chlorophyll distribution and other surface conditions, including sea surface temperature and wind data, from regional to global scales but little information on the dynamics below the surface. As a result estimates of global production tend to use regional profile averages but these methods oversimplify the smaller scale dynamics, particularly in coastal regions where productivity is highly variable on time scales of weeks. A pilot study by computer science honours students in 2006 showed the viability of using a Dynamic Bayesian Network (DBN) in predicting a representative profile per pixel of a satellite map based on a database of time series satellite surface data. In this study, 5813 in situ profiles were obtained from the highly dynamic upwelling region around the southwestern coastline of southern Africa. The samples were collected between 1988 and 2006 between the coast and the continental slope. The region was divided into three sub-regions according to biophysical processes: the west Coast; the west Agulhas Bank; and the east Agulhas Bank. Of the 5813 profiles, 5557 were included in the sub-regions. Two consecutive processes were then applied to the profile database. First, the profiles were clustered using a k-means clustering program which produced 16 representative clusters.