Includes abstract. / Includes bibliographical references. / The aim of this thesis is to produce fine resolution estimates of primary production in three-dimensional space at the temporal scale that these events develop. It is hypothesized that complex relationships among time sequences of physical and biological processes that influence primary production can be automatically discovered from archives of data. This study uses an archive of in situ ship-board data containing subsurface temperature and phytoplankton distribution profiles. Each profile is associated in time and space with satellite remotely-sensed wind, sea surface temperature and surface chlorophyll a data. The bottom depth, season and location of each profile are also recorded. The archive of depth profiles is simplified by mapping each profile onto one of twelve representative profile clusters obtained using the k-means clustering algorithm so that each cluster contains a set of similar profiles and their corresponding data. Relationships between remotely sensed surface features and chlorophyll a profiles are first obtained from a static Bayesian network using same day data. This is then taken further by analysing time-series of satellite data to predict likely temperature and chlorophyll a profiles for each pixel of a 4 km resolution satellite image.

Includes abstract. / Includes bibliographical references. / The model outputs and the satellite data have shown a number of cyclonic and anticyclonic eddies being generated within the Mozambique Channel. The eddies were identified using a newly designed eddy detection algorithm. The algorithm has shown that cyclonic eddies appeared to be more ubiquitous than the anticyclonic and had a single mode sizedistribution. On the other hand, the anticyclonic eddies seemed to have a favorite site for their formation, and have shown a bi-modal size-distribution.

Includes bibliographical references (p. 119-132). / Satellite remote sensing datasets including more than 6 years of high frequency Sea Surface Temperature (SST) imagery as well as surface current observations derived from 18 years of merged-altimetry and over 2 years of Advanced Synthetic Aperture Radar (ASAR) observations are combined to study the variability of the Agulhas Current. The newly available rangedirected surface currents velocities from ASAR, which rely on the careful analysis of the measured Doppler shift, show strong promise for monitoring the meso to sub-mesoscale features of the surface circulation. While the accuracy of ASAR surface current velocities suffers from occasional bias due to our current inability to systematically account for the wind-induced contribution to the Doppler shift signal, the ASAR surface current velocities are able to consistently highlight regions of strong current and shear. The synaptic nature and relatively high resolution of ASAR acquisitions make the ASAR derived current velocities a good complement to altimetry for the study of sub-mesoscale processes and western boundary current dynamics. Time-averaged range-directed surface currents derived from ASAR provide an improved map of the mean Agulhas Current flow, clearly showing the location of the Agulhas Current core over the 1000 m isobath and identifying the region at the shelf edge of the north-eastern Agulhas Bank as one of the most variable within the Agulhas Current. To determine the variability of the Agulhas Current, an algorithm to track the position of the current is developed and applied to the longer merged-altimetry and SST records. Limitations associated with altimetry near the coast favour the use of the SST dataset to track the position of the Agulhas Current in its northern region. In the southern Agulhas, where the current lies further from the coast, altimetry is suited to monitoring the position of the Agulhas Current. The front detection analysis conducted on the SST dataset in the northern Agulhas reveals the complex nature of Natal Pulses. The downstream passage of the Natal Pulses is associated with the generation of secondary offshore meanders at the inshore edge of the current. Perturbations formed during the passage of Natal Pulses evolve rapidly to either dissipate, re-merge with the initial Natal Pulse or in some rare occasion, detach from the Agulhas Current.

Includes bibliographies at end of chapters. / The following objectives are covered in the study: (i) the description of the seasonal hydrological changes in the survey area and a comparison between years. (ii) an examination of the seasonal distribution and abundance of the larval stages in relation to hydrological conditions. (iii) the determination of the preferential temperature and salinity ranges for the larvae. (iv) an examination of seasonal shift in location and intensity of spawning from the geographic distribution, abundance and size composition of the larvae. (v) the establishment of dispersal trends of developing larvae from the spawning grounds. (vi) the provision of information on the identity and development of important fish eggs and larvae. (vii) the determination of diurnal changes in abundance and size composition of various larval species. The results reported are regarded as scientifically significant in view of the paucity of basic information on the early life history of any fish species off South West Africa. Many aspects such as identity, development, distribution, abundance, hydrological affinities, diurnal variation and dispersal are given for the first time. The findings make a positive contribution not only to knowledge of the early stages and biology of the species but also provide an insight into the general ecology of fish larvae in what is probably the most productive and lucrative fishing grounds in the South East Atlantic.

The Southern Ocean forms a vital component of the earth system as a sink of CO2 and heat, taking over 40% of the annual oceanic CO2 uptake (75% of global heat uptake), slowing down the accumulation of CO2 in the atmosphere and thus the rate of climate change. However, recent studies based on the Coupled Model Intercomparison Project version 5 (CMIP5) Earth System Models (ESMs) show that CMIP5 ESMs disagree on the phasing of the seasonal cycle of the CO2 flux (FCO2) and compare poorly with available observation estimates in the Southern Ocean. Notwithstanding these differences, the seasonal cycle is a dominant mode of CO2 variability in the Southern Ocean, and hence this is an important bias. Previous studies suggest that these biases of FCO2 in ESMs might be a significant limitation to the long-term simulation of CO2 characteristics in the Southern Ocean. Consequently, this study has three primary objectives: first, to develop a process-based diagnostic method to analyze and isolate key biases and their underlaying mechanisms in the model-observations seasonal cycle of FCO2 differences for forced ocean models and ESMs. Second, to use this framework to examine sources of biases responsible for the limited skill of CMIP5 models in simulating the seasonal cycle of FCO2 with respect to observed estimates. Thirdly, to investigate how these present-day biases in the seasonality and drivers of CO2 in CMIP5 ESMs affect modelled longterm changes in the mechanisms of CO2 uptake in the Southern Ocean. In the first part of the dissertation, an objective diagnostic framework was established to analyze model-observation biases in the seasonal scale of FCO2 using the NEMO PISCES ORCA2LP model output, and Takahashi et al. (2009) observed estimates. The diagnostic framework focuses on examining the relative contributions of the competing drivers (SST and DIC) and related processes (solubility, biological and mixing) to instantaneous monthly changes in surface pCO2 (and FCO2) at the seasonal scale. In the second part of the dissertation, this approach is applied to 10 CMIP5 models in the Southern Ocean, to investigate the mechanistic basis for the seasonal cycle of FCO2 biases. It was found that FCO2 biases in CMIP5 models can be grouped into two main categories, i.e. group-SST and group-DIC. Group-SST models are characterized by an exaggeration of the seasonal rates of change of Sea Surface Temperature (SST) in autumn and spring during the cooling and warming peaks, respectively. These faster-than-observed rates of change of SST tip the control of the seasonal cycle of pCO2 and FCO2 towards SST and result in divergence between the observed and modelled seasonal cycles, particularly in the Sub-Antarctic Zone. While almost all analyzed models show these SST-driven biases, 3 out of 10 (namely NorESM1-ME, HadGEM2-ES and MPI-ESM, collectively the group-DIC models) compensate the solubility bias because of their exaggerated primary production, such that biologically-driven DIC changes become the regulators of the seasonal cycle of FCO2. It was also found that despite significant differences in the spatial characteristics of the mean annual fluxes, CMIP5 models show a zonal homogeneity in the seasonal cycle of FCO2 at the basin-scale in contrast to observed estimates. In the final third of the dissertation, using five CMIP5 ESMs from the RCP8.5 scenario, it was found that CMIP5 models present climate biases in the seasonality and drivers of FCO2 are fundamental to how models simulate long-term changes in the mechanisms of CO2 uptake in the Southern Ocean. Although all five analyzed models show an increased annual mean CO2 uptake by the end of the century, they show significant differences in the mechanisms. The present-day temperature biased models (group-SST) generally maintain the dominance of the temperature driver in the seasonal variability of FCO2 to end of the century. But show enhanced CO2 uptake due to increased anthropogenic atmospheric CO2 and decreased surface CO2 buffering capacity but they display a weak to null role of biological activity in the increased CO2 sink. On the other hand, the increased CO2 uptake at the end of the century in group-DIC models is explained increased biological driven CO2 uptake in spring, linked to increased Revelle factor and solubility driven CO2 uptake in winter. Increased Revelle factor at the end of the century enhance pCO2 changes for even smaller DIC changes.

Includes bibliographical references (p. 190-206). / Moisture input from the South Atlantic and Indian Oceans over southern Africa is examined through zonal water vapour transport. Along the west coast, variations in intensity and latitudinal position of the South Atlantic anticyclone/modulations of the westerly flow that penetrates from the tropical Atlantic, contribute the most about 25% and 11% of the variance explained respectively), in January-February to variability in moisture advection from the South/tropical Atlantic, thus affecting rainfall at subtropical/tropical latitudes respectively. The southern extension of the AEJ could play a role in transfering moisture from the tropics southwards during wet phases, while events related to low phases of the Southern Oscillation are marked by an eastward shift of the ascending branch of the Walker circulation, suppressing convection and thus reducing rainfall over the subcontinent.

Bibliography: leaves 107-119. / An individual based modelling approach was used to study environmental factors and processes influencing the early life history of anchovy in the southern Benguela region and on the Agulhas Bank. The intention was to then establish the link between these factors and processes and the recruitment success of anchovy in the southern Benguela region. Specific factors that were explored were transport from the spawning grounds to the nursery area, advection, temperature- dependent growth and mortality, vertical migration behaviour, retention in the nursery area, as well as the possibility of a second nursery area on the Eastern Agulhas Bank. Eight individual based models were coupled to the output of a 3-D hydrodynamic model to study dispersion processes. Particles representing eggs and larvae were released (spawned) over the Agulhas Bank, and their movements were tracked during their transport to the west coast (the recruitment area). Although the eggs and larvae were initially considered to be neutrally-buoyant, passive particles, increasing levels of complexity were progressively incorporated by adding processes such as particle buoyancy, temperature-dependency of growth and mortality of eggs and larvae, vertical behaviour and retention. A series of experiments was run by setting the parameters representing the factors being investigated by the model, and estimating a primary, quantifiable response variable representing the dynamics of the system (e.g. particles successfully reaching the nursery area). An analysis of variance was employed to assess the significance and the sensitivity of each model to changes in the parameter values. A pattern-oriented analysis was then systematically applied to assess the validity of the results of the model. The results indicate that five processes and their interactions strongly influence the transport of spawning products arriving at and subsequently being retained in the nursery area: (1) the location of the spawning, (2) the buoyancy of the eggs, (3) transport by the jet current and its inter-annual variability; (4) the 3-D structure of the current in the nursery area on the west coast, (5) The swimming abilities of the pre-recruits in both the vertical and the horizontal planes. Two factors appear to be of major importance in effecting mortality during the period leading up to recruitment, namely temperature and offshore losses through advective processes. A conceptual model of the life history of anchovy in southern Benguela is presented and discussed in the light of the hypothesis proposed by Hutchings et al. (1998). A number of modifications to this hypothesis are proposed, specifically an extension of the spawning area, and the addition of several key biological processes. A new element that is proposed in this thesis is the possibility of the Eastern Agulhas Bank as an additional nursery and spawning area.

Includes bibliographical references. / Underwater Sound Velocity Profiles (SVP) are used throughout the world by their respective navies for submarine and surface vessel strategic operations and exercises. Together with the sonar equations, the sound velocity profiles are of paramount importance to solve underwater sound detectability problems as they provide insight into the highly variable sound transmission loss. Oceanographic records of sea temperature-depth profiles are ordinarily incorporated into a sonar propagation model to determine the sound level at any point (range and depth). The ability to predict these environmental conditions with a defined level of confidence and accuracy significantly increases the situational awareness to in-theatre naval operators and fleet planners. The hypothesis in this thesis is that thermal characteristics of the water column in the southern Benguela can be numerically modeled and deduced from a single Sea Surface Temperature (SST) value, if provided with sufficient historic temperature-depth profiles for that region. For operational use, the SST would ideally be provided from near real time remotely sensed satellite derived data.

Mid-latitude storms are common in the Southern Ocean (SO) and have been shown to drive substantial vertical mixing, leaving behind wakes of perturbed upper ocean. The vertical extent and duration of the impact of these storms on the upper ocean remains unknown in this region, partly due to lack of observations in this remote part of the world. The mixed-layer depth (MLD) is used widely as proxy for vertical extent of upper-ocean mixing, with the assumption that it integrates the variability of atmospheric forcing. Recent studies have shown that this shear-driven mixing associated with storms can actually extend below the base of the MLD into the transitional layer (TL). Knowledge about the TL would help improve the mixing models of the upper ocean because it acts as a window/mediator between the deep ocean and the surface mixed layer (ML). However, the responses of the MLD and the transitional layer depth (TLD) have been shown to vary substantially between different storm events at similar locations. In this study, these two diagnostics, the MLD and TLD, have been used to investigate the response of the upper ocean mixing to storms in the Sub-Antarctic Zone (SAZ) and to further interrogate the relevance of the MLD as a proxy for mixing extent at these short temporal scales. This is explored during the summer period when the storm-driven mixing is thought to maintain primary production via enhanced nutrient supply. I used data collected from high-resolution autonomous gliders in pseudo-mooring mode, which remotely sampled the SAZ from spring to summer documenting the passage of storm events. Four storms of different magnitude were analysed in summer, and two different modes of the upper ocean response were identified. In the first mode, the MLD deepened during a storm, with little or no changes in the vertical structure of temperature and salinity in the layer below. The second mode was characterized by changes in the TL properties, which deepened at times; the MLD however did not respond to this storm forcing. In the pair of storms that was more in line with the classical response (i.e first mode), the vertical stratification in the upper ocean structure was eroded during the storm and after the storm. In the other case (i.e the 5second mode), however, the vertical stratification was enhanced during the passage of the storm and after the storm. These contrasting responses from both these storms can be linked to a number of atmospheric and oceanic factors; the atmospheric factor was the wind forcing extent (magnitude and duration). The oceanic factor that might have played a role is the pre-existing vertical stratification (depth and strength) within the water column. These two factors conspired to bring about upper ocean changes associated with the passing of storms. It has been shown here that most of the changes are indeed occurring in the transitional layer below the MLD. The MLD, which is used widely by the oceanographic community as a proxy for the integrated effect of surface mixing on many temporal scales, does not always capture the full response of upper-ocean mixing driven by the transient synoptic events.

Includes bibliographical references / The Mascarene Plateau is a submerged volcanic plateau to the east of Madagascar which extends over 2200 km between the Seychelles and Mauritius. It is a complex feature, which is composed of 4 banks separated by 3 channels - namely the Seychelles, Saya de Malha, Nazareth and Cargados-Carajos Banks. The main objective of this thesis is to analyze cruise data obtained during the October/November 2008 ASCLME (Agulhas Somali Current Large Marine Ecosystem) cruise on board the Dr Fridtjof Nansen which surveyed the region around the Mascarene Plateau. Due to the paucity of data in the region, the cruise was a routine cruise with no specific scientific questions to be answered. A comparison is also made between sea surface temperature (SST) and Acoustic Doppler Current Profiler (ADCP) derived currents on board to satellite estimate to possibly extend cruise results in space and time. Although the resolution of satellite estimate is low compared to cruise measurements, satellite estimate of geostrophic velocities and sea surface temperatures compare well with cruise data and can therefore be used in the region with confidence. This is invaluable since the Mascarene Plateau is relatively poorly understood and it allows us to link cruise data with Rossby waves and currents impacting the region. This is the second cruise in the region as there was a research cruise on board the RRS Charles Darwin during June/July 2002. However, the June/July 2002 cruise did not sample the banks of the Mascarene Plateau.