Atmospheric and climatic drivers of tide gauge sea level variability along the east and south coast of South Africa

Atmospheric forcing and climate modes of variability on various timescales are important drivers of sea level variability. However, the influence of such drivers on sea level variability along the South African east and south coast has not yet been adequately investigated. Here, we determine the timescales of sea level variability and their relationships with various drivers. Empirical Mode Decomposition (EMD) was applied to seven tide gauge records and potential forcing data for this purpose. The oscillatory modes identified by the EMD were summed to obtain physically more meaningful timescales—specifically, the sub-annual (less than 18 months) and interannual (greater than two years) scales. On the sub-annual scale, sea level responds to regional zonal and meridional winds associated with mesoscale and synoptic weather disturbances. Ekman dynamics resulting from variability in sea level pressure and alongshore winds are important for the coastal sea level on this timescale. On interannual timescales, there were connections with ENSO, the Indian Ocean Dipole (IOD) and the Southern Annular Mode (SAM), although the results are not consistent across all the tide gauge stations and are not particularly strong. In general, El Niño and positive IOD events are coincident with high coastal sea levels and vice versa, whereas there appears to be an inverse relationship between SAM phase and sea level.publishedVersio

Developing ocean particle tracking tools for cross-disciplinary oceanic research with applications in the Agulhas current region

Lagrangian ocean analysis is a powerful way to study ocean processes from in-situ observations and numerical model simulations. As numerical modelling capabilities develop and physical mechanisms of the ocean are better understood, the importance of particle trajectory modelling continues to increase. Therefore, developing cross-disciplinary particle trajectory model applications for the Greater Agulhas System is highly relevant due to its potential contribution to scientific studies and operational applications. This thesis presents the results of developing particle trajectory model applications in the Greater Agulhas System towards better understanding the physical mechanisms that drive ocean processes in the region. The model is used in three applications that demonstrate their cross-disciplinary potential. These applications include a search and rescue scenario, the study of ocean dynamics and the study of the fate of juvenile turtles. Introducing spatially and temporally varying stochastic motion to account for the processes not resolved in the ocean surface current products, as well as including more appropriate boundary conditions, were shown to improve the accuracy of virtual drifters in representing the trajectory of a real surface drifter. Next, implementing the spatially and temporally varying stochastic motion in the particle trajectory model and applying it to a search and rescue scenario of a capsized catamaran revealed that including both winds and surface ocean currents in the particle trajectory model allowed for an improved prediction of the capsized vessel’s trajectory. By comparing a pair of real surface drifters with the particle trajectory model and analysing high resolution sea surface temperature (SST) fields it was shown that the formation of an eddy on the Agulhas Plateau combined with the weakening of the core current velocity resulted in enhanced eddycurrent interactions facilitating the separation of the real surface drifter-pair as they passed through this region. Lastly, the particle trajectory model was used to study the importance of including active swimming characteristic when studying the fate of juvenile turtles. It was found that including active swimming resulted in a change in the distribution of juvenile turtles and, therefore, needs to be included to provide a proper understanding of the fate of juvenile turtles in the ocean. With further development and refinement of the particle trajectory model, Lagrangian ocean analysis has the potential to provide valuable information towards improving our understanding of physical and biological ocean processes at a range of spatial and temporal scales with potential operational oceanography applications

Scaling Observation Error for Optimal Assimilation of CCI SST Data into a Regional HYCOM EnOI System

South Africa currently possesses no operational ocean forecasting system for the purpose of predicting ocean state variables including temperature,salinity and velocity. Substantial initial efforts towards this goal have been made and resulted in a system using a regional Hybrid Coordinate Ocean Model (HYCOM) along with the Ensemble Optimal Interpolation (EnOI)assimilation scheme. Assimilating only sea surface temperature (SST) observations from the Operational Sea Surface Temperature and Sea Ice Analysis (OSTIA) product into the system resulted in a degraded forecast. Aiming to address this, Climate Change Initiative (CCI) SSTs are assimilated into the system in an effort to improve the forecast skill. Observation errors in the assimilated product are used in the EnOI to determine whether more confidence should be placed in the model or observations in producing the analysis, but overconfidence in observations can shock the model and result in failure. To tweak the impact of the assimilation, a scaling factor is applied in the assimilation code. A scaling factor of 25 was found to produce a favourable result with lowest mean root mean square error (RMSE;1.098C) between the model and observations over time. Postulating the error to be overconfident, a floor value is introduced in order to set a minimum value for the observation error thereby reducing confidence in the observations. These experiments fared less favourably with a floor value of 0.5 and a scaling factor of 15 producing the best mean RMSE (1.118C)

Assessing the accuracy of satellite derived ocean currents by comparing observed and virtual buoys in the Greater Agulhas Region

In this study, we assess the accuracy of a combined geostrophic and Ekman current product (GlobCurrent) that estimates ocean currents at 15 m depth, by coupling it to a synthetic particle tracking tool and comparing the virtual trajectories to those of surface drifting buoys drogued at 15 m in the Greater Agulhas Current Region. The velocities from a total of 1041 drifters are compared and evaluated to the synthetic particle-derived velocities for the period 1993–2015. On average the GlobCurrent underestimates the velocity in the Greater Agulhas Current by approximately 27%. The underestimation ranges from 4 to 64% in different regions, with the smallest error found in the Agulhas retroflection region, and the highest in the Benguela Upwelling System. Furthermore, we compare the time taken for the separation between the virtual and real drifters to reach 35 km. The mean separation time was found to be 78 h, with the shortest time (35 h) found in the Agulhas Current and the longest time (116 h) located in the Agulhas Return Current. Deploying 10,000 virtual drifters in a 1° × 1° box within the southern Agulhas Current shows a convergence of trajectories towards the core of the current, while higher divergence is evident in the Agulhas retroflection. To evaluate the utility of this synthetic particle tracking tool coupled with GlobCurrent in open ocean search and rescue operations, two test cases are examined: (1) a capsized catamaran spotted south of Cape Recife and recovered 5 days later south of Cape Agulhas; and (2) a drifter trajectory in the same region. The comparison suggests that the GlobCurrent forced synthetic particle tracking tool is not appropriate for predicting the trajectory of a capsized catamaran that does not have the same drift characteristics as a surface drifting buoy drogued to 15 m

Modes of the southern extension of the East Madagascar Current

Data sets from satellite observations and a nested high-resolution model are used to study a source region of the Agulhas Current. Altimeter-derived geostrophic surface currents are averaged over varying periods, providing evidence of the persistence of flow patterns in the extension of the southern branch of the East Madagascar Current (SEMC). South of Madagascar, the SEMC separates into one branch toward the Agulhas Current and into a second branch retroflecting and connecting to the Subtropical Indian Ocean Countercurrent (SICC). Good agreement is found between long-term mean patterns of observational and model dynamic heights. Two basic modes are identified in the SEMC extension, with anticyclonic motion favoring retroflection in the northern Mozambique Basin when the extension is in a southwestward direction and cyclonic motion occurring in the case of the SEMC flowing westward along the southern Madagascar slope. A cross-correlation sequence between model SEMC transports and the modal changes in the extension region displays a correlation at about 1-month lag which agrees with eddy propagation time from the SEMC to the outflow region. Mean model SEMC transports are determined using floats released at 21 degrees S, and the contribution of the SEMC to the SICC is obtained using floats injected at 55 degrees E with the model running backward. Almost half of the SEMC volume transport contributes to the Agulhas system, and about 40% of SICC water originates from the SEMC

A taxonomic backbone for the global synthesis of species diversity in the angiosperm order Caryophyllales

The Caryophyllales constitute a major lineage of flowering plants with approximately 12500 species in 39 families. A taxonomic backbone at the genus level is provided that reflects the current state of knowledge and accepts 749 genera for the order. A detailed review of the literature of the past two decades shows that enormous progress has been made in understanding overall phylogenetic relationships in Caryophyllales. The process of re-circumscribing families in order to be monophyletic appears to be largely complete and has led to the recognition of eight new families (Anacampserotaceae, Kewaceae, Limeaceae, Lophiocarpaceae, Macarthuriaceae, Microteaceae, Montiaceae and Talinaceae), while the phylogenetic evaluation of generic concepts is still well underway. As a result of this, the number of genera has increased by more than ten percent in comparison to the last complete treatments in the Families and genera of vascular plants” series. A checklist with all currently accepted genus names in Caryophyllales, as well as nomenclatural references, type names and synonymy is presented. Notes indicate how extensively the respective genera have been studied in a phylogenetic context. The most diverse families at the generic level are Cactaceae and Aizoaceae, but 28 families comprise only one to six genera. This synopsis represents a first step towards the aim of creating a global synthesis of the species diversity in the angiosperm order Caryophyllales integrating the work of numerous specialists around the world

Review of the projected impacts of climate change on coastal fishes in southern Africa

The coastal zone represents one of the most economically and ecologically important ecosystems on the planet, none more so than in southern Africa. This manuscript examines the potential impacts of climate change on the coastal fishes in southern Africa and provides some of the first information for the Southern Hemisphere, outside of Australasia. It begins by describing the coastal zone in terms of its physical characteristics, climate, fish biodiversity and fisheries. The region is divided into seven biogeographical zones based on previous descriptions and interpretations by the authors. A global review of the impacts of climate change on coastal zones is then applied to make qualitative predictions on the likely impacts of climate change on migratory, resident, estuarine-dependent and catadromous fishes in each of these biogeographical zones. In many respects the southern African region represents a microcosm of climate change variability and of coastal habitats. Based on the broad range of climate change impacts and life history styles of coastal fishes, the predicted impacts on fishes will be diverse. If anything, this review reveals our lack of fundamental knowledge in this field, in particular in southern Africa. Several research priorities, including the need for process-based fundamental research programs are highlighted

Mesoscale variability study of the Agulhas Current from satellite radar altimetry and a high resolution model

Towards understanding the dynamics and eddy evolving processes in the greater Agulhas Current system, a Hybrid Coordinate Ocean Model (HYCOM) system has been set up to simulation the ocean circulation around Southern Africa in a hindcast experiment. In a region characterised by a general paucity of hydrographic observations, model validation from satellite remote sensing data products play an important role. In particular, radar altimetry observations from satellites are of beneficial use in the Agulhas Current regime, since it is known to exhibit some of the strongest mesoscale variability in the global ocean. Model validation from available in-situ data is presented with the focus on evaluating and implementing satellite altimetry data products for the purpose of validating the model mesoscale variability. An initial comparison of along-track sea level anomaly data from the Jason-1 satellite to merged gridded multi−altimeter data for the Agulhas Current suggested no significant loss of information in the generation of the merged maps. Thus allowing the use of the gridded data product in further model evaluation. It was found that the altimeter data provides good temporal and spatial comparisons, and as a by-product to the validation process, a frequency and variability study of the Agulhas Current regime was undertaken. Additionally to confirming strong seasonal signals in the region, they revealed that mesoscale eddies in the Mozambique Channel frequently interact at the Agulhas Retroflection. These observations are quantified statistically with the application of a Fourier analysis, which additionally provided a further method of validating the model simulation. The model simulation was able to represent the general characteristics of the circulation in the Agulhas regime, and supports many of the findings in the altimetry variability study. However, with the development of a large anticyclonic circulation feature upstream of the Agulhas Plateau in the current proper, the model simulation deteriorates in the later years. Available hydrographic data suggests a salinity deficit in the model fields, resulting in reduced baroclinic gradients, which in addition to other numerical instabilities may provide an explanation for the development of this feature. With continuously improving numerical schemes, increased computing power, and improved data assimilation techniques these models become increasingly realistic. As an oceanographic tool, the development of numerical models is vital, the first steps towards setting up and validating a regional HYCOM model for the oceans around Southern Africa are presented