>Magister Scientiae - MSc / Two species of Chrysaora are described from the northern Benguela ecosystem: C. fulgida and C. africana. These species can be diagnosed by a combination of morphological features including lappet and tentacle number, shape oflappets, colouration patterns (alive), shape of the proximal portion of radial septa, gastrovascular pouch shape, point of attachment of gonads and the presence or absence of small raised nematocyst warts on the exumbrellar surface. Objective, quantitative statistical analyses coupled with molecular sequence data support the qualitative morphological dissimilarity observed, as these analyses unambiguously diagnose C. fulgida and C. africana as two distinct species. There is a strong superficial resemblance between the C. fulgida material described here and the preserved specimens of C. hysoscella examined at the Natural History Museum, London. Thorough investigation does however allow the separation of these two species. morphological features found to be dissimilar were the proximal portion of the manubrium, gastrovascular pouch shape and the presence or absence of sperm sacs. Objective, quantitative statistical analyses support these findings. Nuclear sequence variation suggests considerable divergence between the two species but additional molecular work is needed.

La distribution d'espèces benthiques intertidales est contrainte par l'océanographie côtière. On connaît moins les effets sur l'écologie des prédateurs. Les côtes sud de l'Afrique sont caractérisées par des contrastes de production primaire et d'assemblages intertidaux dus aux deux courants majeurs qui les longent. Le prédateur apical de ces côtes est un oiseau limicole endémique, l'huîtrier noir africain (Haematopus moquini), qui présente un polymorphisme favorable à la spécialisation alimentaire. Ces travaux ont étudié l'effet des variations spatiales de structure de communautés benthiques sur l'écologie alimentaire de l'huîtrier à l'aide des isotopes stables. Les oiseaux répondent aux fluctuations qualitative et quantitative des communautés de proies à plusieurs échelles. A large échelle ils montrent de forts contrastes entre les côtes ouest et sud-ouest où le régime alimentaire est dominé par les moules, notamment l'espèce invasive Mytilus galloprovincialis et le sud-est où un mélange de moules et patelles est consommé. Localement les individus montrent des différences faibles d'alimentation liées à l'abondance relative des moules et patelles. Cela s'explique par le caractère généraliste de l'espèce et le relâchement de compétition intra-spécifique pour les ressources. La transition alimentaire d'H. moquini vers une consommation quasi-exclusive à l'ouest d'une moule introduite et la multitude de comportements alimentaires ailleurs indiquent un fort potentiel d'adaptation aux modifications de son habitat d'alimentation. En revanche la dégradation des plages par l'Homme augmente la compétition pour l'espace et affecterait aujourd'hui le succès reproducteur de l'espèce. / The distribution of intertidal benthic species is constrained by coastal oceanography. Less is known about the effects on the ecology of predators. Along the southern coasts of Africa the two main currents constraint both the patterns of primary production and the structure of benthic communities. The top predator on these coasts is an endemic shorebird, the African Black Oystercatcher (Haematopus moquini), which exhibits a polymorphism favourable for food specialization. This study investigates the effect of spatial variations in benthic community structure on the feeding ecology of oystercatchers using stable isotopes. Birds respond to changes in quality and quantity of prey at multiple scales. At large scale they show strong contrasts between west and southwest coasts where the diet is dominated by mussels, including the invasive species Mytilus galloprovincialis, and south-east shores where a mixture of mussels and limpets is consumed. Locally individuals show weak dietary differences related to relative abundances of mussels and limpets. This reflects the generalist foraging behaviour of the species and the release of intra-specific competition for resources. The dietary shift of H. moquini on the west coast toward the invasive mussel and the multiplicity of foraging behaviours elsewhere reveal strong capacities to face changes in its foraging habitat. On the other hand the degradation of beaches by humans increases the competition for space and today affects the reproductive success of the species

Sandy beaches are often highly allochthonous, depending on external subsidies of carbon and nutrients. Despite this, sandy beach macrofaunal assemblages have received little attention regarding their response to enhanced primary productivity generated from coastal upwelling. This thesis investigates the influence of upwelling on macrofaunal assemblages over a variety of spatial and temporal scales. Spatially, four regions were examined across two biogeographic provinces to remove temperature as a confounding factor, and limit biogeography-specific effects. A nested hierarchical design enabled both large and small scales to be examined and generalities about upwelling effects across multiple areas to be considered. Sampling was conducted in two seasons, and over two years, to test the persistence of any effects. Biogeography and region had the strongest influences on macrofaunal biodiversity. Upwelling influenced macrofaunal assemblages in every region when analyses were conducted at the species level. However, the particular effect, positive or negative, differed among regions depending on local factors, and between the response variables, abundance and biomass. Coarser scales of taxonomy, feeding guild and developmental mode were investigated; however, the influence of upwelling generally became weaker and more varied, and occasionally disappeared. Seasonality was greater on the South Coast but was still important in some analyses on the West Coast. At the small-scale, variation within-beaches was lower than between beaches, assemblage structure remained stable over time, and consistent zonation was not present. The influence of temperature on filtration rate and oxygen consumption of Donax serra was investigated to test a driving mechanism for assemblage responses to upwelling. Feeding ability was significantly reduced at colder temperatures indicating an important factor which may be involved in determining assemblage structure. These results suggest that alterations to upwelling regimes predicted under climate change scenarios will impact sandy beach macrofauna, however the specific outcome will depend on multiple contextual factors.

Late Pleistocene sediments recovered from ODP Leg 175, Site 1085 are used to generate a high-resolution (500 yr) record of continental climate change in Southern Africa. The location of Site 1085, the SW African continental slope, provides a continuous hemipelagic section with a significant terrigenous component. Terrigenous sediments are transported via fluvial and/or eolian transport mechanisms with MIS 1 being dominated by eolian transport. Analyses, including grain-size, color reflectance, biogenic sediment geochemistry (%CaCO3, %TOC, and C/N), bulk sediment geochemistry, and clay mineralogy, are used to identify continental climate conditions in southern Africa. Analyses indicate glacial/interglacial variation. Median grain-size peaks are associated with changes in transport. Clay mineralogy indicates the presence of kaolinite, smectite, and illite in varying percentages. Smectite and illite dominate the clay mineral assemblages except during MIS 2. Maximum kaolinite was found during MIS 2 and is associated with poleward transport by the Angola Counter Current.

A systematic approach to planning, decision-making and management has become best-practice in conservation over the past two of decades. The field of ‘systematic conservation planning’ is concerned with identifying cost-effective places and actions to protect biological diversity. Past research has focused on static assessments. However, given the fact that biological diversity and processes that threaten its persistence vary in space and time, conservation assessments might need to be made in a dynamic context. In addition, we must explicitly account for the trade-offs associated with implementing conservation actions and investing in improved knowledge and learning to reduce uncertainty on where, how and when to act. The aim of this thesis was to develop novel approaches for accounting for both ecosystem dynamics and uncertainty in conservation planning. Ecosystems are generally treated as static in conservation planning despite many being spatially and temporally dynamic. For example, pelagic marine ecosystems are quite dynamic because ecological processes, such as eddies, that produce resources that many species depend on can be erratic. In chapter two we explored the issue of developing a system of fixed protected areas that consider the physical and biological dynamics typical of the pelagic realm. The approach was to maximize the representation of key fisheries species and species of conservation concern due to significant declines in their abundance, within a network of protected areas. We also ensured that protected area design reflected system dynamics and this was achieved by representing key oceanographic process (such as upwellings and eddies), and biological processes (such as the abundance of small pelagic fish) in protected areas. To account for the variability where these processes occur, we used time series data to find both predictable areas and anomalies, assuming that their past location was somewhat reflective of their future locations. Implementing conservation actions that are fixed in space and time are probably not the most effective strategy in ecosystems that are dynamic. This is because of the movements of particular species. For example, many species have distributions and abundances that change seasonally and might only require temporary management in particular areas. In chapter three, we tested the utility of three approaches to implementing fisheries closures to reduce bycatch in the South African Longline Fishery; 1) time closures, 2) permanent spatial closures and 3) episodic spatial closures. In chapter three, we identified these closures using an existing database containing catch and bycatch data from 1998 to 2005. There was variation where and when different species were caught as bycatch, and it was determined seasonal area closures were the best strategy. This was because it achieved the same conservation objectives for bycatch species as the other types of closures, but impacted less on the long-lining industry. While this result is intuitive, it demonstrated quantitatively, how much more effective moveable management can be. Decisions on where conservation actions are implemented are always based on incomplete knowledge about biological diversity. It is generally assumed that gathering more data is a good investment for conservation planning. However, data can take time and incur costs to collect and given habitat loss, there are both costs and benefits associated with different levels of investments in knowledge versus conservation implementation. In chapter four, the aim was to determine the return on investment from spending different amounts on survey data before undertaking a program of implementing new protected areas. We found that, after an investment of only US$100,000, there was little increase in the effectiveness of conservation actions, despite the full species dataset costing at least 25 times that amount. Surveying can take time because of expertise limitations, logistics and funding shortfalls. Biological diversity may be lost while data collection occurs conversely, not collecting enough data can lead to erroneous decisions. Additionally, resources spent on learning may be better spent on other actions. In chapter five, in a series of retrospective simulations, we compared the impact of spending different amounts of time collecting biological data prior to the implementation of new protected areas. The aim was to find the optimal survey period given the trade-off between gaining knowledge to improve conservation decisions while there is concurrent loss of habitat. We discovered that surveying beyond two years rarely increased the effectiveness of conservation decisions, despite a substantial increase in the knowledge of species distributions. Often there are choices between different actions and uncertainty as to which are the most effective. In chapter six, we discuss how the principles of adaptive management might be applied to conservation planning. Improving future management decisions through learning should be viewed as essential in all conservation plans but such learning is often included as a minor step, or is completely ignored. In this chapter we provide a brief overview of an adaptive framework for conservation planning and ideas for future research.

A systematic approach to planning, decision-making and management has become best-practice in conservation over the past two of decades. The field of ‘systematic conservation planning’ is concerned with identifying cost-effective places and actions to protect biological diversity. Past research has focused on static assessments. However, given the fact that biological diversity and processes that threaten its persistence vary in space and time, conservation assessments might need to be made in a dynamic context. In addition, we must explicitly account for the trade-offs associated with implementing conservation actions and investing in improved knowledge and learning to reduce uncertainty on where, how and when to act. The aim of this thesis was to develop novel approaches for accounting for both ecosystem dynamics and uncertainty in conservation planning. Ecosystems are generally treated as static in conservation planning despite many being spatially and temporally dynamic. For example, pelagic marine ecosystems are quite dynamic because ecological processes, such as eddies, that produce resources that many species depend on can be erratic. In chapter two we explored the issue of developing a system of fixed protected areas that consider the physical and biological dynamics typical of the pelagic realm. The approach was to maximize the representation of key fisheries species and species of conservation concern due to significant declines in their abundance, within a network of protected areas. We also ensured that protected area design reflected system dynamics and this was achieved by representing key oceanographic process (such as upwellings and eddies), and biological processes (such as the abundance of small pelagic fish) in protected areas. To account for the variability where these processes occur, we used time series data to find both predictable areas and anomalies, assuming that their past location was somewhat reflective of their future locations. Implementing conservation actions that are fixed in space and time are probably not the most effective strategy in ecosystems that are dynamic. This is because of the movements of particular species. For example, many species have distributions and abundances that change seasonally and might only require temporary management in particular areas. In chapter three, we tested the utility of three approaches to implementing fisheries closures to reduce bycatch in the South African Longline Fishery; 1) time closures, 2) permanent spatial closures and 3) episodic spatial closures. In chapter three, we identified these closures using an existing database containing catch and bycatch data from 1998 to 2005. There was variation where and when different species were caught as bycatch, and it was determined seasonal area closures were the best strategy. This was because it achieved the same conservation objectives for bycatch species as the other types of closures, but impacted less on the long-lining industry. While this result is intuitive, it demonstrated quantitatively, how much more effective moveable management can be. Decisions on where conservation actions are implemented are always based on incomplete knowledge about biological diversity. It is generally assumed that gathering more data is a good investment for conservation planning. However, data can take time and incur costs to collect and given habitat loss, there are both costs and benefits associated with different levels of investments in knowledge versus conservation implementation. In chapter four, the aim was to determine the return on investment from spending different amounts on survey data before undertaking a program of implementing new protected areas. We found that, after an investment of only US$100,000, there was little increase in the effectiveness of conservation actions, despite the full species dataset costing at least 25 times that amount. Surveying can take time because of expertise limitations, logistics and funding shortfalls. Biological diversity may be lost while data collection occurs conversely, not collecting enough data can lead to erroneous decisions. Additionally, resources spent on learning may be better spent on other actions. In chapter five, in a series of retrospective simulations, we compared the impact of spending different amounts of time collecting biological data prior to the implementation of new protected areas. The aim was to find the optimal survey period given the trade-off between gaining knowledge to improve conservation decisions while there is concurrent loss of habitat. We discovered that surveying beyond two years rarely increased the effectiveness of conservation decisions, despite a substantial increase in the knowledge of species distributions. Often there are choices between different actions and uncertainty as to which are the most effective. In chapter six, we discuss how the principles of adaptive management might be applied to conservation planning. Improving future management decisions through learning should be viewed as essential in all conservation plans but such learning is often included as a minor step, or is completely ignored. In this chapter we provide a brief overview of an adaptive framework for conservation planning and ideas for future research.

Using simulation data of a regional ocean model, Nardini et al. applied pathline predicates for a detailed post-hoc analysis of the Benguela upwelling system. In this work, we evaluate the accuracy of this technique. Using different temporal samplings, we aim at finding minimum requirements for the temporal resolution of the flow data in the context of retroactive particle pathline techniques. Besides the flow field, our simulation data contains synthetic tracer fields for different tracer source regions. Using the flow data, dense trajectories are computed to enable deriving ”emulated tracer fields” based on the local ratio of pathline particles originating from tracer source regions to other ones, which can then be compared to the original tracer fields. We find that the emulated tracer concentrations are overestimated in comparison to the original ones. However, the shape of the regions with high tracer concentration can be reproduced.

The Benguela Current is a cold eastern boundary current located on the south-western coast of the African continent. The establishment of its present day features approximately two million years ago has triggered allopatric events which have driven genetic and/or phenotypic differentiation in many of the warm-temperate organisms that previously had continuous distributions along the south and west coast of southern Africa. However, since many of these species have responded differently, despite similar isolation times, research in this region provides a unique opportunity to increase our understanding of evolutionary processes. The common octopus (Octopus vulgaris, Cuvier 1797) is a coastal, sedentary species, inhabiting coral reefs or rocky environments at depths of up to a 100m. It is considered to be one of the most extensively studied cephalopod species due to its worldwide distribution. However, very little research has been conducted on O. vulgaris in southern Africa. In order to gain a holistic understanding of the effects of the Benguela Current on population connectivity, genetic and phenotypic diversity, and evolutionary history of O. vulgaris, a comparative genetic and morphological study was conducted across the Benguela region. A total of 168 specimens of O. vulgaris were collected from four different regions across the Benguela system. A small tissue sample was preserved in ethanol for molecular analysis, and the specimen was frozen whole for morphometric analysis in the laboratory. Octopus vulgaris genetic population structure and evolutionary history was investigated using a 580bp fragment of the mitochondrial cytochrome b (cytb) gene for 76 individuals located within the Benguela region, yielding 10 different haplotypes. AMOVA and pairwise FST analyses revealed significant genetic differentiation suggesting a northern-southern Benguela divergence. Estimates of time since most recent common ancestor, based on biogeographical calibrators and coalescent analyses, indicated that isolation between the Angolan and South African population occurred between ~231 Ka and 1 Ma. Mismatch distribution analyses revealed a past population expansion within the South African O. vulgaris roughly 129.31 Ka, whilst Bayesian skyline plots were indicative of gradual demographic growth within the Angolan population in the last ~100 Ka. Observed O. vulgaris population structure and demographic history was likely the result of historical climate-induced change within the system. Reconstruction of phylogenetic relationships within the Octopus genus, using cytb and COI suggest that O. vulgaris is not a monophyletic group and a major systematic revision is required. Furthermore, unidentified individuals from South Africa were found to group with species from Indo-West Pacific Oceans and were therefore considered to have been translocated through ballast water from Asia. While the molecular analysis indicated a significant northern-southern Benguela structure results from the principle component analysis (PCA) and discriminate function analysis (DFA) were unable to distinguish between O. vulgaris from different sampling localities throughout the Benguela Current region based on soft-parts, hard-parts and meristic characters. The lack of phenotypic variation, despite significant genetic divergence, highlights the importance of multi-method approaches in gaining a holistic understanding of the taxonomy and biogeography of species.

La distribution d'espèces benthiques intertidales est contrainte par l'océanographie côtière. On connaît moins les effets sur l'écologie des prédateurs. Les côtes sud de l'Afrique sont caractérisées par des contrastes de production primaire et d'assemblages intertidaux dus aux deux courants majeurs qui les longent. Le prédateur apical de ces côtes est un oiseau limicole endémique, l'huîtrier noir africain (Haematopus moquini), qui présente un polymorphisme favorable à la spécialisation alimentaire. Ces travaux ont étudié l'effet des variations spatiales de structure de communautés benthiques sur l'écologie alimentaire de l'huîtrier à l'aide des isotopes stables. Les oiseaux répondent aux fluctuations qualitative et quantitative des communautés de proies à plusieurs échelles. A large échelle ils montrent de forts contrastes entre les côtes ouest et sud-ouest où le régime alimentaire est dominé par les moules, notamment l'espèce invasive Mytilus galloprovincialis et le sud-est où un mélange de moules et patelles est consommé. Localement les individus montrent des différences faibles d'alimentation liées à l'abondance relative des moules et patelles. Cela s'explique par le caractère généraliste de l'espèce et le relâchement de compétition intra-spécifique pour les ressources. La transition alimentaire d'H. moquini vers une consommation quasi-exclusive à l'ouest d'une moule introduite et la multitude de comportements alimentaires ailleurs indiquent un fort potentiel d'adaptation aux modifications de son habitat d'alimentation. En revanche la dégradation des plages par l'Homme augmente la compétition pour l'espace et affecterait aujourd'hui le succès reproducteur de l'espèce.

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