Historically the nutrient rich Benguela ecosystem supported large stocks of commercially important fish which sustained the Namibian fishing sector. Recently, non-exploited species i.e. bearded goby (Sufflogobius bibarbatus) and jellyfish (Chrysaora fulgida and Aequorea forskalea) have become more apparent and are described as key-species in this ecosystem. Empirical evidence for understanding the stock abundance and dynamics of S. bibarbatus and jellyfish are still sparse, as research focus has been mainly on commercially important fish. The abundance of these non-exploited species in relation to the environment and commercial species are also not well understood. Lack of methods to effectively assess jellyfish and S. bibarbatus have furthermore limited our knowledge. Acoustics can cover large water volumes and observe many trophic groups and interactions simultaneously hence currently proposed as the most reliable observation tool available to remotely study multiple species that are overlapping and widely distributed in marine ecosystems. For acoustic assessments using echo sounders, the ability to detect, identify and distinguish targets from each other and the echo ability (target strength: TS) of individual targets is pivotal to convert acoustic data from a calibrated system into significant biological measures. The lack of effective acoustic identification (ID) techniques and knowledge about TS of species may limit the application of acoustics. The swimbladder generally contributes more than 90% to the backscattered energy from fish, which makes knowledge of the swimbladder vital for understanding the acoustic properties of a fish. Prior to this study, the presence or absence of a swimbladder within S. bibarbatus has been uncertain. This thesis is an exploratory study addressing 1) the acoustic identification challenge of species in aggregating in mixed assemblages and 2) the acoustic characteristics of the target species. The latter two are of essence to assess the biomass, distributions and ecological interactions of these non-exploited. The multiple frequency data (18, 38, 70, 120 and 200 kHz) and trawl data used in this study were collected on a survey conducted by the RV G.O.Sars during April 2008 in the northern Benguela. Fifteen validated assumed to be ‘single species' trawl and acoustic datasets were selected and used in the application and developing of ID techniques. Traditional acoustic identification techniques (Sᵥ-differencing and relative frequency response r(f)) were adopted and found ineffective as standalones to discriminate the species under study. The overlaps in the Sᵥ differences of the three species complicated separation. A multivariate statistical approach, Linear Discriminant Analysis (LDA) was applied to predict which of the variables s[subscript(A)], S[subscript(A)], Δs[subscript(A)] and r(f) discriminated the three species groups from each other with a higher accuracy. It was found that by combining backscattering strength S[subscript(A)] and r(f) a correct classification accuracy of up to 95% could be obtained. Limitation is that the LDA technique as any classification method is not applicable in “real time” during surveys. A new technique, here within referred to as the Separator Technique, which incorporates the standard techniques, LDA results, a novel r(f) similarity comparison technique and a threshold s[subscript(A)] response technique was established. The effectiveness of the Separator Technique is in the recognition of similarities and stability in frequency response by simple correlation of the observed frequency response at systematic Sᵥ-threshold levels. Accurate acoustic classification depends on good and valid training datasets and there has so far not been a simple way of acoustically detecting if the selected assumed “pure” datasets is contaminated or not. Only available reliable source are the trawl samples. The r(f) similarity comparison method showed that some of the assumed ‘single species' trawls were mixed and that presence of <1% of strong scatterers could mask a weaker scatterer. By evaluating the threshold s[subscript(A)] frequency response, the proportion of thresholded backscattering could be quantified. A frequency which is more appropriate for the acoustic assessment of the respective species in mixed aggregations could also be identified. Further improvements of the Separator Technique are required in terms of the precise Sᵥ-cut levels. The presence of S. bibarbatus' swimbladder was confirmed from two thawed specimens. From further investigations on 26 dissections of sampled S. bibarbatus, the swimbladder was identified as a physoclist (closed swimbladder) with an extensive gas gland, and its morphology was roughly described as prolate spheroid shaped and with about 5ᴼ negatively tilted compared fish vertebra. This means that the strongest echo from a goby will be found when the fish is at about 5ᴼ head down relative to the horizontal. The in situ TS of 8 cm sized S. bibarbatus and the two jellyfish species: C. fulgida [umbrella diameter: 21.7 cm] and A. forskalea [16 cm] at multiple frequencies (18, 38, 70, 120 and 200 kHz) was estimated. At 38 kHz, the TS was -53 dB for S. bibarbatus, -58 dB for A. forskalea and -66 dB for C. fulgida. The single echo detection (SED) approach which is assumed to be a more accurate method for estimating TS than the previously applied methods for jellyfish. The TS results for S. bibarbatus are of similar magnitude to other published TS values of C. fulgida. This suggests that estimates of jellyfish may be overestimated due to inaccuracies in target identification. This thesis established the acoustic characteristics of jellyfish and S. bibarbatus within the northern Benguela which makes it possible to acoustically assess and monitor jellyfish and/or fish. The identification technique though still in early phases of development, can be applied to enhance quality of training datasets (samples) used in classification. This piece of work can reduce variability in biomass estimates that arises from masking or misclassification of echoes.

Two species of hake (Merluccius capensis and Merluccius paradoxus) account for most of Namibia’s fisheries catch, and they are important secondary consumers in the Benguela Current ecosystem. Inferences on their trophic relationships have been based mainly on stomach content analyses. However, such data are limited temporally because they represent only snapshots of recent feeding, and are quantitatively biased because of variation in the digestion rates of different prey. The principal aim of the thesis was to understand the trophic relationships of two hake species relative to each other, their known prey and top predators (demersal sharks) in the northern Benguela Current ecosystem (Namibia), using time-integrating trophic biomarkers. By using stable isotope (carbon and nitrogen) and fatty acid signatures of their muscle tissues, my overall objectives were to produce new knowledge about 1) hake ontogenic trophic relationships, 2) the contributions of different prey to hake diets, 3) hake dietary differences, and 4) some aspects of hake’s trophic relationships with demersal sharks. Tissues of hake (n=358), their potential prey (n=455), and demersal sharks (n=42) were collected between 2008 and 2012 during demersal bottom trawl surveys off Namibia, for stable isotope and fatty acid analyses. And more...

Thesis (M.A.)--Stellenbosch University, 1988. / ENGLISH ABSTRACT: The Benguela upwelling system off southern and south western Africa is a zone of strong and extensive upwelling. Owing to the greater fIsh numbers found along the front between the upwelling and South East Atlantic Ocean the frontal zone is a key element in the ecology of the upwelling area. This discourse focuses on the perturbations of this front. The major data source used was the daily Meteosat satellite imagery for the years 1978, 1979 and 1982 to 1985 in the visible and infrared wavebands. These data enable the investigation of cross frontal activity for the entire Benguela Upwelling System at various spatial and temporal scales. NOAA satellite infrared imagery was also used. At the macroscale two upwelling zones are described. The fIrst is the upwelling core along the coast which exhibits well-developed and persistent upwelling. Offshore of this is an area in where the more transient fllament activity predominates. This outer zone is one of constant change and presents highly variable frontal boundary locations. As far as the persistent upwelling is concerned, the northern boundary closely approximates that suggested by Shannon (1985) of l7oS. Cape Agulhas was the effective southern boundary of any regular upwelling. The mean offshore extent of the outer upwelling is 270 kilometres off Liideritz and 45 kilometres off Cape Town. An analysis of the seasonal location of the front shows that the greatest upwelling extent at both Liideritz and Cape Town is observed in winter. Although the winter upwelling extent is the greater of the two seasons, the summer frontal location at Cape Town, in turn, exhibits remarkable stability. The upwelling off Liideritz, on the other hand, is prone to almost constant frontal location fluctuations. . Most of the variation occurs as a result of the growth and decay of fllaments. Filaments were seen along the entire upwelling zone from Cape Agulhas to Cape Frio. On average, the fllament sector was 270 kilometres wide off Liideritz. Between Cape Point and Cape' Agulhas the southwards extent of the upwelling rarely exceeded 40 kilometres, while the maximum fllament off Cape Point was about 200 kilometres. A fllament at Cape Point generally extends about 40 kilometres westwards and the upwelling zone off Walker Bay stretches about 20 kilometres southwards, onto the Agulhas Bank. Along the coast between Cape Agulhas and Cape Point the fllaments rapidly react to changes in the wind speed and direction. Mesoscale weather systems are therefore important factors in determining fllament activity there. This also true to some extent at Liideritz. The berg wind can induce rapid fllament growth off Liideritz. Despite an upwelling positive wind direction it is the wind speed that determines whether upwelling will develop at Cape Town at all. At Liideritz the wind speeds appear to determine the cross frontal temperature gradient. The greater the wind speed, the steeper the temperature gradient. Cross frontal temperature gradient of between 0.020C and .006oC per kilometre were calculated for Liideritz, which compares well with readings in the Californian upwelling zone (Koblinsky et al. 1984). In the way fllaments extend the length of the frontal zone greatly and the manner in which these cold water streams react to the changing winds, they are complex upwelling frontal features of great variability and importance in the Benguela upwelling system. / AFRIKAANSE OPSOMMING: geen opsomming

Oceanographic features such as currents, fronts and upwelling cells have been recognised as possible factors driving population differentiation within species. The Benguela Current is one of the oldest upwelling systems in the world, located off the west coast of Southern Africa, and represents a biogeographical boundary between the Atlantic and Indo-Pacific Oceans. Previous studies have reported the influence of this system in isolating several marine taxa between the two oceans. However, few have been conducted within the Benguela Current boundaries, in order to understand its role in shaping population genetic structure of fish species at a regional level. The present study documents the influence of the Benguela Current oceanographic features on the genetic differentiation, population connectivity and evolutionary history of five coastal fish species (Diplodus capensis, Argyrosomus inodorus, Argyrosomus coronus, Atractoscion aequidens and Lichia amia), and one oceanic pelagic fish species (Thunnus albacares). Results for both mitochondrial and nuclear marker variation in all coastal species revealed a similar geographical pattern of population genetic structuring despite distinct differences in life history features. The oceanic species exhibited shallow population differentiation between Atlantic and Indian Oceans. For coastal species, different depths of differentiation were observed, ranging from speciation events (A. aequidens, A. coronus and A. japonicus) to shallow structuring (A. inodorus and T. albacares). Furthermore, in these cases, population structures were coincident with the Benguela Current oceanographic features, suggesting that the system may represent a vicariant barrier to dispersal of coastal fish species. Congruence between mitochondrial and nuclear markers suggests that population isolation was not a single historical event, but has persisted over large timescales and is still active. The existence of cryptic speciation events, and the high levels of genetic diversity and differentiation documented make the Benguela Current a natural laboratory to study evolutionary mechanisms shaping biodiversity and genetic population structure of marine fish species.

Philosophiae Doctor - PhD / Although jellyfish are recognised recently as key components that can influence ecosystem functioning and trophic flows in the northern Benguela upwelling ecosystem, the number of published studies on their abundance, seasonality, life history and ecological roles off Namibia is strictly limited. Chrysaora fulgida is one of the most common and conspicuous medusae in the plankton off Namibia, and has flourished in the region, following the decline of the pilchard fishery at the end of the 1960s. It is said that their biomass (together with Aequorea forskalea) exceed that of the commercially important fish stocks off Namibia. In addition, this species is also capable of forming large swarms in northern Benguela where they are a nuisance to fisheries operations. The objective of this study is to try and fill gaps regarding our knowledge of the biology and ecology of Chrysaora fulgida off Namibia, with a view to improve our understanding of its success in the northern Benguela ecosystem. In the Chapter 1, a general overview on the current knowledge and population dynamics of jellyish blooms and their ecology is compiled. Other key topics of the thesis such as jellyfish life cycles and their reproduction are also introduced. Chapter 2 investigates the temporal changes in the jellyfish community in Walvis Bay over a 23-month period from biweekly plankton samples. All twelve of the recovered taxa were characteristically neritic, and included meroplanktonic Hydrozoa and Scyphozoa, as well as cydippid ctenophores and shallow water siphonophores. Whilst, ephyrae of Chrysaora fulgida were dominant overall, and peaked in abundance during mid-spring (Year 2012: 168 933 ind. 100 m-3) and late winter (Year 2013: 23 389 ind. 100 m-3), they were not present all year round, being replaced (in part) by Obelia in summer and autumn, Bougainvillia in spring and summer, and Muggiaea atlantica in summer. Seasonal changes in the composition and structure of the community were driven primarily by bottom water temperature and day length (explaining 24% of the variability in community structure), with wind speed and moon illumination playing a secondary role. The recruitment of ephyrae of C. fulgida to the plankton off Walvis Bay is confirmed not to be continuous throughout the year. Chapter 3 present the first detailed investigation on the identification, morphological development and growth of wild caught ―ephyrae‖ of the scyphozoan Chrysaora fulgida and Chrysaora africana in Walvis Bay, off Namibia. Concrete morphological dissimilarities are documented to distinguish C. africana from C. fulgida, despite the limited sample size of C. africana: coloration differences and the presence/absence of branched canals on the periphery of velar and rhopalial canal tips. In the case of C. fulgida the morphological development from an ephyra (Stage 0) to a juvenile medusa could be described successfully in six stages, whilst missing stages were noted for C. africana. In general, the development of ephyrae described here agrees with patterns described for other species in the genus from elsewhere. The ephyrae stages of C. fulgida illustrated a low overall growth rate (4.33 and 3.45% d-1, respectively) and longer ontogenic development (~164 days), respectively, than most other jellyfish species. Through the histological examination of medusa gonads, Chapter 4 investigates the sexual reproduction and maturation of both Chrysaora species, collected off Walvis Bay, Namibia. Both species were non-brooding, gonochoristic, displayed a 1:1 sex ratio and exhibited no clear sexual dimorphism features. Gametogenesis in both species was similar to that displayed by other Discomedusae, whilst some differences in gonad maturity were evident between them – Chrysaora fulgida displayed aseasonal, reproductive heterogeneity (maturing at ~300 mm diameter) and individuals were semelparous, whilst C. africana appeared strongly seasonal but iteroparous. Through stable isotope analysis (𝛿13C, 𝛿15N and C:N ratios), Chapter 5 examines the presence of tissue, ontogenetic, seasonal, spatial and interspecific variability in medusae of Chrysaora fulgida and Chrysaora africana off Walvis Bay, in the northern Benguela, Namibia. This study did not only illustrate size-associated shifts in trophic ecology, but also revealed spatial, inter-species and some tissue differences in the northern Benguela upwelling system. Size would appear to be the over-riding factor that influences the isotope signatures of Chrysaora fulgida; size being linked in turn to space. A clear negative relationship is illustratred between 𝛿15N and individual size for two scyphozoans (C. fulgida and C. africana) off central Namibia, indicating that larger jellyfish feed lower down the food chain than smaller ones in both species. This is explained by the need and ability of ephyrae and small medusae to access the microbial food web which consists of many trophic steps and hence numerous opportunities for enrichment of nitrogen isotopes, resulting in higher 𝛿15N values of smaller individuals. Chapter 6 provides a synthesis of the main findings of the thesis, and makes recommendations on ways that the research can be carried forward. / 2020-08-31

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.