Browsing by Author "Moloney, Coleen L"

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    Combined fishing and climate forcing in the southern Benguela upwelling ecosystem: an end-to-end modelling approach reveals dampened effects
    (Public Library of Science, 2014) Travers-Trolet, Morgane; Shin, Yunne-Jai; Shannon, Lynne J; Moloney, Coleen L; Field, John G
    The effects of climate and fishing on marine ecosystems have usually been studied separately, but their interactions make ecosystem dynamics difficult to understand and predict. Of particular interest to management, the potential synergism or antagonism between fishing pressure and climate forcing is analysed in this paper, using an end-to-end ecosystem model of the southern Benguela ecosystem, built from coupling hydrodynamic, biogeochemical and multispecies fish models (ROMS-N 2 P 2 Z 2 D 2 -OSMOSE). Scenarios of different intensities of upwelling-favourable wind stress combined with scenarios of fishing top-predator fish were tested. Analyses of isolated drivers show that the bottom-up effect of the climate forcing propagates up the food chain whereas the top-down effect of fishing cascades down to zooplankton in unfavourable environmental conditions but dampens before it reaches phytoplankton. When considering both climate and fishing drivers together, it appears that top-down control dominates the link between top-predator fish and forage fish, whereas interactions between the lower trophic levels are dominated by bottom-up control. The forage fish functional group appears to be a central component of this ecosystem, being the meeting point of two opposite trophic controls. The set of combined scenarios shows that fishing pressure and upwelling-favourable wind stress have mostly dampened effects on fish populations, compared to predictions from the separate effects of the stressors. Dampened effects result in biomass accumulation at the top predator fish level but a depletion of biomass at the forage fish level. This should draw our attention to the evolution of this functional group, which appears as both structurally important in the trophic functioning of the ecosystem, and very sensitive to climate and fishing pressures. In particular, diagnoses considering fishing pressure only might be more optimistic than those that consider combined effects of fishing and environmental variability.
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    Community composition, migration and trophic positions of micronekton in two biogeochemical provinces of the South West Indian Ocean
    (2015) Annasawmy, Pavanee; Moloney, Coleen L; Menard, Frederic; Ternon Jean-Francois; Potier, Michel
    Micronekton fauna was investigated as part of a multi-disciplinary research project carried out in two different bioregions of the South West Indian Ocean: the East African Coastal Province (EAFR) and the Indian South Subtropical Gyre (ISSG). Food web structure was addressed using stable isotopes. Since particulate organic matter had high δ 15 N values in the ISSG province, copepods were chosen as baseline in trophic level estimations. Feeding regime and size were shown to influence the trophic position of micronekon. In the ISSG, carnivores (fishes and squids) and omnivores (crustaceans) had higher δ 15 N values and trophic positions than filter feeder s (gelatinous organisms such as salps and pyrosomes) and detritivores (leptocephali larvae). Fishes and squids encompassed a wide range of overlapping isotopic niches suggesting that organisms across different trophic levels feed on the same resources. Estimated trophic levels ranged from 1.67 to 4.73, showing that micronekton in the ISSG can be tertiary consumers. An average enrichment value of 6.7 ‰ was recorded between the sampled micronekton specimens and swordfish Xiphias gladius in the ISSG. Trawls, being selective in nature, were shown to sa mple smaller - sized micronekton with a lower trophic position than the micronekton being eaten by swordfish. In the EAFR, mean δ 15 N values of micronekton were higher than in the ISSG, exhibiting slightly higher trophic levels. Mesoscale dynamics in the EAFR provide mechanisms that enrich surface layers in nutrients and chlorophyll - a, therefore contributing to a higher abundance and micronekton species richness. In the ISSG, the large - scale wind - driven anticyclonic gyre pushes the nitracline, thermocline and deep chlorophyll maximum deeper in the water column , influencing the diel migration patterns of micronekton , with a significant proportion of micronekton staying in deep layers or slightly above the thermocline at dusk . Regardless of the differences in the ISSG and EAFR in δ 15 N values and trophic positions of micronekton, larger - sized swordfish sampled from these two provinces had similar mean δ 15 N values since swordfish are highly migratory and forage in different p arts of the Indian Ocean. However, smaller - sized swordfish specimens had lower mean δ 15 N values. With a combination of trawl surveys, stable isotope estimates, stomach content and acoustic analyses, this study shed new light on trophic interactions in the oligotrophic ISSG province.
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    Developing dynamic energy budget (DEB) models for small pelagic fishes in the Southern Benguela
    (2021) Groenewald, Grea; Moloney, Coleen L; van der Lingen, Carl D
    Dynamic energy budget models are useful for describing energy flow in individual organisms as functions of their state (e.g., age, size, and energetic reserves) and environment (e.g., food and temperature). Anchovy (Engraulis encrasicolus), redeye round herring (Etrumeus whiteheadi) and sardine (Sardinops sagax) are short-lived fish species co-occurring in the Southern Benguela upwelling system, where they experience marked environmental variability. This study developed full life cycle dynamic energy budget models of these species in the Southern Benguela, which could be compared to the same or similar species in other ecosystems and investigated trade-offs between temperature and feeding conditions in influencing the growth and reproductive outputs of the three species. The key hypothesis was that there would be niche differences among bioenergetic factors for the three species that allow them to cooccur. Models were created and calibrated using published information and survey data (recruitment, biomass, weight-at-length) from 2012-2016. Best visual fit values were estimated for five parameters, using von Bertalanffy growth models and length-weight relationships of each species. Results indicated that redeye round herring invested less than anchovy and sardine in reproductive storage capacity (larger maintenance ratio) and had lower assimilation rates. Sardine had higher structural growth costs than anchovy and redeye round herring. Larval redeye round herring took longer to reach metamorphosis than anchovy and sardine. In all three species, decreased growth rates of larvae in cool waters were mitigated by increased growth from good food availability. Good feeding condition associated with cooler temperatures halved the time spent as recruits in all three species. Thus, increased growth rates from good food availability outweighed decreased growth rates from cool temperatures and resulted in higher egg batch production in adults. Comparisons of Southern Benguela anchovy and sardine to similar species in other ecosystems showed differences in core parameters between regions because of the influence of environmental inputs and species differences, indicating that model parameters may not be species-specific or transferable between ecosystems. Differential responses of small pelagic fish species to environmental factors help in understanding the variable population dynamics of these species and can help predict the impacts of climate change.
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    Distribution and predictors of non-indigenous marine species within South Africa's MPA network
    (2016) Brooker, Ben; Robinson, Tamara; Moloney, Coleen L
    Considering the continual dissemination of marine non-indigenous (NIS) species across biogeographic borders, little is known about the status of these species within the network of South African marine protected areas (MPAs). Using the most recent data, a target list of NIS was set up for each MPA. Nineteen of the 23 South African MPAs were surveyed intertidally for alien and invasive species. The intertidal zone was divided into high-, mid- and low-shore and surveys were conducted during spring low tide. The presence and location in the intertidal zone of alien and invasive species were recorded. Additionally, invasive species' biomasses were quantified at sites at which they were found. Classification and regression tree (CART) analysis was used to assess which factors result in high numbers of NISs within MPAs. The invasive Mediterranean mussel, Mytilus galloprovincialis, was the most widespread species, occurring in 13 of the 19 sampled MPAs. It was most prominent on the island MPAs of the West Coast National Parks and had an overall highest biomass in the mid-shore. The bryozoan, Bugula dentata, was also widespread - present in MPAs across all three ecoregions. The invasive acorn barnacle, Balanus glandula, and bisexual mussel, Semimytilus algosus, both exhibited high levels of invasion in MPAs on the west coast. Extensions of known ranges were recorded for a number of species: the bryozoans Bugula dentata, Watersipora subtorquata and Cryptosula pallasiana, the polychaete Neodexiospira brasiliensis, the amphipod Orchestia gammarellus and the hydrozoan Obelia dichotoma. Certain species were recorded outside of harbours for the first time: the hydrozoans Obelia dichotoma and Obelia geniculata, the bryozoan Cryptosula pallasiana and the ascidians Microcosmus squamgiger and Diplosoma listerianum. CART analysis indicated that the size of the nearest port was an important indicator of the number of alien species in an MPA. When the nearest port is bigger than 0.4 km², more alien species are likely to occur within that MPA. For invasive species, the distance to the nearest yacht marina was the most important factor, with MPAs within 3.7 km of a yacht marina being more likely to have more invasive species in their borders. For all NISs, the highest numbers in an MPA were expected when the nearest port was greater than 2.1 km² and the nearest yacht marina was within 3.7 km of that MPA. Using these findings, spatial planning of future MPAs can further be prioritised to minimise the risk of introduction and spread of NIS therein. MPAs at risk as defined by these findings require structured monitoring regimes. A proactive measure would be establishing an interdisciplinary forum between relevant management authorities in order to enable dissemination of information on NIS. While controlling established NIS is difficult, the creation of task groups to act as rapid response teams for NIS, and the possibility of small-scale fisheries from edible invasive species are practical avenues that could be explored as mitigation efforts.
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    Effects of cannibalism, maternal age and varying fish selectivity in age structured models of deep water hake populations
    (2011) Koch, Erich; Moloney, Coleen L
    An Age Structured Model (ASM) was develop in which dynamic and density-dependent cannibalism was included as a top-down control on a modeled population of M. paradoxus which used spawner biomass and maternal based recruitment. The ASM was used to evaluate the effects cannibalism had on age structure, recruitment and spawner biomass of the modeled population. The development of the model was described and evaluated with special emphasis on incorporating cannibalism and maternal based recruitment.
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    Environmental influences on banana shrimps of the Sofala Bank, Mozambique Channel
    (2015) Malauene, Bernardino Sergio; Moloney, Coleen L; Roberts, Michael J; Marsac, Francis; Penven, Pierrick; Lett, Christophe
    The Sofala Bank in the western Mozambique Channel is an essential habitat for shallow-water penaeid shrimps. It supports an important multi-sector and -species fishery, with Fenneropenaeus indicus and Metapenaeus monoceros (banana shrimp) being the two main target species. Over the past decade this valuable resource has been declining, which has been attributed to environmental changes, but no conclusive evidence has been found. This PhD thesis aims to understand the interactive roles of biophysical processes on recruitment of banana shrimps, par ticularly their larvae on the Sofala Bank. It is hypothesized that shrimp larvae can be advected offshore by passing mesoscale eddies to regions where they are unable to survive and are thus lost. In the absence of both physical and biological observations, a modelling approach is used. A high-resolution, nested, coastal, Regional Ocean Modeling System (ROMS) of the Sofala Bank is developed. In general, the model agrees well with available observations and literature. The ROMS outputs and self-organizing map analysis indicate that the shelf circulation, structure and river plumes are strongly influenced by the highly energetic o_shore eddy activity. A biophysical, individual-based model (IBM) coupled to the ROMS was developed for early life stages of banana shrimps on the Sofala Bank. The IBM uses spawning patterns identified from analyses of both commercial and research survey data. Simulations indicate that shrimp larvae are lost offshore by entrainment in mesoscale eddies at inter- and intra-annual scales and eddies therefore are unlikely to produce a continuous declining in the catch. In contrast, these eddies induce onshore transport of larvae, promoting coastal settlement, compared with periods without eddies. Locations for simulated larval coastal settlement are identified: northern, central and southern. The roles of tides and larval diel vertical migration in influencing simulated larval settlement success was not conclusive; further research considering a selective tidal stream is needed. Simulated larvae were sensitive to low lethal temperature and river plumes. A conceptual model for the Sofala Bank circulation and another for the banana shrimps, early life history dynamics are proposed based on the results of this thesis.
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    Environmental variables influencing spatial and temporal patterns of fish spawning and recruitment
    (2017) Mbatha, Fisokuhle Lungile; Moloney, Coleen L; Ostrowski, Marek; Lipinski, Marek
    ABSTRACT Spawning times and spawning intensity during the life cycles of some fish species found off South Africa and Norway were synthesized using data collected from the literature. The comparison of temporal patterns in spawning of South African fish species showed variable spawning times and intensity depending on the environmental conditions within that spawning habitat. Their spawning migration durations were suggested to be short since they inhabit a dynamic coastal upwelling ecosystem with intra-seasonal differences caused by changes in upwelling strength enhanced by south-easterly winds, nutrient-limited waters on the spawning grounds and stable thermal conditions. This contrasts with Norwegian fish species, which showed patterns of spawning times and durations that are restricted and confined to spring (February – May), probably due to strong, consistent seasonality, depending on primary production. This explains the inter-annual differences observed in their spawning periods, where strong south-westerly winds (downwelling), light intensity and salinity stratification could influence long spawning migrations. For Cape hakes, environmental variability influencing recruitment was further investigated on the west coast nursery grounds of the southern Benguela, particularly for deep-water Cape hake (Merluccius paradoxus). Biophysical characteristics of the west coast nursery grounds were assessed in relation to distribution of deep-water Cape hake juveniles (< 15 cm) using physical data (CTD, alongshore wind speed anomalies) and biological data (abundance/density of hake juveniles, recruitment estimates). Distinct spatial patterns of hake distribution were evident in relation to near-bottom environmental factors (temperature, salinity and oxygen). Nansen surveys conducted from 2003 – 2013 during summer (January – February) showed greater abundance of hake juveniles over the Orange Banks than in other nursery areas. The hake juveniles occurred in mid-shelf waters with oxygen depletion (2 – 3 mL O₂.L⁻¹) and hypoxic conditions (< 2 mL O₂.L⁻¹) and temperature ranges of 7 – 11 ⁰C. Salinity appeared to have less influence on hake juveniles' distribution. During spring surveys, hake catches were reduced on all nursery grounds except near Cape Columbine. There was a strong positive correlation between deep-water Cape hake recruitment indices and summer wind speed anomalies for the same year (Lag = 0 year) and with autumn wind speed anomalies of the previous year (Lag = 1 year). The relationship between winds and near-bottom oxygen concentrations on the Orange Banks is unclear and needs to be investigated.
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    Growth and otolith zone formation of Namibian hake, merluccius capensis
    (2012) Wilhelm, Margit Renate; Jarre, Astrid; Moloney, Coleen L; Roux, Jean-Paul; Durholtz, M Deon
    Life history traits and tactics of commercially important Namibian shallow-water hake, Merluccius capensis, were investigated in relation to their environment. A time series of length-frequency distributions (LFDs) from otoliths collected from fur seal scat samples was used to identify cohorts and calculate the approximate hatchdates and growth rates of young M. capensis from 1994 to 2009. Monthly otolith samples of five of these cohorts (1996, 1998, 2002, 2005 and 2006) were used to evaluate the translucent zone periodicity over the first 21 months of their life. Additionally, LFDs from research surveys and commercial samples were used to calculate growth rates for M. capensis up to 65 cm total length (TL), and to further validate the translucent zone formation of three of the five cohorts (1996, 1998 and 2002) on fish up to 3.5 years old.
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    Measurements of the branchial sieve of sardine (Sardinops sagax ocellatus) from the west and south coasts of southern Africa
    (2010) Idris, Izwandy; Moloney, Coleen L; Van der Lingen, Carl D
    Branchial sieves of southern African sardine (Sardinops sagax ocellatus) were collected from three geographical regions along the southern African coast: Namibia, the south coast and the west coast of South Africa. Sardine from Namibia represented the northern Benguela upwelling ecosystem while sardine from the west and south coasts of South Africa represented the southern Benguela upwelling ecosystem. Morphometric measurements (gill arch length and gill raker spacing) and counts (number of gill rakers) of branchial sieves on the left side of the first gill arch were taken to determine whether the sardine from these regions have different branchial sieve structures.
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    Meristic and morphometric variation among sardine Sardinops sagax around the coast of southern Africa
    (2009) Wessels, Grea; Moloney, Coleen L; Van der Lingen, Carl D
    Meristic counts and morphometric measurements were made on previously frozen sardine Sardinops sagax to determine whether there is a difference in the shape of sardine from different areas around southern Africa. Because freezing influences body size, eight different freezing periods were examined to determine the effects of freezing duration on the caudal length, weight and 21 morphometric measurements of sardine collected from commercial catches at Gans Bay and Saldanha Bay, South Africa. The relative weight loss of sardine ranged between 0.86 and 2.49% and the relative loss in caudal length ranged between 1.57 and 2.54%. Most of the morphometric measurements showed small changes with increasing freezing period and, if they decreased, the decrease was gradual. Samples for the morphometric study were frozen between 12 and 17 weeks before analysis. Independent sample t-tests between these freezing periods confirmed that there was no change in the morphometric measurements over this five week period. In total, 35 samples were collected from three main regions: Namibia, the South African west coast and the South African south and east coast.
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    Modelling the effects of spatio-temporal spawning variability on the transport and retention success of sardine (Sardinops sagax) eggs and larvae around South Africa
    (2018) McGrath, Alice; Moloney, Coleen L; Van der Lingen, Carl D; Hermes, Juliet C; Roy, Claude
    The transport and retention of sardine (Sardinops sagax) eggs on the west and south coasts of South Africa were investigated using a Lagrangrian, particle tracking, individual-based model (IBM), coupled with two 3-D hydrodynamic Regional Ocean Modeling System (ROMS) model configurations of different generations. The same IBM is coupled with PLUME, an older ROMS model configuration used in a previous sardine IBM for the southern Benguela, as well as BENGSAFE, a more recent, better resolved ROMS model configuration. Results from the two runs were compared to see if and how the underlying ocean model affects modelled retention and transport. An updated IBM, extended spatially and temporally to better represent sardine spawning and recruitment, was then coupled with the BENGSAFE model configuration, and assessed. The effects of spawning area, and month, year and depth of particle release, were investigated for each coupled 3D-IBM simulation using linear models. The portion of particles transported from the south coast to the west coast was a focus throughout, as this is of great importance to the management of the sardine fishery. In all simulations, three main systems were identified depending on where particles were released and recruited. Two of these systems were retention-based: particles released on the west coast and retained in the west coast recruitment area (WC-WC), and particles released on the south coast and retained in the south coast recruitment area (SC-SC). The other system is transport-based and represents particles released on the south coast and transported by ocean dynamics to recruit in the west coast recruitment area. Results were similar for the west coast when either hydro- dynamic model configuration was used; depth of release proved to be important in this system with its effect varying depending where on the west coast particles were released. Differences occurred on the south coast, with more transport to the west coast and more offshore loss in the higher resolved BENGSAFE IBM than the PLUME IBM. The difference was attributed to the positioning of the PLUME model's boundary in close proximity to the Agulhas Current, and the conditions at this boundary not properly resolving the current. The initial BENGSAFE IBM was spatially restricted to match the PLUME IBM, and therefore south coast spawning and recruitment was not fully represented. Therefore, the BENGSAFE IBM was spatially extended on the south coast and run for a longer time period. Similar results were obtained in the extended BENGSAFE IBM and the initial BENGSAFE IBM. However south coast retention increased and the average percentage of particles transported to the west coast decreased slightly. Spawning area proved to be an important determinant of retention and transport success in all recruitment systems, and the further east a particle was spawned the less likely it was to be transported to the west coast, and the more likely it was to be retained on the south coast. Transport to the west coast was most successful in late winter; a significant monthly effect on transport success was present. Correlations between standardised anomalies for stock assessment model estimated recruitment and IBM modelled retention/transport for the west and south coast were not significant, highlighting that retention and transport are not the only determinants of recruitment success. The extended BENGSAFE IBM can act as a base level to which extra layers of biological complexities can be added, such as horizontal and vertical egg distribution matching observations, incorporating gonadosomatic index (GSI) values, diurnal vertical migration and buoyancy.
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    Progress towards marine ecosystem observing systems in South Africa
    (2007) Moloney, Coleen L; Shillington, Frank A
    Marine ecosystem observing systems combine measurements, observations and models through a data management and interpretation process to provide information on the status of marine ecosystems. Both biotic and abiotic aspects of the marine environment need to be considered. Single variables typically can be used to represent aspects of the physical and chemical environment, but ecosystem indicators are required for the living components. There are no true marine ecosystem observing systems globally, because most observing systems focus on the physical environment. In South Africa, some fledgling systems are being developed, using the knowledge base provided by focused marine ecosystem research over the past 30 years. Further development should be based on international guidelines, which highlight three interrelated elements : (i) Measurements, obtained directly from ships, drifters or buoys, or remotely from satellites. In South Africa, sustained, long-term measurements are hampered by limited available ship's time, lack of suitable instruments, and insufficient qualified personnel. (ii) Models and other analytical tools to augment observations. South Africa is making progress in marine modelling, but not in marine data assimilation; qualified persons need to be attracted, trained and retained. (iii) Archived and disseminated data generated from measurements and models. The infrastructure and human and institutional capacity for data management and communication in South Africa needs to be enhanced. Existing programmes contribute towards the development of an effective marine ecosystem observing system, but its sustainability requires support at an institutional level.
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    A re-evaluation of the life history strategy of Cape horse mackerel, Trachurus capensis in the southern Benguela
    (2012) Mc Laverty, Kathryn J; Moloney, Coleen L; Van der Lingen, Carl D
    The life history strategy of the Cape horse mackerel, Trachurus capensis in the southern Benguela, relating to distribution and reproductive ecology, was re-evaluated. It is possible that certain aspects of the species' life history may have changed since the previous assessment by Barange et al. (1998), as a result in this study, the conceptual hypotheses about the life history of horse mackerel proposed by Barange et al. (1998) were re-evaluated and possible revisions proposed. Distribution patterns were analysed using acoustic and midwater trawl data (1997-2010), and demersal trawl data (1984-2011) collected during biannual surveys of pelagic and demersal fish.
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    Short-term dynamics of nano- and picoplankton in the southern Benguela upwelling system
    (2022) Dames, Nicole Rebecca; Moloney, Coleen L; Rocke, Emma; Rybicki, Edward; Pfaff, Maya
    Wind driven coastal upwelling influences the overall physical and chemical properties of coastal regions, as well as the small phytoplankton and microbial communities responsible for the productivity and biogeochemistry governing many of these properties. These environmental changes can influence picoplankton (0.3–3 µm) and nano-picoplankton (0.3–10 µm) at different time scales; in this thesis daily changes were of interest because of the cyclic (3–7 days) nature of wind-driven upwelling. Daily variability of picoplankton was studied during an upwelling cycle at a single station in Elands Bay. Using amplicon sequencing of the 16S and 18S rRNA gene region, as well as additional supplementary environmental data, it was found that picoplankton diversity, community structure and primary metabolism varied between the active and relaxation periods of an upwelling cycle. The results highlighted the complexity of picoplankton dynamics in variable environmental settings. However, the question then became whether nano-picoplankton dynamics were as complex in a post-upwelling setting. This was assessed in autumn (post-upwelling period) in St. Helena Bay by measuring primary productivity and nitrogen cycling over five days from three depths at a single station. Using stable isotope tracer and flow cytometry analyses it was determined that primary productivity was supported by regenerated production and that nano-picoplankton were responsible for up to 90% of the net primary production, with nanoeukaryotes and heterotrophic bacteria dominating at the surface and at depth. Increased resolution of nano-picoplankton community composition, structure and potential metabolism was obtained using metagenomic analyses of samples taken at the same depths and days as the productivity study. A strong depth-differentiation in community structure and potential metabolism was found over the five-day period, with little variability observed from day to day. Metagenome abundances of transporter genes for processes like ammonium uptake and nitrite oxidation were found to be good indicators of measured process rates using isotope tracers. This research has highlighted the complex structure of picoplankton and nano-picoplankton communities in a coastal setting, and has shown how diversity, function and biotic interactions are strongly influenced by the properties of the surrounding water column.
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    The effects of escape panels on commercial catches of juvenile hakes (Merluccius spp.) off South Africa
    (2005) Popose, Gcobani; Moloney, Coleen L
    The South African hake fishery has experienced a decline in catches in recent times and juvenile catches now constitute a large portion of the catches. This study was undertaken to test three different juvenile exclusion panels (square mesh, plastic grid and large mesh) in minimizing the volumes of juvenile hake (primarily Merluccius paradoxus) caught in otter trawl nets. Five trawling vessels were used for this experiment and their catches were compared to those immediately prior to the experiment, and to catches of nine trawling vessels (control vessels) fishing in the same general location during the same period. The control of the deployment of these trawling vessels was a limiting factor in the study, and that influenced the results of this experiment. The results of comparing the proportions of small hake caught by each vessel before and during the experiment indicated that two of the five vessels caught fewer small hake during the experiment. However, this was probably caused by reduced availability of small hake during the experiment. When the different gear types were compared with the controls using a normal approximation of a chi-square test, there were no significant differences in the proportions of small hake caught (square mesh, p = 0.4344; large mesh, proportion increased and plastic grid, p = 0.5617). When a general linear model was applied to the catches and other explanatory variables, no significant differences in the catches of small hake could be attributed to gear type. More investigations of gear selectivity in otter trawl nets are needed, using a more comprehensive data set, and a better-controlled deployment of fishing.
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    Trace metal effects on phytoplankton in subpolar seas with special emphasis on coccolithophores
    (2017) Harington, Amy; Poulton, Alex; Lucas, Michael I; Moloney, Coleen L
    Coccolithophores are a biogeochemically important phytoplankton group, fulfilling an important role in the global carbon cycle through primary production and the formation and export of calcium carbonate. Despite this biogeochemical importance, relatively little is known about their ecophysiology, for example their response to nutrient availability in terms of both macronutrient (nitrate, phosphate) and micronutrient (trace metal) or how this impacts on their competition with other phytoplankton groups (e.g. diatoms, Synechococcus). Hence, this study investigated the response of coccolithophores to trace metal (iron, zinc and cobalt) additions in the high latitude North Atlantic (Iceland and Irminger basins) and the Southern Ocean (Great Calcite Belt, Scotia Sea). The response of coccolithophores to environmental conditions was investigated by examining distribution patterns in situ and in targeted bioassays where natural communities were incubated with elevated levels of trace metal concentration. The wide range of initial conditions for these bioassays (e.g. temperature, macro- and micro-nutrient availability and phytoplankton community composition), provided valuable insights into coccolithophore responses to trace metal addition across a range of different biogeographic regions. These responses were investigated in terms of coccolithophore cell abundances, species composition, calcite production and growth rates, and were contrasted with responses of the total phytoplankton community (chlorophyll α) and abundances of diatoms and other phytoplankton groups (e.g. Synechococcus). The major finding of this thesis is that iron addition positively enhances coccolithophore growth rates and calcite production in both the Northern and Southern subpolar oceans. Another significant finding was that zinc addition also positively enhanced growth rates of coccolithophores (and diatoms) in a number of bioassays across the Great Calcite Belt (Southern Ocean). Thus, the trace metals iron and zinc are important micronutrients to consider in regulating coccolithophore growth and calcite production. As climate change potentially altering the flux of such trace metals to the ocean it is therefore important to further investigate the role of these micronutrients in regulating coccolithophore communities and their biogeochemical impact.
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    Trophic models of the Benguela upwelling system : towards an ecosystem approach to fisheries management
    (2000) Shannon, Lynne Jane; Field, John G; Moloney, Coleen L; Jarre, Astrid
    Periods of anchovy and sardine abundance alternate in many upwelling areas. In the southern Benguela ecosystem, anchovy were dominant in the 1980s whereas sardine abundance increased in the 1990s. Mass-balanced models were constructed of the trophic flows in the southern Benguela ecosystem for 1980-1989 and 1990-1997 and in the northern Benguela ecosystem for the 1980s, based on the best available data and estimates. Comparing biomass per trophic level, transfer efficiencies, mixed trophic impacts and several other ecosystem-level attributes suggests that trophic functioning of the southern Benguela ecosystem was similar in the 1980s and 1990s. However, because stocks and catches of small pelagic fish and model zooplankton biomass were larger in the 1990s, the ecosystem was less tightly constrained by predators and food availability than in the 1980s. An extension ofOdum's development theory also suggests that the ecosystem was more mature in the 1990s. Using the trophic models, indices quantifying interactions between species and trophic groups were developed to provide useful measures for the comparison of marine ecosystem structure and function. A new trophic similarity index for anchovy and sardine explains the strong similarities in trophic functioning of the southern Benguela ecosystem in the 1980s and 1990s. Modelling experiments using the dynamic ecosystem simulation tool Ecosim, suggest that observed changes in pelagic fish catches between the 1980s and 1990s are unlikely to have played a large role in driving changes in abundance of anchovy and sardine in the southern Benguela ecosystem. It is hypothesized that changed environmental conditions may have influenced the size composition of planktonic food of anchovy and sardine, thus changing their relative abundance, with some signs of a "regime shift' from anchovy to sardine dominance. Steady-state models show that there are structural and functional differences between the northern and southern Benguela sub-systems. Dynamic simulations of altered fishing strategies show that in the south, heavy fishing on model hake and small pelagic fish has larger negative effects on horse mackerel and large pelagic fish respectively than in the north. There are large differences between the effects of altered fishing simulated under different assumptions oftop-down and bottom-up flow control. A new way of approaching fisheries management is proposed according to a 4-step plan using information from ecosystem modelling studies to address the call for "responsible fishing" and the need to take ecosystem effects into account in managing fisheries.
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    Using cell size to represent phytoplankton diversity in studies of nitrogen dynamics in the southern Benguela
    (2017) Atkins, Josephine ffion; Moloney, Coleen L; Bernard, Stewart; Machu, Eric
    Phytoplankton are a key component in the functioning of marine ecosystems and play a central role in the cycling of nitrogen and other elements. Metrics that can adequately represent the biogeochemical processes associated with phytoplankton diversity are needed in order to make use of remote sensing and modeling platforms. A single-value size proxy, effective diameter (Deff ), represents the mean volume to surface area ratio across the nano and micro plankton size fraction (2-200µm) in the southern Benguela, but has yet to be tested regarding its biogeochemical relevance. Cell size imposes overarching constraints on phytoplankton metabolism; there are therefore strong grounds for evaluating the usefulness of the metric (Deff ) in studies of nitrogen dynamics in diverse, natural assemblages. Three case studies were used to explore the nitrogen dynamics in naturally occurring assemblages and to evaluate the relationships between Deff and the uptake of the different sources of nitrogen. Two of the case studies comprised high biomass, harmful algal blooms observed off Lamberts Bay during an upwelling/downwelling cycle. The third case study used bi-monthly sampling over a full year in Saldanha Bay. The Lamberts Bay case studies involved blooms occasionally dominated by HAB-forming species: a mixotrophic ciliate, Myrionecta rubra, and a dinoflagellate, Prorocentrum triestinum. The nitrogen uptake rates followed the well observed pattern of high nitrate uptake by large cells and regenerated nitrogen uptake by small cells. Myrionecta rubra had a wide range of nitrate (O₃⁻ ) uptake rates (0.02-0.3 µmol N L⁻¹ h⁻¹). Prorocentrum triestinum showed slower rates of O₃⁻ uptake (0.01-0.2 µmol N L⁻¹ h⁻¹) and dominated in low O₃⁻ , stratified conditions. Diatoms were the most efficient utilisers of O₃⁻ and total nitrogen in these cases. The effective diameter was significantly related to the uptake rates of ammonium (NH₄⁺ ) (r=-0.54, p<0.005) and urea (r=-0.59, p<0.005), but not O₃⁻ (r=0.27, p=0.11). This was attributed to some instances of bi-modality in observed size distributions as well as potentially specialist nutrient uptake strategies employed by diatoms. The year-round data from Saldanha Bay indicated the system was diatom-dominated and was used to assess 1 how well Deff could represent the nitrogen uptake strategies employed by the diverse diatom assemblages. The Saldanha Bay system has O₃⁻ limited surface waters during summer, and light-limited bottom waters during winter. No significant relationship was found between Deff and the mass-specific uptake rates of the different nitrogen species in this data set. This was attributed to the complex shapes of the size distributions and the comparatively low biomass observed. Uptake kinetic experiments revealed high variability for maximum uptake rates (Vmax) and half saturation values (Ks) for both O₃⁻ and NH₄⁺ . For O₃⁻ : Vmax ranged 0.007-0.17 µmol N L⁻¹ h⁻¹, and Ks ranged between 0.2-42.5 µmol N L⁻¹. For NH₄⁺ Vmax was observed between 0.02-2.7 µmol N L⁻¹ h⁻¹; and Ks values ranged 0.1- 14.02 µmol N L⁻¹. Variability was observed in association with the availability of the ambient sources of nitrogen, but some variation was accounted for by the presence of different diatom species. From these three case studies it was concluded that the single-value size proxy was an adequate metric to quantify the uptake of regenerated nitrogen in scenarios of high biomass algal blooms. Such blooms are a pervasive feature in the southern Benguela Ecosystem. For lower biomass blooms, however, Deff did not adequately represent the nutrient dynamics of diverse diatomdominated assemblages. The variable shape of the size spectrum is an important factor in determining the rates of nutrient uptake and, in cases of bi- or multi-modality, this information could be lost when represented by a single descriptor such as Deff . It was subsequently hypothesised that size spectra could be used to accurately represent the nitrogen dynamics in diverse phytoplankton assemblages. This was tested by comparing the observed uptake rates of the three case studies to estimated uptake rates based on size spectra. Observed particle size distributions were used to estimate the uptake of O₃⁻ and NH₄⁺ , based on theoretical relationships to calculate size-dependent values of Vmax and Ks. Michaelis-Menten models were applied to measured ambient nutrient concentrations and particle size distributions, generating size-integrated estimates of O₃⁻ , NH₄⁺ and total N uptake rates. The variability in the estimated uptake rates was similar to that of the measured values. It was thus concluded that the representation of phytoplankton diversity by size spectra allowed modification of model parameters, such that improved estimates of uptake rates of O₃⁻ and NH₄⁺ could be obtained for a dynamic eutrophic environment.
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    Using mark-recapture methods to estimate population size and survival of pyjama sharks (Poroderma africanum) in Mossel Bay, South Africa
    (2017) Grusd, Samantha; Gennari, Enrico; Moloney, Coleen L; Distiller, Greg B
    Sharks are vulnerable to exploitation as a result of their biological characteristics. Markrecapture models were applied to conventional tag recapture data and acoustic telemetry data to estimate abundance, apparent survival, recapture probability and temporary emigration for the pyjama shark, Poroderma africanum in Mossel Bay, South Africa over a five-year period. This study applied Pollock's robust design (with the conventional tag data) and Cormack-Jolly-Seber (CJS) models (with the acoustic tag data) to analyze the mark-recapture data. In addition, a von Bertalanffy model was fit to the data to estimate individual growth. The best-fit robust design model showed the population as having no temporary emigration, survival probability that is dependent on the length at first capture, and time-constant capture probabilities. The best-fit CJS model showed the population also having time-constant survival, but sex dependent capture probabilities. Robust design abundance estimates (with 95% C.I.) in Mossel Bay varied from 279 (102-787) sharks to 733 (320-1777) sharks, although confidence intervals were quite large. CJS apparent annual survival (95% C.I.; CJS) was estimated to be 0.271 year⁻¹ (0.04 to 0.56) and annual recapture probability (95% C.I.) was estimated to be 0.008 year⁻¹ (0.003-0.20), indicating that survival and recaptures for this endemic species are relatively low. Annual somatic growth rate (k) was estimated to be 0.213 year⁻¹, indicating that this population is slow growing, a characteristic common in most shark species. Overall, the results in this study provide baseline knowledge on this population in Mossel Bay and can be used to implement proper management techniques. This knowledge can be further expanded upon to give a more in-depth understanding of all size and age classes in the population and the role that the environment and anthropogenic activities play in the population structure.
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    Variability of copepod abundance and growth in the southern Benguela upwelling system and implications for the spawning of the Cape anchovy
    (1998) Richardson, Anthony J; Field, John G; Verheye, Hans M; Moloney, Coleen L
    In the southern Benguela upwelling system, anchovy spawn serially between September and February each year. It has been suggested that this energy-intensive reproductive strategy requires continual ingestion of copepods, which dominate the diet of anchovy at this time. This thesis investigates the spatial and temporal variability of copepod abundance and growth, and their impact upon the spawning of anchovy. Sampling was conducted monthly between August-March 1993/94 and 1994/95 .. It is noteworthy that the primary spawning ground of anchovy, the western Agulhas Bank, had a significantly smaller biomass of copepods than the adjacent West Coast region. In terms of the growth rates of copepods, the effect of food-limitation on fecundity and somatic growth outweighed that of temperature.