Browsing by Author "Shannon, Lynne"

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    Assessing the effects of internal (trophic structure) and external (fishing and environment) forcing factors on fisheries off central Chile : basis for an ecosystem approach to management
    (2008) Alarcón, Sergio Eduardo Neira; Moloney, Coleen; Cury, Philippe; Shannon, Lynne; Jarre, Astrid; Christensen, Villy
    Human perception of sea fisheries has evolved from an inexhaustible resource paradigm towards a generalized concern on the degraded state of fish stocks and ecosystems. Accordingly, fisheries science and management are expanding from the traditional single-species approach towards an ecosystem approach to fisheries. Marine communities are organized as webs of interactions that are affected by external natural (climate) and anthropogenic (fishing) forcing, with their relative effects poorly known, but hypothesised to strongly depend on internal food web structure (i.e., who eats and controls whom). This thesis approaches relevant ecological considerations for an ecosystem approach to fisheries in the upwelling ecosystem off central Chile (33ºS-39ºS). The main objective is to assess the effects of internal (trophic structure) and external (fishing and environment) forcing factors at the fish stock and food web level in the study area. The methodology includes i) the construction of snapshot and dynamic food web models to test hypothesis of changes in the food web in the last century, and the relative contribution of fishing, trophic controls and bottom-up environmental variability to those changes, ii) the computation and analysis of a set of ecosystem indicators to test hypotheses of changes in different aspects of the exploited community (mean trophic level, age and length at maturity, network properties and system variability), iii) the analyses of the relationships between time series of abundance of species with known trophic interactions (Chilean hake-red squat lobster and Chilean hake-small pelagic fish) to test hypothesis of top-down and bottom-up control versus alternative hypotheses of fishing and/or environmental control in the same populations, and iv) simulation experiments to test hypotheses of ecosystem change and recovery under fishing and environmental forcing. Models and indicators are constructed using data series of abundance, catches, production, consumption and diets of the main functional groups in the study area. Snapshot and dynamic food web models are constructed and analyzed using the Ecopath with Ecosim software version 5.1 and routines therein. The observed trends in indicators and model results are in accordance with what is theoretically expected in stressed ecosystems (shift towards a food web dominated by short-lived, low trophic level and high turnover rate species), and suggest that the food web could be in a state that is more susceptible to external forcing. Fishing and the environment (bottom-up anomaly in PP) may have affected the upwelling ecosystem off central Chile both at the stock and at the food web level between 1970 and 2004. The effects of these forcing factors may have been mediated by trophic controls operating in the food web. There is also evidence to support the hypothesis that trophic controls beyond fishing, e.g., trophic (internal) and environment (external) may operate in the analysed populations and this information should be considered in their assessment and management. While target objectives are set and agreed, it is proposed that the main objective for the ecosystem approach to fisheries should be to avoid fishing-induced regime shifts, since results from simulation experiments suggest that fishing can induce ecosystem changes of lower recovery than bottom-up forcing.
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    Changes in food web structure and energy flow in kelp forest ecosystems on the south-west coast of South Africa following the invasion of Jasus lalandii
    (2019) Steyn, Clara; Shannon, Lynne; Blamey, Laura
    In the early 1990s the west coast rock lobster Jasus lalandii underwent an eastward shift in distribution into an area known as East of Cape Hangklip where they had previously been rare. This shift has also been termed an invasion and resulted in a complete change in the benthic community structure, changing from one state dominated by herbivores and encrusting algae, to another state dominated by lobsters, sessile species, kelp and understory foliose algae. Using the trophic modelling software Ecopath with Ecosim, baseline models of the pre- and Post-invasion systems were created to better understand trophic pathways between the two different states and assess how fishing pressure may have driven the shift in ecosystem state. Using the baseline models, different fishing management strategies were tested to see whether the post lobster-invaded ecosystem could be shifted back or close to the pre-invasion state. Baseline models that were developed to describe the shift in ecosystem state reflected an increase in the presence of kelp, sessile species and lobsters, and the decline of encrusting algae and herbivores. Furthermore, the baseline models reflect the Postinvasion system as more productive and less diverse than the pre-invasion system. Simulations using an Ecosim model showed that, with a reduction in fishing pressure on reef fish and abalone and a simulated increase in fishing pressure on rock lobster, reef fish and adult abalone recovered to pre-invasion levels, whereas juvenile abalone and urchin biomass did not recover, likely due to the difficulty in capturing non-trophic interactions in the trophic models. Further functional groups such as sessile species, turf and foliose algae, also did not return to the pre-invasion state. This study concluded that a reduction in fishing pressure on abalone and reef fish, and the removal of rock lobster through increased fishing pressure, would allow the post-invasion ecosystem to partially recover to the pre-invasion state, but not completely, suggesting a hysteresis effect. Further exploration of management strategies through model simulations is needed, including those that can account for non-trophic links.
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    Ecosystem effects of bottom trawling in the Benguela current system : experimental and retrospective data analyses
    (2011) Mafwila, Samuel Kakambi; Field, John G; Jarre, Astrid; Shannon, Lynne
    This thesis investigates ecosystem effects of bottom-trawling on demersal fish assemblages (1990-2006) off Namibia and their relationship to environmental variables.
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    Effects of demersal trawling on marine infaunal, epifaunal and fish assemblages: studies in the southern Benguela and Oslofjord
    (2009) Atkinson, Lara Jane; Field, John G; Jarre, Astrid; Shannon, Lynne; Hutchings, Larry
    This thesis investigates the impacts of the demersal trawl fishery on infaunal, epifaunal and fish assemblages in the southern Benguela upwelling system for the first time. In the absence of representative areas of similar habitat protected from trawling in the southern Benguela region, infaunal and epifaunal assemblages were compared between heavily and lightly trawled areas to assess the impacts of the otter-trawl fishery. Infauna were sampled at four sites, from southern Namibia to near Cape Town by means of five replicate grab samples at each paired heavily and lightly trawled area. Invertebrate epifauna were sampled at two sites in heavily and lightly trawled areas using a finemeshed otter trawl. Sites ranged in depth from 350-450 m in unconsolidated sediment habitat. Epifaunal assemblages showed greater differences at heavily trawled areas with significantly reduced species diversity, average number of species and individuals. Several epifaunal species were absent from heavily trawled areas highlighting their vulnerability to impacts of trawling. Multivariate analyses show significant differences in composition of both infaunal and epifaunal assemblages among the sites and between trawling treatments at all sites. The results of this study suggest that intense trawling activities are at least partially responsible for significantly altering benthic community composition, affecting epifauna to a greater measurable extent than infauna. Biological Traits Analysis (BTA) was used to explore potential changes in ecological functioning of benthic assemblages, comparing areas exposed to heavy and light trawl intensities in the Benguela system. BTA incorporates biological traits (life-history, morphology and behaviour) of infaunal and epifaunal species with biomass, capturing a broad range of information of marine benthic assemblages. Seventeen percent of the infaunal traits analysed showed a significant difference between heavily and lightly trawled areas. Twenty-four percent of epifaunal biological traits investigated were significantly different between areas of heavy and light trawling. This study suggests that more intense trawling modifies some trait constituents of the benthic assemblage in the southern Benguela region, confirming the sensitivity of functional traits analysis in detecting changes induced by trawling disturbance. Biological traits analysis of benthic invertebrates shows promise as a practical technique for incorporation into monitoring programmes and for developing indicators of benthic ecosystem health, needed for implementation of an ecosystem approach to fisheries management in South Africa. A lack of representative untrawled areas in the trawl grounds of southern Africa precluded investigations comparing trawl impacts with unfished reference sites. A bilateral agreement between South Africa and Norway (NORSA) provided the opportunity to conduct experiments in an untrawled area of Oslofjord, Norway, where a shrimp trawl fishery for Pandalus borealis operates nearby. Infauna Abstract 2 were sampled at four untrawled sites in Oslofjord with five replicate grabs after which an Agassiz beam sled was dragged across two of the sites (impact sites) four times, simulating a trawl disturbance. Infauna were re-sampled at all four sites immediately after trawling (post-impact), 14 days and 64 days after the impact to monitor recovery of infaunal populations. Multivariate analyses comparing the impact sites with paired control sites for each sampling occasion showed no significant differences in infaunal assemblages at any stage of the experiment. Whilst it is considered possible that the trawl simulation was not a sufficient impact to represent that of a commercial trawl effect, it is considered more likely that trawl activities in Oslofjord do not inflict measurable impacts on infaunal assemblages. However, the impact of trawling on epifaunal assemblages in Oslofjord was not investigated in this study. Annual research survey data collected over the past 24 years (1986-2009) provide an opportunity to explore long-term demersal fish assemblage composition changes on the west coast of South Africa. Differences in spatial (latitude and depth) and temporal (seasonal and annual) factors were examined using multivariate analyses. Possible long-term changes were investigated using the Sequential T-test Algorithm to detect Regime Shifts (STARS). Results indicate geographic differences in fish assemblage composition from the northern to the southern region on the west coast of South Africa. The fish community composition is also clearly influenced by depth with a distinct change in fish assemblages in the shelf break region between 300 m and 400 m. Multivariate analyses also show two clear temporal changes in assemblage composition, firstly, in the early 1990s and secondly, in the mid- 2000s. STARS analyses detect long-term shifts in 27% of demersal species with the majority of speciesâ shifts detected either in the early- to mid-1990s or in the past decade (2002 to 2009). Multivariate analyses among year groups reveal an increase in three fast-growing, early maturing species and decreases in two slow-growing, long-lived species. STARS analysis detected increases in two of the same fast-growing species, decreases in an additional four slow-growing, long-lived species, but four other slow-growing, long-lived species showed the opposite trend (i.e. increases). The hypothesis of an increase in fast-growing, early maturing species and a decline in slow-growing, longlived species in fished systems is therefore only partially supported by these findings. Shifts in demersal fish assemblages coincide temporally with spatial shifts observed in small pelagic species and west coast rock lobster. The shifts in the demersal fish assemblage composition detected in this study are probably a reflection of long-term indirect effects of fishing in combination with environmental changes. Abstract 3 The response of benthic invertebrate assemblages to two levels of fishing intensity in the southern Benguela region justifies regular monitoring of epifauna during existing annual demersal research surveys and infaunal monitoring through dedicated, periodic sampling initiatives. Demersal fish assemblage data should be regularly assessed for changes in community composition. Representative protected areas can serve as reference areas against which fishing impacts could be assessed and improve our understanding of ecosystem effects of demersal fishing.
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    Investigating the trophic ecologies of early life stages of small pelagic fishes in the Benguela upwelling ecosystem
    (2024) Horton, Matthew; Shannon, Lynne
    The Benguela upwelling system, located on the west coast of southern Africa, harbours large biomasses of three small pelagic fishes; anchovy Engraulis encrasicolus, sardine Sardinops sagax and west coast round herring Etrumeus whiteheadi. Despite fisheries management interventions, stocks of sardine have been low for the past decade following consecutive years of poor recruitment. This has highlighted that despite low fishing mortality, variance in recruitment may be largely governed by fluctuations in early-stage mortality rates. Therefore, examining early life traits that may explain a fraction of this mortality could be fundamental to understanding the underlying mechanics of recruitment. This study seeks to investigate the ontogenetic development in morphology and trophic ecology of early life stages of these three small pelagic fish species in the Benguela, and how they compare interspecifically and spatially. Increasing our temporal resolution of the ecological ontogeny of a species will enable accurate future analysis of trophic pathways and linkages within ecosystems and their feedback to vital ecosystem services such as fisheries. Results show that there is a high likelihood of trophic partitioning between sardine and anchovy larvae through distinct differences in their ecomorphology. Sardines exhibit traits in their development such as increased relative gut length, that would suggest a higher degree of herbivory compared to anchovy. Contrastingly, anchovy display positive allometric growth patterns in their cranial development at a younger age, suggesting a greater importance of particulate feeding on larger prey. These results provide an anatomical basis of how both the feeding ability and behaviour of these two species may differ which would predispose them to distinct diets. Both species exhibited trophic progression inferred through (a) a 15N enrichment and (b) an increase in carnivory fatty acid trophic markers. Interspecific partitioning is facilitated through distinctions in prey-size composition, with anchovy consuming comparatively larger prey than sardine. Surprisingly, sardine exhibit a higher δ15N, arising from the increased presence of smaller carnivorous copepods in their diet, which highlights the complexity of the food web dynamics in the Benguela. Prey-size selection is an important regulator of both intra- and interspecific competition in these species. Round herring pre-recruits are further trophically disassociated from sardine than anchovy, consuming on average larger particles with very little herbivory compared to sardine and anchovy. This was corroborated by (a) a 15N enrichment from sardine to anchovy to round herring indicative of feeding at higher trophic levels, and (b) 13C depletion in the opposite order, indicative of a reduced dependence on autotrophic components. Stomach content analysis suggested substantial filter-feeding for anchovy and sardine, but relatively little for round herring. Therefore, the compounding effect of the feeding mode with the functional traits provides potential answers for variances seen in their trophic ecology. The Ecopath model that included a finer life history of anchovy, sardine and round herring exhibited substantially more small pelagic fish-centred trophic pathways that were previously grouped into plankton groups than the model that did not. As a consequence, there was an improvement in model fit of 14 out of the 19 functional group time series analysed. In terms of overall model function, there was no change in biomass or system variability. However, there was a significant change in the trophic level estimation of functional groups, that had system-wide ramifications. This study has shown that despite the relative mass insignificance of small pelagic larvae in the system, they still have a considerable effect on the ecosystem dynamics. However, it seems that when disaggregating functional groups into life history stanza, if the same increase in resolution is not reflected in their prey, then vital trophic relationships can be lost. This research has highlighted crucial distinctions between the ecology of anchovy and sardine early life stages that may give rise to differences in condition and starvation and hence mortality in the face of varying prey compositions. The foundational work detailed here will contribute to future studies aimed at understanding the population dynamics of these species, and so contribute to the already multi-faceted toolkit that aims to sustainably manage the small pelagic fisheries of the Benguela.
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    Using seasonal mass-balanced models of the Algoa Bay ecosystem to investigate African penguin and small pelagic fish interactions
    (2019) Weigum, Emily; Shannon, Lynne; Jarre, Astrid
    Ecopath with Ecosim is a modeling software that allows the creation of mass-balanced models of the trophic flows of an ecosystem to explore the past and present impacts of fishing and environmental change on the trophic flows of a given food web. Currently, Algoa Bay supports the world’s largest breeding colony of endangered African penguins (Spheniscus demersus). The breeding success of African penguins is largely dependent on the availability of their food, mainly anchovy (Engraulis encrasicolus) and sardine (Sardinops sagax). African penguins breed year-round however, peak breeding season begins during the summer months (January to March) in Algoa Bay, when penguins begin building up fat reserves and laying eggs. In order to investigate the interaction between the small pelagic fish and penguin population, mass-balanced trophic models of the Algoa Bay ecosystem were constructed using the software Ecopath with Ecosim. Input parameters were derived from data compiled from published literature and survey data collected by DAFF (Department of Agriculture, Forestry, and Fisheries; formerly Marine and Coastal Management, MCM) and SAEON (the South African Environmental Observation Network). Two seasonal models were created to depict the summer (January to March) and winter (June to August) seasons from 2010-2014. Additionally, two seasonal models were created to represent a marine protected area where all fishery catch was set to zero. These static marine protected area models were created to investigate how the removal of fishery predation impacts the trophic structure of the Algoa Bay ecosystem by comparing ecotrophic efficiency values to those of the fished system. Two Ecosim simulations were used in fishery sensitivity analyses. The first, by setting all fishery catches to zero over a period of 30 years for each season to investigate the sensitivity of trophic groups to the removal of fishing pressure. The second, by setting fishery mortalities of anchovy and sardine to levels reported in the west coast (also over a period of 30 years) to investigate the sensitivity of trophic groups to an increase in small pelagic fishing pressure. Seasonal differences were observed with an increase in primary production and zooplankton biomass in the summer season compared to the winter season. The increase in plankton biomass resulted in an approximately 3x greater summer total system throughput, and total net primary production. Transfer efficiencies were higher than the average of 10% for aquatic ecosystems at trophic levels II and III with the seasonal averages being 17% and 19% respectively. The greatest seasonal change in modeled biomass occurred at trophic level III with summer biomass being 72% larger, indicating that small pelagic fishes benefit the most from the increase in summer plankton biomass. Linefish ecotrophic efficiency values were smaller in the marine protected area models in the summer and winter respectively, reflecting the reduced mortality on linefish under MPA conditions. Although the removal of fisheries resulted in an overall drop in predation pressure of 27% in the static MPA models, predation by other predatory trophic groups in the bay increased by 13% as a result of their subsequent biomass increases after the removal of fishery predation. Ecosim results showed the greatest change in biomass occurred in linefish which increased in both seasons when fishery catch was set to zero. The increase in linefish biomass can be attributed to the removal of fishery pressure on themselves and their prey, and may be an indication that linefish are overexploited in the bay. As a result of the biomass increase of some predator groups, some lower trophic level fish groups decreased despite the removal of fishery pressure. The results of the marine protected area analyses indicate that fisheries do not necessarily only have direct impacts on a target species as food-webs can have moderating effects. When fishing mortalities for sardine and anchovy were increased to west coast values, African penguins had the largest decrease in modeled biomass followed by other seabirds. Although, the observed decrease in modeled biomass of African penguins over the 30-year period does not fall within IUCN criteria for major concern, African penguins are already listed as endangered. An added decline of 10% on the largest breeding colony could have major implications on the future of the species. This study was a preliminary attempt at constructing mass-balanced trophic models of the Algoa Bay ecosystem, highlighting seasonal differences while investigating the possible impact of implementing a marine protected area in the bay and the sensitivity of trophic groups to fishing. Future research is needed to improve the more uncertain model parameters; however, these models are a good base for future work and the application of spatialized modeling of the bay using EcoSpace