L. J. Shannon

University of Cape Town, Kaapstad, Western Cape, South Africa

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Publications (71)150.49 Total impact

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    ABSTRACT: The African penguin (Spheniscus demersus) population in southern Africa has experienced rapid decline in the 20th century and as of 2010 is listed as “endangered” on the IUCN Red List. There is an urgent need for decision support tools to enable effective management of colonies. We present a system dynamics model of the penguin population on Robben Island, South Africa, that combines a demographic simulation with the modelling of multiple pressures including food availability and food competition by commercial fisheries, oil spills, predation by terrestrial and marine predators, and extreme climate events. The model is stochastic, stage-specific and resource-driven, and incorporates both well-defined, quantitative field data and qualitative expert opinion. Survival rates for eggs, chicks, immatures and adults were adapted from field data and an earlier model of this population to create a simulation of a stable population used in a variety of scenarios and sensitivity tests. The modelled population was found to be strongly driven by food availability and to a lesser degree by oiling and marine predation, while climate events and terrestrial predation had low impacts. Food biomass levels (small pelagic fish) in the penguins’ foraging area around the island (used during nesting) and further afield (used during the rest of the year) had an equal influence in driving population development in the short and long run. The impact of short-term (three years) fishing restrictions currently being trialled around the island was found to be generally beneficial to the modelled population, but easily masked by food-driven variability in population growth. The model produced population dynamics similar to those observed in 1988–2009 when immigration and a plausible change in predation pressure during this period were simulated. The model is being extended to other colonies to provide tools for specific management decisions and to enable the study of meta-populations by modelling migration between colonies. Our results suggest that improving food availability and mitigating the impact of oiling would have the highest beneficial impact on this penguin population.
    Ecological Modelling 02/2014; 277:38–56. · 2.07 Impact Factor
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    ABSTRACT: 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-N2P2Z2D2-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.
    PLoS ONE 01/2014; 9(4):e94286. · 3.53 Impact Factor
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    ABSTRACT: A 22-group Ecopath model representing the southern Humboldt (SH) upwelling system in the year 1970 is constructed. The model is projected forward in time and fitted to available time series of relative biomass, catch and fishing mortality for the main fishery resources. The time series cover the period 1970 to 2004 and the fitting is conducted using the Ecopath with Ecosim (EwE) software version 5.1. The aim is to explore the relative importance of internal (trophic control) and external (fishing, physical variability) forcing on the dynamics of commercial stocks and the Southern Chilean food web. Wide decadal oscillations are observed in the biomass of commercial stocks during the analyzed period. Fishing mortality explains 21% of the variability in the time series, whereas vulnerability (v) parameters estimated using EwE explain an additional 20%. When a function affecting primary production (PP) is calculated by Ecosim to minimize the sum of squares of the time series, a further 28% of variability is explained. The best fit is obtained by using the fishing mortality time series and by searching for the best combination of v parameters and the PP function simultaneously, accounting for 69% of total variability in the time series. The PP function obtained from the best fit significantly correlates with independent time series of an upwelling index (UI; rho = 0.47, p < 0.05) and sea surface temperature (SST; rho = −0.45, p < 0.05), representing environmental conditions in the study area during the same period of time. These results suggest that the SH ecosystem experienced at least two different environmentally distinct periods in the last three decades: (i) from 1970 to 1985 a relatively warm period with low levels of upwelling and PP, and (ii) from 1985 to 2004 a relatively cold period with increased upwelling and PP. This environmental variability can explain some of the changes in the food webs. Fishing (catch rate) and the environment (bottom-up anomaly in PP) appear to have affected the SH both at the stock and at the food web level between 1970 and 2004. The vulnerability setting indicates that the effects of external forcing factors may have been mediated by trophic controls operating in the food web.
    Ecological Modelling 01/2014; 274:41–49. · 2.07 Impact Factor
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    ABSTRACT: This paper assesses changes in the southern Humboldt system (33–39 °S) in the 20th century by constructing and comparing food web models representing four historical periods: (i) lightly exploited (<1900s), (ii) altered by removal of marine mammals (1950), (iii) development of industrial fisheries (1992), and (iv) the more recent state (2005) when main stocks are fully or overexploited. Models are constructed with a standard structure in terms of functional groups using the Ecopath with Ecosim (EwE) software version 5.1. Model components include: the fisheries, cetaceans, sea lions, marine birds, cephalopods, large-sized pelagic fish (swordfish), medium-sized pelagic fish (e.g., horse mackerel, mackerel, and Pacific grenadier), small-sized pelagic fish (e.g., anchovy and Araucanian herring), demersal fish (e.g., Chilean hake, black conger-eel), benthic invertebrates (red squat lobster, yellow squat lobster, pink shrimp) and other groups such as zooplankton, phytoplankton and detritus. Input data are gathered from published and unpublished (grey) literature. Inter-model comparison is based on individual and community indicators obtained by means of network analysis. The biomasses of target species (with the exception of small pelagic fish) and top predators decrease in more recent models. Although predation mortality is the main cause of total mortality for the majority of the fish groups in all models, fishing mortality of target species is high in the 1992 and 2005 models. This has led to a decrease in the importance of predation removal of the most important fish stocks compared with fishing, which is found to assume the role of the main predator in the system in the more recent state. Changes in system energetics could have resulted in loss of productivity by increased flow to detritus. Prior to heavy fishing, long-living and high-trophic level species were abundant compared to the most recent models in which species with small body size, short life span and low trophic level dominate. These fishing-induced trends are in accordance with what is theoretically expected in stressed ecosystems and, if correct, the food web could now be more susceptible to external forcing and negative ecological interactions.
    Ecological Modelling 01/2014; 278:52–66. · 2.07 Impact Factor
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    ABSTRACT: There is growing interest in models of marine ecosystems that deal with the effects of climate change through the higher trophic levels. Such end-to-end models combine physicochemical oceanographic descriptors and organisms ranging from microbes to higher-trophic-level (HTL) organisms, including humans, in a single modeling framework. The demand for such approaches arises from the need for quantitative tools for ecosystem-based management, particularly models that can deal with bottom-up and top-down controls that operate simultaneously and vary in time and space and that are capable of handling the multiple impacts expected under climate change. End-to-end models are now feasible because of improvements in the component submodels and the availability of sufficient computing power. We discuss nine issues related to the development of end-to-end models. These issues relate to formulation of the zooplankton submodel, melding of multiple temporal and spatial scales, acclimation and adaptation, behavioral movement, software and technology, model coupling, skill assessment, and interdisciplinary challenges. We urge restraint in using end-to-end models in a true forecasting mode until we know more about their performance. End-to-end models will challenge the available data and our ability to analyze and interpret complicated models that generate complex behavior. End-to-end modeling is in its early developmental stages and thus presents an opportunity to establish an open-access, community-based approach supported by a suite of true interdisciplinary efforts. Yes Yes
    Marine and Coastal Fisheries Dynamics Management and Ecosystem Science 05/2013; 2(1):115-130. · 1.79 Impact Factor
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    ABSTRACT: Changes in two contrasting ecosystems of the Benguela upwelling region, one dominated at mid-trophic level by jellyfishes (Namibia, northern Benguela ecosystem, where small pelagic fish abundance has been severely depleted) and one still dominated by small pelagic fishes (South Africa, southern Benguela) were compared in an effort to determine ecosystem trajectories under different exploitation regimes. The role of small pelagic fishes (clupeoids) was highlighted in the context of their importance in maintaining interactions in marine ecosystems. In particular, we examined trophic cascades and possible irreversible changes that promote the proliferation of jellyfishes in marine systems. We found that the presence of large populations of small pelagic fishes has a fundamental role in preserving beneficial trophic interactions in these marine ecosystems. The implications of trophic cascades, such as those observed in the northern Benguela, for ecosystem-based management were apparent. In addition, this comparison provides contrasting case studies to inform the development of management scenarios that avoid ecosystem shifts that affect predators and reduce the value of fisheries production. Considerable attention has been given in the last decade to the perceived increases in jellyfish populations and frequency of jellyfish outbreaks worldwide, and their po-tential causes (Arai 2001, Brodeur et al. 2002, Parsons and Lalli 2002, Attrill et al. 2007, Purcell et al. 2007, Richardson et al. 2009, Brotz et al. 2012). Because these outbreaks have negative impacts on many human activities and can affect the func-tioning of marine ecosystems (Purcell et al. 2007, Richardson et al. 2009), identify-ing and mitigating the effects of the potential human causes of increased jellyfish abundance (Hay 2006, Richardson et al. 2009) has become a research focus with important management implications. Of the many possible such causes (ranging from global climate change to coastal developments), those linked to the trophic im-pacts of overfishing are of particular concern, as most marine ecosystems have been profoundly modified by fishing (see e.g., Pauly et al. 1998). As attempts are made to implement an ecosystem approach to fisheries to improve the sustainability of world fisheries (FAO 2001, 2003, Pauly et al. 2002, Pikitch et al. 2004), and jellyfishes are now often viewed as a threat to fishing, the potential linkages between fisheries and jellyfish populations are increasingly relevant. The northern Benguela (NB) ecosystem is often highlighted as an example of a system where increased jellyfish abundance may have resulted from overfishing (Bakun and Weeks 2006, Lynam et al. 2006, Richardson et al. 2009, Utne-Palm et al. 2010, Jensen et al. 2012). Although the southern Benguela (SB) has also been
    Bulletin of Marine Science -Miami- 01/2013; 89:249-284. · 1.30 Impact Factor
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    ABSTRACT: We show that the EcoTroph model based on trophic spectra is an efficient tool to build ecosystem diagnoses of the impact of fishing. Using the Southern Benguela case study as a pretext, we present the first thorough application of the model to a real ecosystem.We thus review the structure and functioning of EcoTroph and we introduce the user to the steps that should be followed, showing the various possibilities of the model while underlining the most critical points of the modelling process. We show that EcoTroph provides an overview of the current exploitation level and target factors at the ecosystem scale, using two distinct trophic spectra to quantify the fishing targets and the fishing impact per trophic level. Then, we simulate changes in the fishing mortality, facilitating differential responses of two groups of species within the Southern Benguela ecosystem to be distinguished. More generally, we highlight various trends in a number of indicators of the ecosystem's state when increasing fishing mortality and we show that this ecosystem is moderately exploited, although predatory species are at their MSY. Finally, trophic spectra of the fishing effort multipliers EMSY and E0.1 are proposed as tools for monitoring the ecosystem effects of fishing.
    Journal of Marine Systems 05/2012; 90(1):1-12. · 2.48 Impact Factor
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    ABSTRACT: Highlights ► There is strong need for interdisciplinary assessment of exploited marine ecosystems. ► Governance and management must be linked to the ecological status of fished ecosystems. ► Developing country marine ecosystems, in particular, are facing considerable challenges. ► Incorporating local expertise in global ecosystem assessments has major advantages. ► IndiSeas is incorporating multi-disciplinary indicators for policy and decision makers.
    Current Opinion in Environmental Sustainability 01/2012; 4:292-299. · 3.17 Impact Factor
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    ABSTRACT: Determining the form of key predator-prey relationships is critical for understanding marine ecosystem dynamics. Using a comprehensive global database, we quantified the effect of fluctuations in food abundance on seabird breeding success. We identified a threshold in prey (fish and krill, termed "forage fish") abundance below which seabirds experience consistently reduced and more variable productivity. This response was common to all seven ecosystems and 14 bird species examined within the Atlantic, Pacific, and Southern Oceans. The threshold approximated one-third of the maximum prey biomass observed in long-term studies. This provides an indicator of the minimal forage fish biomass needed to sustain seabird productivity over the long term.
    Science 12/2011; 334(6063):1703-6. · 31.20 Impact Factor
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    ABSTRACT: Low-trophic level species account for more than 30% of global fisheries production and contribute substantially to global food security. We used a range of ecosystem models to explore the effects of fishing low-trophic level species on marine ecosystems, including marine mammals and seabirds, and on other commercially important species. In five well-studied ecosystems, we found that fishing these species at conventional maximum sustainable yield (MSY) levels can have large impacts on other parts of the ecosystem, particularly when they constitute a high proportion of the biomass in the ecosystem or are highly connected in the food web. Halving exploitation rates would result in much lower impacts on marine ecosystems while still achieving 80% of MSY.
    Science 07/2011; 333(6046):1147-50. · 31.20 Impact Factor
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    ABSTRACT: South Africa is committed to moving towards an Ecosystem Approach to Fisheries (EAF) and has laid the foundations for this using a three-pronged approach: through a project (EAF Feasibility Study) under the Benguela Current Large Marine Ecosystem Programme; through a dedicated scientific working group established by the Marine and Coastal Management branch of South Africa's Department of Environmental Affairs and Tourism; and through collaborative scientific and modelling studies within the joint French-South African 'Upwelling Ecosystems' Programme. This contribution provides an overview of the progress made towards developing an EAF in South Africa, both on the scientific front in terms of improved understanding of the functioning of the Benguela ecosystem and the ways in which its ecosystem components interact, and regarding the practical ways being explored to enable scientific advice to feed in to South African fisheries management while taking into account broad stakeholder concerns. The paper focusses particularly on the role played by scientific contributions (research and monitoring) to address these ecosystem issues in three important South African fisheries — pelagic, demersal and rock lobster — so that the appropriate management measures can be put into place. Socio-economic concerns are included for the rock lobster fishery.
    African Journal of Marine Science 01/2010; April 2006(Vol. 28):115-157. · 0.93 Impact Factor
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    Ices Journal of Marine Science. 01/2010; 67(4):692-716.
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    ICES Journal of Marine Science 01/2010; · 2.28 Impact Factor
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    ABSTRACT: South Africa’s commitment to implementation of the ecosystem approach to fishing (EAF) requires a solid scientific basis comprised of a toolkit assembled through concerted efforts from which management measures can be carefully considered and put into place. A series of workshops was held to assist in the identification of issues in South Africa’s key fisheries that are cause for concern and may have EAF implications. Several of these issues were addressed under various projects. Food-web studies have been undertaken and models have been constructed of the changes in the structure and functioning of the Southern Benguela upwelling system. The combined effects of fishing and environmental change on South African fisheries have been examined using various observation-based and modelling methods. These are contributing to assessment of changes at multiple spatial and temporal scales, from the impact of pelagic fishing in key foraging areas of critically-dependent predators, to impacts of demersal trawls on the benthos and demersal fish assemblages, to decadal-scale dynamics, and global comparative classifications of ecosystem status. To address some of the EAF issues, practical implementation measures are being developed and applied in collaboration with stakeholders. Stakeholders are also actively involved in the process leading to development of indicators to address the human dimensions of EAF, and knowledge-based systems are being developed as decision support tools. Future priorities for South African EAF research will include placing more emphasis on conservation and biodiversity aspects, linking of environmental/oceanographic knowledge to management objectives, spatial aspects, as well as increased focus on the human dimension and transdisciplinary approaches. Indicators are a promising means of synthesizing multi-disciplinary information for consideration in the management process, providing measures of anthropogenic (including fishing) pressures including social and economic pressures, in combination with environmental drivers, and providing a means of assessing how these affect the Benguela ecosystem. Respectful scientific collaboration will be required to bridge the gap between classical single-species fisheries management approaches and broader ecosystem approaches.
    Progress In Oceanography 01/2010; · 3.71 Impact Factor
  • ICES Journal of Marine Science 01/2010; · 2.28 Impact Factor
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    ABSTRACT: J. 2010. Comparing data-based indicators across upwelling and comparable systems for communicating ecosystem states and trends. – ICES Journal of Marine Science, 67: 807– 832. A suite of ecological indicators was selected for communicating, in a comparable way, how fishing affects the state of several upwelling ecosystems and others in which small pelagic fish play key ecological roles. Detailed background and understanding of system-specific processes and changes is needed for proper interpretation of results. In particular, environmental forcing is important in driving dynamics in upwelling systems; fishing impacts cannot be understood without understanding the corresponding dynamics of the environment. The Saharan Coastal (Morocco) and southern Benguela, both having experienced upsurges in low-trophic-level species, differed from other ecosystems when considering indicator trends. The ecosystem off Portugal emerged as showing reduced signs of fishing impacts in recent years, although the change may also be reflecting climate change favouring recruitment and abundance of demersal stocks. The indicator suite confirmed general understanding that the Mediterranean ecosystems have been notably degraded for several decades. Results and conclusions from this descriptive synthesis are compared with other compari-sons of more complex, model-derived indicators. Even in upwelling and comparable systems, the simple data-based indicators are useful in synthesizing information on the status of an ecosystem, in particular on the ecosystem effects of fishing, to provide an eco-logical diagnosis at the ecosystem level, to be used in decision-making. Indicators of recent ecosystem state and trends over time are needed to assess the effects of fishing, but more indicators measuring biodiversity attributes and environmental change would comp-lement the suite, providing fuller assessment of the status of upwelling and comparable ecosystems.
    ICES Journal of Marine Science 01/2010; 67:807-832. · 2.28 Impact Factor
  • ICES Journal of Marine Science 01/2010; 67:745-768. · 2.28 Impact Factor
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    ABSTRACT: Ecosystem models provide a platform allowing exploration into the possible responses of marine food webs to fishing pressure and various potential management decisions. In this study we investigate the particular effects of overfishing on the structure and function of the southern Benguela food web, using two models with different underlying assumptions: the spatialized, size-based individual-based model, OSMOSE, and the trophic mass-balance model, Ecopath with Ecosim (EwE). Starting from the same reference state of the southern Benguela upwelling ecosystem during the 1990s, we compare the response of the food web to scenarios of overfishing using these two modelling approaches. A scenario of increased fishing mortality is applied to two distinct functional groups: i) two species of Cape hake, representing important target predatory fish, and ii) the forage species anchovy, sardine and redeye. In these simulations, fishing mortality on the selected functional groups is doubled for 10 years, followed by 10 years at the initial fishing mortality. We compare the food web states before the increase of fishing mortality, after 10 years of overfishing and after a further 10 years during which fishing was returned to initial levels. In order to compare the simulated food web structures with the reference state, and between the two modelling approaches, we use a set of trophic indicators: the mean trophic level of the community and in catches, the trophic pyramid (biomass per discrete trophic level), and the predatory/forage fish biomass ratio. OSMOSE and EwE present globally similar results for the trophic functioning of the ecosystem under fishing pressure: the biomass of targeted species decreases whereas that of their potential competitors increases. The reaction of distant species is more diverse, depending on the feeding links between the compartments. The mean trophic level of the community does not vary enough to be used for assessing ecosystem impacts of fishing, and the mean trophic level in the catch displays a surprising increase due to the short period of overfishing. The trophic pyramids behave in an unexpected way compared to trophic control theory, because at least two food chains with different dynamics are intertwined within the food web. We emphasize the importance of biomass information at the species level for interpreting dynamics in aggregated indicators, and we highlight the importance of competitive groups when looking at ecosystem functioning under fishing disturbance. Finally, we discuss the results within the scope of differences between models, in terms of the way they are formulated, spatial dimensions, predation formulations and the representation of fish life cycles.
    Journal of Marine Systems 01/2010; 79:101-111. · 2.48 Impact Factor
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    Ices Journal of Marine Science - ICES J MAR SCI. 01/2010; 67(4):787-795.
  • Y. J. Shin, L. J. Shannon
    Ices Journal of Marine Science - ICES J MAR SCI. 01/2010; 67(4):686-691.

Publication Stats

1k Citations
150.49 Total Impact Points

Institutions

  • 2003–2014
    • University of Cape Town
      • • Marine Research Institute
      • • Department of Biological Sciences
      Kaapstad, Western Cape, South Africa
  • 2009
    • Dalhousie University
      Halifax, Nova Scotia, Canada
  • 2004
    • University of British Columbia - Vancouver
      • Fisheries Centre (FC)
      Vancouver, British Columbia, Canada