L. J. Shannon

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

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Publications (87)211.38 Total impact

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    ABSTRACT: Understanding how external pressures impact ecosystem structure and functioning is essential for ecosystem based approaches to fisheries management. We quantified the relative effects of fisheries exploitation and environmental conditions on ecological indicators derived from two different data sources, fisheries catch data (catch-based) and fisheries independent survey data (survey-based) for 12 marine ecosystems using a partial least squares path modeling approach (PLS-PM). We linked these ecological indicators to the total biomass of the ecosystem. Although the effects of exploitation and environmental conditions differed across the ecosystems, some general results can be drawn from the comparative approach. Interestingly, the PLS-PM analyses showed that survey-based indicatorswere less tightly associated with each other than the catch-based ones. The analyses also showed that the effects of environmental conditions on the ecological indicatorswere predominantly significant, and tended to be negative, suggesting that in the recent period, indicators accounted for changes in environmental conditions and the changes were more likely to be adverse. Total biomass was associated with fisheries exploitation and environmental conditions; however its association with the ecological indicators was weak across the ecosystems. Knowledge of the relative influence of exploitation and environmental pressures on the dynamicswithin exploited ecosystemswill help us to move towards ecosystem-based approaches to fisheries management. PLS-PMproved to be a useful approach to quantify the relative effects of fisheries exploitation and environmental conditions and suggest it could be used more widely in fisheries oceanography.
    Journal of Marine Systems 08/2015; 148:101-111. DOI:10.1016/j.jmarsys.2015.01.004 · 2.48 Impact Factor
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    ABSTRACT: Thirty years of progress using the Ecopath with Ecosim (EwE) approach in different fields such as ecosystem impacts of fishing and climate change, emergent ecosystem dynamics, ecosystem-based management, and marine conservation and spatial planning were showcased November 2014 at the conference “Ecopath 30 years-modelling dynamic ecosystems: beyond boundaries with EwE”. Exciting new developments include temporal-spatial and end-to-end modelling, as well as novel applications to environmental impact analyses, in both aquatic and terrestrial domains. A wide range of plug-ins have been added to extend the diagnostic capabilities of EwE, and the scientific community is applying EwE to a diversified range of topics besides fishing impact assessments, such as the development of scientific advice for management, the analysis of conservation issues, and the evaluation of cumulative impacts of environmental and human activities in marine food webs (including habitat modification and the invasion of alien species). Especially promising is the new potential to include the EwE model in integrated assessments with other models such as those related to climate change research. However, there are still many challenges, including the communication of scientific results in management procedures. In addition, other important scientific issues are how to improve model result validation and perform model quality control. During the conference, the Ecopath International Research and Development Consortium was presented as a way for the EwE user community to become involved in the long-term sustainability of the EwE approach. Overall, exciting times are facing the ecosystem modelling scientific community, and as illustrated by the conference: synergistic cooperation is the future path for the EwE approach.
    Reviews in Fish Biology and Fisheries 06/2015; 25(2). DOI:10.1007/s11160-015-9386-x · 2.56 Impact Factor
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    ABSTRACT: Overfishing and human-induced climate change are putting severe pressure on marine ecosystems. In the southern Benguela, most of South Africa's commercial fisheries have a long history of exploitation and this, coupled with spatio-temporal changes in key species over the last three decades has severely impacted some of South Africa's fisheries and ecosystems. This review summarizes these spatio-temporal changes and investigates possible drivers thereof. It incorporates both past and current research, with a large portion of the latter having formed part of the University of Cape Town's Ma-Re BASICS (Marine Research in the Benguela and Agulhas Systems for supporting Interdisciplinary Climate-change Science) 2010–2013 program. Almost all described changes involve a temporal decline or a spatial shift in species. Fishing seems to have played a role in many of the observed stock declines, for example through geographically disproportionate catches in relation to stock distribution. In some cases, changes in the physical environment seem to have played an additional role, e.g., rock lobsters on the west coast have been affected by fishing as well as changes in the physical environment. In almost all cases these changes have taken place since the 1980s/1990s, except for one or two resources, which have experienced declines since at least the mid 20th century. Spatial shifts in species have either involved an eastward expansion of cool-water species, including kelps, rock lobster and pelagic fish, or a retraction of warm-water species such as the brown mussel, suggesting a cooling of inshore waters along the south-west coast since the 1980s. This suggested cooling is revealed in ocean temperature (SST Pathfinder), wind and upwelling data for the Cape Peninsula and south-west coast region during the same period. The absence or inconsistency of long-term data is problematic when trying to identify drivers of ecosystem change, and actual ecosystem change itself. We discuss this using ocean temperature in the southern Benguela as an example. In addition, the complex interplay between climate and anthropogenic (notably fishing) drivers makes identification of drivers difficult and disentangling these combined effects will require interdisciplinary collaboration, co-ordinated ecosystem projects, increased modelling effort and the continuation, but also establishment, of new, long-term monitoring studies.
    Journal of Marine Systems 04/2015; 144:9-29. DOI:10.1016/j.jmarsys.2014.11.006 · 2.48 Impact Factor
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    ABSTRACT: Ecosystem-based management of marine fisheries requires the use of simulation modelling to investigate the system-level impact of candidate fisheries management strategies. However, testing of fundamental assumptions such as system structure or process formulations is rarely done. In this study, we compare the output of three different ecosystem models (Atlantis, Ecopath with Ecosim, and OSMOSE) applied to the same ecosystem (the southern Benguela), to explore which ecosystem effects of fishing are most sensitive to model uncertainty. We subjected the models to two contrasting fishing pressure scenarios, applying high fishing pressure to either small pelagic fish or to adult hake. We compared the resulting model behaviour at a system level, and also at the level of model groups. We analysed the outputs in terms of various commonly used ecosystem indicators, and found some similarities in the overall behaviour of the models, despite major differences in model formulation and assumptions. Direction of change in system-level indicators was consistent for all models under the hake pressure scenario, although discrepancies emerged under the small-pelagic-fish scenario. Studying biomass response of individual model groups was key to understanding more integrated system-level metrics. All three models are based on existing knowledge of the system, and the convergence of model results increases confidence in the robustness of the model outputs. Points of divergence in the model results suggest important areas of future study. The use of feeding guilds to provide indicators for fish species at an aggregated level was explored, and proved to be an interesting alternative to aggregation by trophic level.
    African Journal of Marine Science 01/2015; 37(1):65--78. DOI:10.2989/1814232X.2015.1013501 · 1.06 Impact Factor
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    ABSTRACT: Trophic level (TL)-based indicators have been widely used to examine fishing impacts in aquatic ecosystems and the induced biodiversity changes. However, much debate has ensued regarding discrepancies and challenges arising from the use of landings data from commercial fisheries to calculate TL indicators. Subsequent studies have started to examine survey-based and model-based indicators. In this paper, we undertake an extensive evaluation of a variety of TL indicators across 9 well-studied marine ecosystems by making use of model- as well as survey and catch-based TL indicators. Using detailed regional information and data on fishing history, fishing intensity, and environmental conditions, we evaluate how well TL indicators are capturing fishing effects at the community level of marine ecosystems. Our results highlight that the differences observed between TL indicator values and trends is dependent on the data source and the TL cut-off point used in the calculations and is not attributable to an intrinsic problem with TL-based indicators. All 3 data sources provide useful information about the structural changes in the ecosystem as a result of fishing, but our results indicate that only model-based indicators represent fishing impacts at the whole ecosystem level.
    Marine Ecology Progress Series 10/2014; 512:115-140. DOI:10.3354/meps10821 · 2.64 Impact Factor
  • LJ Shannon, W Osman, A Jarre
    Marine Ecology Progress Series 10/2014; 512:217-237. DOI:10.3354/meps10879 · 2.64 Impact Factor
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    ABSTRACT: The marine pelagic social-ecological system in the southern Benguela, which supports important forage fisheries, has been undergoing both human-induced and environmentally-induced long-term, system-scale changes. While people have learnt to adapt to the high interannual variability in the natural system, the effects of long-term changes have largely been detrimental, and have led to a stressed social-ecological system particularly on SA’s west coast. An integrated approach to marine social-ecological systems requires collaboration across a wide range of stakeholders, and we explore the possibilities for collaborative research and management programmes. We provide an overview of methodology developed in support of an EAF in the southern Benguela, including (i) mediated modelling of the links between small pelagic fisheries and a dependent predator, African penguins, whose breeding colonies support ecotourism, (ii) ecosystem modelling for management strategy evaluation including system-scale changes, and (iiii) ecosystem indicators and their combined evaluation in decision trees and expert systems. Focussing on long-term collaboration between universities, the relevant government departments and NGOs, we reflect on social learning in the fisheries and conservation management systems towards an integrated approach to management of human activities in the southern Benguela.
    American Fisheries Society 144th Annual Meeting; 08/2014
  • Kate E. Watermeyer, Astrid Jarre, Lynne J. Shannon
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    ABSTRACT: A number of ecologically and economically important species in the southern Benguela, including sardine Sardinops sagax and anchovy Engraulis encrasicolus, have undergone southward/eastward shifts in their distribution in recent decades. In addition to the effects of changes in prey availability to top predators, the spatially-distinct nature of the system means the location of a stock has implications for its productivity. The spatial dynamics of small pelagic fish are of particular importance because they are thought to exert wasp-waisted trophic control on the system. An objective-driven frame-based model was constructed to investigate the ability of the approach to describe spatial and population dynamics of sardine and anchovy, and to explore the implications of possible management options. Climate variability and fishing pressure were assumed as drivers. A frame-based approach appears to be useful within this context. Results suggest that the productivity of the sardine resource within the model is highly dependent on the spatial characteristics of fishing pressure. The role of anchovy within the model system has not yet been fully developed. Increasing our understanding of the relative suitability of environmental conditions of different regions is also important if we are to increase our capacity to predict trends in abundance and distribution.
    American Fisheries Society 144th Annual Meeting; 08/2014
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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 04/2014; 9(4):e94286. DOI:10.1371/journal.pone.0094286 · 3.53 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 04/2014; 278:52–66. DOI:10.1016/j.ecolmodel.2014.01.003 · 2.07 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 02/2014; 274:41–49. DOI:10.1016/j.ecolmodel.2013.09.022 · 2.07 Impact Factor
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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. DOI:10.1016/j.ecolmodel.2014.01.013 · 2.33 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. DOI:10.1577/C09-059.1 · 1.81 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.
    Bulletin of Marine Science -Miami- 01/2013; 89(1):249-284. DOI:10.5343/bms.2011.1145 · 1.33 Impact Factor
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    Lynne Shannon, Yunne Shin
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    ABSTRACT: An investigation into the impacts of depleting key species in the Southern Benguela Upwelling System has been carried out using two modelling approaches, Ecopath with Ecosim (EwE) and OSMOSE. In EwE depletion simulations, F MSY was usually close to the estimated F 40 level and largest in absolute terms in the case of cephalopods and anchovy. Fishing mortality resulting in depletion was lowest in the case of the " other small pelagic fish " group, which is only lightly fished in the southern Benguela. Depletion of redeye round herring (Etrumeus whiteheadi) occurred at F=1y
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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. DOI:10.1016/j.jmarsys.2011.07.012 · 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. DOI:10.1016/j.cosust.2012.05.003 · 2.76 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. DOI:10.1126/science.1212928 · 31.48 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. DOI:10.1126/science.1209395 · 31.48 Impact Factor

Publication Stats

3k Citations
211.38 Total Impact Points

Institutions

  • 2006–2015
    • University of Cape Town
      • • Department of Biological Sciences
      • • Marine Research Institute
      • • Animal Demography Unit
      Kaapstad, Western Cape, South Africa
  • 2010
    • Dalhousie University
      Halifax, Nova Scotia, Canada