Contributing to ecosystem-based management: a personal scientific journeyTrenkel, Verena M
doi: 10.1093/icesjms/fsae065pmid: N/A
After three decades of working as a research scientist, I am stepping back to consider the events, questions, and principles that have guided my scientific journey. Important questions and research objectives have been how to implement the ecosystem approach to fisheries management in practice, the development of new data uses, the application of new observation methods and models, and estimating and accounting for uncertainty. Stakeholder engagement—why and how—is a topic that has increased in importance over time. While our observation methods did not change much over many decades, they are now changing rapidly due to new technological developments, but also societal and environmental changes.
Incorporation of observation uncertainty in stock assessment using spatio-temporal modeling of catch-at-length and age-at-length survey dataBreivik, Olav Nikolai; Zimmermann, Fabian; Johannesen, Edda; Ono, Kotaro; Fall, Johanna; Howell, Daniel; Nielsen, Anders
doi: 10.1093/icesjms/fsae079pmid: N/A
Spatio-temporal models are essential tools for estimating abundance indices and quantifying the associated uncertainty. Time series of index uncertainties can be used to objectively determine the influence each index has on the assessment. This can involve reducing the influence of indices in years with limited data. However, incorporating uncertainty in age-length conversion into assessment models has remained a challenge. In this research, we propose an index estimation approach that combines an abundance-at-length model with a model for age-at-length to generate age-specific abundance indices. By jointly modeling abundance-at-length and age-at-length, we address uncertainties in both components of the index-at-age. Using North East Arctic haddock (Melanogrammus aeglefinus) as a case study, we validate the uncertainty of the indices by integrating them into the state space assessment model SAM. The results indicate that the uncertainty estimates are realistic, and we further demonstrate that incorporating uncertainty in age conversion has effects on the assessment results. Our case study demonstrates that incorporating the uncertainty in age-at-length data improves the characterization of uncertainty in stock assessment, and hence better accounts for risk in precautionary management.
Empirical dynamic modeling for sustainable benchmarks of short-lived speciesTsai, Cheng-Han; Munch, Stephan B; Masi, Michelle D; Stevens, Molly H
doi: 10.1093/icesjms/fsae080pmid: N/A
The abundance dynamics of short-lived marine species often exhibit large-amplitude fluctuations, potentially driven by unknown but important species interactions and environmental effects. These complex dynamics pose challenges in forecasting and establishing robust reference points. Here, we introduce an empirical dynamic modeling (EDM) framework using time-delay embeddings to recover unspecified species interactions and environmental effects, and use walk-forward simulations with varying harvest rates to estimate maximum sustainable yield (MSY). Firstly, we apply our framework to simulated data under various dynamics scenarios and demonstrate the statistical robustness of EDM-based MSY. Secondly, we apply our framework to abundance and catch time series (>30 years) of federally managed brown shrimp stocks in the US Gulf of Mexico. We identify nonlinear signals and achieve high prediction accuracy in the empirical dynamics of brown shrimp. Lastly, based on the EDM of brown shrimp dynamics, we obtain MSY for timely and effective management. Our results highlight the utility of EDM in deriving reference points for short-lived species, particularly in situations where stock abundance and catch dynamics are influenced by unobserved species interactions and environmental effects in a complex ecosystem.
Otoliths as chemical archives through ontogeny reveal distinct migratory strategies of Atlantic halibut within the Gulf of St. LawrenceGauthier, Charlotte; Fisher, Jonathan A D; Robert, Dominique; Sirois, Pascal
doi: 10.1093/icesjms/fsae081pmid: N/A
In marine fishes of commercial interest, defining habitat use and migration strategies through ontogeny can help better understand the structure and dynamics of harvested populations and guide their management. The present study relied on otolith chemistry to identify three contingents within the Atlantic halibut (Hippoglossus hippoglossus) stock in the Gulf of St. Lawrence (GSL). We differentiated two chemical signatures from otolith edges, one for shallow (<100 m) and another one for deep (>100 m) waters. By identifying transitions between the deep and shallow habitats, we found that most halibut display migrations from the deep waters to shallow waters during the first 3 years of life. After reaching maturity, most halibut distributing in northern regions of the GSL became full-time residents in deep areas of the GSL. In contrast, halibut found in summer on the shallow plateau of the southern GSL displayed migrating behaviour between shallow (summer) and deep (winter) waters throughout their lives, either on an annual or irregular basis. Overall, our results demonstrate that otolith chemical signatures serve as natural markers of geographically distinct marine environments, facilitating the identification and reconstruction of environmental histories of long-lived marine fishes.
Adding the risk of stock collapse over time to stock assessments and harvest allocation decisionsBlanz, Benjamin; Cormier, Roland; Swain, Douglas; Held, Hermann
doi: 10.1093/icesjms/fsae084pmid: N/A
Globally, many fisheries have experienced collapse even though most of these fisheries had management plans with harvest control rules and were supported by scientific modelling that explicitly accounted for uncertainty. Recognizing that an informed decision on risks of a stock collapse versus harvest is only possible when the outcomes of the technical measures are described explicitly. We propose that the cumulative probability of stock collapse over a range of harvest levels would provide a perspective of the future consequences of harvesting decisions. Adding to the harvest level negotiations the consideration of how long a fishery should sustain the livelihoods of fishers may provide managers, fishers, and other stakeholders with a more tangible understanding of the risks within the context of precautionary principles in decision-making. We use a time series from the Canadian Cod fishery of the Southern Gulf of St. Lawrence, from which we construct and calibrate a simplified model as an emulator of more comprehensive models to demonstrate the approach. The implications of adding an analysis of the probabilities of stock collapse for a range of harvest levels and using a risk matrix to inform decision-making are discussed for four selected years 1974, 1986, 1993, and 2017.
Weakly supervised classification of acoustic echo-traces in a multispecific pelagic environmentLekanda, Aitor; Boyra, Guillermo; Louzao, Maite
doi: 10.1093/icesjms/fsae085pmid: N/A
In trawl-acoustic methods, machine learning can objectively assign species composition to echo-traces, providing a reproducible approach for improving biomass assessments and the study of schooling behaviour. However, the automatic classification of schools in multispecies environments is challenging due to the difficulty of obtaining ground truth information for training. We propose a weakly supervised approach to classify schools into seven classes using catch proportions as probabilities. A balancing strategy was used to address high dominance of some species while preserving species mixtures. As the composition of schools from multispecific catches was unknown, model performance was evaluated at the school and haul level. Accuracy was 63.5% for schools from single-species catches or those identified by experts, and a 20.1% error was observed when comparing predicted and actual species proportions at the haul level. Positional and energetic descriptors were highly relevant, while morphological characteristics showed low discriminative power. The highest accuracies were obtained for juvenile anchovy and Muller’s pearslide, while sardine was the most challenging to classify. Our multioutput approach allowed the introduction of a metric to assess the confidence of the model in classifying each school. As a result, we introduced a method to classify echo-traces considering prediction reliability.
Predicted ecological consequences of wave energy extraction and climate-related changes in wave exposure on rocky shore communitiesWant, Andrew; Waldman, Simon; Burrows, Michael T; Side, Jonathan C; Venugopal, Vengatesan; Bell, Michael C
doi: 10.1093/icesjms/fsae086pmid: N/A
Wave energy has the potential to contribute in the transition to decarbonized electricity generation. Extracting wave energy might be expected to have ecological impacts on rocky shore intertidal communities where exposure is one of the most important factors determining species structure and composition. With global climatic change, coastal exposure is predicted to increase with greater significant wave height. The wave-exposed west coast of Orkney, Scotland, UK, is the site of pre-commercial wave device testing. Surveys of 39 rocky shore sites along this coast identified key species and abundances, and quantified exposure-modifying topographic variables. A spectral wave model was constructed to compare baseline, wave extraction, climate change, and combined scenarios. Generalized additive modelling was used to describe the relationship between species, topography, and exposure. Results show that individual species differentially respond to exposure changes with ‘winners’ and ‘losers’ at site level. Overall, community responses are expected to be far greater following predicted climatic change than to industrial-scale wave energy extraction, depending on spatial scale. In combination, energy extraction may reduce the effects of climate-change-related increases in wave exposure of rocky shores. Predicting how location-specific biotic assemblages respond to changes in wave energy as a result of long-term forcing agents provides a valuable marine resource management tool.
Identifying fish and estimating abundance and swim velocities of migrating Pacific salmon using adaptive resolution imaging sonar in mobile surveysXie, Yunbo; Hornsby, Rachael L; Hanot, William H; Bartel-Sawatzky, Michael; Nelitz, Jacqueline L
doi: 10.1093/icesjms/fsae088pmid: N/A
Mobile acoustic sounding is an effective survey method for fish abundance residing or migrating in large riverine basins and marine areas. A long-standing challenge in acoustic fish surveys with conventional sonar is the uncertainty in identifying fish targets from acquired echo data. Identification errors of fish targets can significantly bias estimates of fish abundances and negatively impact the management of fisheries. In contrast to conventional sonar, adaptive resolution imaging sonar (ARIS), if deployed properly with appropriate settings, can yield high-quality images of fish targets. ARIS images acquired with adequate frame rates can form video recordings to allow for confident identification of fish targets from recorded morphological features, sizes, direction of movements, and speeds. In this paper, we present an approach of using ARIS sonar for mobile surveys of fish passage in a riverine environment. Applications of this approach are demonstrated for its practical values with results from an ARIS-based mobile survey of upstream migrating salmon at an acoustically challenging fish-counting site on the lower Fraser River in British Columbia, Canada.