Evaluating acoustic-trawl survey strategies using an end-to-end ecosystem model

Fisheries independent surveys support science and fisheries assessments but are costly. Evaluating the efficacy of a survey before initiating it could save costs. We used the NORWECOM.E2E model to simulate Northeast Atlantic mackerel and Norwegian spring spawning herring distributions in the Norwegian Sea, and we ran vessel transects in silico to simulate acoustic-trawl surveys. The simulated data were processed using standard survey estimation software and compared to the stock abundances in the ecosystem model. Three existing real surveys were manipulated to demonstrate how the simulation framework can be used to investigate effects of changes in survey timing, direction, and coverage on survey estimates. The method picked up general sources of biases and variance, i.e. that surveys conducted during fish migrations are more vulnerable in terms of bias to timing and changes in survey direction than during more stationary situations and that increased effort reduced the sampling variance.publishedVersio

Modeling and Simulation of American Lobster in the Gulf of Maine: Spatial Distribution, Monitoring, and Conservation

In spite of the high fishing pressure and landings, the Gulf of Maine (GOM) American lobster (Homarus americanus) population abundance has increased dramatically since the early 1990s. Various hypotheses have been developed to explain such an increase, ranging from improved habitat to conservation measures that protect female spawners. However, no systematic study has been done to evaluate these hypotheses. This study aims to examine roles of environmental drivers and conservation measures in regulating the dynamics of lobster population, and evaluate the performance of monitoring programs. A geographical weighted regression model was developed to examine the non-stationary environmental effects on the lobster distribution. An individual-based lobster simulator was used to assess the impact of minimum and maximum legal sizes on the lobster population dynamics from 1982 to 2013. Various quantitative measures were used to evaluate the effectiveness of existing sampling design for the lobster monitoring programs and the accuracy of modeled bottom water temperatures in the GOM. This study shows that bottom water temperature had a more significant positive impact on the increase of lobsters in the eastern GOM than in the western GOM. Minimum and maximum legal sizes also made a great contribution to the dramatic increase of the GOM lobster fishery. An increase of 2 mm carapace length in minimum legal size with no changes in maximum legal size would result in a 279.92% increase in landings compared with the reference landings in 2013. The current lobster and temperature monitoring programs could capture the temporal trend of lobster catches and bottom water temperature. A systematic subsampling of only 50% of the reference samples could produce similar information on lobster catches and size composition for the Lobster Sea Sampling Program. The estimation of locally varying relationships can further improve regionally informed management plans. The estimated impacts of conservation measures address some concerns from stakeholders regarding the necessity of these measures in the fishery. This study also provides spatial-temporal specific sampling advice for the monitoring programs and optimization which can be applied to other monitoring programs to facilitate the development of cost-effective surveys

Improving Management and Conservation of Cusk (Brosme brosme): Habitat Distribution, Bycatch Interactions, and Conservation Practices

Cusk (Brosme brosme) are a National Oceanic and Atmospheric Administration species of concern, currently under internal status review for the Endangered Species Act, but are considered data limited. Current concerns for cusk include: decline in abundance, increase in fishing mortality relative to survey biomass, increased patchiness in habitat, and lack of management (72 FR 10710). Future management will require an improved understanding of cusk distribution, habitat use, spatial distribution of bycatch interactions, and the impact of bycatch on the population. This study set out to evaluate changes in cusk distribution and habitat, locations and levels of bycatch, and the feasibility of implementing conservation measures to reduce discard mortality of cusk bycatch. Data limited approaches were developed to map cusk habitat and potential areas of bycatch. A spatio-temporal delta-Generalized Linear Mixed Model (GLMM) was used to combine observations from the Northeast Fisheries Science Center (NEFSC) spring and fall research bottom trawl survey with the NEFSC western Gulf of Maine (GOM) co-operative research longline survey. The resulting density estimates were then used to develop model-based habitat suitability index (HSI) maps for cusk with increased data resolution. The American lobster (Homarus americanus) fishery is thought to be a significant source of mortality for cusk, as such bycatch of cusk within this fishery was evaluated. Bycatch ‘hotspots’ were predicted based on the overlap of cusk and American lobster high quality habitat. Field studies were conducted in collaboration with Maine lobster fishermen to evaluate the ability of cusk to survive incidental catches within the lobster fishery. These studies resulted in an estimated 75% survival rate in the medium-term (4 – 14 days) if recompressed. To evaluate the impact of implementing the recompression of cusk as a conservation measure throughout the Maine lobster fleet stock assessment simulations were conducted. Cusk bycatch was first estimated for the Maine lobster fishery to develop the simulation scenarios. These estimates indicate 2 – 9 cusk are caught per 10,000 trap hauls, depending on location. Life history parameters were also estimated for cusk for the simulations. The stock assessment simulations indicated that a decrease in fishing mortality would be beneficial to the population, but only decreasing mortality from the Maine lobster fishery would not be enough to significantly improve the population status

The Past, Present and Future of Conservation in the Maine Lobster Fishery

Understanding both the social and biological factors surrounding conservation is important for informing effective fisheries management. This dissertation examines conservation in the American lobster (Homarus americanus) fishery in a changing Gulf of Maine (GOM) using computer simulations informed by interviews with lobster fishers. In this fishery, v-notching, an important conservation measure intended to protect the spawning stock, has been hypothesized to have contributed to the dramatic increase in lobster landings and stock biomass since the 1990s in the GOM. Semi-structured and oral history interviews were analyzed to understand v-notching compliance and lobster fishers’ perceptions of v-notching. All lobster fishers interviewed described v-notching as important for the lobster fishery’s sustainability, while also reporting that the v-notching practice has been declining in recent years. Interviews suggest that the decline in v-notching was due to a decrease in the net benefits of v-notching resulting from increased lobster abundance. Given this decline in v-notching practice, evaluating the effect of v-notching on the fishery is important. An individual-based lobster simulator (IBLS), which can capture complex processes with a flexible probabilistic approach, was modified, parameterized, and applied to the fishery. To evaluate the impact of v-notching, scenarios examining different v-notching compliance rates and v-notch definitions were simulated using the IBLS with different recruitment dynamics scenarios. These simulation results suggest that the lobster fishery would not have experienced the observed large positive increases in biomass and landings without a high v-notching compliance rate (i.e. 90 or 100% compliance) or a strict definition of the notch. Although v-notching has contributed to the increases in the fishery and population, to fully understand the role of conservation, the stock-recruitment relationship (SRR) in a changing GOM needs to be better understood. The GOM bottom water temperatures have increased at a rate of 0.2°C per decade, which caused lobster settlement area to expand and size at maturity to change, adding to the complexity of understanding recruitment dynamics. To give more effective advice for fisheries management, the SRR for lobster was further investigated by including bottom water temperature as a covariate. The results showed that temperature had a strong effect on recruitment resulting in a temporal shift in productivity in the SRR in 2009. This dissertation also used a size-structured stock assessment model to assess the effect of a decrease in size at maturity and the resulting change in growth on the American lobster stock assessment model and SRR. Projections of the lobster fishery under different v-notching scenarios show that in the near future, although v-notching does not increase landings, v-notching still preserves the spawning stock. These results show that the v-notching conservation measure is a valuable tool for precautionary management. Overall, these results suggest that input controls, such as protecting the spawning stock, can provide benefits to both the fish population and fishery. The implications of a decline in the v-notching practice may have negative impacts for the future sustainability of the fishery if the spawning stock and productivity were to decline. Additionally, this dissertation demonstrates that climate driven SRRs and biological reference points should be considered for American lobster management. This dissertation highlights the importance of considering changes in compliance and productivity and the interactions between the two factors. The framework proposed in this study can be extended to evaluate the protection of spawning females in many other commercial fisheries influenced by climate change

ABS-FishCount: An Agent-Based Simulator of Underwater Sensors for Measuring the Amount of Fish

[EN] Underwater sensors provide one of the possibilities to explore oceans, seas, rivers, fish farms and dams, which all together cover most of our planet's area. Simulators can be helpful to test and discover some possible strategies before implementing these in real underwater sensors. This speeds up the development of research theories so that these can be implemented later. In this context, the current work presents an agent-based simulator for defining and testing strategies for measuring the amount of fish by means of underwater sensors. The current approach is illustrated with the definition and assessment of two strategies for measuring fish. One of these two corresponds to a simple control mechanism, while the other is an experimental strategy and includes an implicit coordination mechanism. The experimental strategy showed a statistically significant improvement over the control one in the reduction of errors with a large Cohen's d effect size of 2.55.This work acknowledges the research project Desarrollo Colaborativo de Soluciones AAL with reference TIN2014-57028-R funded by the Spanish Ministry of Economy and Competitiveness. This work has been supported by the program Estancias de movilidad en el extranjero José Castillejo para jóvenes doctores funded by the Spanish Ministry of Education, Culture and Sport with reference CAS17/00005. We also acknowledge support from Universidad de Zaragoza , Fundación Bancaria Ibercaja and Fundación CAI in the Programa Ibercaja-CAI de Estancias de Investigación with reference IT24/16. We acknowledge the research project Construcción de un framework para agilizar el desarrollo de aplicaciones móviles en el ámbito de la salud funded by University of Zaragoza and Foundation Ibercaja with grant reference JIUZ-2017-TEC-03. It has also been supported by Organismo Autónomo Programas Educativos Europeos with reference 2013-1-CZ1-GRU06-14277. We also aknowledge support from project Sensores vestibles y tecnología móvil como apoyo en la formación y práctica de mindfulness: prototipo previo aplicado a bienestar funded by University of Zaragoza with grant number UZ2017-TEC-02. Furthermore, we acknowledge the Fondo Social Europeo and the Departamento de Tecnología y Universidad del Gobierno de Aragón for their joint support with grant number Ref-T81.García-Magariño, I.; Lacuesta Gilabert, R.; Lloret, J. (2017). ABS-FishCount: An Agent-Based Simulator of Underwater Sensors for Measuring the Amount of Fish. Sensors. 17(11):1-19. https://doi.org/10.3390/s17112606S1191711Lloret, J. (2013). Underwater Sensor Nodes and Networks. Sensors, 13(9), 11782-11796. doi:10.3390/s130911782Akyildiz, I. F., Pompili, D., & Melodia, T. (2005). Underwater acoustic sensor networks: research challenges. Ad Hoc Networks, 3(3), 257-279. doi:10.1016/j.adhoc.2005.01.004Santos, R., Orozco, J., Micheletto, M., Ochoa, S., Meseguer, R., Millan, P., & Molina, C. (2017). Real-Time Communication Support for Underwater Acoustic Sensor Networks. Sensors, 17(7), 1629. doi:10.3390/s17071629Das, A. P., & Thampi, S. M. (2017). Simulation Tools for Underwater Sensor Networks: A Survey. Network Protocols and Algorithms, 8(4), 41. doi:10.5296/npa.v8i4.10471Kawahara, R., Nobuhara, S., & Matsuyama, T. (2016). Dynamic 3D capture of swimming fish by underwater active stereo. Methods in Oceanography, 17, 118-137. doi:10.1016/j.mio.2016.08.002Schaner, T., Fox, M. G., & Taraborelli, A. C. (2009). An inexpensive system for underwater video surveys of demersal fishes. Journal of Great Lakes Research, 35(2), 317-319. doi:10.1016/j.jglr.2008.12.003Shinoda, R., Wu, H., Murata, M., Ohnuki, H., Yoshiura, Y., & Endo, H. (2017). Development of an optical communication type biosensor for real-time monitoring of fish stress. Sensors and Actuators B: Chemical, 247, 765-773. doi:10.1016/j.snb.2017.03.034Chen, Z., Zhang, Z., Dai, F., Bu, Y., & Wang, H. (2017). Monocular Vision-Based Underwater Object Detection. Sensors, 17(8), 1784. doi:10.3390/s17081784Saberioon, M. M., & Cisar, P. (2016). Automated multiple fish tracking in three-Dimension using a Structured Light Sensor. Computers and Electronics in Agriculture, 121, 215-221. doi:10.1016/j.compag.2015.12.014Pais, M. P., & Cabral, H. N. (2017). Fish behaviour effects on the accuracy and precision of underwater visual census surveys. A virtual ecologist approach using an individual-based model. Ecological Modelling, 346, 58-69. doi:10.1016/j.ecolmodel.2016.12.011Burget, P., & Pachner, D. (2005). FISH FARM AUTOMATION. IFAC Proceedings Volumes, 38(1), 137-142. doi:10.3182/20050703-6-cz-1902.02113Simon, Y., Levavi-Sivan, B., Cahaner, A., Hulata, G., Antler, A., Rozenfeld, L., & Halachmi, I. (2017). A behavioural sensor for fish stress. Aquacultural Engineering, 77, 107-111. doi:10.1016/j.aquaeng.2017.04.001Petreman, I. C., Jones, N. E., & Milne, S. W. (2014). Observer bias and subsampling efficiencies for estimating the number of migrating fish in rivers using Dual-frequency IDentification SONar (DIDSON). Fisheries Research, 155, 160-167. doi:10.1016/j.fishres.2014.03.001Garcia, M., Sendra, S., Lloret, G., & Lloret, J. (2011). Monitoring and control sensor system for fish feeding in marine fish farms. IET Communications, 5(12), 1682-1690. doi:10.1049/iet-com.2010.0654Lloret, J., Garcia, M., Sendra, S., & Lloret, G. (2014). An underwater wireless group-based sensor network for marine fish farms sustainability monitoring. Telecommunication Systems, 60(1), 67-84. doi:10.1007/s11235-014-9922-3Bharamagoudra, M. R., Manvi, S. S., & Gonen, B. (2017). Event driven energy depth and channel aware routing for underwater acoustic sensor networks: Agent oriented clustering based approach. Computers & Electrical Engineering, 58, 1-19. doi:10.1016/j.compeleceng.2017.01.004Gallehdari, Z., Meskin, N., & Khorasani, K. (2017). Distributed reconfigurable control strategies for switching topology networked multi-agent systems. ISA Transactions, 71, 51-67. doi:10.1016/j.isatra.2017.06.008Jurdak, R., Elfes, A., Kusy, B., Tews, A., Hu, W., Hernandez, E., … Sikka, P. (2015). Autonomous surveillance for biosecurity. Trends in Biotechnology, 33(4), 201-207. doi:10.1016/j.tibtech.2015.01.003García-Magariño, I., & Plaza, I. (2015). FTS-SOCI: An agent-based framework for simulating teaching strategies with evolutions of sociograms. Simulation Modelling Practice and Theory, 57, 161-178. doi:10.1016/j.simpat.2015.07.003Cooke, S. J., Brownscombe, J. W., Raby, G. D., Broell, F., Hinch, S. G., Clark, T. D., & Semmens, J. M. (2016). Remote bioenergetics measurements in wild fish: Opportunities and challenges. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, 202, 23-37. doi:10.1016/j.cbpa.2016.03.022García, M. R., Cabo, M. L., Herrera, J. R., Ramilo-Fernández, G., Alonso, A. A., & Balsa-Canto, E. (2017). Smart sensor to predict retail fresh fish quality under ice storage. Journal of Food Engineering, 197, 87-97. doi:10.1016/j.jfoodeng.2016.11.006Tušer, M., Frouzová, J., Balk, H., Muška, M., Mrkvička, T., & Kubečka, J. (2014). Evaluation of potential bias in observing fish with a DIDSON acoustic camera. Fisheries Research, 155, 114-121. doi:10.1016/j.fishres.2014.02.031Rakowitz, G., Tušer, M., Říha, M., Jůza, T., Balk, H., & Kubečka, J. (2012). Use of high-frequency imaging sonar (DIDSON) to observe fish behaviour towards a surface trawl. Fisheries Research, 123-124, 37-48. doi:10.1016/j.fishres.2011.11.018Cenek, M., & Franklin, M. (2017). An adaptable agent-based model for guiding multi-species Pacific salmon fisheries management within a SES framework. Ecological Modelling, 360, 132-149. doi:10.1016/j.ecolmodel.2017.06.024Gao, L., & Hailu, A. (2011). Evaluating the effects of area closure for recreational fishing in a coral reef ecosystem: The benefits of an integrated economic and biophysical modeling. Ecological Economics, 70(10), 1735-1745. doi:10.1016/j.ecolecon.2011.04.014Helbing, D., & Balietti, S. (2011). From social simulation to integrative system design. The European Physical Journal Special Topics, 195(1), 69-100. doi:10.1140/epjst/e2011-01402-7Reynolds, C. W. (1987). Flocks, herds and schools: A distributed behavioral model. ACM SIGGRAPH Computer Graphics, 21(4), 25-34. doi:10.1145/37402.37406Beltran, R. S., Testa, J. W., & Burns, J. M. (2017). An agent-based bioenergetics model for predicting impacts of environmental change on a top marine predator, the Weddell seal. Ecological Modelling, 351, 36-50. doi:10.1016/j.ecolmodel.2017.02.002Berman, M., Nicolson, C., Kofinas, G., Tetlichi, J., & Martin, S. (2004). Adaptation and Sustainability in a Small Arctic Community : Results of an Agent-based Simulation Model. ARCTIC, 57(4). doi:10.14430/arctic517Kadir, H. A., & Arshad, M. R. (2015). Cooperative Multi Agent System for Ocean Observation System based on Consensus Algorithm. Procedia Computer Science, 76, 203-208. doi:10.1016/j.procs.2015.12.343Trygonis, V., Georgakarakos, S., Dagorn, L., & Brehmer, P. (2016). Spatiotemporal distribution of fish schools around drifting fish aggregating devices. Fisheries Research, 177, 39-49. doi:10.1016/j.fishres.2016.01.013De Kerckhove, D. T., Milne, S., & Shuter, B. J. (2015). Measuring fish school swimming speeds with two acoustic beams and determining the angle of the school detection. Fisheries Research, 172, 432-439. doi:10.1016/j.fishres.2015.08.001Source Code of the Agent-Based Simulator of Underwater Sensors for Measuring the Amount of Fishes Called ABS-FishCounthttp://dx.doi.org/10.17632/yzmt73x8j8.1Cossentino, M., Gaud, N., Hilaire, V., Galland, S., & Koukam, A. (2009). ASPECS: an agent-oriented software process for engineering complex systems. Autonomous Agents and Multi-Agent Systems, 20(2), 260-304. doi:10.1007/s10458-009-9099-4García-Magariño, I., Palacios-Navarro, G., & Lacuesta, R. (2017). TABSAOND: A technique for developing agent-based simulation apps and online tools with nondeterministic decisions. Simulation Modelling Practice and Theory, 77, 84-107. doi:10.1016/j.simpat.2017.05.006García-Magariño, I., Gómez-Rodríguez, A., González-Moreno, J. C., & Palacios-Navarro, G. (2015). PEABS: A Process for developing Efficient Agent-Based Simulators. 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smartR: An r package for spatial modelling of fisheries and scenario simulation of management strategies

Abstract Overfishing or exploitation patterns with high juvenile mortalities often negatively impact demersal fish stocks. Meanwhile, the increased availability and diffusion of georeferenced information is propelling a revolution of marine spatial planning. A spatial‐explicit approach to the management of fishing effort should protect the Essential Fish Habitats and minimize the impact of trawlers on areas where juveniles of commercial species concentrate. The smartR package is a data‐driven model that implements the Spatially explicit bio‐economic Model for Assessing and managing demeRsal Trawl fisheries to edit and format the raw data; construct and maintain coherent datasets; to numerically and visually inspect the generated metadata; to simulate management scenarios and forecast the possible effects in terms of resources status and economic performances of the fleets. Explicit inclusion of the spatial dimension is essential to improve the understanding of the fishery system, and to enhance the ability of management plans to improve stocks statuses

Real-time Simulation of Cable Pay-Out and Reel-In with Towed Fishing Gears

[Abstract] Achieving real-time simulation of fast cable pay-out and reel-in manoeuvres with towed fishing gears is a challenging task. This work presents two new simulation methods based on simplified cable models for this kind of application. First, three numerical techniques are proposed to enhance a classical spring-based cable model, increasing its computational efficiency in manoeuvres that involve reeling the cable around a winch drum. Second, the development of an efficient multibody modelling approach based on natural coordinates is reported. The performance of these methods was assessed with two realistic examples. The numerical experiments involved different values of cable axial stiffness and spatial discretization levels, since these parameters were found to have a major impact on computational efficiency. The proposed methods achieved real-time performance in the simulation of systems modelled with up to a few thousand variables. Each modelling approach has advantages and limitations that must be considered when addressing a given application.MINECO; JCI-2012-1237

Development of seabed friendly bottom trawls

Concerns over the impacts of fishing practices, especially bottom trawling, on the ocean environment have been expressed at the local, national and international scale. While physical alterations of the seabed by bottom trawling are known to occur, the biological effects on benthic communities and their recovery rates depend on substrate types, depth, and natural disturbance in the fishing area, as well as how trawl gears are designed and operated. In this thesis, I investigate different key research aspects regarding the subject of development of seabed friendly bottom trawls, in particular shrimp trawling in Newfoundland and Labrador, Canada. The complementary use of different research approaches (e.g., underwater video observations, numerical modeling and simulation, flume tank testing, and at-sea experiments) were applied for each of the research questions. First, I investigated the behavioural interactions of individual snow crab in response to the rockhopper footgear of a traditional inshore shrimp trawl used in Newfoundland and Labrador, Canada. I found that snow crab were quickly overtaken under the footgear of the approaching trawl and over half of the snow crab (i.e., 54%) observed experienced an encounter with the rockhopper footgear components. The majority of the snow crab observed appeared to be aware of the trawl and were actively responding and/or reacting to the approaching threat. Second, the strengths and limitations of different commercially available trawl simulation software (i.e., DynamiT, SimuTrawl, and Trawl Vision PRO) in terms of design capability, simulation capability, and reliability of results, were investigated and interpreted. The study provides valuable knowledge and reference for stakeholders (e.g., gear designers, researchers, and educators) who are considering using numerical simulation methods to optimize their gear design concepts during the early stages of development of seabed friendly bottom trawls (e.g., predict expected mechanical stresses of trawl components on the seabed). Next, I addressed the question of how well computer simulation and flume tank testing of scale engineering models actually predict full-scale at-sea performance of bottom trawls. The results demonstrated that the complementary use of two or three methods should be encouraged for assisting the gear development cycle given their own weakness and merits. For instance, the flume tank testing method was successfully utilized to estimate the percentage of contact area made by trawl footgear with the seabed, while at-sea experiments were not designed to measure such impacts. Moreover, I clarified that the precision and accuracy of the predictions depends on many factors. Thus, thoroughness and care must be emphasized in order to reduce bias in predicted performance. Finally, I examined the effectiveness of a reduced seabed impact footgear (i.e., drop chain) over a traditional rockhopper footgear on identical bottom trawls targeting northern shrimp (Pandalus borealis) in Newfoundland and Labrador, Canada. The results demonstrated that seabed impacts of shrimp trawling can be reduced if the trawl footgear is made lighter and/or designed to have less contact with the seabed. In particular, it was revealed that with the experimental drop chain footgear trawl we are able to reduce the interaction or encounter of snow crab. In summary, the knowledge presented in this thesis is believed to significantly contribute to the research and development of low-impact bottom trawls both in theoretical and practical aspects. While the potential impact of bottom trawling activities on habitats and benthic communities is not easy to predict and characterize for various reasons, I do believe that further development and application of fishing gears and techniques that reduce impacts on seabed habitats and associated benthic communities will be essential to achieve ecosystem objectives

Report of the Workshop on Survey Design and Data Analysis (WKSAD) [21- 25 June, 2004, Aberdeen, UK]

Contributors: Knut Korsbrekke, Michael Penningto