A Stepwise Fitting Procedure for automated fitting of Ecopath with Ecosim models

The Stepwise Fitting Procedure automates testing of alternative hypotheses used for fitting Ecopath with Ecosim (EwE) models to observation reference data (Mackinson etal. 2009). The calibration of EwE model predictions to observed data is important to evaluate any model that will be used for ecosystem based management. Thus far, the model fitting procedure in EwE has been carried out manually: a repetitive task involving setting >1000>1000 specific individual searches to find the statistically ‘best fit’ model. The novel fitting procedure automates the manual procedure therefore producing accurate results and lets the modeller concentrate on investigating the ‘best fit’ model for ecological accuracy

Modelling the Mediterranean marine ecosystem as a whole: addressing the challenge of complexity

An ecosystem modelling approach was used to understand and assess the whole 16 Mediterranean marine ecosystem structure and functioning. In particular, two food web 17 models for the 1950s and 2000s periods were built to investigate: 1) the main structural and 18 functional characteristics of the Mediterranean food-web during these time periods; 2) the key 19 species/functional groups and interactions; 3) the role of fisheries and its impact; and 4) the 20 ecosystem properties of the Mediterranean Sea in comparison with other European Regional 21 Seas. Results show that among all functional groups the highest trophic levels were observed 22 for marine mammals and large predatory fish. The ecosystem flows were mainly dominated by 23 lower trophic level organisms, as benthic invertebrates, zooplankton and phytoplankton while 24 small pelagic fish, mainly European sardines and anchovies, prevailed in terms of biomasses and 25 catches. Large pelagic fish, sharks and medium pelagic fish seemed to play a key role in the past 26 ecosystem, replaced in more recent year by large pelagic fish, benthopelagic and benthic 27 cephalopods. Fisheries showed large impacts on most living groups of the ecosystem in both 28 time periods. Also, when comparing the Mediterranean to the other European Regional Seas, 29 the Mediterranean stood alone in relation to the type of flows driving the system and the 30 cycling indices, suggesting higher levels of community stress induced by intensive fishing 31 activities. In the near future, effort should be dedicated to implement spatial and temporal 32 dynamic simulations to evaluate the exploitation status of the Mediterranean Sea and explore 33 different management policies and future scenarios.JRC.H.1-Water Resource

New, flexible and open-source fisheries self-reporting app: The Shiny4SelfReport

Self-reporting applications are considered a promising solution for fisheries data monitoring. However, they are still failing in providing accurate information and engaging users. We introduce the Shiny4SelfReport, an application for self-reporting data in fisheries that aims to address these shortcomings. Instead of using expensive proprietary software, we demonstrate how common and affordable technologies can be used to fill gaps in fisheries management of developing nations. The tool, developed in R, works by gathering fishers’ inputs and storing them in the cloud. It was designed to be simple and adaptable. Our application improves the data assembly on small-scale fisheries, provides fishers’ engagement and data accuracy, and may integrate fisheries’ knowledge worldwide while filling the gaps on data-poor fisheries. The app is available at http://triatlas.shinyapps.io/Shiny4SelfReport under a General Public License (GPLv3).Postprint (published version

A century of fish biomass decline in the ocean

Contribution to the Theme Section ‘Trophodynamics in marine ecology’.-- 12 pages, 7 figures, 3 tables, supplementary material https://doi.org/10.3354/meps10946We performed a global assessment of how fish biomass has changed over the last 100 yr, applying a previously developed methodology using ecological modeling. Our assessment built on more than 200 food web models representing marine ecosystems throughout the world covering the period from 1880 to 2007. All models were constructed based on the same approach, and have been previously documented. We spatially and temporally distributed fish biomasses delivered by these models based on fish habitat preferences, ecology, and feeding conditions. From these distributions, we extracted over 68000 estimates of biomass (for predatory and prey fishes separately, including trophic level of 3.5 or higher, and trophic level between 2.0 and 3.0, respectively), and predicted spatial-temporal trends in fish biomass using multiple regression. Our results predicted that the biomass of predatory fish in the world oceans has declined by twothirds over the last 100 yr. This decline is accelerating, with 54% occurring in the last 40 yr. Results also showed that the biomass of prey fish has increased over the last 100 yr, likely as a consequence of predation release. These findings allowed us to predict that there will be fish in the future ocean, but the composition of fish assemblages will be very different from current ones, with small prey fish dominating. Our results show that the trophic structure of marine ecosystems has changed at a global scale, in a manner consistent with fishing down marine food webs. © Inter-Research 2014This is a contribution from Sea Around Us, a scientific cooperation between the University of British Columbia (UBC) and the Pew Charitable trust. V.C. acknowledges support from the Natural Sciences and Engineering Research Council of Canada. M.C. was partially funded by the EC Marie Curie Career Integration Grant Fellowships to the BIOWEB project and the Spanish National Program Ramon y Cajal.Peer Reviewe

Using ecosystem models to inform ecosystem-based fisheries management in Europe: a review of the policy landscape and related stakeholder needs

The need to implement an ecosystem-based fisheries management (EBFM) is enshrined in numerous regulations and strategies, at both global and European level. In practice, it is challenging to implement EBFM because it requires a complex evaluation of interlinked management effects and environmental and climate forcing on multi-species interactions, habitat status and human activities. Ecosystem models are one of the most critical research tools to inform EBFM, because they can integrate a wide variety of data, examine multiple and complex ecosystem interactions, and can make forecasts based on specific management scenarios. However, despite clear progress in marine ecosystem modelling, many models do not address policy goals and targets, which hinders uptake in policy. In this paper, we review the global and European policies and implementing bodies which directly or indirectly have a repercussion on the implementation of EBFM. Moreover, we highlight specific stakeholder needs related to the implementation of EBFM in European waters, which ecosystem models could help address. We review the policy commitments that drive these needs and the concerns raised by stakeholders during a survey and dedicated workshop. Key topics of concern were effects of climate change; bycatch; protected areas/fisheries restricted areas; and reducing the impacts of trawling. Stakeholders also provided specific questions related to these topics which ecosystem models could help address. Scenario and data results visualizations, as well as specific barriers in using the results of ecosystem models for decision-making are also discussed. A close involvement of stakeholders in scenario development and in designing graphical outputs is important, and can help overcome some of the main barriers that can hinder uptake of models and scenarios, including a lack of understanding of the benefits and limits of ecosystem models; insufficient involvement and interaction with stakeholders; and inadequate characterization of uncertainties.publishedVersio

The Biodiversity of the Mediterranean Sea: Estimates, Patterns, and Threats

The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterra- nean Sea. However, our estimates of marine diversity are still incomplete as yet—undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterra- nean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well.Comisión Europea Marie Curie Call FP7-PEOPLE-04/01/2007-IOFMinisterio de Ciencia e Innovación GRACCIE C5D2007-00067Ministerio de Ciencia e Innovación CGL2008-05407-C03-03Generalitat de Catalunya 2009SRG665 y 2009SGR484Ministerio de Ciencia e Innovación CTM2007-6663

Combining ecosystem modeling with serious gaming in support of transboundary maritime spatial planning

The Maritime Spatial Planning (MSP) Challenge simulation platform helps planners and stakeholders understand and manage the complexity of MSP. In the interactive simulation, different data layers covering an entire sea region can be viewed to make an assessment of the current status. Users can create scenarios for future uses of the marine space over a period of several decades. Changes in energy infrastructure, shipping, and the marine environment are then simulated, and the effects are visualized using indicators and heat maps. The platform is built with advanced game technology and uses aspects of role-play to create interactive sessions; it can thus be referred to as serious gaming. To calculate and visualize the effects of planning decisions on the marine ecology, we integrated the Ecopath with Ecosim (EwE) food web modeling approach into the platform. We demonstrate how EwE was connected to MSP, considering the range of constraints imposed by running scientific software in interactive serious gaming sessions while still providing cascading ecological feedback in response to planning actions. We explored the connection by adapting two published ecological models for use in MSP sessions. We conclude with lessons learned and identify future developments of the simulation platform

Modelling marine trophic transfer of radiocarbon (14C) from a nuclear facility

Sellafield marine discharges of 14C are the largest contributor to the global collective dose from the nuclear fuel industry. As such, it is important to understand the fate of these discharges beyond the limitations and scope of empirical analytical investigations for this highly mobile radioactive contaminant. Ecopath with Ecosim (EwE) is widely used to model anthropogenic impacts on ecosystems, such as fishing, although very few EwE studies have modelled the fate of bioavailable contaminants. This work presents, for the first time, a spatial-temporal 14C model utilising recent developments in EwE software to predict the ecological fate of anthropogenic 14C in the marine environment. The model predicted observed trends in 14C activities between different species and through time. It also provided evidence for the integration of Sellafield 14C in species at higher trophic levels through time

Changes in Life History Traits of Small Pelagic Fish in the Western Mediterranean Sea

21 pages, 8 figures, 3 tables, supplementary material https://www.frontiersin.org/articles/10.3389/fmars.2021.570354/full#supplementary-material.-- Data Availability Statement: The datasets presented in this article are not readily available because the dataset is available by request to the Spanish Institute of Oceanography. Requests to access the datasets should be directed to [email protected] pelagic fish (SPF) in the western Mediterranean Sea are key elements of the marine food web and are important in terms of biomass and fisheries catches. Significant declines in biomass, landings, and changes in the age/size structure of sardine Sardina pilchardus and anchovy Engraulis encrasicolus have been observed in recent decades, particularly in the northern area of the western Mediterranean Sea. To understand the different patterns observed in SPF populations, we analyzed key life history traits [total length at age, length at maturity, gonadosomatic index (GSI), and body condition (Kn)] of sardine and anchovy collected between 2003 and 2017, from different fishing harbors distributed along a latitudinal gradient from northern to southern Spain. We used Generalized Linear Models (GLM) to estimate the length at maturity and Generalized Additive Models (GAMs) to test the relationship with environmental variables (seawater temperature, water currents, and net primary productivity). The life history traits of both species presented seasonal, interannual and latitudinal differences with a clear decline in length at age, length at first maturity, and body condition, for both species in the northern part of the study area. In the southern part, on the contrary, life history traits did not present a clear temporal trend. The environmental conditions partially explained the long-term changes in life history traits, but the selected variables differed between areas, highlighting the importance of regional oceanographic conditions to understand the dynamics of small pelagic fish. The truncated length-at-age pattern for both species with the disappearance of the larger individuals of the population could have contributed to the poor condition of small pelagic fish populations in the northern part of the western Mediterranean Sea in recent years. In the south area, recent declines in body condition for sardine and anchovy were observed and could be a possible first sign for future population declines. This study highlights the importance of understanding the trade-off between the energy invested in reproduction, maintenance and growth at seasonal and interannual level to advance our knowledge on how environmental and human pressures influence population dynamics of small pelagic fish at local and regional scalesThis study was carried out within the Spanish Research project PELWEB (CTM2017-88939-R) funded by Spanish Ministry of Science, Innovation and Universities and the European Research Contract SPELMED (SC NR 02-TENDER EASME/EMFF/2016/032XXX) funded by EC EASME. Fisheries data collection has been co-funded by the EU through the European Maritime and Fisheries Fund (EMFF) within the National Program of collection, management and use of data in the fisheries sector and support for scientific advice regarding the Common Fisheries Policy (Regulation, EU 2017/1004)With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

Global ensemble projections reveal trophic amplification of ocean biomass declines with climate change

While the physical dimensions of climate change are now routinely assessed through multimodel intercomparisons, projected impacts on the global ocean ecosystem generally rely on individual models with a specific set of assumptions. To address these single-model limitations, we present standardized ensemble projections from six global marine ecosystem models forced with two Earth system models and four emission scenarios with and without fishing. We derive average biomass trends and associated uncertainties across the marine food web. Without fishing, mean global animal biomass decreased by 5% (±4% SD) under low emissions and 17% (±11% SD) under high emissions by 2100, with an average 5% decline for every 1 °C of warming. Projected biomass declines were primarily driven by increasing temperature and decreasing primary production, and were more pronounced at higher trophic levels, a process known as trophic amplification. Fishing did not substantially alter the effects of climate change. Considerable regional variation featured strong biomass increases at high latitudes and decreases at middle to low latitudes, with good model agreement on the direction of change but variable magnitude. Uncertainties due to variations in marine ecosystem and Earth system models were similar. Ensemble projections performed well compared with empirical data, emphasizing the benefits of multimodel inference to project future outcomes. Our results indicate that global ocean animal biomass consistently declines with climate change, and that these impacts are amplified at higher trophic levels. Next steps for model development include dynamic scenarios of fishing, cumulative human impacts, and the effects of management measures on future ocean biomass trends