Using the ISIS-Fish fisheries dynamics model to explore the consequences on Bay of Biscay demersal fisheries and ecosystem of spatial closures aiming to reduce bycatch of protected species

The present repository makes available the model, material and outputs of the ISIS-Fish modeling work showcased in the peer-reviewed scientific article by Bastardie et al. 2025. As part of the SEAwise research project (seawiseproject.org), we used an ISIS-Fish database (Mahevas et al 2003, Pelletier et al. 2009, isis-fish.org) previously developed within the MACCO project which describes the mixed demersal fishery in the Bay of Biscay. For this application, the spatial extent of the fishery is the Bay of Biscay, defined here by ICES divisions 8a, 8b and 8d and the resolution chosen is 1/16 ICES statistical rectangle. The biological module (Vajas et al. 2024) includes 7 species of economic interest in the mixed demersal fishery: European hake (Merluccius merluccius), common sole (Solea solea), Norway lobster (Nephrops norvegicus), megrim (Lepidorhombus whiffiagonis), anglerfish (Lophius piscatorius) and two ray species (Raja clavata, Leucoraja naevus). The fishing activities module (Mahevas et al. 2024) is made up of 41 demersal fleets (including all French vessels < 12 meters and > 12 meters fishing in this area, Spanich, UK and Belgium fleets) and 431 métiers (combination of a gear, location and mix of target species) catching these 7 species, as target or bycatch. Monthly effort of a fleet distributes among the possible métiers (those historically practiced). The biological and fishing activity modules are identical to the published version. The original model used here has been calibrated on historical catch data 2015-2018 by tuning accessibility and catchability parameters. In the present application the Bay of Biscay model is used to investigate the spatial- and effort- based fisheries management strategies. Consistently with for a task of the SEAwise project (Bastardie et al. 2024) simulations were conducted from 2021 onwards, projecting the effect of an implementation of 3 different closures from 2022 to 2050, under current fishing effort conditions or in a context of fishing effort reduction. Outcomes of these simulations are averaged over short/medium (10 year horizon) and long-term period (20 year horizon). The data project includes: 1) the database including the biological module and fishing activity module; 2) 8 .properties files, each corresponding to one combination of management measure and closure, to restore the simulations parameters in the ISIS-Fish interface and reproduce the simulation runs; 3) the .java scripts to force effort dynamics and simulate spatio-temporal closures, as well as generate the main output files - they will be called by the ISIS-Fish software once the simulations restored 4) the .rds containing the main outputs of the simulations and the associated .html document displaying the R code to compute the indices of interest at different levels of aggregation and reproduce the figures in Bastardie et al. 2025. All files are provided in the Zip. Associated with this material, a study summary and a readme .docx are provided. The first one provides context on the present work and describes the model and simulations' design. The second provides guidelines to reproduce the simulations and their derived outcomes from the data project material made available in this repository. They are both directly downloadable from this repository and are also copied to the zipped folder containing the data project. All the data are reproducible using isis-fish-4.4.8.1 (isis-fish.org; available at forge.codelutin.com) and R 4.2.0.