1. We present a seasonal stock assessment model, which allows the user to initiate a stochastic age-based model inside the R programming language. 2. The model is currently the official stock assessment model for five small pelagic stocks in the North Sea. The seasonality component enables within year changes in weight, natural mortality and recruitment, which is commonly missing from existing methods. 3. We show through simulation analysis that including seasonality can lead to lower bias in stocks with strong interannual dynamics. 4. We provide a variety of useful functions and applications that let the user perform diagnostics and evaluate the goodness-of-fit of the model. The software contains functions used for catch forecasting and management strategy evaluation. The stock assessment model is written in Template Model Builder (TMB), which enables rapid parameter estimation and the potential to estimate parameters as random effects. 5. Practical implication. The model offers a tool for consistent and transparent stock assessments for populations with strong seasonal dynamics.

Oxygen depletion in marine ecosystems, known as hypoxia, is an escalating form of marine pollution driven by eutrophication and climate-induced warming that threatens coastal ecosystems worldwide. Although the ecological impacts of hypoxia are well documented, its broader environmental consequences remain less understood, including how oxygen stress alters human use of marine habitats. Based on an extensive oxygen monitoring dataset integrated with bottom-trawl activity and catch records from the Western Baltic Sea (2010-2023), we assess how fisheries respond to varying levels of hypoxia as an indicator of ecosystem degradation and its consequences for fishing activities. Fishing activity declined to 20% of baseline levels under moderate hypoxia (2-4 mg/L) and to 10% under severe hypoxia (<2 mg/L). Fishers also delayed their return to previously hypoxic areas by an average of 1.9-2.7 weeks, respectively. These behavioral shifts mirror known ecological responses of demersal fish and benthic invertebrates to sublethal oxygen stress. While the resumption of fishing activity suggests some short-term recovery, likely reflecting the return of some fish species to affected areas, long-term degradation of benthic communities may further compromise habitat quality and fish stock productivity. Our findings highlight the importance of incorporating oxygen dynamics into environmental and fisheries management, pollution mitigation, and marine spatial planning, particularly as hypoxia intensifies under the combined pressures of climate change and nutrient loading.

Bycatch of cetaceans in gillnet fisheries is a global problem that can be a major cause of mortality for some species like the harbour porpoise (Phocoena phocoena). To avoid cetacean bycatch, one can enhance the reflectivity of the netting material to make the net barrier more audible in the marine environment. Plastic spheres made of acrylic glass are highly reflective to sound underwater and can be designed species-specifically to be particularly reflective in the frequencies used for echolocating by the species of concern. “PearlNets” are gillnets incorporating such plastic spheres on the twines and have the potential to reduce bycatch rates by making cetaceans aware of the presence of gillnets in their surroundings. However, PearlNets should also be at least as effective as traditional nets at catching target fish species if fishers are to accept using this new mitigation tool. In this study, we compared the catch rates of target species and the bycatch rates of non-target species between control and PearlNets in a set net fishery for Atlantic cod (Gadus morhua) off the Western Baltic Sea. The analysis of the data collected during this trial did not demonstrate a significant difference in catch rates between pearl and control nets (p-values >0.05). In other words, assuming that PearlNets effectively reduce cetacean bycatch, we show that they also maintain catch rates, making this mitigation tool likely acceptable for fishers.

Bottom trawling (hereafter trawling) is the dominant human pressure impacting continental shelves globally. However, due to ongoing data deficiencies for smaller coastal vessels, the effects of trawling on nearshore seabed ecosystems are poorly understood. In Europe, the Water Framework Directive (WFD) provides a framework for the protection and improvement of coastal water bodies. It requires member states to track the status of 'biological quality elements' (including benthic macrofauna) using WFD-specific ecological indicators. While many of these metrics are sensitive to coastal pressures such as nutrient enrichment, little is known about their ability to detect trawling impacts. Here, we analysed a comprehensive data set of 5885 nearshore benthic samples - spatiotemporally matched to high-resolution trawling and environmental data - to examine how these pressures affect coastal benthos. In addition, we investigated the ability of 8 widely-used benthic monitoring metrics to detect impacts on benthic biological quality. We found that abundance (N) and species richness (S) were strongly impacted by bottom trawling. A clear response to trawling was also observed for the WFD-specific Benthic Quality Index (BQI). Relationships between N and S, and trawling were particularly consistent across the study area, indicating sensitivity across varying environmental conditions. In contrast, WFD indices such as AZTIs Marine Biotic Index (AMBI), multivariate AMBI (M-AMBI), and the Danish Quality Index (DKI), were unresponsive to trawling. In fact, some of the most heavily trawled areas examined were classified as being of 'high/good ecological status' by these indices. A likely explanation for this is that the indices are calculated using species sensitivity scores, based on expected species response to eutrophication and chemical pollution. While the BQI also uses species sensitivity scores, these are based on observed responses to disturbance gradients comprising a range of coastal pressures. Given the prominent use of AMBI and DKI throughout Europe, our results highlight the considerable risk that the metrics used to assess Good Ecological Status (GES) under the WFD may fail to identify trawling impacts. As trawling represents a widespread source of coastal disturbance, fishing impacts on benthic macrofauna may be underestimated, or go undetected, in many coastal monitoring programmes around Europe.

Physical and topographic characteristics can structure pelagic habitats and affect the plankton community composition. For example, oxygen minimum zones (OMZs) are expected to lead to a habitat compression for species with a high oxygen demand, while upwelling of nutrient-rich deep water at seamounts can locally in -crease productivity, especially in oligotrophic oceanic waters. Here we investigate the response of the gelatinous zooplankton (GZ) assemblage and biomass to differing oxygen conditions and to a seamount in the Eastern Tropical North Atlantic (ETNA) around the Cape Verde archipelago. A total of 16 GZ taxa (>1100 specimens) were found in the upper 1000 m with distinct species-specific differences, such as the absence of deep-living species Atolla wyvillei and Periphylla periphylla above the shallow seamount summit. Statistical analyses consid-ering the most prominent groups, present at all stations, namely Beroe spp., hydromedusae (including Zygocanna vagans, Halicreas minimum, Colobonema sericeum, Solmissus spp.) and total GZ, showed a strong positive corre-lation of abundance with temperature for all groups, whereas oxygen had a weak negative correlation only with abundances of Beroe spp. and hydromedusae. To account for size differences between species, we established length-weight regressions and investigated total GZ biomass changes in relation to physical (OMZ) and topo-graphic characteristics. The highest GZ biomass was observed at depths of lowest oxygen concentrations and deepest depth strata at the southeastern flank of the seamount and at two stations south of the Cape Verde ar-chipelago. Our data suggest that, irrespective of their patchy distribution, GZ organisms are ubiquitous food web members of the ETNA, and their habitat includes waters of low oxygen content.

There is a need to improve fishing methods to select for certain sizes and species while excluding others. Experiments are conducted to quantify selectivity of fishing gears and how variables such as gear design (e.g. mesh size, mesh shape), environmental parameters (e.g. light, turbidity, substrate) or biological parameters (e.g. fish condition) alter selectivity; the resulting data need to be analyzed using specialized statistical methods in many cases. Here, we present a new tool for analyzing this type of data: an R package named selfisher. It allows estimating multiple fixed effects (e.g. fish length, total catch weight, environmental variables) and random effects (e.g. haul). A bootstrapping procedure is also provided. We demonstrate its use via four case studies including (A) covered codend analyses of four gears, (B) a paired gear study with numerous covariates, (C) a catch comparison study of unpaired hauls of gillnets and (D) a catch comparison study of paired hauls using polynomials and splines. This software will make it easier to model selectivity, teach statistical methods, and make analyses more repeatable.

To effectively future-proof the management of the European Union fishing fleets we have explored a suite of case studies encompassing the northeast and tropical Atlantic, the Mediterranean, Baltic and Black Seas. This study shows that European Union (EU) fisheries are likely resilient to climate-driven short-term stresses, but may be negatively impacted by long-term trends in climate change. However, fisheries’ long-term stock resilience can be improved (and therefore be more resilient to increasing changes in climate) by adopting robust and adaptive fisheries management, provided such measures are based on sound scientific advice which includes uncertainty. Such management requires regular updates of biological reference points. Such updates will delineate safe biological limits for exploitation, providing both high long-term yields with reduced risk of stock collapse when affected by short-term stresses, and enhanced compliance with advice to avoid higher than intended fishing mortality. However, high resilience of the exploited ecosystem does not necessarily lead to the resilience of the economy of EU fisheries from suffering shocks associated with reduced yields, neither to a reduced carbon footprint if fuel use increases from lower stock abundances. Fuel consumption is impacted by stock development, but also by changes in vessel and gear technologies, as well as fishing techniques. In this respect, energy-efficient fishing technologies already exist within the EU, though implementing them would require improving the uptake of innovations and demonstrating to stakeholders the potential for both reduced fuel costs and increased catch rates. A transition towards reducing fuel consumption and costs would need to be supported by the setup of EU regulatory instruments. Overall, to effectively manage EU fisheries within a changing climate, flexible, adaptive, well-informed and well-enforced management is needed, with incentives provided for innovations and ocean literacy to cope with the changing conditions, while also reducing the dependency of the capture fishing industry on fossil fuels. To support such management, we provide 10 lessons to characterize ‘win-win’ fishing strategies for the European Union, which develop leverages in which fishing effort deployed corresponds to Maximum Sustainable Yield targets and Common Fisheries Policy minimal effects objectives. In these strategies, higher catch is obtained in the long run, less fuel is spent to attain the catch, and the fisheries have a higher resistance and resilience to shock and long-term factors to face climate-induced stresses.

Bycatch of protected species, particularly small cetaceans, in gillnets is a worldwide concern. One hypothesis for this is that echolocating cetaceans entangle because they do not perceive conventional gillnets as impenetrable barriers, owing to the gillnet’s faint echo. A gillnet modified for improved acoustical visibility was tested in a first pilot trial in a commercial gillnet fishery targeting turbot (Scophthalmus maeoticus) on the Turkish Black Sea coast. This study is the first demonstration of the viability of using a gillnet equipped with small acrylic glass spheres to reduce bycatch of harbor porpoises in a commercial fishery and provides the basis for full-scale sea trials of the gear in commercial fisheries through a power analysis. In these pilot experiments, the focus lied on the handling of the gear and identification of requirements for a full-scale trial, but results include promising bycatch data for an endangered echolocating marine mammal (Phocoena phocoena) and no reduction in catch efficiency of a bottom-dwelling, vulnerable species (Raja clavata).

Bottom trawling results in widespread impacts to the structure and composition of benthic communities. Although an ecosystem approach to fisheries management aims to conserve marine biodiversity and ecosystem function, there remains a lack of empirical evidence regarding the effects of trawling on benthic functional properties. Here, we examined the sensitivity of benthic macrofauna communities to trawling using their biological traits, and compared trait responses across size-categories and survey types. We collected 84 benthic soft-sediment samples by Van Veen grab (0.1 m 2 ) in the Kattegat in 2016, and complemented with 827 Haps cores (0.0143 m 2 ) gathered over a long-term monitoring programme between 2006 and 2013. By analysing trait response in 3 size categories (small: 1-4 mm fraction; large: ≥4 mm fraction; full community: all individuals combined), we demonstrate a size-dependent effect of trawling on benthic trait composition, where the traits of large-bodied fauna (≥4 mm) were more sensitive. Specifically, larger sessile, deep-living, suspension-feeding, tube-dwelling, subsurface deposit-feeding, burrow-dwelling, and long-lived (≥10 yr) individuals were among the most affected. Our results based on large fauna were largely in agreement with trait responses observed in the multi-year monitoring data, suggesting that trait data gathered from a targeted one-time sampling event can convey information on both acute (short-term) and chronic (long-term) trawling impacts. Given that most trawling impact assessments do not consider size-based effects, we outline how size-separating the community can be used to improve the detectability of trawling impacts, and provide new insights into the functional impacts of fishing on the seabed.

Biomass limit reference points are widely used in fisheries management and define the biomass threshold (BT) below which stock productivity (i.e. recruitment) is likely to be impaired. Scientifically sound and transparent methods for estimating BTs are therefore needed together with ways of quantifying uncertainties. The main focus of the study was placed on two methods currently applied to several small-bodied pelagic species in the Northeast Atlantic. These methods have not formerly been described in the scientific literature and are in the present study being compared with some already described methods, of which one is broadly applied outside the Northeast Atlantic. Using a combination of data simulations and data from 51 small-bodied pelagic fish stocks, we analysed the sensitivity of estimated BTs to (a) the choice of method, (b) time-series length and (c) stock development (e.g. rebuilding or declining). It was demonstrated that estimated BTs are associated with considerable uncertainty not previously quantified. Furthermore, the level of the estimated threshold and the amount of uncertainty depended on choice of method, time-series length and stock development trends. Hence, this study contributes to improving the quality of future biomass limit reference points by providing guidance regarding choice of method and how to demonstrate stock-specific uncertainties.

Climate effects on marine fish depend on life stage, particularly when life stages differ in habitat utilization. In the present study, we investigated life stage-dependent responses of lesser sandeel (Ammodytes marinus) to temperature at contrasting geographical scales. We related population density and individual growth to temperature and found different temperature responses between the first and the second years of life. During the first year of life, fish size was the single most important factor influencing sandeel abundances, indicating a positive relationship between growth and survival. In contrast, during the second year of life, autumn bottom temperature was negatively correlated with sandeel abundance, suggesting elevated mortality in warm years. Southerly areas, experiencing higher temperatures in general, were also the areas showing the strongest response to temperature. This study sheds light on how warming impacts population dynamics of one of the most important forage fishes in the North Sea and supports the discussion of underlying mechanisms.

Reproduction by individuals is typically recorded as count data (e.g., number of fledglings from a nest or inflorescences on a plant) and commonly modeled using Poisson or negative binomial distributions, which assume that variance is greater than or equal to the mean. However, distributions of reproductive effort are often underdispersed (i.e., variance < mean). When used in hypothesis tests, models that ignore underdispersion will be overly conservative and may fail to detect significant patterns. Here we show that generalized Poisson (GP) and Conway-Maxwell-Poisson (CMP) distributions are better choices for modeling reproductive effort because they can handle both overdispersion and underdispersion; we provide examples of how ecologists can use GP and CMP distributions in generalized linear models (GLMs) and generalized linear mixed models (GLMMs) to quantify patterns in reproduction. Using a new R package, glmmTMB, we construct GLMMs to investigate how rainfall and population density influence the number of fledglings in the warbler Oreothlypis celata and how flowering rate of Heliconia acuminata differs between fragmented and continuous forest. We also demonstrate how to deal with zero-inflation, which occurs when there are more zeros than expected in the distribution, e.g., due to complete reproductive failure by some individuals.

Bottom trawling alters the abundance, diversity, size-composition, and function of benthic communities. However, the ability to detect these impacts over large spatial scales can be obscured by various complicating factors, such as community adaptation to disturbance and co-varying environmental conditions. An ecosystem-based approach to fisheries management therefore requires ecological indicators which can 'disentangle' trawling effects from other natural and human drivers, and respond effectively to shifts in ecological quality. We collected benthic macrofaunal samples at 21 sites across a Norway lobster Nephrops norvegicus fishing ground in the Kattegat, and separated the benthic community into small (1-4 mm) and large ( > 4 mm) size fractions. Four taxonomic indicators (total density, species density, Shannon diversity, and biomass) and four functional indicators (functional diversity, functional richness, functional evenness, and functional dispersion) were calculated based on each size fraction, and the two fractions combined (pooled community). Here, we compare the ability of these indicators to detect trawling impacts across size categories. We show that indicators derived from large macrofauna were highly effective in this regard, and were less influenced by other environmental drivers, such as depth, sediment grain size, bottom current velocity, salinity, and temperature. This suggests that the taxonomic and functional characteristics of benthic communities display a size-dependent sensitivity to trawling disturbance, and therefore community metrics based on large benthic macrofauna may provide useful indicators. By contrast, indicators derived from the small fraction performed poorly, and those based on the pooled community demonstrated a varied ability to detect trawling. Small macrofauna are typically characterised by high density, diversity, and population growth rates, and their relative resilience to trawling may mask the response of the more sensitive macrofauna. This highlights an underlying issue with calculating indicators based on the whole benthic community. The approach outline here is easily applied, improves indicator performance, and has the potential to reduce laboratory workloads due to the fewer taxa and individuals required for analyses.