Many coastal ecosystems are impacted by several human pressures that are increasing in coverage and rate. Rocky reefs are structurally complex habitats that often support elevated fish abundance and biodiversity. In the Baltic Sea, rocky reefs have suffered from extraction for decades, leading to a decrease in hard substrata and complex habitat availability. This study is the first to restore cobble reefs and examine the biological effects. Ecosystem restoration was undertaken by deploying cobble reefs in January 2018. Baited and unbaited underwater video systems (BRUVS and UBRUVS, respectively) were employed across five years to monitor fish communities before reef deployment in 2017 and after reef deployment in 2018 and 2021. Using a before-after control-impact (BACI) study design with replicates, relative abundances of Atlantic cod (Gadus morhua), herring (Clupeidae sp.), goldsinny wrasse (Ctenolabrus rupestris), two-spotted goby (Gobiusculus flavescens), shore crab (Carcinus maenas), and flatfish (Pleuronectiformes spp.) were determined and compared across time and test sites. Comparisons were conducted across 1) restored cobble reefs, 2) natural cobble reefs, and 3) sand-bottom test sites. This study found positive reef restoration effects revealed both by BRUVS and UBRUVS in three of our six focal species: Atlantic cod, goldsinny wrasse and two-spotted goby. These findings indicate that A) it is possible to restore cobble reefs and the associated fauna, but also that B) continued marine extraction of cobble degrades complex habitats to the detriment of a range of marine species. Cobble reef restoration might be a potential conservation tool to be applied in areas that have undergone cobble extraction. In order to preserve Atlantic cod, and other sensitive species, we emphasise ecosystem restoration and warn against marine cobble reef extraction in vulnerable areas.

Hard-bottom habitats span a range of natural substrates (e.g., boulders, cobble) and artificial habitats (e.g., the base of wind turbines, oil platforms). These hard-bottom habitats can provide a variety of ecosystem services, ranging from the enhancement of fish biomass and production to providing erosion control. Management decisions regarding the construction or fate of hard-bottom habitats require information on the ecological functions of these habitats, particularly for species targeted in ecosystem-based fisheries management. This study provides a systematic review of the relationships of various hard-bottom habitats to individual commercially harvested species that are managed jointly across the Atlantic by the International Council for the Exploration of the Sea (ICES). We systemically reviewed peer-reviewed publications on hard-bottom habitats including both natural and artificial reefs, after applying various exclusion criteria. Most studies were conducted on near-shore hard-bottom habitats, and habitat importance varied according to fish species and region. We quantified the frequency with which studies demonstrate that natural and artificial hard-bottom habitats function as spawning grounds, settlement and nursery areas, and foraging grounds, as well as provide stepping-stones during migration, or new home ranges. Hard- bottom habitats generally support higher fish densities than surrounding habitat types, although not all fish species benefit from hard-bottom habitats. Of the commercially important species, cod (Gadus morhua) was the most frequently studied species, with enhanced biomass, density, feeding, and spawning on hard-bottom habitats compared to unstructured habitats. Moreover, hard-bottom habitats appear to be of particular importance for spawning of herring (Clupea harengus). Collectively, data indicate that loss of hard-bottom habitats may translate into less-favourable conditions for spawning and biomass of diverse commercial species, including cod and herring.

Estuaries are complex environments that provide important nursery areas for several fish species, but anthropogenic activities as well as low salinities may affect fish reproductive potential. This study investigated spawning migrations of turbot (Scophthalmus maximus) and European flounder (Platichthys flesus) in the estuary of Roskilde Fjord using acoustic telemetry. For turbot, migratory behaviour was coupled with salinity measurements to estimate likelihood of successful spawning. Turbot in Roskilde Fjord are stocked fish, whereas the European flounder represents a naturally occurring population. Telemetry data suggested that the two species exhibited different migration behaviours towards the spawning season. The migratory behaviour of turbot indicates that they remain in the southern parts of Roskilde Fjord where successful development of eggs and larvae may be limited by low salinity. In contrast, the majority of European flounder migrated towards more marine waters prior to the spawning season, and only a minority of the fish remained inside Roskilde Fjord during the spawning season. Consistent with previous studies, the present results indicate that European flounder perform partial spawning migration. Thus, European flounder may utilize a diversity of spawning areas, including the brackish waters inRoskilde Fjord estuary as well as more marine waters with elevated salinities. Our results are important for future management of spawning areas, recruitment dynamics and selection of suitable turbot populations for stocking.

Understanding satisfaction is an important aspect of the management of recreational fisheries. We investigated fishing trip satisfaction from data collected via a Danish citizen science platform that allows anglers to report information from their fishing trips through a smartphone application and a webpage. Trip satisfaction was related to a set of predictor variables covering classical catch constructs such as trip outcomes, angler motives to capture angler-specific expectations, and contextual conditions (e.g., air temperature, and water body/species combinations). We hypothesized that catch, motives, and general trip context would jointly affect trip satis faction, with motives serving as a moderator, such that the relative importance of catch in driving angler satisfaction varies with the leading motive. Using mixed ordinal logistic regression, we identified several significant predictors of trip satisfaction, specifically catch outcomes at the trip level, trip motivation, trip context, year of the trip, recall period, air temperature and angling effort (hours spent fishing). As expected, trip-level catch was an important and positive driver of satisfaction, but catch also interacted with trip motivation, trip context, and angling effort. The perceived angler benefit from catch was much higher for anglers fishing for activity-specific motivations (e.g., to experience the excitement of catching a fish) compared to anglers fishing for activity-general motivations (e.g., to experience and be close to nature). The benefit from catch was also higher in some trip contexts (e.g., trips for salmonids in streams) compared to others (e.g., trips for predatory fish in lakes). The benefit from catch was also higher on shorter fishing trips (e.g., 1 h) compared to longer fishing trips (e.g., 5 h), which indicate that higher catch rates yields higher satisfaction (i.e., an effect of catch per unit effort). We also found a recall period effect (i.e., days between conducting and logging a fishing trip), in which the trip satisfaction was generally higher as the recall period increased. Additionally, increasing air temperature had a positive effect on satisfaction. We conclude that angler satisfaction is affected by external (trip context and catch outcomes) and a range of internal factors (e.g., motives). Managers are unlikely to be able to manage internal factors (e.g., motivations) and some contextual factors (e.g., air temperature) and hence a focus on external factors, specifically catch, seems important if the aim is to generate or maintain satisfied anglers.

Targeted sequencing is an increasingly popular next-generation sequencing (NGS) approach for studying populations that involves focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R- package supeRbaits, which encompasses our considerations and guidelines for bait design for the benefit of researchers and practitioners. The supeRbaits R-package is user-friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaitssupeRbaits

1. Acoustic telemetry data often contain erroneous detections, which need to be addressed before further analysis. It is important that this process is systematic, standardised and reproducible.
2. The r package actel provides a systematic conditional pipeline to filter and analyse acoustic telemetry data in a reproducible fashion, for animals moving between receiver arrays.
3. actel outputs a standardised report containing the main results and the steps taken by the user, in addition to summary information for each animal and other content such as efficiency estimations for each receiver array.
4. actel improves the reproducibility of the acoustic data filtering and analysis, and simplifies the integration of acoustic data sets originating from different studies (in time and/or in space).

The Atlantic salmon (Salmo salar) population of the River Minho represents the southern natural distribution edge of the species. In line with the general trend for Atlantic salmon, this population has been declining over the years and is now at a critically low level. With river connectivity compromised by a large dam just 80 km upstream the River Minho's outlet, and an expected deterioration of climatic conditions, it is urgent to increase our knowledge of this population and identify survival bottlenecks that can be addressed. In this study, we used radio and acoustic telemetry to track Atlantic salmon smolts during their migration towards the sea and record both survival rates and possible causes of mortality. The recorded survival for the tagged migrating Atlantic salmon remained below 55% in the three studied years, indicating that the in-river loss of smolts is likely a strong constraint to this population. From the smolts to which a likely cause of mortality could be attributed (34%), most appear to have been removed from the river (25%), with two confirmed events of bird predation and one of mammal predation. Interestingly, eight tags were recorded moving back upstream, likely indicating predation by larger fish. Increasing predator populations (e.g. cormorants, Phalacrocorax carbo) and invasive predators (e.g. American mink, Neovison vison) lead to elevated predation pressure on this already strained Atlantic salmon population, and further studies quantifying their impact in more detail could prove crucial for future management considerations.

1. Acoustic telemetry enables spatial ecologists to collect movement data from a variety of aquatic species. In estuaries and rivers, accounting for the complex shape of water bodies is challenging. Current methods for analysing utilization distributions (UDs) are restricted to using the locations of receivers where animals have been detected, which limits the information available to estimate movement paths.
2. We present a new r package (RSP—Refined Shortest Paths) for analysing the movements of animals tracked with acoustic transmitters in environments constrained by landmasses. The method estimates the shortest in water locations of monitored animals between pairs of detections using least-cost path analysis. It then applies dynamic Brownian Bridge Movement Models to calculate UD areas. Intra- and interspecific overlaps in space and time are calculated and can be used, for example, to investigate potential influencing environmental factors.
3. Tracks refined with RSP follow the estuary shape, yielding substantially longer, but more realistic travel distances. Showcased examples demonstrate how RSP can be used to analyse intra- and interspecific movement patterns; determine similarities in habitat use; identify the environmental conditions responsible for influencing the size of the space use areas; and assess levels of spatial overlap between different species.
4. The RSP toolkit generates more realistic movements of tracked animals than those derived using receiver locations alone. An incidental benefit is its ability to deal with receiver loss, a common problem in acoustic telemetry studies. The analysis can be readily customized to suit different study species, array configurations and habitat shapes.

Remote underwater video systems (RUVS) are increasingly used in scientific studies to monitor marine ecosystems. RUVS can be deployed baited (BRUVS) or unbaited (UBRUVS) and allow for an estimation of the MaxN metric, a relative measure of species abundance. Recording species MaxN in a variety of marine habitats provides associations between species abundance and habitat type, known as ‘species-habitat relationships’. However, the introduction of bait in BRUVS could obscure such relationships by inadvertently attracting fish from neighbouring habitats. Here, we investigate the species-habitat relationships of seven temperate marine species: Atlantic cod (Gadus morhua), right-eyed flatfish (Pleuronectinae spp.), Atlantic herring (Clupea harengus), whiting (Merlangius merlangus), goldsinny wrasse (Ctenolabrus rupestris), two-spotted goby (Gobiusculus flavescens) and shore crab (Carcinus maenas) as revealed by BRUVS and UBRUVS. Video systems were deployed in coastal areas in the Western Baltic, with a cobble coverage ranging from 0% to 100%. Results show that all focal species responded to changes in cobble coverage, highlighting the importance of benthic habitat for a range of animals including benthopelagic species. Specifically, mean abundances of goldsinny wrasse and two-spotted goby were positively associated with cobble coverage, whilst right-eyed flatfish, herring, whiting and shore crab showed a negative association. Atlantic cod was found to be most abundant at intermediate cobble coverage between 65 and 70%, showing a unimodal trend with the mean abundance decreasing again at higher coverage. The relationships suggest that anthropogenic activities modifying benthic habitats, including extraction of material from the seabed and bottom trawling, likely change abundances of a range of marine species. Our comparative analysis suggests that both BRUVS and UBRUVS can identify previously documented species-habitat relationships. However, BRUVS demonstrated some superiority by confirming documented relationships for Atlantic cod and whiting, whilst UBRUVS failed to record any patterns for those species. Our data highlight the ability of BRUVS to identify changes in abundance across different habitats for a variety of species. Although the bait plume serves to attract organisms to the field of view, current results suggest that the use of BRUVS does not obscure species-habitat relationships in patchy coastal habitats. Therefore, future studies examining the importance of different marine areas may benefit from using BRUVS to quantify relationships between habitat variables and species abundance. Developing a better understanding of such relationships will be crucial in ensuring adequate management and protection of ecologically important marine habitats.

The River Bush (Northern Ireland) is an index river for the estimation of Atlantic salmon, Salmo salar L., stock size, population dynamics and marine survival rates. Marine survival estimates are based on the number of smolts counted at a trap 3.5 km upstream of the river outlet. The survival from release to coastal inshore waters for acoustic-tagged smolts released at the Bushmills trap varied between 32% and 68%, with both year and brightness during river exit playing a significant role in explaining the variations in survival. This constitutes an important survival bottleneck. Contrary to true marine mortality, this significant loss of smolts in the river and nearshore environments could be reduced by focused management actions. More studies on other rivers, where smolts are enumerated above the head of tide, could further partition smolt and post-smolt mortality, help differentiate true marine survival and help understand fluctuations in adult returns.

The survival rates of three groups of seaward-migrating Salmo salar smolts were investigated in 2005, 2016, and 2017 in the River Skjern and River Omme, as well as in the Ringkøbing Fjord using acoustic telemetry. Ringkøbing Fjord extends for approximately 300 km², and has a narrow, regulated outlet to the sea. Smolts of three different origins: (a) wild smolts, (b) hatchery-reared smolts previously released at half-year-old, and (c) hatchery-reared smolts previously released at 1-year-old were captured in rotary screw traps and surgically implanted with acoustic transmitters. The progress during seaward migration was monitored with a network of automatic listening stations deployed in the river estuary, fjord mouth and sea opening.
The smolts' probability of survival in the river was related to their length, with larger smolts being more likely to reach the fjord. Once in the fjord, the probability of reaching the sea was related with the smolt's group, with smolts previously released at half-year-old being more likely to succeed than wild smolts. However, none of the biometric or behavioural variables explained the difference between the studied smolt groups, masking the potential reasons behind this difference in survival probability.
Overall, approximately 47% of the tagged smolts were registered at the last array of automatic listening stations (i.e., entered the sea), demonstrating the early migration as a critical bottleneck for the local Atlantic salmon population. Ultimately, this limits the number of Atlantic salmon that survive to adulthood and return to River Skjern and River Omme for spawning.

Kelts – individuals of anadromous fish species which have successfully spawned and may return to sea to repeat the cycle – are perhaps the least studied life stage of iteroparous fish species. To date, our understanding of what makes them successful in their return migration to sea is limited. We investigated the relationship between three physiological parameters (baseline cortisol, baseline glucose and low molecular weight antioxidants) and the timing and success of Atlantic salmon (Salmo salar) and sea trout (Salmo trutta) kelt migration. To do so, we combined blood samples obtained within 3 minutes of capture and acoustic telemetry to track 66 salmon and 72 sea trout as they migrated out of rivers, into fjords and out at sea. We show that baseline cortisol may be a good predictor of migration success. Individuals with high baseline cortisol levels exited the river earlier but were less likely to successfully reach the sea. Similar relationships were not observed with glucose or antioxidants. We provide the first evidence to support the role of physiological status in migration success in Atlantic salmon and sea trout kelts. Our findings contribute to our understanding of the relationship between physiology and fitness in wild animals. Further, we suggest that migration timing is a trade-off between stress and readiness to migrate.

Agriculture is widespread across the EU and has caused considerable impacts on freshwater ecosystems. To revert the degradation caused to streams and rivers, research and restoration efforts have been developed to recover ecosystem functions and services, with the European Water Framework Directive (WFD) playing a significant role in strengthening the progress.

Analysing recent peer-reviewed European literature (2009–2016), this review explores 1) the conflicts and difficulties faced when restoring agriculturally impacted streams, 2) the aspects relevant to effectively reconcile agricultural land uses and healthy riverine ecosystems and 3) the effects and potential shortcomings of the first WFD management cycle.

Our analysis reveals significant progress in restoration efforts, but it also demonstrates an urgent need for a higher number and detail of restoration projects reported in the peer-reviewed literature. The first WFD cycle ended in 2015 without reaching the goal of good ecological status in many European water-bodies. Addressing limitations reported in recent papers, including difficulties in stakeholder integration and importance of small headwater streams, is crucial. Analysing recent developments on stakeholder engagement through structured participatory processes will likely reduce perception discrepancies and increase stakeholder interest during the next WFD planning cycle.

Despite an overall dominance of nutrient-related research, studies are spreading across many important topics (e.g. stakeholder management, land use conflicts, climate change effects), which may play an important role in guiding future policy. Our recommendations are important for the second WFD cycle because they 1) help secure the development and dissemination of science-based restoration strategies and 2) provide guidance for future research needs.