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The Atlantic goliath grouper (Epinephelus itajara) is the largest grouper species in the Atlantic and exhibits high site fidelity and limited range of movement. By 1990, the goliath grouper population in US waters had declined approximately 95% relative to unfished levels, leading to a harvest ban in 1990. Since then, the south Florida population has grown but the magnitude of recovery remains unknown due to uncertainties about life history characteristics. However, despite these unknowns, the state of Florida approved a limited recreational harvest of goliath grouper. In 2021, fine-scale habitat use of three juvenile goliath grouper was investigated using acoustic telemetry and a positioning solver. All three individuals exhibited high site fidelity as well as a diel habitat use pattern, utilizing seagrass habitat during the night and mangrove habitat during the day. Fine-scale acoustic telemetry provides insight into not only habitat use, but broader habitat preferences as well. This study illustrates the need to consider deep seagrass-dominated channels lined with red mangroves when protecting juvenile goliath grouper populations within Florida Bay, especially as the population is opened to harvest.

The global population of European eel (Anguilla anguilla) is rapidly declining, and migration barriers in rivers are believed to be one of several key causes. While progress has been made in the development of bypass solutions, they are often constructed based on a limited knowledge of swimming behaviour. A bypass close to the stream bed is often recommended at fish passage facilities to accommodate downstream eel migration. The results of this recommendation are poorly studied, and the few studies that exist show varying bypass efficiencies. The current study used acoustic telemetry with depth sensors to explore the three-dimensional migratory behaviour of downstream-migrating silver eels. The eels were tracked as they approached a hydropower plant with a state-of-the-art angled bar rack and full-depth bypass. Downstream and upstream swimming differed in preferred vertical and lateral positions. During periods of local downstream movement, the density of observations was largest in the upper middle section, away from the river boundaries and in higher velocities. Conversely, when moving upstream, eels tended to avoid the upper layers of the middle part of the river, swimming closer to the riverbed and using the bank areas to a greater extent. Downstream-moving fish swam higher in the water column during night and in turbid conditions (high discharge). When approaching the impassable bar rack and the full-depth bypass, the eels searched most intensely but not exclusively along the bottom third of the rack, often exploring at new depths after changing direction. The impediment passage efficiency was 100% when both bypass solutions were considered. The study provides knowledge of the swimming behaviour of silver eels, which is relevant for the design of bypass solutions for eels at migration barriers.

Natal homing, a strategy in which individuals return to breed in the same river as they were born, is prevalent among salmonids. However, some individuals may not return to their natal river, and instead stray to non-natal rivers. To date, there is limited documentation on patterns of straying among iteroparous salmonids that have returned to spawn over multiple years. In this study, 21538 out-migrating juvenile anadromous brown trout (Salmo trutta L.) were tagged over two years with passive integrated transponder (PIT) tags, and followed as they returned to either their natal or three non-natal rivers in a fjord system, over multiple years. In total, 206 individuals were detected returning for more than one year, of which 43% were strayers. A divergence in migratory strategies among strayers was documented: a smaller proportion of strayers were only detected in non-natal rivers, while the majority (67%) displayed high variability in their migratory patterns as they were detected in both their natal and non-natal rivers, sometimes within the same reproductive season. This study documents high variability in the migratory patterns of repeat spawners and high probability for them to stray, and suggests that straying is an important life-history strategy possibly affecting individual fitness.

Temporary summer stratification is probably a common, but easily overlooked phenomenon in many shallow lakes, because short-term temperature stratification and mixing events are not easily discovered by routine samplings. We used two years of high frequency measurements and monitoring of 5-m deep and hypereutrophic Lake Ormstrup, Denmark to study the dynamics of temporary stratification and its effects on oxygen concentrations, nutrient cycling, greenhouse gas emissions and fish habitat use. Temporary stratification followed by complete mixing of the water column occurred several times each summer, but its duration was highly variable between years despite only small climatic variations. Anoxia at depths greater than 2–3 m developed within a few days after stratification. During anoxia fish accumulated in the upper 2 m and high accumulation of phosphate (up to 1.34 mg/l), ammonia (up to 2.32 mg/l) and greenhouse gases (methane up to 5 mg/l) occurred at depths greater than 2–3 m that were released at mixing. Lake Ormstrup is an example of how very dynamic, unpredictable, and variable mixing conditions develop each summer with significant implications for fish habitat use, nutrient dynamics and greenhouse gas emissions. This might adjust our view of these lakes in a management and climate change perspective.

Anadromous brown trout display a continuum of life-history strategies with high intraspecific variability across their distribution range. While many of these strategies have been widely studied, some have received considerably less attention. In this study, we investigated intraspecific differences in two overlooked life-history strategies—outmigration phenology (spring vs. autumn migrants) and the prevalence of straying—in brown trout originating from four rivers flowing into the same fjord system. Juvenile brown trout ( Salmo trutta) were tagged with passive integrated transponder (PIT) tags in their natal river, and were subsequently followed during their outmigration and subsequent return to freshwater. We found that patterns of outmigration (spring vs. autumn migrant, day of season) and return to freshwater (return likelihood, strayers vs. nonstrayers) differed between rivers, as did the factors (length, condition) affecting these outcomes. We also found evidence that outmigration phenology was linked to the likelihood of returning in a river-specific way. Our findings suggest that the costs and benefits of autumn migration and straying differ depending on an individual's home river.

Natal homing is a prevalent life-history strategy among salmonids. However, not all individuals return to their natal river, a behaviour known as straying. In this study, we investigated the prevalence of straying and its connection to different life-history characteristics in an anadromous brown trout (Salmo trutta) population. In total, 21 538 juvenile out-migrating brown trout were tagged with Passive Integrated Transponder (PIT) tags in two years. Individuals were grouped according to their developmental status (parr, pre-smolt, and smolt) at the time of out-migration to investigate the effect of such life-history characteristic on the likelihood of straying. High number of anadromous brown trout (36%) were detected in non-natal rivers. Individuals spending longer time at sea were less likely to stray. Additionally, the likelihood of straying was dependent on the developmental status during out-migration, with parr having lower likelihood to stray compared to pre-smolt and smolt. However, the latter is further dependent on length and timing of juvenile out-migration. These results indicate that straying is an inherent part of this anadromous brown trout population and it is influenced by several life-history characteristics at different life stages. This may have significant implications to genetic structure within and between populations and to population dynamics.

1. Fine-scale tracking with passive acoustic telemetry can yield great insights into the movement ecology of aquatic animals. To predict fine-scale positions of tagged animals in continuous space from spatially discrete detection data, state-space modelling through the R package YAPS provides a promising alternative to frequently used positioning algorithms. However, YAPS cannot currently classify multiple kinds of movement that may be used as proxies for individual behaviours of study animals (behavioural states), an endeavour that is of increasing interest to movement ecologists.2. We advance YAPS by incorporating the functionality to predict behavioural states by using an iterative maximization framework. Our model, which we call YAMS, occurs in continuous-time and therefore we adapt current HMM machinery to accommodate this while remaining within a likelihood framework that provides rapid fitting. We test our model using simulations and approximately six days worth of Northern pike data from Hald Lake, Denmark.3. YAMS is shown to produce accurate parameter estimates and random effect predictions when model results were compared to simulated data, with behavioural state accuracies of 0.94 and 0.79 for two- and three-state models, respectively, and location state root mean squared errors of 1.8 m for both models. In addition, the behavioural states are shown to reflect varying speeds of the pike, yielding a highly interpretable classification.4. This research has the potential to be broadly applicable to both ecologists interested in identifying fine scale space use and behavioural states from acoustic telemetry data, as well as to statisticians who may wish to use standard HMM machinery to fit continuous-time HMMs to animal movement data.

1. The longstanding debate in conservation biology on the importance of single large or several small (SLOSS) habitats for preserving biodiversity remains highly relevant, given the ongoing degradation and loss of natural habitats worldwide. Restoration efforts are often constrained by limited resources, and insights from SLOSS studies therefore have important implications if restoration efforts can be optimized by manipulating the spatial configuration of restored habitats. Yet, the relevance of SLOSS for habitat restoration remains largely unexplored.2. Here, we report the effects of spatial reef configuration on early colonization of marine organisms after restoring boulder reef habitats. Reefs were restored in single large (SL) and several small (SS) designs in the western Baltic Sea, where century-long boulder extraction has severely degraded large reef areas and likely exacerbated regional declines in commercially important gadoids (Gadidae spp.). We sampled the field sites using remote underwater video systems in a before-after control-impact (BACI) design and obtained probabilistic inferences on restoration and SLOSS effects from Bayesian hierarchical models.3. Probabilities of a positive restoration effect were high (>95%) for gadoids, labrids and demersal gobies, moderate (60-75%) for species richness and sand gobies, and low (4. Spatial reef configuration had the strongest effect on small-bodied mesopredators, including gobies, which were more abundant at SS and driving distinct species assemblages between the reef designs. In addition to providing suitable conditions for reef species, results suggest that SS can also benefit soft-bottom taxa, possibly through a dispersed predator-mediated effect relative to SL.5. Synthesis and applications. This study demonstrates that boulder reef restoration can strongly promote the abundance of exploited gadoids and is therefore a promising management tool to support top-down controls by predatory fishes in degraded marine systems. The higher abundance of mesopredators at reefs with a ‘several small’ configuration suggests that the ‘Single Large or Several Small’ (SLOSS) dilemma could have long-term implications for trophic structure and resilience of restored habitats, and should therefore become an important facet within restoration strategies.

PIT-tagging is commonly used in behavioural studies of fish, although long-term evaluations of effects from tagging under natural conditions are scarce. We PIT-tagged common bream Abramis brama, European perch Perca fluviatilis, pike Esox lucius and roach Rutilus rutilus, released them in their lakes of origin and recaptured them after 103-3269 days. Overall, tagged fish did not differ in condition from non-tagged fish, except for small R. rutilus that weighed less in one lake in one year. We conclude that PIT-tagging in general has negligible long-term effects on fish condition. This article is protected by copyright. All rights reserved.

Understanding animal movement is essential to elucidate how animals interact, survive, and thrive in a changing world. Recent technological advances in data collection and management have transformed our understanding of animal "movement ecology" (the integrated study of organismal movement), creating a big-data discipline that benefits from rapid, cost-effective generation of large amounts of data on movements of animals in the wild. These high-throughput wildlife tracking systems now allow more thorough investigation of variation among individuals and species across space and time, the nature of biological interactions, and behavioral responses to the environment. Movement ecology is rapidly expanding scientific frontiers through large interdisciplinary and collaborative frameworks, providing improved opportunities for conservation and insights into the movements of wild animals, and their causes and consequences., This work was supported by the Minerva Center for Movement Ecology, the Minerva Foundation, grants ISF-3277/21, ISF-1272/21, ISF-965/15, ISF-1259/09, ISF-1316/05, MOST 3-17405, JNF/KKL 60-01-221-18, GIF 1316/15, and the Adelina and Massimo Della Pergola Chair of Life Sciences to R.N.; the Marine Science programme within the Research Council of Norway, grant 294926 (CODSIZE) to C.T.M.; the German Ministry of Education and Research (projects Besatzfisch) and Leibniz Community (project BType) to R.A.; the Danish Rod and Net Fishing License Funds to H.B.; DFG-GRK Biomove 2118/1 to F.J, ISF-1919/19 and ISF-965/15 to S.T.; and SCHL 2259/1-1 to U.E.S.

Internal seiches are common in stratified lakes, with significant effects on stratification patterns, hydrodynamics and vertical nutrient transport. In particular, seiche can change the vertical distribution of the thermocline and the cold hypolimnetic and warm epilimnetic water masses by several meters on a timescale of a few hours. The results are rapid and strong changes in temperature profiles and oxygen availability that can have profound effects on vagrant and sessile organisms. Internal seiche dynamics could therefore affect fish communities directly through physiological stress and elevated mortality, and indirectly through prey distribution.The aim of this study was to analyze the effects of internal seiche dynamics on lacustrine fish behaviour, and to characterize fish reaction patterns, with the main focus on vertical movement of fish in the vicinity of a shifting thermocline, and avoidance of cold hypolimnetic water.The analysis was based on acoustic telemetry data from Lake Milada, a post-mining lake in the Czech Republic, with a total of 55 tracked individuals of four species: northern pike (Esox lucius), wels catfish (Silurus glanis), tench (Tinca tinca) and rudd (Scardinius erythropthalmus).The effects of seiche dynamics on the four species studied were weak but significant during the day, but only on rudd during the night. Upward seiche produced stronger reactions in fish than downward seiche, and the effects were manifested only during the strongest seiche events.Thermocline shifting during seiche events may induce a transient reduction in habitat for seiche-reacting species, thus potentially affecting predation and other inter- and intra-specific interactions, and probably affecting fish community dynamics.Graphical abstract

Since in 1980s, the number of great cormorants (Phalacrocorax carbo sinensis) has increased all over its European distribution area. This has led to conflicts between bird conservation and fisheries. Mariager fjord in Denmark is an important feeding and transition area for a large population of migrating seatrout (Salmo trutta), but it also provides resting and breeding places for cormorants. Thus, juvenile anadromous salmonids migrating from the river to the sea may be exposed to high predation risk during a critical and vulnerable time in their development. A total of 31 123 down-migrating wild seatrout were tagged with Passive Integrated Transponder (PIT) tags in 2008, 2009, 2015, and 2016 in river Villestrup, the main tributary flowing into Mariager fjord. Tagged fish were measured and grouped by their developmental stage as parr, pre-smolt, or smolt. To quantify cormorant predation, nearby cormorant colonies and roosting sites were repeatedly scanned for PIT tags with a manual antenna to record tags from predated fish. Minimum predation rate was 27% but varied among years. Body length of the fish and predation risk were negatively correlated and the latter was dependent on the group of the fish. This study demonstrates a potential negative effect of predation by great cormorants on an important population of wild trout.

Patterns of animal migration and the ecological forces that shape them have been studied for centuries. Yet ecological impacts caused by the migration, such as altered predator–prey interactions and effects on community structure, remain poorly understood. This is to a large extent due to the scarcity of naturally replicated migration systems with negative controls, that is, ecosystems without migration. In this study, we tested whether partial migration of certain species within the overall prey community affects foraging ecology of top predators and thereby alters energy pathways in food webs. We carried out the study in independent replicated freshwater lake systems, four with and four without opportunity for prey migration. Specifically, we compared predator foraging mode in lakes where cyprinid prey fish perform seasonal partial migrations into connected streams with lakes lacking migratory opportunities for prey fish. We found clear seasonal bottom-up effects of prey migration on predators, including changes in size structure and total biomass of ingested prey, size-specific changes in littoral versus pelagic origin of diet, and a higher degree of feast-and-famine for predators in systems with migratory prey. Our analyses further showed that partially migratory prey species constitute a larger part of the prey community in systems that allow migration. Hence, prey migrations have important implications for predator foraging ecology and may cause seasonal shifts in the importance of their supporting energy pathways. We suggest that such bottom-up effects of partial migration may be a widespread phenomenon both in aquatic and in terrestrial ecosystems.

Genetic data have great potential for improving fisheries management by identifying the fundamental management units—that is, the biological populations—and their mixing. However, so far, the number of practical cases of marine fisheries management using genetics has been limited. Here, we used Atlantic cod in the Baltic Sea to demonstrate the applicability of genetics to a complex management scenario involving mixing of two genetically divergent populations. Specifically, we addressed several assumptions used in the current assessment of the two populations. Through analysis of 483 single nucleotide polymorphisms (SNPs) distributed across the Atlantic cod genome, we confirmed that a model of mechanical mixing, rather than hybridization and introgression, best explained the pattern of genetic differentiation. Thus, the fishery is best monitored as a mixed‐stock fishery. Next, we developed a targeted panel of 39 SNPs with high statistical power for identifying population of origin and analyzed more than 2,000 tissue samples collected between 2011 and 2015 as well as 260 otoliths collected in 2003/2004. These data provided high spatial resolution and allowed us to investigate geographical trends in mixing, to compare patterns for different life stages and to investigate temporal trends in mixing. We found similar geographical trends for the two time points represented by tissue and otolith samples and that a recently implemented geographical management separation of the two populations provided a relatively close match to their distributions. In contrast to the current assumption, we found that patterns of mixing differed between juveniles and adults, a signal likely linked to the different reproductive dynamics of the two populations. Collectively, our data confirm that genetics is an operational tool for complex fisheries management applications. We recommend focussing on developing population assessment models and fisheries management frameworks to capitalize fully on the additional information offered by genetically assisted fisheries monitoring.

Determining the mechanisms driving range-wide reductions in Atlantic salmon marine survival is hindered by an insufficient understanding of their oceanic ecology and distribution. We attached 204 pop-up satellite archival tags to post-spawned salmon when they migrated to the ocean from seven European areas and maiden North American salmon captured at sea at West Greenland. Individuals migrated further north and east than previously reported and displayed increased diving activity near oceanographic fronts, emphasizing the importance of these regions as feeding areas. The oceanic distribution differed among individuals and populations, but overlapped more between geographically proximate than distant populations. Dissimilarities in distribution likely contribute to variation in growth and survival within and among populations due to spatio-temporal differences in environmental conditions. Climate-induced changes in oceanographic conditions will alter the location of frontal areas and may have stock-specific effects on Atlantic salmon population dynamics, likely having the largest impacts on southern populations.

Fish swimming performance is strongly influenced by flow hydrodynamics, but little is known about the relation between fine-scale fish movements and hydrodynamics based on in-situ investigations. In the presented study, we validated the etho-hydraulic fish swimming direction model presented in the River Mandal from Southern Norway, using similar behavioral and hydraulic data on salmon smolts from the River Orkla in Central Norway. The re-parametrized model explained the variation of the swimming direction of fish in the Orkla system in same degree as the original model performed in the Mandal system (R2: 84% in both cases). The transferability of the model when using it from one river to predict swimming direction in the other river was lower (R2: 21% and 26%), but nevertheless relatively high given that the two localities differed in hydraulic conditions. The analyses thus provide support for the fact that the identified hydraulic parameters and their interaction affected smolt behavior in a similar way at the two sites, but that local parametrization of the base model is required. The developed etho-hydraulic models can provide important insights into fish behavior and fish migration trajectories and can be developed into prediction models important for the future development of behavioral downstream migration solutions.

Movement ecology is increasingly relying on experimental approaches and hypothesis testing to reveal how, when, where, why, and which animals move. Movement of megafauna is inherently interesting but many of the fundamental questions of movement ecology can be efficiently tested in study systems with high degrees of control. Lakes can be seen as microcosms for studying ecological processes and the use of high-resolution positioning systems to triangulate exact coordinates of fish, along with sensors that relay information about depth, temperature, acceleration, predation, and more, can be used to answer some of movement ecology's most pressing questions. We describe how key questions in animal movement have been approached and how experiments can be designed to gather information about movement processes to answer questions about the physiological, genetic, and environmental drivers of movement using lakes. We submit that whole lake telemetry studies have a key role to play not only in movement ecology but more broadly in biology as key scientific arenas for knowledge advancement. New hardware for tracking aquatic animals and statistical tools for understanding the processes underlying detection data will continue to advance the potential for revealing the paradigms that govern movement and biological phenomena not just within lakes but in other realms spanning lands and oceans. Correction published here, October 2021: https://doi.org/10.1186/s40462-021-00285-3

Repeat spawners constitute an important component of Atlantic salmon populations, but survival of post-spawning individuals (kelts) are often compromised by anthropogenic structures such as hydropower plants (HPPs). Potential effects of HPPs include migration delays and associated increased energy depletion, which potentially results in increased overall mortality. We combined a detailed 3D hydraulic model with high-resolution 3D tracking of tagged kelts (length 73&ndash, 104 cm) to obtain estimates of kelt movement through water. These estimates were then used in an energetics model to estimate hourly energy expenditure while negotiating the HPP area. Hourly kelt energy expenditure varied between 0.8 and 10.1 kJ &times, h&minus, 1 and was dependent on kelt length. Degree of additional energy depletion can amount to several percent of remaining energy content (our study indicates 4&ndash, 5 percentage points) potentially leading to reduced post-spawning survival. In turn, this can nullify the iteroparous breeding strategy and jeopardize long-term stability and persistence of Atlantic salmon populations inhabiting HPP rivers.

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 suggestthat 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.

Background Acoustic positioning telemetry allows to collect large amounts of data on the movement of aquatic animals by use of autonomous receiver stations. Essential in this process is the conversion from raw signal detections to reliable positions. A new advancement in the domain is Yet Another Positioning Solver (YAPS), which combines the detection data on the receivers with a model of animal movement. This transparent, flexible and on-line available positioning algorithm overcomes problems related to traditional point-by-point positioning and filtering techniques. However, its performance has only been tested on data from one telemetry system, providing transmitters with stable burst interval. To investigate the performance of YAPS on different system parameters and settings, we conducted a simulation study. Results This paper discusses the effect of varying burst types, burst intervals, number of observations, reflectivity levels of the environment, levels of out-of-array positioning and temporal receiver resolution on positioning accuracy. We found that a receiver resolution better than 1 ms is required for accurate fine-scale positioning. The positioning accuracy of YAPS increases with decreasing burst intervals, especially when the number of observations is low, when reflectivity is high or when information out-of-array is used. However, when the burst interval is stable, large burst intervals (in the order of 1 to 2 min) can be chosen without strongly hampering the accuracy (although this results in information loss). With random burst intervals, the accuracy can be much improved if the random sequence is known. Conclusions As it turns out, the key to accurate positioning is the burst type. If a stable burst interval is not possible, the availability of the random sequence improves the positioning of random burst interval data significantly.

Removal of cyprinid fish is a widely used biomanipulation tool to transform turbid shallow eutrophic lakes in north temperate regions into a clear water state. We here evaluate the removal of cyprinids from streams as a supplement to lake fishing. Since cyprinids often aggregate in high densities in lake inlet/outlet streams during winter migration, removal of fish in this space-confined habitat may be cost-efficient as compared to fish removal in the lake habitat. In two consecutive years, we annually removed up to 35% of the dominant cyprinids from an inlet stream to a lake and argue that this could easily be increased with a more targeted fishing effort. Concurrently, we monitored species- and length-specific variation in migration propensity, to explore how this relates to efficient fish removal. Smaller planktivores generally had a much higher migratory propensity than larger benthivores. Hence, stream fishing specifically targets species and size groups that are less efficiently controlled with traditional lake fishing methods. As a rule of thumb, stream fishing is most efficient when water temperature is 2–6°C. Prior to implementing fish removals from streams, the potential evolutionary consequences of the targeted removal of migratory phenotypes should be considered.

Eutrophication of coastal areas as a consequence of the agricultural use of fertilizers is a widespread problem. The development of artificial lakes and constructed wetlands in nutrient‐rich rivers is a widely used management tool in the fight to decrease eutrophication. Juvenile salmonids that have to negotiate these lakes during their downstream migration to the sea are commonly subjected to high mortality due to increased predation pressure and delayed passage. In this study, we double tagged 39 brown trout smolts with passive integrated transponder and radio tags to gain further insight into predation rates and migration patterns during their passage of an artificial lake in a Danish lowland stream in the spring of 2016. Thirty‐four of the tagged smolts, caught and released upstream, entered the lake, of which 22 (65%) successfully exited the lake. Four smolts (12%) returned upstream to the river. Three smolts were predated in the lake by two northern pike (Esox lucius). Three tags were recovered from the lake bottom, and two disappeared out of the study area after a last detection in the lake. Tracking the smolts manually and by automatic listening stations showed highly erratic movement patterns during lake passage. Further, we observed long delays of up to 27 days after the smolts reached the river mouth and before they entered the sea, potentially due to low sea water temperature or due to the stocking of a large amount of hatchery‐reared brown trout smolts. The results are discussed in the context of abiotic and biotic factors, which differed considerably in the year 2016 compared with previous years.

Today's river systems have been extensively modified, requiring us to rethink how we approach the management of these important ecosystems. We evaluated the effects of removing 6 weirs in River Villestrup (Jutland, Denmark) on the smolt run of brown trout (Salmo trutta) over the course of 12 years. During 5 of these years, we evaluated the number, size, and timing of smolts during their downstream migration. We found an increase in smolt output following the weir removals, along with a decrease in average length and indications of an earlier peak migration. Our results suggest that barrier removal has led to an increase in spawning success by adults, fry survival, recruitment, and smolt migration success. Weir removal is therefore a viable management approach to restore connectivity in freshwater streams and rivers, which promotes the passage of smolts as they migrate to marine environment

During migration, animals are typically limited by their endogenous energetic resources that must be allocated to the physiological costs associated with locomotion, as well as avoiding and (or) compensating for oxidative stress. To date, there have been few attempts to understand the role of oxidative status in migration biology, particularly in fish. Semi-anadromous brown trout (Salmo trutta L., 1758) exhibit partial migration, where some individuals smoltify and migrate to sea, and others become stream residents, providing us with an excellent model to investigate the link between oxidative stress and migration. Using the brown trout, we obtained blood samples from juveniles from a coastal stream in Denmark in the fall prior to peak seaward migration that occurs in the spring, and assayed for antioxidant capacity (oxygen radical absorbance capacity) and oxidative stress levels (ratio of oxidized to reduced glutathione). We found that individuals that migrated had higher antioxidant capacity than residents and that future migration date was negatively correlated with both antioxidant capacity and body length in the fall. This study provides the first evidence that oxidative status is associated with migration strategy and timing, months in advance of the actual migration, and provides insight into the role of oxidative status in animal migration.

Aquatic positional telemetry offers vast opportunities to study in vivo behaviour of wild animals, but there is room for improvement in the data quality provided by current procedures for estimating positions. Here we present a novel positioning method called YAPS (Yet Another Positioning Solver), involving Maximum Likelihood analysis of a state-space model applied directly to time of arrival (TOA) data in combination with a movement model. YAPS avoids the sequential positioning-filtering-approach applied in alternative tools by using all available data in a single model, and offers better accuracy and error control. Feasibility and performance of YAPS was rigorously tested in a simulation study and by applying YAPS to data from an acoustic transmitter towed in a receiver array. Performance was compared to an alternative positioning model and proprietary software. The simulation study and field test revealed that YAPS performance was better and more consistent than alternatives. We conclude that YAPS outperformed the compared alternative methods, and that YAPS constitute a vast improvement to currently available positioning software in acoustic telemetry. Additionally, in contrast to vendor-supplied solutions, YAPS is transparent, flexible and can easily be adapted and extended for further improvements or to meet study specific requirements such as three-dimensional positioning.

The R package yaps was introduced in 2017 as a transparent open source alternative to closed source manufacturer-provided solutions to estimate positions of fish (and other aquatic animals) tagged with acoustic transmitters.Although yaps is open source and transparent, the process from raw detections to final tracks has proved to be challenging for many potential users, effectively preventing most users from accessing the benefits of using yaps. Especially, the very important process of synchronizing the hydrophone arrays have proven to be an obstacle for many potential users.To make yaps more approachable to the wider fish tracking community, we have developed and added user-friendly functions assisting users in the complex process of synchronizing the data.Here, we introduce these functions and a six-step protocol intended to provide users with an example workflow that can be used as a template enabling users to apply yaps to their own data. Using example data collected by an array of Vemco VR2 hydrophones, the protocol walks the user through the entire process from raw data to final tracks. Example data sets and complete code for reproducing results are provided.

Spring migrating sea trout juveniles can be classified as parr, pre-smolt or smolt based on body morphology and osmoregulatory capacity. In this respect, parr are assumed to be less prepared for a marine life and to have lower survival at sea than pre-smolts and smolts. However, the behaviour and survival of these trout phenotypes upon entering the sea is not well known. Using passive integrated transponder telemetry, this study found that the return rate from the sea to the natal river was higher for parr compared to pre-smolts and smolts. Additionally, trout classified as parr generally migrated earlier to the sea and a larger proportion returned to the river after less than one year at sea. The daily mortality rate at sea was comparable among the different phenotypes of trout, suggesting that the higher proportion of returning parr to the river was linked to their shorter duration at sea. These results provide evidence of different life-history strategies for seaward-migrating juvenile sea trout, ultimately affecting their return rate to the natal river. Investigations failing to consider downstream migrating parr and pre-smolts risks neglecting a large part of the anadromous population and may result in inaccurate assessments of sea trout stocks in rivers.

The foraging activity of large-bodied benthivorous fish has been suggested to be of key importance for maintaining shallow lakes in a turbid state. Since especially the spring ecosystem dynamics determines the successive state of shallow lakes, such impact could depend on seasonality in benthivore activity patterns. However, we do not yet know to what extent the activity of large-bodied benthivorous fish affects lake turbidity across the year. In order to investigate seasonal dynamics in bream activity and its impact on water turbidity under natural conditions, bream daily activity was studied in a small (39 ha) shallow Danish lake using passive biotelemetry technology, i.e. a modified Passive Integrated Transponder (PIT)-tag antenna system. We tracked the activity of 448 benthivorous bream over a period of four years (2012 to 2016) and during the same period wind conditions, water turbidity and temperature was measured. Results showed a clear relationship between bream activity and water turbidity at water temperature below 15°C indicating that winter season activity of benthivorous bream may play an important role for maintaining lake ecosystems in a turbid state. Also wind speed and wind direction affected water turbidity, suggesting that wind induced resuspension can be important even in small shallow lakes. This is to our knowledge the first full-scale study under natural conditions to describe how bream activity influence lake turbidity on a day-to-day basis. Our findings also add a seasonal component to previous findings by showing that benthivorous feeding bream have the potential to increase water turbidity also in the winter season and thereby, ultimately, impact ecosystem functioning within shallow lakes.

Anthropogenic structures in rivers are major threats for fish migration and effective mitigation is imperative given the worldwide expansion of such structures. Fish behaviour is strongly influenced by hydrodynamics, but little is known on the relation between hydraulics and fish fine scale-movement. We combined 3D Computational fluid dynamics modelling (CFD) with 2D and 3D fish positioning to investigate the relation between hydrodynamics and the downstream movement of Atlantic salmon smolts (Salmo salar). We show that fish use fine-scale flow velocity and turbulence as navigation cues of fine-scale movement behaviour. Tri-dimensional swimming speed and swimming direction can be explained by adjustments of fish to flow motion, which are linked to fish swimming mode. Fish diverge from the flow by swimming at speeds within or higher than their prolonged speeds (0.38–0.73 m s−1). Flow direction plays a pivotal role on fish swimming performance, with high upstream and downwards velocities impacting swimming the most. Turbulence is also influential, by benefiting swimming performance at low TKE (< 0.03 m2 s−2) or constraining it at higher levels. We show that fish behaviour is affected by interactions of several hydraulic variables that should be considered jointly.

Background Understanding fish movements and migrations are paramount for management and conservation efforts. By applying Hidden Markov Models (HMMs) on records from electronic tags, migration routes of tagged fish can be reconstructed and new insights to the movement ecology of a species can be gained. We demonstrate the usability of HMMs on a widespread, iteroparous salmonid (sea trout, Salmo trutta) in a complex marine area with highly variable temperatures and salinities within small geographic distances. Understanding how the highly adaptable sea trout cope with these complex conditions could shed new light on factors driving the movement ecology of salmonids. Migration tracks of fish migrating at sea are reconstructed by applying an HMM on temperature and depth records from eight wild post-spawned sea trout from four Danish rivers. Results The fish migrated at sea for 47–142 days. Estimated positions of all fish were close to the coast (−1 (range 0–58 km day−1). Conclusions The results corroborate the expectation that sea trout are more coastally orientated than other salmonids, but also suggest that longer migrations occur in the seas surrounding Denmark compared to elsewhere. This could be a consequence of the fish seeking out habitats with optimal conditions (e.g. salinity, temperature, predation and foraging options) for growth in different parts of the year. The coinciding movement from shallow or stratified marine areas that heat up fast during spring to deeper, more well-mixed areas that heat up slow during summer suggested that some habitat selection had occurred. These results shed new light on factors influencing marine migrations in salmonids and demonstrate how HMMs can expand our knowledge on behaviour and movement ecology of marine fishes.