Henrik Baktoft

Technical University of Denmark | DTU · National Institute of Aquatic Resources

Temperate lakes can be ice covered for several months each year, yet little is known about the behaviour and activity of the fish during the cold season. As northern pike represents the top of the food web in many northern temperate lakes and may structure the ecosystem both directly and indirectly, a detailed understanding of the behaviour of this...

Ongoing climate change is affecting animal physiology in many parts of the world. Using metabolism, the oxygen- and capacitylimitation of thermal tolerance (OCLTT) hypothesis provides a tool to predict the responses of ectothermic animals to variation in temperature, oxygen availability and pH in the aquatic environment. The hypothesis remains cont...

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-sp...

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 algo...

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,...

Salmonids are well known for their natal homing behaviour, meaning they return to breed in the same area where they originated. However, not all individuals return to their natal breeding grounds—a behavioural trait known as straying. The prevalence of straying is difficult to explore and therefore quantitative estimates for straying are seldom rep...

Animal movement is a multifaceted process that occurs for multiple reasons with powerful consequences for food web and ecosystem dynamics. New paradigms and technical innovations have recently pervaded the field, providing increasingly powerful means to deliver fine-scale movement data, attracting renewed interest. Specifically in the aquatic envir...

Geolocating aquatic animals with acoustic tags has been ongoing for decades, relying on the detection of acoustic signals at multiple receivers with known positions to calculate a 2D or 3D position, and ultimately recreate the path of an aquatic animal from detections at fixed stations. This method of underwater geolocation is evolving with new sof...

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, there are some that have received proportionally less attention. In this study, we investigate intraspecific differences in two overlooked life-history st...

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...

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 on swimming behaviour. A bypass close to the stream bed is often r...

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...

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 t...

Atlantic bluefin tuna (Thunnus thynnus; ABFT) is one of the most iconic fish species in the world. Recently, after being very rare for more than half a century, large bluefin tunas have returned to Nordic waters in late summer and autumn, marking the return of the largest predatory fish in Nordic waters. By tagging 18 bluefin tunas with electronic...

Internal seiches are common in stratified lakes, with significant effects on stratification patterns, hydrodynamics and vertical nutrient transport. In particular, seiches can change the vertical distribution of the thermocline and the cold hypolimnetic and warm epilimnetic water masses by several metres on a timescale of a few hours, leading to ra...

Accurate knowledge on spatiotemporal distributions of marine species and their association with surrounding habitats is crucial to inform adaptive management actions responding to coastal degradation across the globe. Here, we investigate the potential use of environmental DNA (eDNA) to detect species–habitat associations in a patchy coastal area o...

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 ju...

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 world‐wide. Restoration efforts are often constrained by limited resources, and insights from SLOSS studies therefore have...

Structural complexity is known to influence prey behaviour, mortality and population structure, but the effects on predators have received less attention. We tested whether contrasting structural complexity in two newly colonised lakes (low structural complexity lake—LSC; high structural complexity—HSC) was associated with contrasting behaviour in...

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 ar...

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 mi...

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...

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 be...

Atlantic bluefin tuna (ABFT) have recently returned to waters in the Skagerrak-Kattegat area between Denmark and Sweden and the western English Channel, where they have been rare for over five decades. To understand the factors that affect their distribution, ecology, population structure and survival, we conducted a tagging study to track their mi...

Structural complexity is known to influence prey behaviour, mortality and population structure, but the effects on predators has received less attention. We tested whether contrasting structural complexity in two newly colonised lakes (low structural complexity lake – LSC; high structural complexity - HSC) was associated with contrasting behaviour...

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. The r package actel provides a systematic conditional pipeline to filter and analyse acoustic telemetry data in a reproducible fashion, for animals moving bet...

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 o...

Citizen science platforms, including smartphone applications, that allow anglers to report information about fishing trips and catches may be a low-cost source of data that can feed into the science and management of recreational fisheries. However, information about potential biases in these data, such as the representativeness of user characteris...

Different migratory species have evolved distinct migratory characteristics that improve fitness in their particular ecological niches. However, when such species hybridize, migratory traits from parental species can combine maladaptively and cause hybrids to fall between parental fitness peaks, with potential consequences for hybrid viability and...

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 detect...

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 provide...

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...

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 day...

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 fo...

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 YAPS (Yet Another Positioning Solver), which combines the detec...

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 YAPS (Yet Another Positioning Solver), which combines the detec...

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 YAPS (Yet Another Positioning Solver), which combines the detect...

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 wi...

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 mode...

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...

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 w...

There is no generic solution to establish safe passage of downstream migrating fish passed hydropower facilities and mitigation measures are species‐ and site‐specific. Development of solutions is thus often based on “trial and error” and modelling based approaches may significantly reduce cost and time to arrive at successful mitigation. Here we e...

The interaction between hydrodynamics and the upstream migration of fish has been investigated in several studies over the past few years, but there has been a relative lack of investigation into the effects of hydraulics on the downstream migration of fish. In Norway, mortality associated with downstream migration is strongly related to hydropower...

Juvenile salmonids experience high mortality when negotiating lentic waters during their downstream migration to the sea. The development of artificial lakes and wetlands in streams has become a widely used management tool to reduce nutrient load to coastal areas. Such wetlands may threaten anadromous populations. In this study we quantify net grou...

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...

Genetic data have great potential for improving fisheries management by identifying the fundamental management units – i.e. 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 appli...

We tagged 125 sea trout kelts (length: 460−925 mm) in Danish rivers with positively buoyant, depth- and temperature-sensing data storage tags. Eight tags were recovered from fish that had completed a full marine cycle (exit and return to natal river). Mean duration of the post-estuary marine cycle was 96.1 d (range: 47−142 d). The trout resided at...

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...

There is increasing evidence that phenotypic variation can strongly impact community structure and ecosystem functions. Alewife Alosa pseudoharengus is a planktivorous fish species that strongly impact lake ecosystems. It has previously been demonstrated that phenotypic variation related to differences in life history among landlocked and anadromou...

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,...

In many animal species, performance in the early life stages strongly affects recruitment to the adult population; however, factors that influence early life history stages are often the least understood. This is particularly relevant for lake sturgeon,Acipenser fulvescens, living in areas where environmental calcium concentrations are declining, p...

Species integrity can be challenged, and even eroded, if closely related species can hybridize and produce fertile offspring of comparable fitness to that of parental species. The maintenance of newly diverged or closely related species therefore hinges on the establishment and effectiveness of pre-and/or post-zygotic reproductive barriers. Ecologi...

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 f...

Abstract Pike in the western Baltic Sea live on the edge of their salinity tolerance. Under physiologically challenging conditions, organism may respond by moving to environmentally more benign areas during critical periods, such as during spawning. We hypothesised that pike in a brackish lagoon (8–10 ppt salinity) would perform spawning- and feedi...

Artificial lake development is often used as a management tool to reduce nutrient runoff to coastal waters. Denmark has restored more than 10 000 ha of wetlands and lakes in the last 14 years as a consequence of ‘Action Plans for the Aquatic Environment’, which aim to meet the demands of the European Union's Water Framework Directive. Juvenile, sea...

Recent evidence supports the existence of a downstream autumn-migratory phenotype in juvenile anadromous brown trout (Salmo trutta), however the precise timing, extent and ecological significance of such behaviour remains ambiguous. We investigated the phenology of downstream migration of wild juvenile trout using passive integrated transponder (PI...