Hi! My name is Mahboobeh Hajiesmaeili. I joined the RivEM research group for the second time, as a Visiting Research Project Assistant in December 2020. I worked in this research group in the year 2019, too. I have a PhD in River Engineering from Tarbiat Modares University (TMU), Tehran, Iran. My research interests center around the ecological modeling and river habitat assessment for freshwater fish and benthic invertebrates using individual-based/agent-based modelling (IBM/ABM) and bioenergetics approach, as well as physical habitat simulation models. I’m currently the chair of Ecohydraulics committee of the Iranian Hydraulic Association (https://iha.ir/ecohydraulics/).

During my M.Sc. project my main challenge was to introduce and enhance understanding of the multidisciplinary science of “Ecohydraulics” in Iran, which was completely new in my country. I used PHABSIM (Physical HABitat SIMulation) model for my M.Sc. thesis to investigate the effects of flow hydraulic parameters on rainbow trout. This study was one of the first habitat simulation studies about the interaction between ecology and hydraulics in Iran.

As a result of my interest in ecohydraulics and freshwater aquatic ecosystems, I was interested to focus on more developed habitat selection models for my PhD project and I focused on inSTREAM (individual-based Stream Trout Research and Environmental Assessment Model), which is one of the most important individual-based habitat selection models, and one of the main purposes of my research was to modify inSTREAM in its feeding and growth component to include more about how fish feed and how it depends on spatial variation in invertebrates. Given that the primary food sources of brown trout in my study area (Elarm River in Lar National Park, Iran) were benthic invertebrates and also due to the lack of considering these types of feeding organisms and their associated feeding strategy in other bioenergetics models presented so far, development of a new version of inSTREAM by considering hydraulic parameters affecting biomass of benthic invertebrates was the most important innovation of my PhD research. I was so lucky that one of my PhD supervisors was Steve Railsback, who is the main developer of inSTREAM and helped me a lot to improve my knowledge in individual-based modeling.

Starting in the left top corner, clockwise: Elarm River which is a fabulous trout reproduction habitat with plenty of suitable spawning grounds in Lar National Park (Iran); Identified benthic invertebrates in my study site; Collecting benthic invertebrate samples using a Surber sampler in Elarm River); Identifying benthic invertebrates in the laboratory; Me and my field studies team work in my PhD project
Mahboobehs first book, written from the results of both my M.Sc. and Ph.D. studies with collaboration of my PhD supervisor and my M.Sc. thesis advisor (in Persian)

Immediately after receiving my PhD degree, I was successfully accepted by John Piccolo to work in the KK Eflows project within the RivEM-research group at Karlstad University for a short term employment as a visiting researcher. My work was mostly focused on preparing inSTREAM input data using QGIS for Blankaström (Emån) and also downstream part of Gullspång River (Stora and Lilla Åråsforsen).

Mahboobeh and Kristine Lund Bjørnås  (former RivEM Lic-student) in the Day of the Salmon at Fortum in Gullspång, 2019

As a project assistant in our ongoing project I will focus on ecological and individual-based modelling of Atlantic salmon and brown trout habitat using inSTREAM in the lower part of the Gullspång River (Stora and Lilla Åråsforsen) under hyropeaking conditions. I will collaborate with John Piccolo, Johan Watz, and Louis Addo.

One of my favorite activities during my free time is drawing portraits. Considering that my research work is such that I should spend too much time on my computer, drawing and art help me to relax 🙂 

Some of Mahboobehs drawings

Brown trout (Salmo trutta) eggs with eyed embryos

On Tuesday 8 December Kalle Filipsson, RivEM PhD student, will present his work on how elevated temperatures and predator presence during egg incubation affect development and behaviour of brown trout. The seminar starts at 13:15 and will be streamed live on Zoom. Contact Kalle (karl.filipsson@kau.se) if you are interested in attending the seminar, and he will send you a link.

Our former PhD student Anna Hagelin and several other researchers, amongst them Larry Greenberg, Olle Calles and Eva Bergman, recently published a new paper in the Canadian Journal of Fisheries and Aquatic Sciences.

They examined fishway passage of landlocked Atlantic salmon in River Klarälven, Sweden and brown trout in River Gudbrandslågen, Norway, and the influence of prior experience on passage success in 2012 and 2013. Fishway trap efficiency varied from 18 to 88% and was influenced by river discharge. Most salmon (81%) entered the fishway trap on days without spill, and salmon moved from the turbine area to the spill zone when there was spill, with small individuals showing a stronger reaction than large fish. Analysis of fish with and without prior trap experience showed that a higher percentage of the “naïve” fish (70% of salmon and 43% of the trout) entered the fishway traps than the “experienced” ones (25% of the salmon and 15 % of the trout). Delays for fish that entered the trap ranged from 3-70 days for salmon and 2-47 days for trout.

The paper is not publicly accessible, but can be requested via ResearchGate.

Karl Filipsson, Eva Bergman, Larry Greenberg, Martin Österling, Johan Watz and Ann Erlandsson recently published the paper “Temperature and predator-mediated regulation of plasma cortisol and brain gene expression in juvenile brown trout (Salmo trutta)” in the journal Frontiers in Zoology.

In this study, we tested how temperature and the presence of a cold-water adapted predatory fish (burbot, Lota lota) affected primary stress responses (i.e. cortisol and mRNA levels of stress-related genes) in juvenile brown trout (Salmo trutta). We found that trout had elevated cortisol levels in the presence of burbot, and that stress-related gene expressions varied a lot with temperature. In addition, we found that the predator-induced effects on mRNA levels were temperature dependent for some of the genes. This, together with the directly temperature-mediated effects that we observed in our study, suggest that warming winters can have major impact on primary stress responses in overwintering salmonids, for instance in encounters with predators.

In the abstract of the paper, we wrote that:

“Temperature affects many aspects of performance in poikilotherms, including how prey respond when encountering predators. Studies of anti-predator responses in fish mainly have focused on behaviour, whereas physiological responses regulated through the hypothalamic-pituitary-interrenal axis have received little attention. We examined plasma cortisol and mRNA levels of stress-related genes in juvenile brown trout (Salmo trutta) at 3 and 8 °C in the presence and absence of a piscivorous fish (burbot, Lota lota).

One of the experimental aquaria used for the study.

A redundancy analysis revealed that both water temperature and the presence of the predator explained a significant amount of the observed variation in cortisol and mRNA levels (11.4 and 2.8%, respectively). Trout had higher cortisol levels in the presence than in the absence of the predator. Analyses of individual gene expressions revealed that trout had significantly higher mRNA levels for 11 of the 16 examined genes at 3 than at 8 °C, and for one gene (retinol-binding protein 1), mRNA levels were higher in the presence than in the absence of the predator. Moreover, we found interaction effects between temperature and predator presence for two genes that code for serotonin and glucocorticoid receptors.

We extracted mRNA from the forebrain (telencephalon) of the trout. The picture shows a trout brain after dissection, where the telencephalon is the two upper lobes.

Our results suggest that piscivorous fish elicit primary stress responses in juvenile salmonids and that some of these responses may be temperature dependent. In addition, this study emphasizes the strong temperature dependence of primary stress responses in poikilotherms, with possible implications for a warming climate.”

You can read the paper for free on the journal website, as the paper is published open access through funding provided by Karlstad University.

On Thursday 26 March, Kristine Lund Bjørnås, NRRV PhD-student, will defend her licentiate thesis “Modeling Atlantic salmon and brown trout responses to river habitat alteration”. The defense starts at 10:00. Asbjørn Vøllestad, Professor at the University of Oslo, is the opponent for Kristine’s defense.

Kristine’s defense will be held as an online meeting on Zoom (a video communication system commonly used by universities). You should be able to follow Kristine’s defense using this link:


The defense will also be streamed live on a bigscreen in lecture hall 1B309 (Sjöströmsalen) at Karlstad University, and everyone is welcome to watch the defense from the lecture hall. Please note that Kristine and the opponent will not be in the lecture hall.

On Friday 13 March, Kalle Filipsson, NRRV PhD-student, will defend his (my) licentiate thesis. The thesis has the title ”From behaviour to genes: anti-predator responses of brown trout (Salmo trutta) under winter conditions”. The defense will be held in room 1B309 (Sjöströmsalen) at Karlstad University, and starts at 10:00. Stefán Óli Steingrímsson, Professor at Hólar University, Iceland, is the opponent. The defense is open for everyone who wishes to attend.

Kalle’s licentiate thesis, nailed to one of the “theses trees” at the Biology Department at Karlstad University.
Three juvenile brown trout (Salmo trutta), doing trout stuff in a stream flume at Karlstad University.

On Tuesday 10 March, Kristine Lund Bjørnås, PhD student at Karlstad University, will give a seminar entitled “Modeling Atlantic salmon and brown trout responses to river habitat alteration”. The seminar starts at 13.15 in room 5F416, everyone who wants to is welcome to attend the seminar.

This seminar is a practice seminar in preparation for Kristine’s licentiate defense, which will be held Thursday 26 March at 10:00. More information about the licentiate seminar will be provided closer to the defense.

Kristine Lund Bjørnås and Niclas Carlsson taking point measurements of the physical habitat in Gullspångsforsen.

On Tuesday 25 February, Kalle Filipsson, RivEM PhD student, will give a seminar entitled ”From behaviour to genes: anti-predator responses of brown trout under winter conditions”. The seminar starts at 13.15 in room 5F416, everyone who wants to is welcome to attend the seminar.

This seminar is a practice seminar in preparation for Kalle’s (my) licentiate defense, which will be held Friday 13 March at 10:00. More information about the licentiate seminar will be provided closer to the defense.

Juvenile brown trout (Salmo trutta). Photo: Karl Filipsson
A burbot (Lota lota) in a stream flume at Karlstad University. Photo: Karl Filipsson

Johan Watz, Assistant Professor at Karlstad University, recently published two papers on juvenile salmonid ecology:


Temperature‐dependent competition between juvenile salmonids in small streams

By Johan Watz, Yasuhiko Otsuki, Kenta Nagatsuka, Koh Hasegawa & Itsuro Koizumi, published in the journal Freshwater Biology.

In the abstract, the authors write:

Johan Watz, doing field work during his PostDoc in Japan.

1) Biotic interactions affect species distributions, and environmental factors that influence these interactions can play a key role when range shifts in response to environmental change are modelled.

2) In a field experiment using enclosures, we studied the effects of the thermal habitat on intra‐ versus inter‐specific competition of juvenile Dolly Varden Salvelinus malma and white‐spotted charr Salvelinus leucomaenis, as measured by differences in specific growth rates during summer in allopatric and sympatric treatments. Previous laboratory experiments have shown mixed results regarding the importance of temperature‐dependent competitive abilities as a main driver for spatial segregation in stream fishes, and no study so far has confirmed its existence in natural streams.

3) Under natural conditions in areas where the two species occur in sympatry, Dolly Varden dominate spring‐fed tributaries (cold, stable thermal regime), whereas both species often coexist in non‐spring‐fed tributaries (warm, unstable thermal regime). Enclosures (charr density = 6 per m2) were placed in non‐spring‐fed (10–14°C) and spring‐fed (7–8°C) tributaries.

A forest stream on Hokkaido, northern Japan.

4) In enclosures placed in non‐spring‐fed tributaries, Dolly Varden grew 0.81% per day in allopatry and had negative growth (−0.33% per day) in sympatry, whereas growth rates were similar in allopatry and sympatry in spring‐fed tributaries (0.68 and 0.58% per day). White‐spotted charr grew better in sympatry than in allopatry in both thermal habitats. In non‐spring‐fed tributaries, they grew 0.17 and 0.79% per day and in spring‐fed tributaries 0.46 and 0.75% per day in allopatry and sympatry, respectively.

5) The negative effect of inter‐specific competition from white‐spotted charr on Dolly Varden thus depended on the thermal habitat. However, there was no strong evidence of a temperature‐dependent effect of intra‐ and inter‐specific competition on white‐spotted charr growth.

6) Multiple factors may shape species distribution patterns, and we show that temperature may mediate competitive outcomes and thus coexistence in stream fish. These effects of temperature will be important to incorporate into mechanistic and dynamic species distribution models.


Read more about the Koizumi lab at Hokkaido University (where Johan did his PostDoc) on their website!


Structural complexity in the hatchery rearing environment affects activity, resting metabolic rate and post‐release behaviour in brown trout Salmo trutta

By Johan Watz, published in the Journal of Fish Biology

In the abstract, Johan writes:

The effects of structural enrichment in the hatchery rearing environment of brown trout Salmo trutta was linked to post‐release performance. Enrichment resulted in reduced swimming activity scored in an open field test and reduced movement in a natural river after release. Also, enrichment increased resting metabolic rates, which correlated positively with overwinter growth.


Contact the author to access the papers.


The left photographs show Dolly Varden (a) and white‐spotted charr (b). The right photographs show enclosures in a non‐spring‐fed (c) and a spring‐fed (d) tributary.


The structurally enriched (left) and barren (right) tanks used in the study on how structural complexity in the hatchery environment affects juvenile brown trout.


River Rottnan in winter.

Åsa Enefalk, Ari Huusko, Pauliina Louhi and Eva Bergman recently published the paper “Fine stream wood decreases growth of juvenile brown trout (Salmo trutta L.)” in the journal Environmental Biology of Fishes. In the abstract, the authors write:

A juvenile brown trout (Salmo trutta) hiding in fine stream wood.

“In this study, the growth rate, gut fullness, diet composition and spatial distribution of brown trout was compared between artificial channels with and without fine wood (FW). Access to FW resulted in significantly lower brown trout growth rates over the study period from late summer to early winter as water temperatures declined from 17 °C to 1 °C. Access to FW resulted in minor differences in occurrence of the most common taxa found in brown trout diets, except for chironomid larvae which were found in c. 60% of the brown trout guts from control treatments but in only 30% of the guts from FW treatments in early winter. Diet consisted primarily of case-bearing and free-living Trichoptera larvae, Asellus, chironomid and Ephemeroptera larvae. Brown trout gut fullness was not significantly affected by access to FW bundles. Brown trout aggregated among FW but were more evenly distributed in channels lacking it. Our results suggest that juvenile brown trout use FW as a shelter at a wide range of water temperatures, and that this behaviour may result in reduced growth rates during their first fall and the onset of their first winter. We also show that prey availability and the composition of brown trout diet changes from late summer to early winter and that FW has a small but significant effect on brown trout diet composition.”

Read the paper here, or contact any of the authors.