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The costal populations of perch (Perca fluviatilis) in some parts of the Baltic Sea have been in decline for about two decades. Recruitment failure in the early larval stages has been put forward as a possible cause and the decline has also been suggested to coincide with increases in three-pined stickleback (Gasterosteus aculeatus) densities. The aim of this study was to study the effects of growth and survival of newly hatched perch larvae in the presence of the three-pined stickleback, and if possible determine the main mechanism behind any negative effects the perch may suffer under such conditions. Using large scale experimental ponds as a controlled habitat, an experiment was conducted where perch larvae were being exposed to sticklebacks under four different stages of their development. Results showed that the three- spine stickleback can have a strong negative effect on the survival of young perch. This effect was strongest in the earliest stage of perch development and decreased as they grew bigger. The zooplankton densities didn't differ between the controls and stickleback treatments, suggesting that the young perch didn't suffer from food limitation. Instead predation was identified as the main mechanism behind the high mortality. The results of this study highlight the potential danger of the observed patterns of decreasing predator populations in conjunction with increasing populations of smaller prey species in the Baltic Sea.

Biological diversity is controlled by an array of factors and processes all active at different spatial and temporal scales. Regional factors control what species are available to occur locally, whereas the local factors determine what species are actually capable of colonizing the locality. I have investigated how these local and regional factors affect species richness and diversity, mainly of fish in Swedish lakes and in order to assess the impact of dispersal mode one study on bacteria was also performed. In addition, potential first steps towards speciation were investigated in perch (Perca fluviatilis) from two different habitats. Fish species richness and diversity were found to be regulated by history, dispersal limitation and the local environment. In addition, striking similarities were found in the control of community composition for fish and bacteria. Both were regulated by nearly equal parts regional and local factors. The study of morphological and genetical variation in perch (Perca fluviatilis) revealed genetic differentiation at small spatial scales, suggesting that genetic differences can evolve between groups at strikingly small spatial scales, which might have implications for speciation in a long time perspective. Based on these findings I conclude that space and time matter. Space has the potential to isolate sites. And both dispersal and local extinctions, it seems, might take a long time, as effects of the last ice-age can still be seen on the contemporary fish community richness and composition.

Cette thèse a déterminé les rôles respectifs de la photopériode et de la température lors des différentes et successives étapes du cycle de reproduction (induction du cycle, vernalisation, ponte) chez la perche commune Perca fluviatilis femelle. La photopériode est le facteur environnemental principal qui synchronise l’induction du cycle de reproduction chez la perche commune, la température joue uniquement un rôle modulateur. Une baisse importante de la durée de la photophase de 4-8 heures est recommandée. Le maintien d'une photopériode constante basée sur une photophase longue et constante (17L : 7D) inhibe l’induction, alors que le maintien d’une température élevée et constante (22-23°C) ne le permet pas. Pour la phase de vernalisation, une photopériode de type jour court (8L : 16D) est nécessaire. Concernant les effets de la température, une forte et progressive baisse de la température (de 22 à 6°C sur 16 semaines) est recommandée pour assurer un développement gonadique complet (ovocytes aux stades de vitellogenèse avancée en fin de phase d’induction et de la maturation finale avant la période de ponte). Des baisses de température plus modérées (de 22 à 14-18°C) altèrent la reproduction, notamment pendant la phase de vernalisation. L’augmentation finale de la température après la vernalisation est le facteur principal de synchronisation de la ponte. Cette étude a permis la mise au point d’un protocole photo-thermopériodique fiable garantissant des taux d’induction et de ponte très élevés, proches de 100%, chez les femelles / This PhD thesis has determined the respective roles of photoperiod and temperature at the different and successive steps of the reproductive cycle (induction of the cycle, wintering period, spawning) in female Eurasian perch Perca fluviatilis. Photoperiod is the main environmental factor which synchronizes the onset of the reproduction cycle in Eurasian perch female, temperature plays only a modulating role. A high photoperiod decrease of 4 or 8 hours is recommended. The maintenance of constant photoperiod based on a long photophase (17L: 7D) delays the onset of the reproductive cycle, whereas the maintenance of a warm and constant temperature (22-23°C) does not delay it. For the wintering period, a photoperiod with a short daylight period (8L : 16D) is required. Concerning the effect of temperature variations, a high and progressive temperature decrease (from 22 to 6°C over 16 weeks) is recommended to ensure a complete ovarian development (all oocytes achieved the advanced vitellogenesis stage at the end of the induction phase and and final maturation stage just before spawning). Slight temperature decreases (from 22 to 14-18°C) alter the reproduction, especially during the chilling period (wintering period). The final increase of temperature (up to 14°C) after the wintering period is the main factor for spawning synchronization. This study allowed the development of a reliable photo-thermal protocol for out-of-season spawning with very high rates (close to 100%) of female response and spawning

Although grassland bird populations have steadily declined, little research has examined the effect of oil infrastructure on abundances of grassland songbirds. Even less research has identified mechanisms that explain observed effects. To evaluate this, I sampled abundance of 5 songbird species at oil well sites with different pump mechanisms, power sources, and activity levels; I also evaluated the effects of perch and road density and exotic vegetation, all of which are associated with oil development. Both Baird’s sparrows (Ammodramus bairdii) and Sprague’s pipits (Anthus spragueii) had lower abundances at all sites that contained oil infrastructure. The other 3 species, chestnut-collared longspurs (Calcarius ornatus), western meadowlarks (Sturnella neglecta), and Savannah sparrows (Passerculus sandwichensis), were relatively unaffected by oil wells, linear features, or exotic vegetation. Given that oil well sites negatively affected two species of concern, more research is needed to determine mitigation strategies. / October 2016

This study was conducted to evaluate the relative roles of trophic dynamics and nutrient concentrations in the development of cyanobacteria blooms. The motivation for this research was to gain insights into how food webs respond to ecosystem-scale changes, using Lake Champlain as a case study. I sought to link field-based observations with experimentally derived data on mechanisms to better understand the processes that drive cyanobacteria blooms. My research addressed three specific topics: (1) associations among phytoplankton and nutrient concentration trends over time, (2) the impacts of planktivory by invasive fish on the ambient zooplankton community, and (3) the role of herbivore zooplankton grazers in determining the composition of the phytoplankton community. I found little evidence of a strong association between nutrient concentrations and phytoplankton community composition during summer months in shallow bays of Lake Champlain prone to annual cyanobacteria blooms. Fish diet analysis indicated that invasive white perch (Morone americana) and alewife (Alosa pseudoharengus) selectively graze on large zooplankton, which has likely led to substantial declines in zooplankton biomass. I used these results to inform the design of a mesocosm study, which tested the effects of zooplankton grazing on phytoplankton and provided support for the theory that large zooplankton grazing pressure changes the size structure, abundance and composition of phytoplankton. High nutrient concentrations support increased levels of ecosystem productivity, but cascading trophic dynamics are additional forces that are likely contributing to the determination of phytoplankton community composition. Collectively, my research suggests that in shallow bays of Lake Champlain, selective grazing by invasive planktivorous fish is shifting the size structure of the zooplankton grazer community and has likely contributed to conditions that favor dominance by cyanobacteria in summer.

The intensification of agricultural production in the Mekong Delta has faced serious challenges with respect to increased use of agrochemicals and especially pesticides. The indiscriminate use of pesticide could potentially impact on the long-term food production, environmental and human health in the delta. The aim of this thesis was to investigate the negative side effects of the current use of pesticides on climbing perch (Anabas testudineus) in rice fields using brain acetylcholinesterase (hereafter referred to as AChE) activity as a biomarker. The empirical work, on which this thesis is based, includes structured questionnaires, laboratory and field experiments. First, a field survey using questionnaires was carried out to gain a better understanding of the current state of rice farming systems, the use of pesticides and attitude to pest management strategies among rice and rice-fish farmers, as well as to provide basic information for the set-up of the laboratory and field experiments. Secondly, laboratory studies were conducted to clarify if the selected insecticides applied alone and in mixtures caused negative side effects on climbing perch fingerlings. Thirdly, further toxicity studies were carried out, under rice field conditions, to further investigate the toxicity effects of the insecticides, applied alone, in mixtures and under sequential applications, on climbing perch fingerlings. The results showed that although there were a more selective use of pesticides and an increased awareness among farmers of the negative side effects of pesticides in 2007 as compared to 1999, the current use of pesticide in the Mekong Delta still cause many problems to the environment and human health. Chlorpyrifos ethyl (hereafter referred to as CPF) was found to cause a significant and more prolonged inhibition on the brain AChE activity in climbing perch than fenobucarb (hereafter referred to as F). The inhibition by the mixture of CPF and F were significantly higher than the inhibition by only F, but less prolonged and significant lower than the inhibition by only CPF. The results suggest that the combined effect from a mixture of F and CPF can create both additive effects initially and later antagonistic effects. CPF and F applied at concentrations used by farmers, either as separate doses, in a mixture or in sequential doses, decreased the brain AChE activity, growth and survival rates in climbing perch. The results demonstrate that brain AChE activity in climbing perch is a relevant biomarker for monitoring of exposure to, and sub-lethal impacts from organophosphates and carbamates under tropical conditions. The result also shows that 2-PAM re-activate the brain AChE activity, and can be used as an alternative method to assess the AChE inhibition level in organisms recently exposed to OP’s, in situation where it may be difficult to find unexposed individuals as controls. In conclusion, this thesis shows that the current use of pesticides in the Mekong Delta has a negative effect on climbing perch living in rice fields. It indicates that a sustained long-term food production in the Mekong Delta must be based on ecological principles, taking advantages of ecosystem biodiversity and productivity, and not through intensified use of pesticides. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Submitted. Paper 5: Submitted.</p>

Individuals within fish populations differ in many traits, such as sex, life-history, habitat residence, diet, and morphology. Such trait differences among individuals (i.e. intra-population variation) may be greater than the differences among populations (i.e. inter-population variation). My dissertation examines intra-population variation, with a focus on trophic relationships and morphology; as well as how variation in these attributes may reflect differences in bioaccumulation of contaminants. The second chapter of my dissertation examines the influence of spatial-temporal variation on the trophic structures of round goby (Neogobius melanstomus) and two age classes of yellow perch (Perca flavescens) within Saginaw Bay, Lake Huron. Using stable isotope ratios (δ13C, δ15N, δ2H, δ18O) and stomach contents as trophic indicators, I examined variation of diets. I found that spatial variation had a greater impact on diet indicators than both annual and seasonal variation. This spatial variation could represent a form of compartmentalization within the community of fish residing in Saginaw Bay, and could provide stability to the community. Chapter three of my dissertation examines intra-population variation in yellow perch morphology through a series of mesocosm experiments. My first mesocosm study determined that yellow perch could be experimentally manipulated to display divergent morphologies using simulated habitats, specifically pelagic and littoral habitats. Following this experiment, I focused on specific environmental drivers (structure, prey resources, and predation risk) as possible influences on yellow perch morphology. Within experimental pools, I exposed yellow perch to one of four treatments (an open pool, a structured pool, pools with chironomid prey resources and pools with a perceived, olfactory, predation risk) in the summer of 2015. Following exposure to these treatments I examined the morphological changes in yellow perch in magnitude and direction. I observed that while each treatment induced some difference in morphology, the open and structured treatments had the greatest magnitude of difference. I repeated the open and structure treatments during the following summer (2016). Again, I found that structure and open morphologies could be induced by my mesocosm treatments, but also observed that shapes differed from the previous year’s structure and open treatments. Finally, my fourth chapter examined how variation in trophic niches and morphology may reflect variation in contaminant concentration of fish in their natural environment. In this chapter, I extended my work with yellow perch to also include black crappie (Pomoxis nigromaculatus) and examined fish from 5 northern Indiana glacial lakes. Using model inference techniques, I found that variation in mercury was closely associated with not only fish total length, but also stable isotopes (δ13C and δ15N) and morphology. Interestingly, morphology-related variables of both species were strong predictors of mercury concentration in fish, following total length. Together, the chapters within my dissertation highlight the importance of considering intra-population variation, in which local factors such as habitat conditions and prey availability can influence individual variation in trophic structuring and morphology. These in turn may reflect other attributes of interest, such as the accumulation of contaminants.

Elucidation of habitat and resource use patterns is important for facilitating sustainable management of fisheries. Discrete habitats in large aquatic ecosystems may offer distinct resources and differentially affect performance. Movement of organisms and organic materials links these habitats and potentially leads to spatially complex trophic pathways between basal resources and consumers. Habitat and resource use are commonly explored via two common methods: stable isotopes and morphometric analysis. The first research chapter of this thesis employed both methods to investigate seasonal habitat use of yellow perch <i>Perca flavescens</i>in eastern Lake Michigan and connected waterbodies known as drowned river mouth (DRM) lakes. Landmark-based geometric morphometrics was used to compare shape differences among habitats. Stable isotopes of ambient water, otoliths, and soft tissues were compared to differentiate among habitats. Both methods provided evidence of resident nearshore Lake Michigan fish, resident DRM lake fish occupying the littoral zone, and transient Lake Michigan fish occupying the profundal zone of DRM lakes. The majority of transient Lake Michigan fish moved into the profundal zone of DRM lakes in the fall. These results support previously published genetic data of distinct populations of yellow perch in eastern Lake Michigan and connected waterbodies. The second research chapter of this thesis also employed stable isotopes and morphometric analysis, but to investigate the consistency of resource use of age-0 yellow perch in Saginaw Bay, Lake Huron. These methods served as long-term diet indicators, as compared to short-term stomach contents analysis. Both stable isotopes of soft tissues and morphometric analysis showed spatial consistency in variation among sites. Fish from the two sites closer to the tributary input had higher δ¹⁵N values and more fusiform bodies, while fish from the third site further away from the tributary had lower δ¹⁵N values and were deeper-bodied. This spatial variation supports stomach content analysis of age-0 yellow perch from a previously published study. δ¹³C ratios displayed annual variation, and while inconsistent with stomach content analysis, was consistent with available prey items. The findings from this study suggest that young yellow perch in Saginaw Bay have limited movement and forage in a similar area to where they were collected. Previous studies have found discrepancies among indicators and have cautioned generalization of trophic relationships when only relying on a single metric. Agreement between complementary techniques provided additional support to previously-published genetic results and stomach content data, and thereby helped more fully describe habitat use by yellow perch in these systems.

<p>Recent studies show that populations of the freshwater isopod <em>Asellus aquaticus L. can rapidly become locally differentiated when submerged stonewort (<em>Chara spp.) vegetation expands in lakes. In the novel <em>Chara habitat, isopods become lighter pigmented and smaller than in the ancestral reed stands. In this study, I used laboratory experiments to investigate if selective predation by fish could be a possible explanation for these phenotypic changes. Predation from fish is generally considered to be a strong selective force on macroinvertebrate traits. In the first experiment I measured perch (<em>Perca fluviatilis L.) handling time for three size classes of <em>Asellus to see which size of those that would be the most profitable to feed upon. No difference in handling time was detected between prey sizes, hence the largest size would be the most beneficial to feed upon. In a second experiment I let perch feed on a mixture of <em>Asellus phenotypes in aquaria manipulated to mimic the substrates in either the <em>Chara or the reed habitats. Remaining isopods were significantly smaller and lighter pigmented in the fish aquaria than in the controls, showing that the perch preferred to feed on large and dark individuals. In the <em>Chara habitat, selection on isopod pigmentation was according to what could be expected from background matching, but in the reed habitat selection was quite the opposite. These results support the hypothesis that predation from fish is a strong selective force behind the rapid local adaptation seen in <em>Asellus populations in the novel <em>Chara habitat. </em></em></em></em></em></em></em></em></em></em></p>