La diversification de la production, par la domestication de nouvelles espèces de poissons, constitue l’une des solutions pour une aquaculture durable. Dans ce contexte, l’élevage de la perche Eurasienne, Perca fluviatilis, s’est bien développé ces dernières années permettant aujourd’hui une production stable et croissante. Le progrès de la filière requiert, la mise en œuvre de programmes de sélection génétique pour améliorer, entre-autres, la croissance, la reproduction, et la résistance aux maladies. Pour ce faire, la caractérisation génétique des stocks de poisson actuellement en élevage est un pré-requis indispensable afin d’évaluer si la variabilité génétique est suffisante. Au cours de ce travail, nous avons analysé la variabilité génétique entre les populations sauvages de deux lacs alpins (lacs Léman et Neuchâtel) dont les populations sont utilisées comme fondatrices par les perciculteurs et les stocks de deux fermes d’élevage. Nous avons trouvé une seule population panmictique dans le lac Léman, alors que deux sous-populations ont été identifiées dans le lac Neuchâtel et dont la variabilité génétique est plus forte. Par contre, ces populations sauvages ne sont pas représentées dans les stocks d’élevage bien qu’elles étaient utilisées pour fonder les stocks de géniteurs. De plus, la variabilité génétique est plus forte dans les populations captives. Entre les géniteurs et leurs descendances, la diversité génétique n’a pas diminué malgré une faible augmentation de la consanguinité. Ainsi, ce travail permettra aux perciculteurs de mettre en place une réelle gestion génétique de leurs cheptels et par la suite de développer des programmes de sélection. De plus, il a permis de mieux comprendre les liens possibles entre le processus de domestication et l’évolution de la variabilité génétique / The diversification of production, by the domestication of new fish species, is one of the possible solutions for sustainable aquaculture. In this context, the farming of the Eurasian perch, Perca fluviatilis, has developed well in recent years allowing today a stable and increasing production. The progress of the sector requires, among others, the establishment of breeding programs to improve, growth, reproduction and disease resistance. For this, the genetic characterization of currently farmed fish stocks is an essential prerequisite to assess whether genetic variation is sufficient. In this work, we analyzed the genetic variability among wild populations of two alpine lakes (lakes Geneva and Neuchâtel) whose populations are used by fish farmers to establish their stocks. We found one panmictic population in Lake Geneva, while two sub-populations were identified in Lake Neuchâtel, whose genetic variability is higher. However, those wild populations are not found in captive stocks. In addition, the genetic variability is higher in captive populations. Between parents and their offspring, the genetic diversity has not decreased despite a small increase in inbreeding. Thus, this work will allow fish farmers to set up a real genetic management of their stocks and subsequently to develop breeding programs. Moreover, it provides a better understanding of the possible links between the process of domestication and the evolution of genetic variability

Food culture emerges as a social culture and can be summarized through its historicaldevelopment process. The exploration of socio-cultural analysis of food with sociologicalapproaches has emerged in research due to the increased awareness of modern societies’motivations to discover other cultures through food. However, in the context of Sweden,limitations exist in analyzing the continuous ongoing process of a food product’s cultural valueand its potential ‘added value to local cultural expression. This research focuses on evaluatingPike-Perch’s culture value through its historical developed process and how utilization of theproduct has established present brand identity. By targeting the local stakeholder community, theperception of Pike-Perch’s recognized cultural value could be captured and utilized as addedvalue for local cultural expression. The stakeholder’s perspectives were collected via interviewsand observations through the geographical boundaries connected to the lakes of Mälaren andHjälmaren. The findings point towards a recent transformation of Pike-Perch market value,giving the fish a new sociological appearance. As a result, a change of traditional utilization hasreinvented/reproduced Pike-Perch with a different positioning within its socio-cultural setting.The stakeholders acknowledge the success in its development process that has establishedpresent identity; however, to the cost of preserving its intangible heritage. In return, thetraditional food culture appeared fragmented. By reintroducing traditional elements from the pastthat satisfy the imaginations and need for visitors to acknowledge its distinctiveness, the brandcould be strengthened and potentially justify its new market position. This research contributedto understanding the value of food culture from a stakeholder perspective and how post-modernsocieties influence its potential for sustainable destination development.

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The study of spatiotemporal dynamics of fish populations is important for both stock assessment and fishery management. I explored the impacts of environmental and anthropogenic factors on spatiotemporal patterns of fish populations, and contributed to stock assessment and management by incorporating the inherent spatial structure. Hierarchical models were developed to specify spatial and temporal variations, and Bayesian methods were adopted to fit the models. Yellow perch (Perca flavescens) is one of the most important commercial and recreational fisheries in Lake Erie, which is currently managed using four management units (MUs), with each assessed by a spatially-independent stock-specific assessment model. The current spatially-independent stock-specific assessment assumes that movement of yellow perch among MUs in Lake Erie is statistically negligible and biologically insignificant. I investigated whether the assumption is violated and the effect this assumption has on assessment. I first explored the spatiotemporal patterns of yellow perch abundance in Lake Erie based on data from a 27-year gillnet survey, and analyzed the impacts of environmental factors on spatiotemporal dynamics of the population. I found that yellow perch relative biomass index displayed clear temporal variation and spatial heterogeneity, however the two middle MUs displayed spatial similarities. I then developed a state-space model based on a 7-year tag-recovery data to explore movements of yellow perch among MUs, and performed a simulation analysis to evaluate the impacts of sample size on movement estimates. The results suggested substantial movement between the two stocks in the central basin, and the accuracy and precision of movement estimates increased with increasing sample size. These results demonstrate that the assumption on movements among MUs is violated, and it is necessary to incorporate regional connectivity into stock assessment. I thus developed a tag-integrated multi-region model to incorporate movements into a spatial stock assessment by integrating the tag-recovery data with 45-years of fisheries data. I then compared population projections such as recruitment and abundance derived from the tag-integrated multi-region model and the current spatial-independent stock-specific assessment model to detect the influence of hypotheses on with/without movements among MUs. Differences between the population projections from the two models suggested that the integration of regional stock dynamics has significant influence on stock estimates. American Shad (Alosa sapidissima), Hickory Shad (A. mediocris) and river herrings, including Alewife (A. pseudoharengus) and Blueback Herring (A. aestivalis), are anadromous pelagic fishes that spend most of the annual cycle at sea and enter coastal rivers in spring to spawn. Alosa fisheries were once one of the most valuable along the Atlantic coast, but have declined in recent decades due to pollution, overfishing and dam construction. Management actions have been implemented to restore the populations, and stocks in different river systems have displayed different recovery trends. I developed a Bayesian hierarchical spatiotemporal model to identify the population trends of these species among rivers in the Chesapeake Bay basin and to identify environmental and anthropogenic factors influencing their distribution and abundance. The results demonstrated river-specific heterogeneity of the spatiotemporal dynamics of these species and indicated the river-specific impacts of multiple factors including water temperature, river flow, chlorophyll a concentration and total phosphorus concentration on their population dynamics. Given the importance of these two case studies, analyses to diagnose the factors influencing population dynamics and to develop models to consider spatial complexity are highly valuable to practical fisheries management. Models incorporating spatiotemporal variation describe population dynamics more accurately, improve the accuracy of stock assessments, and would provide better recommendations for management purposes. / Doctor of Philosophy / Many fish populations exhibit complex spatial structure, but the spatial patterns have been incorporated into stock assessment only in few cases. A full understanding of spatial structure of fish populations is needed to better manage the populations. Stock assessment and management strategies should depend on the inherent spatial structure of the target fish population. There have been many approaches developed to analyze spatial structure of fish populations. In this dissertation, I developed quantitative models to analyze fish demographic data and tagging data to explore spatial structure of fish populations. Yellow perch (Perca flavescens) in Lake Erie and Alosa group including American Shad (Alosa sapidissima), Hickory Shad (A. mediocris) and river herrings (Alewife A. pseudoharengus and Blueback Herring A. aestivalis) in selected tributaries of the Chesapeake Bay were taken as examples. Fishery-independent data for yellow perch displayed spatial similarities in the central basin of Lake Erie. Distinct temporal trends were observed in relative abundance data for Alosa sp. in different tributaries of the Chesapeake Bay. Substantial yellow perch movement among the central basin of the Lake was observed in tagging data. Ignoring the inherent spatial structure may cause fish to be overfished in some regions and underfished in others. To maximize the effectiveness of management in all regions for fish populations, I highly recommend incorporating spatial structure into stock assessment and management such as the ones developed in this dissertation.

Detta examensarbete syftade till att ta fram ett underlag för en regional åtgärdsplan avseende dibenso-p-dioxiner och dibensofuraner, gemensamt benämnda som PCDD/F eller dioxiner, i Gävleborgs län. Länet har historiskt varit ett av de mest utsatta områdena i Sverige beträffande dessa föroreningar och höga koncentrationer i bland annat strömming har medfört att denna inte får saluföras i övriga EU.   I arbetet har resultaten från den rådande forskningen på området studerats för att få kunskap om nuvarande källor och möjliga förklaringar till de fortsatt förhöjda koncentrationerna av dioxiner. Därefter har data från tidigare undersökningar av dioxinkoncentrationer i Gävleborgs län samlats in, sammanställts och använts för att studera hur koncentrationerna varierar geografiskt inom länet. Principalkomponentanalys (PCA) av specifika dioxinkongeners koncentrationer har sedan använts för att försöka identifiera verksamhetstyper som potentiellt kan ha bidragit till föroreningarna på olika platser - en analys som dock är behäftad med stora osäkerheter. De insamlade provresultaten har även använts för att genom massbalansmodellering undersöka återhämtningen i två känt förorenade fjärdar i länet; Norrsundet och Gårdsfjärden. Utifrån resultaten av ovanstående analyser diskuterades även nyttan av att genomföra eventuella åtgärder för att reducera halterna i kraftigt förorenade områden.   Proverna som sammanställts visade klara geografiska skillnader i sedimentkoncentration, och till viss del även i koncentration i muskel från abborre, vilket visar på en stark betydelse av lokala källor i vissa områden. Bland strömmingsproverna kunde inget liknande samband ses. Detta kan förklaras av att det migrerande beteendet hos strömming gör att fisken under sin livstid exponeras för varierande föroreningsnivåer i olika områden, medan abborren är mer stationär även som vuxen. Principalkomponentanalysen gav, för vissa prover, indikationer kring vilken typ av verksamhet som bidragit till de uppmätta koncentrationerna. Dessa resultat är dock mycket osäkra och bör inte på egen hand användas som underlag för att fastställa föroreningskällor. Massbalansmodelleringen visade att PCDD/F-koncentrationen i sediment inte har någon betydelse för koncentrationen i vattenmassan utan att inflödet från omgivande hav dominerar även i avgränsade fjärdar. De modellerade jämviktskoncentrationerna mellan sediment och vattenmassa indikerade även att koncentrationerna i sediment kommer fortsätta överskrida somliga gränsvärden tills koncentrationen i vattenmassan reducerats, vilket även stöds av att dessa gränsvärden överskreds i majoriteten av de sammanställda proverna.   Baserat på samtliga ovannämnda resultat drogs slutsatsen att lokala saneringsåtgärder sannolikt inte ger någon effekt på PCDD/F-koncentrationerna i strömming, samt att de inte är tillräckliga för att erhålla sedimentkoncentrationer under samtliga gränsvärden. De kan däremot effektivt minska den exponering som mer stationära organismer som abborre utsätts för i områden med kraftigt förorenade sediment, och kan även ha positiva effekter på förekomsten av andra miljöfarliga ämnen i området. För- och nackdelar måste således övervägas i varje enskilt fall. / The aim of this Master’s Thesis was to provide a basis for a regional plan of action regarding dibenzo-p-dioxins and dibenzofurans, commonly referred to as PCDD/F or dioxins, in Gävle-borg County. This region has historically been one of the Swedish areas most affected by these pollutants, and high concentrations in for example Atlantic herring (Clupea harengus) have resulted in restrictions where some fish species cannot be sold in other EU countries.   In this work, results of current research on the subject were studied in order to gain knowledge about current sources and possible explanations to the continued high concentrations of dioxins. Thereafter, data from earlier investigations of dioxin levels in Gävleborg County have been gathered, compiled and used to study the regional geographic variation of the concentrations. Principal component analysis (PCA) was then used on the concentrations of specific congeners in an attempt to identify source types that might have contributed to the contamination in various sites; this analysis is however marred by uncertainties. The gathered data have also been used to investigate the recovery in two bays with known contaminations, Norrsundet and Gårdsfjärden, using mass balance modelling. The benefits of implementing measures to reduce the PCDD/F-concentrations in highly polluted areas were then discussed based on the results of the above-mentioned analyses.   The measured sediment concentrations, and partly also the concentrations in European perch (Perca fluviatilis), of the compiled samples showed distinct geographic differences, which indicates a strong influence from local sources in some areas. Among the herring samples, no such connection could be seen. This could be explained by the migrating behaviour of adult herring, resulting in an exposure to various levels of contamination in different areas as they migrate, while adult perch has a more stationary behaviour. For some samples, the principal component analysis gave indications on source types that might have contributed to the local contamination levels. These results are however very uncertain and they should not be used as the sole basis when determining emission sources. The mass balance modelling showed that the PCDD/F-concentrations in sediments have no influence on the concentrations in the water body; the inflow from the surrounding sea is predominant also in enclosed bays. The modelled equilibrium concentrations between sediments and water body also indicated that the sediment concentrations will continue to exceed the guideline values until the water concentrations have decreased. This is also supported by the fact that the majority of the samples showed concentrations exceeding these guideline values.   Based on all of the abovementioned results it was concluded that local remediation measures would most likely not affect the PCDD/F-concentrations in herring. It was also concluded that such measures would not suffice to obtain sediment concentrations that fall below all guideline values. They can however be used to lessen the exposure that stationary organisms are subjected to in areas with highly contaminated sediments, and can also have positive effects on the levels of other hazardous substances in the area. Thus, the benefits and disadvantages need to be considered in each specific case.

The work in this thesis deals with the ecology and evolution of adaptive individual variation. Ecologists have long used niche theory to describe the ecology of a species as a whole, treating conspecific individuals as ecological equivalent. During recent years, research about individual variation in diet and morphology has gained interest in adaptive radiations and ecological speciation. Such variation among individual niche use may have important conservation implications as well as ecological and evolutionary implications. However, up to date we know very little about the extension of this phenomenon in natural populations and the mechanisms behind it. The results in this thesis show that the extension of individual diet specialization is widely spread throughout the animal kingdom. The variation in diet is mainly correlated to morphological variation but not always. Furthermore, this variation in diet and morphology among individuals could be both genetically determined and environmentally induced and it mainly comes from trade-offs in foraging efficiency between different prey types. The results from a number of studies of perch also show that individual perch differ in morphology and diet depending on habitat, where littoral perch has a deeper body compared to pelagic perch. This difference in morphology corresponds to functional expectations and is related to foraging efficiency trade-offs between foraging in the littoral and pelagic zone of a lake. The variation in morphology in perch is mainly due to phenotypic plasticity but there are also small genetic differences between the littoral and pelagic perch. Two separate studies show that both predation and competition may be important mechanism for the variation in morphology and diet in perch. In conclusion, the results in this thesis show that individual variation in diet and habitat choice is a common phenomenon with lots of ecological and evolutionary implications. However, there are many mechanisms involved in this phenomenon on which we are just about to start learning more about, and only further research in this area will give us the full insight.

Hydroxylated polybrominated diphenyl ethers (OH-PBDEs) are naturally produced in aquatic ecosystems e.g. by algae. Many OH-PBDEs have been observed to be highly bioactive and to cause adverse effects through several pathways, e.g. via disrupting oxidative phosphorylation (OXPHOS). The levels of some OH-PBDEs have increased in Baltic biota over the past decades. This may be associated with the nutrient enrichment of the Baltic Sea, which has favored growth of some of the OH-PBDE producers. Ceramium tenuicorne has been suggested to be a producer of OH-PBDEs in the Baltic Sea, which is supported by the results presented in this thesis. The levels of OH-PBDEs were observed to fluctuate greatly in C. tenuicorne over the summer season, and to correlate with the levels of pigments in the algae. However, the observed congener pattern in C. tenuicorne questioned theories regarding the mechanism of their biosynthesis. The results indicate a much more selective pathway for biosynthesis than previously suggested for the production of OH-PBDEs. One of the most abundant OH-PBDEs in C. tenuicorne, 6-OH-BDE137, has previously been observed to be toxic to bacteria, fungi, and crustaceans. Furthermore, Baltic gammarids seemed to change their feeding preferences towards less grazing on C. tenuicorne during the production peek of OH-PBDEs in the alga. This suggests that OH-PBDEs may serve as allelochemical defense agents for C. tenuicorne. The transport and fate of OH-PBDEs through a Baltic food chain was also studied, including C. tenuicorne, Gammarus spp., three-spined stickleback (Gasterosteus aculeatus), and perch (Perca fluviatilis). A small portion of the OH-PBDEs were observed to be methylated in the alga, or by associated bacteria. The methylated OH-PBDEs biomagnified in the food chain up to perch, in which they were converted back to the OH-PBDEs via demethylation. The OH-PBDEs and their methylated counterparts were also partially debrominated in the food chain, which resulted in high concentration of 6-OH-BDE47 in the perch. This congener is the most toxic OH-PBDE with regards to OXPHOS disruption. Another biotransformation of OH-PBDEs was identified in Baltic Sea blue mussels (Mytilus edulis). High concentrations of OH-PBDEs were conjugated with lipophilic moieties, e.g. fatty acids. This increases the residence time of the OH-PBDEs in the mussels. Mussels have been suggested to conjugate steroids with fatty acids as a means to regulate hormone levels. The conjugation of OH-PBDEs to fatty acids may occur due to intrusion into this pathway. Methods were developed to include quantification of conjugated OH-PBDEs in the analysis of mussels. OH-PBDEs were also quantified in blood from Baltic Sea grey seals (Halichoerus grypus). Seals originating from the Baltic proper were observed to be more highly exposed to 6-OH-BDE47 than seals from the Gulf of Bothnia. However, the levels of OH-PBDEs were generally low. A major effort was invested into securing these results, including development of a new analytical method. Blood obtained from dead seals is a difficult matrix for quantification of OH-PBDEs, and previous attempts using an established method yielded unsatisfactory results. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

Dams and weirs are widely implicated in large-scale declines in both the range and abundance of aquatic fauna. Although many factors are involved, such declines are commonly attributed to the prevention or reduction of migration, reductions in available habitat, alteration of natural flow regimes and changes to physicochemical characteristics. In Australia, studies into the ecological effects of these impacts are limited, and have concentrated mainly on species of recreational and commercial importance. Subsequently, the adverse effects of dams and weirs, and suitable methods of mitigation, remain largely unknown for many other taxa. Therefore, the major aim of this thesis is to investigate the ecological effects of dam and weir construction on previously unstudied migratory assemblages of fish and macroinvertebrates in the Murray-Darling Basin. It is anticipated that the results of these studies will feed back into improved management strategies that help arrest the previously observed declines of aquatic fauna. Initially, fish communities were sampled, by boat electrofishing, from both reference sites and downstream of Balranald and Redbank weirs on the lower reaches of the Murrumbidgee River, Australia. Sampling was stratified over large spatial and temporal scales to gain a comprehensive understanding of species most affected by the presence of these two barriers. In general, the weirs obstructed fish migrations during summer and autumn and many species of small-bodied fish such as Australian smelt, western carp gudgeon, fly-specked hardyhead and crimson-spotted rainbowfish accumulated downstream of Balranald Weir. In addition, downstream accumulations of juveniles of larger-bodied species such as bony herring, common carp and goldfish were also detected. Although many previous studies had either documented or hypothesised that upstream migrating fish accumulate downstream of migration barriers, none attempted to quantify the size of such populations. Therefore, a simple but efficient method to estimate the size of migratory populations was assessed at the Balranald Weir site. The application of two commonly used estimation techniques yielded relatively reliable results for seven species that accumulated downstream of the weir. Population size estimates were greatest for most species during summer and autumn, where accumulations as high as 800 fish per day were detected. The largest calculated population size estimates, in addition to the greatest temporal variation, of any individual species was observed in bony herring. Given the simplicity of the technique and the relative accuracy of population estimates, it was concluded that these methods could easily be applied to other weirs where the size of migratory populations is of particular interest. A study investigating the effects of Yanco Weir on the diets of three migratory percichthyid species, Murray cod, trout cod and golden perch was also conducted. Observed spatial variation in a number of trophic processes strongly implicated Yanco Weir as a major contributor to increased competition among percichthyid species on the Murrumbidgee River. The greater relative abundance of percichthyids from downstream samples, combined with increases in dietary overlap and a greater percentage of empty stomachs, also suggested percichthyids may be significantly affecting the relative abundance of potential prey items such as freshwater prawns and Australian smelt. These significant changes in dietary composition were likely related to migratory behaviour, as these species accumulated downstream of the weir, and could be readily expected at other sites where passage is obstructed. It was suggested that the construction of suitable fish passage facilities would effectively reduce the probability of migratory fish accumulating and, subsequently, potential effects of dams and weirs on trophic processes. Since it was established that dams and weirs of the Murrumbidgee River were significantly affecting migratory fish communities, an innovative but relatively inexpensive fishway design, the Deelder fish lock (after Deelder, 1958), was constructed and assessed for wider application throughout the Murray-Darling Basin. The Deelder lock was effective at mitigating the effects of Balranald Weir by providing passage for a wide range of size classes and species of fish; but importantly, the structure enabled the passage of most species previously observed to accumulate downstream of the structure. Most significant was the ability of the fish lock to pass substantial numbers of small-bodied fish, which were previously not considered migratory, suggesting that these species should be considered when developing options to mitigate the effects of other dams and weirs throughout the Murray-Darling Basin. A significant finding of this study was the realisation that substantially more species and size classes of Australian native fish are migratory than previously thought. Subsequently, it is recommended that, when designing facilities to mitigate the effects of a dam or weir, the structure of the entire migratory community is considered when developing operating parameters. Various options for mitigating the effects of dams and weirs are discussed, but it was concluded that the construction of effective fishways would be the most appropriate means of restoring migration pathways to Australian native fish. A strategic approach for assessing and adaptively mitigating the effects of dams and weirs is presented and discussed.