Growth retardation in King salmon Oncorhynchus tshawytscha (Walbaum) is a common and significant problem affecting marine farming operations in New Zealand. While the basic marine culture requirements for the King salmon species are well understood, the etiology of seawater adaptation and growth retardation remains understudied. Consequently, this study was established to investigate the physiological state and causative factors of growth retardation in collaboration with a leading New Zealand aquaculture company, New Zealand King Salmon Ltd (NZKS). Hypoosmoregulatory indicators are not currently used by marine farmers in New Zealand due to the belief that King salmon are more adaptable to seawater than their more highly cultured counterparts, Coho and Atlantic, and can be transferred to seawater anytime after a critical weight is achieved. This study sought to investigate changes in hypoosmoregulatory ability and its relation to water temperatures commonly used in the hatchery environment. This was determined by changes in the activity of the predominating seawater-adapting gill enzyme Na+/K+-ATPase, as an indirect measure of its abundance during smoltification. Changes in plasma ion profiles and the ability to regulate ions after abrupt transfer were also measured and compared with enzymatic activity throughout the austral springtime smoltification period in commercial strains of under-yearling King salmon. It was found that King salmon do undergo a distinct austral spring-time temporal increase in hypoosmoregulatory processes. This was characterised by a 2-fold increase Na+/K+-ATPase activity which was concomitant with reduced plasma Na+ in freshwater and following a seawater challenge in fish between fork lengths of 140-160 mm. Despite no consistent reduction in Na±/K+-ATPase activity during desmoltification, it was shown that the percent of ATP dependent activity specific to Na+/K+-ATPase diminished over time. Increased residual ATP dependent activity is hypothesised to be a result of apical H+-VATPase activity as a compensatory mechanism to rapidly normalise plasma Na+ during desmoltification concomitant with elevated basolateral Na+/K+-ATPase. Water temperature has been linked with the advancement and shortening of the smoltification period in several species. Gill Na+/K+-ATPase activity and hypoosmoregulatory ability in King salmon were negatively affected by increasing water temperatures above 12°C in contrast to a constant 12°C. The level of growth retardation was dependent on the time of transfer to seawater and was found to increase during a period of reducing hypoosmoregulatory ability. The transfer of growth retarded King salmon back to freshwater resulted in a complete reversal of the growth retarded state, comparable to that observed in Coho and Atlantic salmon. Growth retarded fish were able to readapt back to freshwater with higher survival and growth rates compared to the transfer of normal growing sub-adult King salmon, strongly demonstrating that growth retarded fish are more adapted to freshwater. Osmoregulatory physiology, and endocrinology during the transfer of growth retarded and normal growing fish were investigated. Overall, these results have fundamental implications for the aquaculture of King salmon that are able to be applied by industry to improve current husbandry practices.

For animals that live in a reasonably variable environment the capacity for learning and memory allow them to adapt to the changes they experience. Ecological factors that vary between habitats can affect a range of learning behaviours. Less attention has been directed at how this variation may affect memory processes, or how different ecological variables might interact when shaping cognition and behaviour. Therefore one aim of this thesis was to investigate how different ecological variables shape memory abilities and to test whether those same variables affect other related behaviours such as learning. In order to test this, I selected natural populations of a temperate freshwater fish, the three-spined stickleback (Gasterosteus aculeatus) from pond and river habitats that were proposed to differ in predation pressure, and assayed their learning, memory and other behavioural traits. Pond and river populations differed in their memory and orientation behaviour. An interaction between pond/river habitat and predation pressure affected learning rate, and a similar interaction affected temperament behaviours. Two further studies were conducted to address how captive rearing environments and typical handling procedures affect behaviour in different species. Rearing environment affected memory, but not learning or temperament behaviours in three-spined sticklebacks. Handling caused stress responses in three-spined sticklebacks, Panamanian bishops (Brachyraphis episcopi) and Rainbow trout (Oncorhynchus mykiss), but handling with a water filled scoop compared to a traditional dip-net decreased these responses in three-spined sticklebacks and Panamanian bishops, and also affected behaviour in Panamanian bishops. The results presented in this thesis suggest that ecological variables play a substantial role in shaping learning, memory and other behavioural traits in fish, and highlight the utility of behavioural assays in answering welfare-based questions.

Microhabitat use by cutthroat trout and macrohabitat use by both cutthroat and rainbow trout were studied i n the Green River below Flaming Gorge Dam during the winters of 1988 and 1989. Microhabitat parameters used by cutthroat trout, such as focal velocity, depth, and fish elevation, differed significantly in eddies, runs, and riffles. Mean focal velocities in runs were 0.79 body lengths/seconds (bl/s), in riffles 0.66 bl/s, and in eddies 0.24 bl/s. Cutthroat trout size also varied significantly with macrohabitat; larger fish were found in riffles. Macrohabitat use by cutthroat trout and rainbow trout differed significantly among species, macrohabitat types, and months. Both rainbow trout and cutthroat trout macrohabitat use shifted from lower velocity habitats during winter to faster velocity habitats in summer. Cutthroat trout and rainbow trout used macrohabitats at seasonally differing rates. Riffles were never selected in proportion to their abundance, especially during high winter discharges. Cutthroat trout implanted with radiotransmitters exhibited little movement during diel monitoring and did not change their occupation of macrohabitats.

Growth retardation in King salmon Oncorhynchus tshawytscha (Walbaum) is a common and significant problem affecting marine farming operations in New Zealand. While the basic marine culture requirements for the King salmon species are well understood, the etiology of seawater adaptation and growth retardation remains understudied. Consequently, this study was established to investigate the physiological state and causative factors of growth retardation in collaboration with a leading New Zealand aquaculture company, New Zealand King Salmon Ltd (NZKS). Hypoosmoregulatory indicators are not currently used by marine farmers in New Zealand due to the belief that King salmon are more adaptable to seawater than their more highly cultured counterparts, Coho and Atlantic, and can be transferred to seawater anytime after a critical weight is achieved. This study sought to investigate changes in hypoosmoregulatory ability and its relation to water temperatures commonly used in the hatchery environment. This was determined by changes in the activity of the predominating seawater-adapting gill enzyme Na+/K+-ATPase, as an indirect measure of its abundance during smoltification. Changes in plasma ion profiles and the ability to regulate ions after abrupt transfer were also measured and compared with enzymatic activity throughout the austral springtime smoltification period in commercial strains of under-yearling King salmon. It was found that King salmon do undergo a distinct austral spring-time temporal increase in hypoosmoregulatory processes. This was characterised by a 2-fold increase Na+/K+-ATPase activity which was concomitant with reduced plasma Na+ in freshwater and following a seawater challenge in fish between fork lengths of 140-160 mm. Despite no consistent reduction in Na±/K+-ATPase activity during desmoltification, it was shown that the percent of ATP dependent activity specific to Na+/K+-ATPase diminished over time. Increased residual ATP dependent activity is hypothesised to be a result of apical H+-VATPase activity as a compensatory mechanism to rapidly normalise plasma Na+ during desmoltification concomitant with elevated basolateral Na+/K+-ATPase. Water temperature has been linked with the advancement and shortening of the smoltification period in several species. Gill Na+/K+-ATPase activity and hypoosmoregulatory ability in King salmon were negatively affected by increasing water temperatures above 12°C in contrast to a constant 12°C. The level of growth retardation was dependent on the time of transfer to seawater and was found to increase during a period of reducing hypoosmoregulatory ability. The transfer of growth retarded King salmon back to freshwater resulted in a complete reversal of the growth retarded state, comparable to that observed in Coho and Atlantic salmon. Growth retarded fish were able to readapt back to freshwater with higher survival and growth rates compared to the transfer of normal growing sub-adult King salmon, strongly demonstrating that growth retarded fish are more adapted to freshwater. Osmoregulatory physiology, and endocrinology during the transfer of growth retarded and normal growing fish were investigated. Overall, these results have fundamental implications for the aquaculture of King salmon that are able to be applied by industry to improve current husbandry practices.

Memoria para optar al título profesional de Ingeniero Agrónomo / Dentro de la acuicultura chilena, una de las especies más relevantes es la trucha arcoíris (Oncorhynchus mykiss), ocupando actualmente el cuarto lugar en producción de de especies comerciales en Chile con un volumen de 94.717 toneladas, registrando un retorno de 606 millones de dólares el año 2015. Los estudios relacionados a la genética de este animal se centran en la búsqueda de genes asociados a rasgos de interés productivo y su aplicación para el mejoramiento de su cultivo. En la actualidad, un área especialmente importante es el desarrollo de dietas más amigables con el medio ambiente, que se enfocan en el remplazo de insumos como proteínas y aceites de origen animal por otros de origen vegetal.

Tesis para optar al Grado de Magíster en Ciencias de la Acuicultura / Se entregan los parámetros genéticos de heredabilidad, correlaciones genéticas, y ganancia genética estimados para peso alevín, peso smolt y peso cosecha de dos líneas, año par e impar, de salmón Coho (Oncorhynchus kisutch), a partir de seis y cuatro generaciones respectivamente, del programa de reproducción de un núcleo comercial, en Chiloé, Región de Los Lagos. Se estima el nivel de consanguinidad alcanzado para cada línea en las cinco generaciones. La metodología utilizada considera el desove de reproductores individualizados, la incubación de ovas y desarrollo inicial de alevines en unidades segregadas por cada familia generada, marcaje individual de ejemplares juveniles y crecimiento en comunidad, con muestreos periódicos de peso corporal. La metodología de evaluación para la estimación de los parámetros genéticos fue el ‘modelo animal’ y los softwares Pedigree Viewer y MTDFREML.

Memoria para optar al título Profesional de Ingeniero Agrónomo. Mención: Producción Animal / En el presente estudio se estimaron heredabilidades, correlaciones genéticas y fenotípicas para un stock de truchas arcoíris que muestran el rasgo doble ciclo reproductivo anual. Se evaluaron las variables de presencia de uno o dos desoves en el transcurso de un año (DCRA), el tiempo que pasa entre dos desoves en una misma hembra (longitud del ciclo reproductivo, LCR), los pesos de las hembras al primer desove, al marcaje, a los 380 y 625 días, las edades de las hembras en su primer y segundo desove. Todo esto con el objetivo de estudiar y comparar la conducta productiva y reproductiva de truchas arcoíris doblecicladoras y monocicladoras. Se trabajó con una población de trucha arcoíris (n = 1570), mantenida en piscícola Huililco Ltda. En la estimación de heredabilidades se utilizó un modelo mixto, el que fue resuelto utilizando el programa DFREML, mientras que en la estimación de las correlaciones genéticas se utilizó el programa MTDFREML. Además, se estimaron las correlaciones fenotípicas junto con la respuesta correlacionada a la selección para las variables de peso al seleccionar solo para LCR. Las heredabilidades obtenidas para presencia de DCRA y LCR fueron medias: 0,19 ± 0,10 y 0,28 ± 0,11, respectivamente; y superiores a lo que se espera para caracteres reproductivos. Esto es positivo, pues permite obtener respuesta a la selección para estos rasgos. Las heredabilidades para las distintas variables de peso y edad, fluctuaron dentro de lo esperado, entre 0,15 y 0,26, excepto para peso al marcaje que dio 0,93 ± 0,12, que puede estar sobreestimada por efectos del ambiente común en la fase de alevinaje. Las correlaciones genéticas y respuestas correlacionadas entre LCR y los pesos fueron positivas, indicando que a mayor LCR se observa un mayor peso. En general las truchas monocicladoras presentaron mayores pesos y edades al primer y segundo desove que las doblecicladoras. Sin embargo, no se observaron diferencias en el peso a los 625 días de edad, indicando que el fenómeno DCRA al parecer no disminuiría los pesos al momento de la cosecha. / In the present study heritabilities, genetic and phenotypic correlations for a rainbow trout stock that show the characteristic double annual reproductive cycle were estimated. Variables evaluated were presence of one or two spawns in the course of one year (DCRA), days between two spawn in the same female (length of the reproductive cycle, LRC), weights of females at first spawning, to tagging, to the 380 and 625 days, and ages of the females in their first and second spawning. The main objective was to study and compare the productive and reproductive behavior of the doublecycler and monocycler rainbow trout. We worked with a rainbow trout population (n = 1570), kept at Huililco Ltd. farm. In the heritability and genetic correlation estimations a mixed model using a derivative free algorithm of restricted maximum likelihood (DFREML) was used. In addition, phenotypic correlations were estimated with correlated response to selection for weight variables selecting only for LCR. Heritabilities obtained for the presence of DCRA and LRC were medium: 0.19 ± 0.10 and 0.28 ± 0.11, respectively, and higher than expected for reproductive characters. These estimations of heritabilities allow higher response to the selection for both traits. Heritabilities for the different age and weight variables fluctuate within the expected range between 0.15 and 0.26, except for weight marking that gave 0.93 ± 0.12, which could be due to common environmental effects in alevín stage. Genetic correlations between LRC and correlated responses and weights were positive, indicating that the higher LRC shows a greater weight. The trout monocycler generally had higher weights and ages at first and second spawning that doublecycler. However, no differences in weight at 625 days of age were observed, indicating that the phenomenon does not seem to diminish DCRA weights at the time of harvest.

There is an increasing scientific acceptance that fish may feel some sort of fear, pain and distress, which in turn feeds a growing concern for their welfare. Humans impact the wellbeing of a large number of fish in various ways, one of them being through research. Welfare legislation in the UK demand welfare considerations for all animals used in scientific procedures. Furthermore, welfare and enrichment needs for fish are included in the Appendix A of the European Convention for the Protection of Vertebrate Animals used for Experimental and Scientific Purposes. As fish are extensively used in research, changing their housing and husbandry to improve welfare is of importance, since fish kept in laboratories are most likely subjected to impoverished environments. Although enrichment programs have been shown to improve health and welfare in various animal species, little is known of their potential for application to juvenile rainbow trout. How best to improve barren experimental tanks for female juvenile rainbow trout used in regulatory research was the broad aim of this PhD. In this thesis, three enrichment strategies for rainbow trout have been examined, using physiological and behavioural welfare indicators. The first study assessed the effects of semitransparent shelters on trout welfare, and a clear message became evident; that shelters of this design should not be considered enrichment for rainbow trout as they had several significant negative impacts, indicating chronic stress in fish from shelter tanks relative to fish in a barren environment. The second study investigated impacts of reduced visual access to conspecifics in the same tank. Habitats with low visual contact between individuals have been suggested to reduce aggression for a range of species, and I have shown that visual barriers appeared to be beneficial to trout as well. The final experiment evaluated effects of high and low water currents on the wellbeing of rainbow trout, and results indicated increased fish welfare when water currents were supplied.

Feeding ecology of organisms has a critical influence on ecosystem structure, function, and stability, but how feeding ecology of a single organism varies over multiple spatial and temporal scales in nature is unknown. Here, I characterize the factors driving and the implications of variability in feeding ecology of juvenile Chinook Salmon (Oncorhynchus tshawytscha) over multiple spatial and temporal scales using stable isotopes and stomach contents. Significant variation in juvenile Chinook salmon feeding ecology at the individual-level was found to occur off of the west coast of Vancouver Island (WCVI) (British Columbia, Canada). This variation is correlated with a diet shift from feeding on invertebrates to feeding on fish, as the salmon increase in size. I developed a novel Bayesian stable isotope method to model this shift while taking into account the time-lag associated with isotopic turnover. I found that this model was able to replicate patterns seen in a simplified coastal food web, and that resource-use estimates from this stable isotope model somewhat diverged from a compilation of stomach content data. Next, I compared the feeding ecology of Chinook Salmon in one season and year along nearly their entire North American range. I found considerable spatial variation in ontogeny and feeding ecology, with individuals of the same size from different geographic regions having different δ13C, δ15N, and trophic levels. These differences likely corresponded to regional variability in sea surface temperature, ocean entry date and size, and growth rates. Subsequently, I quantified temporal shifts in the feeding ecology of Chinook Salmon from WCVI. I found that feeding ecology over winter was different from feeding ecology in the fall, and that this likely corresponds to shifts in the prey field. Finally, I found that WCVI juvenile Chinook Salmon showed significant interannual variability in feeding ecology, and that the interannual variability in the δ13C value of juvenile salmon (indicative of primary productivity or nutrient source) predicts their smolt survival. In turn, large-scale climate variability determines the δ13C values of salmon—thus mechanistically linking climate to survival through feeding ecology. These results suggest that qualities propagated upwards from the base of the food chain have a cascading influence that is detectable in salmon feeding ecology. I conclude that the feeding ecology of juvenile Chinook Salmon varies on individual, spatial, season and interannual scales, and that this variability has impacts on survival rates. These findings have implications for the understanding of ontogeny in natural systems in general, allowing for modelling of ontogeny in previously intractable ecological systems. Furthermore there may also be implications for Chinook Salmon management, considering that feeding ecology showed utility as a mechanistic leading indicator of survival rates. / Graduate

The inter-tissue metabolic responses to hypoxia were determined in lungfish (Protopterus aethiopicus), and trout (Salmo gairdneri). Lungfish respond to hypoxia with a reduction in metabolic rate. It was intended to determine which tissue, or tissues exhibit decreased metabolic rates during hypoxia, and then compare the results with the metabolic reactions observed in trout, which are not reported to reduce metabolic rate during hypoxia. The metabolic potentials of the heart, brain, white muscle and liver in the African lungfish were estimated using enzymatic data. Metabolic effects of a 12 hr submergence were monitored using metabolite measurements. Heart was the most oxidative tissue, but also showed the greatest anaerobic potential. The brain displayed relatively low oxidative capabilities. White muscle remained almost inert. Although high energy phosphate concentrations in brain and heart did not fall during submergence, glycolysis was activated as indicated by cross-over plots, depletion of endogenous glycogen stores, and lactate accumulation. Blood-tissue lactate and glucose gradients indicated (1) that the heart and brain released lactate throughout submergence, (2) that after 12 hr of submersion the brain and heart were probably obtaining all their required glucose from the blood (3) that the liver released glucose throughout submergence, and (4) the white muscle was metabolically isolated from the rest of the body during submergence. The lack of measurable changes in white muscle metabolite concentrations coupled with the low enzyme activities leads to the suggestion that the most significant adaptation to hypoxia in these fishes may not be the capacity for increased anaerobic energy production. Instead, it is likely that the ability of the muscle to prevent the activation of glycolysis during hypoxic dysoxia is the key to the animal's survival. Histochemical and ultrastructural studies were done on the axial musculature of the lungfish. The small wedge of red coloured muscle evident upon gross examination was shown by histochemical demonstrations of lactate and succinate dehydrogenases, of adenosine triphosphatases, and of lipid to be composed of a mosaic of red and intermediate fibres. Respectively, these fibres measured 23.6 and 34.3 microns in average diameter. The bulk of the myotome is composed of white fibres having an average diameter of 67.3 microns. Mitochondrial density, capillarity and lipid content were very low for all fibres. These data suggest that the axial musculature is geared primarily for anaerobic function. The relatively large percentage of white muscle indicates that the overall metabolic rate of the axial muscle is low. The capacity of the muscle to exist with a reduced rate of ATP turnover (as was suggested above) may be related to the large proportion of white fibres present in the myotome. Tissue metabolites were measured in a hypoxia sensitive organism, the Rainbow trout (Salmo qairdneri), before and after exposure for 3 hr to inspired oxygen tensions of 20 torr (at 4°C). There were small changes in the brain but the energy status was maintained. The red muscle was the least affected. White muscle creatine phosphate was depleted. Various data indicate that the white muscle is the major user of glycolytic substrates and the major producer of lactate. The heart is stressed as indicated by a decline in glycogen, ATP, CrP, and the total adenylate pool. The liver exhibited declines in every indicator of metabolic homeostasis. The liver concentrations of glycogen did not decline. The fact that anaerobic glycolysis has been activated in the white muscle, while the muscle remains in metabolic communication with the other tissues via the blood, supports the suggestion that the metabolism of the white muscle will have a pronounced effect on the metabolic status of the whole animal. The trout is maintaining its rate of oxygen uptake while activating anaerobic glycolysis in the attempt to maintain 'normal' rates of energy utilization. The turnover rates of glucose and lactate were measured in trout subjected to the same hypoxic stress as above. Glucose turnover did not change while lactate turnover increased from 2.8 ± 0.4 µmoles/min./kg to 20.6 ± 6.8 µmoles/min./kg. The lack of increase in glucose turnover was attributed to the observation that liver glycogen concentrations do not change and so there is no increase in glucose flux. The increase in lactate turnover emphasizes the fact that anaerobic glycolysis is activated and that some tissues are oxidizing lactate. The problem of when a cell becomes hypoxic and the reactions of the cell to that stress is addressed. The cell (tissue, organ, animal) has two options if oxygen supply drops to a level which prevents oxidative metabolism from supplying all of the requirements for ATP synthesis. The cell may exhibit a decline in requirements, in which case the rate of ATP production need not be as high as in the oxidative state or, conversely, anaerobic energy production may increase in the attempt to maintain ATP production rates. The lungfish muscle appears to be capable of the former, thus preserving substrates for other tissues and reducing the rate of end-product formation. The trout white muscle, on the other hand, exerts a major influence upon the other tissues when the animal is stressed with hypoxia. The term 'energy conformer' is applied to animals which do not maintain oxygen uptake in the face of a declining supply, and which allow ATP production to decline concomittantly by not activating glycolysis to a marked degree. An energy regulator would activate glycolysis in the attempt to maintain oxidative rates of ATP production. The trout is more of an energy regulator than is the lungfish with the main difference in this capacity being in the white muscle. / Science, Faculty of / Zoology, Department of / Graduate