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.

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.

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

Salmonids are a diverse group of fishes whose common ancestor experienced an evolutionarily important whole genome duplication (WGD) event approximately 90 MYA. This event has shaped the evolutionary trajectory of salmonids, and may have contributed to a proliferation of the repeated DNA sequences known as transposable elements (TEs). In this work I characterized repeated DNA in five salmonid genomes. I found that over half of the DNA within each of these genomes was derived from repeats, a value which is amongst the highest of all vertebrates. I investigated repeats of the most abundant TE superfamily, Tc1-Mariner, and found that large proliferative bursts of this element occurred shortly after the WGD and continued during salmonid speciation, where they have produced dramatic differences in TE content among extant salmonid lineages. This work provides important resources for future studies of salmonids, and advances the understanding of two important evolutionary forces: TEs and WGDs. / Graduate / 2019-04-19

Aquatic ecosystems continue to be increasingly affected by climate warming. For salmonids in the Pacific Northwest of North America, increasing temperatures pose tighter thermal constraints on their habitat use as well as aspects of their individual performance, such as disease resistance. This thesis examines the effect of temperature on the phenology of the Ceratomyxa shasta life cycle, the effect of thermal refugia on disease risk in juvenile salmonids in the Klamath River, CA, and the spatial and temporal distribution of C. shasta in the Willamette River, OR. We developed a biological model that predicts an acceleration of the C. shasta life cycle development due to climate shifts in the Klamath River, resulting in more generations per year and earlier seasonal parasite occurrence. We showed that in early summer the Beaver Creek-Klamath River confluence provides juvenile Chinook and coho salmon an area of lower parasite doses and cooler temperatures than the main stem, thus lessening disease risk. By accelerating the development of C. shasta in its hosts, increasing temperatures will result in earlier parasite transmission to juvenile salmonids and a longer season of infectivity. These fish may find disease refuge at cold tributary inflows to the main stem of the Klamath River in early summer, further adding to the benefit of these important thermal habitats. To determine if similar disease patterns occur in other rivers with the parasite, we described spatial and temporal occurrence of C. shasta in the Willamette River. By collecting weekly water sampling at four sites over 28 months we characterize seasonal and annual differences of parasite abundance, which varies with weekly temperature. We also collected samples along the length of the main stem and its tributaries and identified spatial differences in C. shasta spore densities. Identification of spatial and temporal variation of C. shasta in the Willamette River provides a foundation for understanding future patterns of disease occurrence in this river where conservation of anadromous fisheries is also of concern. This thesis identifies likely responses of C. shasta to climate warming in the Klamath River, with useful application to other rivers in the Pacific Northwest. / Graduation date: 2013