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The links between hydrology, hydrochemistry and salmonid ecology were examined in an interdisciplinary study of the effects of hyporheic water quality on the survival and the development of salmonid ova. Three catchments located in the northeast of Scotland were examined. Work focussed on the Newmills Burn, a degraded agricultural catchment. Complementary studies were also undertaken on the Pow Burn, a comparative agricultural catchment, and the Girnock Burn, a contrasting semi-pristine upland catchment. The relative importance of sediment transport, groundwater-surface water (GW-SW) interactions and hydrochemistry, for the survival and development of salmonid ova, was assessed between spawning in autumn, and hatch in spring. Hydrochemical, hydrometric, isotopic and modelling techniques were applied to the problem in an evolving, serial approach to investigation. The infiltration of fine sediment to the streambed was not sufficient to explain observed fine scale spatial variability (<1m), nor complex spatial patterns of sub-surface hydrochemical change. Hydrochemical and piezometric data indicated that the observed spatial and temporal patterns could be explained by variable contributions of chemically reduced groundwater to the hyporheic zone. At the catchment scale, gross differences in land-use and channel characteristics substantially affected GW-SW interactions and consequently in-redd water quality. At the reach scale, local GW-SW interactions were controlled by geomorphology and riparian sedimentary stratigraphy. At the scale of individual redds, the influence of groundwater generally increased with depth into the hyporheic zone. Dissolved oxygen (DO) levels were implicated as the dominant control on in-redd mortality. Embryo survival and development correlated with mean DO concentrations. Mortality rates from samplers located within artificial redds ranged from 0-100% and showed a significant inverse relationship with mean DO concentrations (r2 = 0.85, P < 0.01). Where embryos survived, low DO affected rates of development. Embryos exposed to low DO concentrations retained a higher portion of the yolk sac mass near to hatch than those developing in more favourable conditions.

I examined the genetic architecture and evolutionary significance of the considerable morphological and life history variation in Arctic charr (Salvelinus alpinus) from natural and cultured populations in Iceland. I found that the sex determining locus in Icelandic Arctic charr is located on a different linkage group relative to the majority of the Atlantic lineage Arctic charr, including populations from the Fraser River in Labrador Canada and Swedish and Norwegian strains. In addition, there may be a possible conservation of a sex linkage arrangement in Icelandic Arctic charr and Atlantic salmon. These observations suggest that the differentiation of the sex determination chromosome in salmonids is still in the early stages. I then tested hypotheses regarding the genetic architecture of wild and cultured populations of Icelandic Arctic charr identifying the number and effect size of quantitative trait loci (QTL) and their conservation within and across salmonid species. QTL with genome-wide significance for body size, condition factor and age of maturation in cultured fish from the Icelandic breeding program were detected on multiple linkage groups. Comparisons with a North American cultured strain of Arctic charr and North American populations of Atlantic salmon and rainbow trout revealed some conservation in QTL. Additionally, I compared the genetic architecture of fork lengths in juvenile wild and cultured populations and found moderate conservation of genomic regions among Icelandic populations. I compared linear measurements taken on the cleared and stained heads of benthic and limnetic morphs from two lake populations expressing varying degrees of divergence. I found high genetic variation for craniofacial morphology in all morphs with no significant difference of plasticity levels between them. However, stronger family effects and weaker morph effects in the less derived lake population suggest higher genetic variation for craniofacial traits compared to the more derived system. Overall QTL (suggestive and significant) number and effect size was similar but the morphs hypothesized to be more derived within each lake had about half the number of significant QTL (p<0.01) compared to their sympatric counterpart, suggesting fixation of alleles through canalization.

This research programme aimed to review the nutritional requirements for the main minerals, (namely calcium, phosphorus, magnesium and zinc) formulated in commercial diets that are essential for the health and growth performance for salmonid fish. This was undertaken with the aim of improving our knowledge of their physiology, metabolism and fate in the rainbow trout, Oncorhynchus mykiss. Phosphorous (P) featured strongly in this work due to its adverse role in pollution and the environmental impact of intensive fish farming. The first chapter surveyed the gross nutritional requirements of fish and focused on the mineral requirements in particular. Typically the P requirements for trout were found to range from 0.5-0.8% of the diet. The problems of P loading as a consequence of dietary loses was addressed and the physiological and metabolic roles of both calcium and phosphorous were especially noted in relation to fish health and for phosphorous its environmental implications were addressed. Experimental approaches were evaluated and it was decided to conduct both standard growth trial studies as well as digestibility trials to provide the basis of most investigations with the rainbow trout. Novel approaches and strategies were used in relation to specific experiments such as examining the mineral levels in blood, and various tissues and the testing of different feed ingredients, dietary supplements and mineral sources in successive investigations. Initial investigations appraised commercial diets of varying nutritional profile with respect to mineral retention and availability for rainbow trout under controlled laboratory conditions. The effects of diets containing different fishmeal sources: i.e. brown versus white fishmeals, elevated ash content and also varying in the levels of oil were tested on juvenile rainbow trout in closed recirculated systems. Diet composition caused a significant effect on mineral retention and distribution profile in fish tissues and organs. Typically, both P and Ca were of highest concentration in vertebrae of trout (60mg/g-dry weight), compared with P concentrations for all other major organs/tissues, which were fairly even between 11-20mg/g. A small increase in dietary P level (1.08% vs. 1.22%) did not affect any growth parameters for trout for the first two commercial feeds tested but there were interesting observations with respect to the amount of P excreted in the bile with a 25% increase from 0.8mM to 1.2mM. The P levels in plasma of these fish did not reflect any dietary changes. However, there was a noticeable reduction in the digestibility of P in the diet containing the white fishmeal source (26%) compared with 49% for the higher grade fishmeal diet. High ash content feeds resulted in a marked reduction in the net mineral retention of this element (16% compared to 27% for the lower ash diet). The same was also true for Ca (12% compared with 26%). The effect of oil levels in diets on mineral utilization was investigated under farmed conditions and was of particular interest given the demand for nutrient dense feeds in the industry. There was a strong tendency for improved P and Ca digestibility coefficients at each incremental increase in oil level for juvenile production sized fish (50-l00g). This ranged from 55% to over 70% when oil levels were over 26%. However this was not observed for larger fish of over 200g in weight. Experimental investigations followed are described in (Chapter 4) where fishmeal based diet was supplemented with varying levels of inorganic phosphorous. Phosphorous, calcium and other mineral absorption characteristics in addition to retention were measured in a series of growth and digestibility trials. Interestingly, there was no apparent change in the distribution of P with increasing dietary levels ranging from 1.39-2.16%. These were above known requirements for these fish with minerals being in excess. Similar results were noted for all other minerals measured in rainbow trout. There was a significant rise in the P concentration of plasma of rainbow trout fed a diet containing over 2% P and this may infer that the homeostatic regulation of P is unable to function at this level. Other haemato-logical parameters were not affected. Although not significant, there appeared to be slight trend in elevated bile P with increasing dietary P supplementation. The faecal concentrations for each of the minerals showed that elevated P in fish meal diets led to increased faecal output from 25mg/g to over 40mg/g for the highest P diet. Overall digestibility coefficients were lower as dietary P increased above that in the fishmeal control diet. These ranged from 50% to 39% for P, Ca and Mg were not greatly affected. The net retention of P was calculated and this fell from 30% to just below 20% for the range of dietary P used in the investigation. A preliminary study, reported in chapter 5A, was useful in providing information about the relative absorption profiles for differential mineral absorption from the various regions of the gastro intestinal tract of rainbow trout. A standard commercial diet was fed to large trout (&gt;200g) and subsequently, digesta was removed from fish and analysed. For all minerals and protein, the pyloric and mid intestinal region was the main site for digestion, release and absorption of the macro elements concerned. The protein and mineral digestibility of suitable feedstuffs commonly employed in the formulation of complete diets for trout resulting from a sequence of experimental trials are presented in chapter 5B. These included a selection of marine, animal and plant by-products which were substituted into a reference basal diet designed for salmonids. This involved the inert marker- yttrium oxide and calculations based on nutrient digestibility from diet and faecal concentrations. Mineral digestibility coefficients were found to vary considerably and a number of anomalies such as negative values were obtained for Ca and Zn in certain feedstuffs. Combined diets (reference and test ingredient) gave values that were more consistent and P digestibility ranged from 47-59% in marine and animal protein concentrates compared with plant sources (24-37%). Negative values for Ca and Zn were thought to be attributable to complex interactions with other feed components. Additionally, a group of inorganic mineral supplements were tested by inclusion into a series of diets. These included mono calcium phosphate, di-calcium phosphate (DCP), mono di-calcium phosphate and magnesium phosphate. DCP produced lower Ca and P digestibility values, 31 and 50% respectively, compared with the other sources (44-62%), indicating the importance of choice of mineral supplement in aquafeeds. A critical appraisal of this work is provided in Chapter 6 and formed a retrospective review of the results generated and integrated these findings into a foundation for further research and development. Nutritional investigations using the rainbow trout as the model salmonid species raised many more questions and possibilities and broadened the scope of the topic. The subject of mineral requirements for fish is very complex and numerous factors are involved at several physiological and biochemical levels in fish. Although the research on rainbow trout involved whole animal studies under both laboratory and commercial farm conditions, the need to explore alternative in vitro methods and to utilize larger scale farm and sea cage trials for salmon were suggested. The advent of more advanced diet formulations and feeding strategies were mentioned and the scope for more scientific investigations to improve the utilization and reduce phosphorous discharge into the environment proposed.

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Renibacterium salmoninarum, the etiological agent of bacterial kidney disease (BKD) of salmonid fish, is a pathogen of great concern among fisheries and the aquaculture industry worldwide. Previous investigations have indicated the pathogenesis of BKD is complex. It is a chronic, multisystemic, granulomatous disease with a number of potential immunomodulatory effects on the host. Given the current limitations for treatment and control of BKD, it is imperative that the pursuit of development of methods of prevention, namely management strategies and vaccination, be continued. To do so, the immunology of BKD must be elucidated in order to better understand and manipulate the associated immune responses to our advantage. This dissertation is composed of four chapters which relate to BKD and the associated immune responses of three species of susceptible salmonid fish as follows: Exogenous stress factors, through stress-induced immunosuppression, have been shown to influence BKD development in cultured salmonids. Chapter 1 examines the effects of two environmental stressors common to fish culture, overcrowding and overfeeding, as they affect BKD development and R. salmoninarumantigen prevalence among juvenile chinook salmon (Oncorhynchus tshawytscha) Immunomodulatory interaction between pathogen and host in BKD is widely reported and merits further investigation. Particularly, the immunological parameters affected and the role of the extracellular protein (ECP) of R. salmoninarum are of interest. Chapter 2 examines the in vivo immune response of rainbow trout (Oncorhynchus mykiss) following exposure to the ECP in terms of both humoral and cell-mediated immunological parameters, including the immune response against another bacterial pathogen. Chapter 3 addresses the in vitro effects of the ECP upon specific splenic immunocyte functions, phagocytosis and respiratory burst activity, in brook trout (Salvelinus fontinalis). The immune-complex mediated hypersensitivity reported to occur with BKD has considerable ramifications for control measures involving immunostimulation via antigen exposure. Further investigation is warranted to discern the significance and consistency of immunological hypersensivity in BKD pathogenesis. Chapter 4 examines the renal lesions, including immunopathologic changes and indications of immune-mediated disease, of brook trout exposed to R. salmoninarum. / Ph. D.

River flow regime is fundamental in determining lotic fish communities and populations, and especially of salmonid fishes. Quantifying the effects of human induced flow alteration on salmonids is a key question for conservation and water resources management. While qualitative responses to flow alteration are well characterised, a more intractable problem is quantifying responses in a way that is practical for environmental management. Using data drawn from the Environment Agency national database, I fitted generalised linear mixed models (GLMMs) using Bayesian inference to quantify the response of salmonid populations to the effects of impounding rivers, flow loss from rivers due to water abstraction, and the mitigating effects of flow restoration. I showed that in upland rivers downstream of impounded lakes, the magnitude of antecedent summer low flows had an important effect on the late summer abundance of 0+ salmonids Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). In contrast, the abundance of 1+ salmon and brown trout appeared to be largely unresponsive to the same flows. I demonstrated that short-term flow cessation had a negative impact on the abundance of 1+ brown trout in the following spring, but that recovery was rapid with negligible longer-term consequences. I further established that flow restoration in upland streams impacted by water abstraction provided limited short-term benefits to salmonid abundance when compared with changes at control locations. However, while benefits to salmonid abundance were limited, I detected important benefits to the mean growth rates of 0+ and 1+ brown trout from flow restoration. I discuss the implications of my findings for salmonid management and conservation and propose a more evidence-based approach to fishery management based on robust quantitative evidence derived using appropriate statistical models. The current approach to flow management for salmonids requires revision and I recommend an alternative approach based on quantitative evidence.

Conventional fish monitoring requires considerable investments of equipment and labour, and often harmful and potentially fatal techniques. Emerging methods allow detection of aquatic animals by collecting water and extracting DNA that has been shed to the environment (eDNA). Present knowledge gaps in the field include minimum densities necessary for consistent detection, and persistence of eDNA after a target species has left a site. I conducted three experiments at a salmon hatchery in British Columbia to address these knowledge gaps. Water samples were taken from flow-through tanks with juvenile Coho Salmon densities ranging from 38.0g/1000L to 0.6g/1000L. To simulate field surveys in recently abandoned habitats, I sampled water from tanks after removing fish, at flow-through volumes ranging from 20,000L to 1,000,000L. Post removal sampling occurred starting at one hour and ending after just over four days of flow-through time. Water samples from tanks containing one or more fish tested positive for Coho DNA at least 70% of the time, increasing at higher densities. Samples taken after removing the fish had detection probability of 75% at flow-through volume of 40,000L. Detection failed at flow-through volumes greater than 80,000L. In stream samples, all sites with Coho or salmonid presence confirmed by conventional trapping also tested positive for target species’ eDNA. Two sites tested positive for Coho eDNA where conventional methods failed, indicating a possible higher sensitivity of eDNA sampling. I also mapped the distribution of juvenile Coho Salmon through multiple tributaries of a productive salmon system with conventional and eDNA detections. This study improves on an emerging method with a new species by addressing existing uncertainties regarding eDNA detection threshold, and signal persistence through dilution in a simulated stream pool habitat. It also demonstrates that eDNA methods can be used to assess coastal streams for presence of juvenile and resident salmonid fishes. / Graduate

I examined the relationship between landscape attributes and population differentiation among lake trout (Salvelinus namaycush) populations inhabiting a hierarchically structured dendritic freshwater system in northern Labrador, the Kogaluk River system. Samples were collected from a total of 10 lakes which differed in size, elevation, level of connectivity, and position within the system. STRUCTURE analysis provided evidence of significant population structure within the system likely attributed to a varying degree of asymmetric gene flow. Gene flow estimates were generally low and appear to be influenced by the presence of waterfalls as well as geographic distance. Isolation by distance tests coupled with decomposed pairwise regression analysis suggest a significant influence of geographic distance on population differentiation. Mantel testing also showed that population differentiation is significantly correlated with the position of waterfalls. Estimates of effective population size reveal significantly smaller population sizes in headwater lakes, a pattern not attributed to lake size.