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The molecular basis for heritable variation in quantitative traits is poorly understood in most species of fish. This is the case even for salmonids such as the Atlantic salmon <i>(Salmo salar </i>L.), one the most intensively studied and economically important aquaculture species. Quantitative genetic studies tell us that traits such as growth, development and morphology are likely to be controlled by a large number of genes, but to date there have only been two loci, the allozyme loci <i>MEP-2* </i>and <i>TRP-2</i>*, which have been shown to consistently influence the salmon phenotype. This thesis sets out to increase understanding of the molecular basis of phenotypic variation in growth performance, development and morphology in the Atlantic salmon. Experiments were performed to look for associations of phenotypic variation with genotypic variation at the molecular level and, thereby, to identify molecular markers linked to regions of the salmon genome containing genes influencing these quantitative traits. This was achieved by analysing phenotypic performance in two F2 backcross families derived from crosses of two outbred wild salmon populations, one from Scotland and one from Canada, which are divergent with respect to growth, development and morphology. The study began with an examination of the relationship between growth prior to first-feeding, utilising endogenous energy supplies, and growth post first-feeding, utilising exogenous energy supplies. The study then focused on growth, development and morphology in individually fish post first-feeding.

The nature of intraspecific biodiversity in the Atlantic salmon was examined, more particularly the issues related to mating between non-natives and natives, and the genetic basis of complex traits, which could be important to aquaculture. These issues were examined in parental, F₁, BC₁ and F₂ crosses between extremely genetically differentiated populations, i.e. a non-anadromous Canadian and anadromous Scottish populations, and the experiments were carried out in a hatchery. Outbreeding depression, which is defined as the reduction in the offspring fitness caused by the mating of unrelated individuals, was measured directly in relation to survival and indirectly through traits associated with early growth and development in parental, F₁ and BC₁ cross types.  The genetic basis of smolification, seawater tolerance and resistance to PKD was investigated in F₂ families. Reduced survival, which was asymmetrical in the BC₁, was observed in the F₁ and BC₁ cross types, with offspring from one backcross being unviable, whilst viable offspring were obtained from the reciprocal backcross.  Growth and development patterns were altered in the F₁ and BC₁ compared to the parental controls, and could be explained by both maternal and additive effects. QTL analysis revealed a number of markers associated with the various phenotypic traits related to smolification, seawater survival and PKD resistance, suggesting polygenic control. Reduced survival and altered growth and developmental patterns in the hybrids could be expected to lead to even more severe outbreeding depression in a selective environment.  However, there was also indirect evidence for outbreeding depression in relation to seawater survival and PKD resistance.

Very little is currently known about how gender is established in Atlantic salmon, and environmental and commercial matters have increased interest in the life history strategies of this ancient fish. It is necessary to assess the sex ratios in populations of Atlantic salmon both before they head out to oceanic feeding grounds and when they return to spawn, before we can begin to understand the mechanisms that govern gender in this species. Much of the challenge faced by those studying gender in the Atlantic salmon lies in the problem of sexing juvenile salmon. It is currently not possible to sex Atlantic salmon without the need to sacrifice the individual. The principle aim of this project was to establish such a method. To this end, several approaches were taken to attempt to develop a non-destructive method of sexing juvenile salmon. The first comprises a PCR-based test to assess whether the Sox9a gene, known to be involved in vertebrate sex determination, is gender-specific in Atlantic salmon. The second strand of work involved the use of genetic markers identified as gender-specific in Pacific salmon to reveal whether any of these sequences segregated with gender in Atlantic salmon. In the final part of the study, a suppressive subtractive hybridisation technique was used to compare male and female Atlantic salmon cDNA, and isolate sequences unique to each. Results from the Sox9a study showed that the Sox9a gene is present in both males and females, and therefore not gender-specific in Atlantic salmon. One of the sequences identified from Pacific salmon showed female-specificity in one of the three strains of Atlantic salmon tested. The suppressive subtractive hybridisation technique successfully yielded two populations of differential sequences from male and female cDNA. The work done in this study thus partially achieved the aim of establishing a non-destructive gender test and lays the foundations of further work exploring gender in Atlantic salmon.

Atlantic salmon is protected under national and European legislation but most populations are declining. The research investigated population size, habitat quality, population structure and stability over time using Atlantic salmon parr in the River Frome (a chalk stream in Dorset, England) surveyed at 15 sites, in summer and autumn over three consecutive years. The hypotheses were: * Abundance of juvenile Atlantic salmon in a chalk stream is related to habitat quality. * There is significant genetic differentiation between Atlantic salmon within one river, despite small geographic distance between sites and no barriers to migration. * Temporal stability of spatial population structure of Atlantic salmon occurs within a river. Habitat quality, assessed using HABSCORE, varied between sites and over time. Habitat quality was not a predictor of juvenile density but presence of adult brown trout reduced juvenile numbers. DNA for molecular analysis was extracted from fin-clips (removed non-lethally) and genetic variation and distribution of genetic variation was assessed using 5 microsatellites. Relatedness tests indicated that some 0+ parr within a site were closely related. It was inferred that 1+ parr had moved from their natal site, as they could not be assigned to a site of origin. Moderate heterozygosity was detected at each sample site. Low, but significant, genetic differentiation over all sites was detected in summer and autumn for three consecutive years. Isolation by distance was detected at two out of the six sample times, despite small distances between sites. This was strong evidence for structuring within the population. Using a new statistical test, no temporal stability of spatial population structure was detected in the River Frome, but significant temporal stability was detected using published data for Atlantic salmon in a Canadian river.

This study examines the dynamics of the Atlantic salmon (Salmo salar L.) population of the Foyle catchment in Ireland, through the analysis of long-term datasets and extensive field data. In chapter 1 the current conservation status of the salmon is discussed with particular reference to the Foyle. Chapter 2 considers the interaction between commercial netting and recreational sport angling and the effect of total combined exploitation on an independent measure of population size (redd counts) using a 49 year dataset. The evidence suggests that year class strength is the principal modulator of variation in commercial catches, sport angling catches and spawning escapement. Chapter 3 examines the role of density-dependence in the Foyle salmon population. A Ricker density-dependent model showed that spawning adult population size significantly predicted variation in the resultant filial generation; however, a significant amount of variation (ca. 68%) remained unexplained. Environmental factors were significant in explaining some of the remaining variance and these influences were linked to specific life stages. Chapter 4 investigates the effect of marine climatic conditions in the North Atlantic on the abundance of returning migrant Atlantic salmon, using a 126 year dataset of commercial catches and an index of climate in the northern hemisphere, the North Atlantic Oscillation (NAOI). The NAOI when below 0.151 explained a significant proportion of variation in five year running mean catches of migrant Atlantic salmon returning to the River Foyle. This indicates that a significant proportion of the variance in population size in the past was the result of variability in conditions in the marine environment. However, when the NAOI was above 0.151 this relationship uncoupled. Chapter 5 tests the capacity of local instream and broadscale catchment characteristics to predict 0+ salmon abundance within the Foyle area. This chapter also highlighted the potential detrimental impact of increasing urbanisation on the salmon stocks of the Foyle area.

Whole salmon scales were analysed using inductively coupled plasma mass spectrometry (ICP-MS) to test for differences in elemental compositions between salmon stocks. The investigation was structured to address stock variation based on fish origin (wild or farmed), farm populations, river origin of wild fish and sea fishery origin (Farces or Greenland). Initial studies were conducted to determine optimal analytical methods and to quantify the effects of fish size, sex, age and interannual variability on trace element composition within a single stock. Although a large number of trace elements were measured in fish scales, only a small number were found to be important predictor elements. The trace element composition of scale samples from wild and farmed fish enabled identification of origin (wild/farmed) to a high degree of accuracy (98 %), with Mn found in significantly higher concentrations in farmed fish and identified as the most influential element. Farmed fish taken from six sites around the west coast of Scotland were also correctly classified with a surprisingly high accuracy using discriminant analysis (87 %). The ability to discriminate between wild stocks was tested using scales from returning fish caught in 12 rivers from around Scotland. Overall classification success was 59 %, but this was found to depend on sample sizes, with elimination of samples comprised of small numbers of individuals improving the classification success to 90 %. The elements showing the highest predictive power differ according to the origin of fish, Mn carries most weight distinguishing farmed from wild fish, Ba, Mn, Zn, Co, Li, Ni and V are important in distinguishing between farms, Li, Sr and Ba strongly influence classification of wild wish and U was found to be the most important predictor element separating out samples recovered from the Farces and West Greenland fisheries. It is suggested that differences in Li and Ba i Abstract contents in scales reflect natural differences in river or catchment water chemistry, Zn, Ni, Co and V are likely to reflect differences in anthropogenic loading within industrialised settings and the high levels of Mn found in farmed fish scales predominantly reflects dietary uptake from supplementation of feed.

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