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I investigated the genetic architecture underlying variation in embryonic developmental rate in rainbow trout ('Oncorhynchus mykiss ') and tested whether there was genetic covariation with age at maturation. Both dams and sires influence the hatching time of their progeny indicating that developmental rate is under significant genetic control. Genome scans with 127 microsatellite loci from all 29 linkage groups in two families detected four significant quantitative trait loci (QTL) for developmental rate. A QTL on linkage group RT-8 explained 23.8% of the phenotypic variation and supports results from previous studies. I found inconsistent support for the hypothesis that embryonic developmental rate is genetically coupled to age of maturation. Maturation background and the maturation schedule of sires did not have a consistent effect on progeny hatching times. However, alleles associated with faster developmental rate were found significantly more often in early maturing rather than typical/later maturing male ancestors from one family.

Three brook charr full sib families were genotyped for 133 microsatellite loci and two 'Clock' genes, resulting in the identification of 43 linkage groups, 35 of which contain two or more markers. While only twelve conserved homeologous linkage groups were identified between brook charr and rainbow trout and six between brook charr and Atlantic salmon, nearly all of the highly supported rainbow trout and Atlantic salmon homeologies were identified. QTL for time to hatch (TTH) were identified in genomic regions of brook charr showing homology to four of the five linkage groups in rainbow trout where QTL for TTH were identified. Additionally, several of the QTL for TTH have been identified in regions of the brook charr genome showing homology to rainbow trout and/or Arctic charr linkage groups associated with maturation timing and/or spawning time. The locations of putative candidate genes in relation to brook charr TTH QTL are discussed.

To identify quantitative trait loci (QTL) influencing early maturation (EM), body weight (BW) and condition factor (K) in rainbow trout (' Oncorhynchus mykiss'), a genome scan approach with 96 microsatellite loci across 29 linkage groups was utilized. The six inter-strain paternal half sib families used were derived from two strains that differ in the propensity for EM. Several significant QTL for EM localized to different regions in males and females, suggesting some sex-specific control. Some QTL for BW and K localized to regions identified in previous studies, as well as where candidate genes for these traits have been identified. QTL for multiple traits often co-localized, suggesting a level of genetic correlation. The highest prevalence of co-localization occurred between EM and BW. Linkage group RT-8, which has strong connections with developmental and early life history traits, had detected effects for all traits studied.

A genome scan, using microsatellite markers, was performed to detect quantitative trait loci for age at sexual maturation in two full-sib families of North American (NA) Atlantic salmon. Furthermore, linkage arrangements were compared between these NA fish and those found in the current European (EU) Atlantic salmon map. I found eleven QTL for age at maturity, as well as a rearrangement of the sex linkage region compared to EU fish. Four of the QTL were localized to two homeologous chromosomal segments. In addition, QTL were localized to linkage groups where similar effects were detected on the homologous linkage group regions in Arctic charr ('Salvelinus alpinus ') and rainbow trout ('Oncorhynchus mykiss'). The conservation of QTL effects across two other species of Salmonidae provide support for the identification of the QTL detected in Atlantic salmon, and suggest that certain regions of the salmonid genome retain ancestrally related syntenies with constrained functions.

A multiplex genotyping system was applied to Atlantic salmon (' Salmo salar') being reared by the Atlantic Salmon Broodstock Development Program in Chamcook, New Brunswick. Nine microsatellite loci were used to determine the parents of 98% of 305 progeny from the 1998 year-class reared in a sea cage. The genotyping system validated family identity of 299 fish, which had been initially identified by branding. The genotyping system was also able to discriminate among all but 5 of 79 families in the 1998 year-class when progeny genotypes were generated from genotypes of known parental pairs. In a second experiment, two quantitative trait loci for body weight were identified, using progeny from two full-sib families of the 1998 year-class. Out of 25 microsatellite loci tested, association between variation and body weight was detected at two of these microsatellite loci. The QTL explained between 9.6 and 14% of the variation in body weight.

Molecular markers can be used to scrutinize both pedigree and population genetic structure, providing important insights into phenotypic evolution and determination in natural populations. Here, microsatellite markers were used to investigate the determination of size, growth, and maturation traits in salmonid fishes. Two marker-assisted methodologies for estimating quantitative genetic parameters were compared in an aquaculture population of rainbow trout ('Oncorhynchus mykiss'). A regression-based model employing estimates of pairwise relatedness effectively detected significant components of genetic variance and covariance for size and spawning time traits. However, numerical estimates of parameters were unreliable. A Markov Chain Monte Carlo (MCMC) procedure to reconstruct families resulted in estimates that did not differ significantly from those obtained with known pedigree, and was therefore deemed the superior method. This method was then used to investigate constraints on the evolution of larger body size in two stunted populations (designated Lower and Upper) of brook charr ('Salvelinus fontinalis') from Freshwater River, Cape Race, Newfoundland, Canada. Population structure of the system was investigated using ecological and genetic methods. Over a 5-year period, mark-recapture data revealed limited movement, with the proportion of recaptured fish migrating from one population area to another being low (0-3.8%). Despite this, microsatellite analysis based on sixteen polymorphic loci provided no evidence of genetic differentiation. These results indicate that while gene flow occurs between the populations, they are relatively isolated on an ecological time frame. Selective and genetic constraints on the evolution of larger body size were investigated by measuring viability selection acting on length-at-age traits, and by estimating quantitative genetic parameters 'in situ' (following reconstruction of sibships using the MCMC procedure). In the Lower population, significant heritabilities were found for several traits, while selection was found to act on length-at-age traits in both populations. However selection does not in general favor larger adult size, and while such size selective mortality does operate on juveniles there is no evidence for a significant heritability of juvenile size in either population. Thus within each population, selection differentials and estimates of heritabilities for length-at-age traits, suggest that evolution of larger size is prevented by both selective and genetic constraints.

I searched for quantitative trait loci (QTL) affecting fitness traits in crosses between the Nauyuk Lake and Fraser River strains of Arctic charr ('Salvelinus alpinus'). A comparative mapping approach using microsatellite loci demonstrated that several chromosomal regions influencing upper thermal tolerance and body size have been conserved in Aredc charr based on previous work with rainbow trout ('Oncorhynchus mykiss'). Thus, genes underlying fitness QTL may antedate the divergence of these two species. QTL for condition factor and relative gonad size (gonadosomatic index) were also identified. In addition, pairs of homeologues (ancestrally duplicated chromosomal segments) have maintained similar functions in Arctic charr since the evolution of salmonids from a tetraploid ancestor 100-25MYA. However, co-occurrence of body size and thermal tolerance QTL on the same linkage group, and high phenotypic correlations between the two traits, suggest that associated genes control a more basic physiological function like metabolism.

I estimated the morphological and genetic differentiation among sympatric morphs of Arctic charr (Salvelinus alpinus) from five Icelandic lakes. Morphological variation was estimated by measuring fifteen characters while genetic differentiation was estimated by determining allele frequencies at five microsatellite loci. The sympatric morphs showed variable degrees of morphological differentiation. Sympatric morphs clustered together on a Neighbour Joining phenogram based on the frequencies of microsatellite alleles and shared some alleles not found in the charr from other lakes. This suggests that the morphs have diverged in their respective lakes. Furthermore, sympatric morphs from different lakes showed variable degrees of morphological and genetic differentiation. The degree of morphological and genetic differentiation was coupled across lakes, suggesting that morphological differences become more pronounced as reproductive isolation becomes established. These results suggest that resource polymorphism is a diversifying force in speciation.

MtDNA diversity in contemporary samples from eight populations of walleye from eastern Lake Huron was negatively associated with the relative amounts of anthropogenic impacts experienced by each. MtDNA diversity was also compared in contemporary and archival samples from two populations. In one instance, contemporary samples had reduced mtDNA diversity compared to archival samples collected before major exploitation. No such difference was detected between contemporary and archival samples from the second population where commercial exploitation and habitat alteration have been more limited. Low mtDNA diversity in artificially produced fish relative to parental sources suggests that culture programmes might be one mechanism lowering mtDNA diversity in populations. A phylogenetic comparison of walleye mtDNA haplotypes revealed that an analysis based on restriction fragment length polymorphisms in two amplified fragments surveyed 554bp and detected almost twice the number of mutations and haplotypes than did a sequence analysis of 513nt of the control region.