Date of Award

Fall 2014

Degree Type


Degree Name

Doctor of Philosophy (PhD)


Biological Science

First Advisor

Krista M. Nichols

Committee Chair

Krista M. Nichols

Committee Member 1

Richard D. Howard

Committee Member 2

Esteban Fernandez-Juricic

Committee Member 3

Greg J. Hunt


Individual differences in behavior can have potential fitness consequences and often reflect underlying genetic variation. My research focuses on three objectives related to individual level variation: 1) evaluating the innate behavioral variation within and between individuals, families, and progeny of different life-history types across time; 2) testing for differences in gene expression within the brain associated with this behavioral variation; and 3) using genetic polymorphisms to test for associations with ecotype, as well as population structure, in polymorphic populations. First, we evaluated the variation in a suite of ecologically relevant behaviors across time in juvenile progeny produced from crosses within and between migratory and resident rainbow trout (Oncorhynchus mykiss). By testing multiple behaviors repeatedly in the same individuals, we better understand the innate behavioral variation in a population containing multiple life history types. Our study shows that there were consistent differences between individuals across time, or personality, for dispersal, aggression, and exploration. The significant repeatabilities of these behaviors indicate that these traits may be heritable. Not only did we find evidence for habituation in all behaviors, but dispersal, aggression and exploration showed significant differences between individuals in the rate of that habituation. The identification of this individual level variation is a step towards understanding which potentially heritable traits selection could influence. ^ Genetic variation for complex phenotypes, such as the behavioral traits identified, can arise as a function of variation in protein coding regions, or as a function of mutation in regulatory regions that modify the expression of genes. By examining the transcriptome within the brains of the fish used in the behavioral trials, we were able to identify genes differentially expressed among individuals with naturally variable behaviors. Moreover, we examined whether there is any overlap in the differentially expressed genes associated with individual differences in behavior and how these gene expression differences fit into biological functions and pathways. The results demonstrated that there are some key genes and pathways associated with the observed behavioral traits, and in many cases associated with multiple behaviors. Neuronal signaling (neurotransmitters such as gamma-aminobutyric acid (GABA) and catecholamines) was involved in multiple behavioral measures, while neuronal function and development were part of habituation in behavioral responses. Hormones (such as androgens, glucocorticoids, and growth hormone) and their related pathways are shown to have expression patterns correlating with behavioral differences in these juvenile fish. The overlap in genes that are differentially expressed between behaviors suggests pleiotropic effects of these genes on behavior with respect to personality traits and habituation. The differences in pathways, biological functions, and specific annotated genes underlying observed behavioral variation provide a starting place to finding possible proximate molecular and physiological mechanisms forming the connection between the heritable genome and the phenotypic differences observed. ^ Understanding patterns of extant genetic diversity is crucial for understanding not only the evolutionary history of populations, but also how populations should be managed and conserved. On a genomic level, we tested the hypothesis that ecotypic differences within and across polymorphic populations of brook trout (Salvelinus fontinalis) in Nipigon Bay, Ontario, Canada, were heritable and linked to allelic variation in the genome. We also evaluated population structure using the same genetic markers. In this study, we found that life history variation in Lake Superior brook trout appears to be heritable, but genome wide association analysis revealed only a few single nucleotide polymorphism (SNP) loci associated with ecotype. Moreover, the population genetic signature from 900 SNP markers distributed across the genome shows existing population structure across the tributaries of Nipigon Bay that should be considered when making stocking decisions. In particular, the Cypress River seems to be the main source of the sampled coaster ecotype captured in Lake Superior. Our study confirms that there is little to no genetic differentiation between life history types on a genome-wide level. By and large, the preponderant genomic signature suggests that coaster brook trout are an ecotype derived from resident populations, rather than a distinct stock. Understanding the genetic variation for ecotypic divergence and existing population structure has important implications for the conservation and restoration of the declining coaster ecotype. ^ In summary, this work can have important consequences for understanding the diversification of alternative life histories, and will contribute to our understanding on the units for conservation and management in these fish species. In juvenile rainbow trout, innate behavioral differences are heritable and also reflected in differential gene expression at the molecular level in the brain. While the fitness consequences of these behaviors at this life stage, which experiences high mortality in nature, remain to be verified, the identification of the molecular mechanisms related to these behavioral differences still has importance. My research shows that there is overall no significant differentiation in behaviors between progeny produced by migratory or resident parents, but that there is considerable individual variation upon which selection could act, and maintenance of this variation would be important for any conservation and management programs. For example, care should be taken to avoid selection against aggression in hatchery breeding programs, which may be correlated with other behaviors (or even a life history variant) due to a shared molecular basis. For both species used in this study – rainbow trout and brook trout – in many areas the migrant life history type is declining (particularly the coaster brook trout in Lake Superior). Importantly, it is necessary to parse out the genetic and environmental contributions to life history decisions to understand how extant populations can be used to conserve or restore populations. In the rainbow trout study, we find little behavioral differentiation between progeny produced by migrant or resident adults; in the brook trout, we find no genetic differentiation between life history types when considering loci distributed across the genome. While the rainbow trout are too young for one to know their eventual life history trajectory or to detect behavior or gene expression differences related to migration, our findings suggest that there are no differences between migrants and residents at this stage that might contribute to differential survival at the fry stage. For the brook trout it is likely that the environmental contribution to the coaster ecotype is the key to conservation efforts, and should be examined more directly. The identification of population structure for the brook trout also informs conservation efforts, emphasizing the need for local sources when stocking, and further examination of how some streams, and the biotic and abiotic variables that influence those streams, in northern Lake Superior may differentially contribute to production of the migratory ecotype. Overall, the findings presented herein provide insight into the molecular mechanisms promoting behavioral diversity among individuals, as well as future directions for research aimed at conserving life history variation among salmonids.