Evolution of genotypes during range expansion is driven in part by colonization dynamics. I investigated genetic patterns of colonization and dispersal during initial expansion of an invasive bunchgrass, Brachypodium sylvaticum, into Oregon. Using microsatellite markers, I sampled plants at two different scales: at regular intervals along three parallel roads spanning about 30km, and in populations identified throughout Oregon. I also collected field-generated progeny from a subset of populations and used molecular identification of outcrossing events to estimate selfing rates in both central and peripheral populations. Dispersal patterns were similar at both scales, with non-contiguous dispersal responsible for colonization of new populations. High levels of differentiation were observed at all scales, though newly-colonized populations were more differentiated than older populations. Corvallis populations were responsible for colonization of a majority of populations throughout Oregon, while individuals from Eugene were only occasionally found in new populations. Admixture occurs between Corvallis and Eugene populations, decreasing differentiation, and potentially creating novel phenotypes and increasing evolutionary potential of populations. Selfing rates were high, but two populations in the areas of original introduction had lower rates of selfing, suggesting that selfing rates may decrease as population density and diversity increases with age. The influences of founder effects and bottlenecks on phenotypic evolution during range expansion require further investigation, as inbreeding, lag times, and selection may influence evolutionary trajectories of populations.

It is common knowledge that invasive species cause worldwide ecological and economic damage, and are nearly impossible to eradicate. However, upon introduction to a novel environment, alien species should be the underdogs: They are present in small numbers, possess low genetic diversity, and have not adapted to the climate and competitors present in the new habitat. So, how are alien species able to invade an environment occupied by native species that have already adapted to the local environment? To discover some answers to this apparent paradox I conducted four ecological genetic studies that utilized the invasive species Brachypodium sylvaticum (Hudson) Beauv. to determine mechanisms contributing to adaptation and success in the novel habitat. The first study used simulations and experiments to test the hypothesis that genetic purging, the process where genetic load is reduced by selection against the recessive deleterious alleles expressed in the homozygous state, promotes invasive range expansion. I found that homozygous populations on B. sylvaticum's range periphery displayed lower inbreeding depression compared to heterozygous populations near introduction sites. Empirical tests with B. sylvaticum further demonstrate that purging of genetic load is a plausible scenario promoting range expansion during invasion. Next, I explored how the interaction between population genetic diversity and the environment contributed to the establishment and spread of Brachypodium sylvaticum. I found that nitrogen application increases both final size and shoot biomass for B. sylvaticum individuals from source populations with low HS levels to levels found in individuals from populations with high HS. A coefficient of relative competition intensity index (RCI) displayed reduced effects of interspecific competition on B. sylvaticum biomass in high nitrogen plots. Results show that elevated nitrogen deposition is a factor that increases establishment of introduced species with historically small effective population sizes. Thirdly, I investigated phenotypic differentiation during the establishment and range expansion of Brachypodium sylvaticum. Utilizing a novel approach, unique alleles were used to determine the genetic probability of contribution from native source regions to invasive regions. These probabilities were integrated into QST-FST comparisons to determine the influence of selection and genetic drift on twelve physiological and anatomical traits associated with drought stress. Phenotypic divergence greater than neutral expectations was found for five traits between native and invasive populations, indicating selective divergence. Results from this study show that the majority of divergence in B. sylvaticum occurred after introduction to the novel environment, but prior to invasive range expansion. The final chapter of my dissertation investigates the adaptive role of genetic differentiation and plasticity for Brachypodium sylvaticum invasion. Plasticity was measured across treatments of contrasting water availability. Linear and nonlinear selection gradients determined the effect of directional and quadratic selection on plasticity and genetic differentiation. Invasive trait divergence was a consequence of post-introduction selection leading to genetic differentiation, as there were no plastic responses to contrasting water availability for any measured traits. Genetic divergence of invasive plants was not consistently in the direction indicated by selection, suggesting limitations of selection that may be a consequence of physical constraints and/or tradeoffs between growth and abiotic tolerance. Results suggest that selection, rather than plasticity, is driving phenotypic change in the invaded environment. The combined volume of these studies contributes significantly to the field of invasion and plant biology by providing novel insights into the processes underlying range expansion, adaptation, and ultimately, evolution of introduced species.

Transcriptomics and gene expression profiling enables the elucidation of the genetic response of an organism to various environmental cues. Transcriptomics enables the deciphering of differences between two closely related organisms to the same environment and in contrast, enables the elucidation of genetic responses of the same organism to different environmental cues. Two major methods are utilized for the study of transcriptomes, high-throughput sequencing and microarray analysis. High-throughput sequencing technologies such as the Illumina platform are relatively new and protocols must be developed for the analyses of transcriptomes (RNA-sequencing). A RNA-seq protocol was developed and refined for the Illumina sequencing platform. This protocol was then utilized for the de novo sequencing of the steelhead salmon transcriptome. Hatchery steelhead exhibit a reduced fitness compared to wild steelhead that has been shown to be genetically based. Consequently, the steelhead transcriptome was assembled, annotated, and used to identify gene expression differences between hatchery and wild fish. We uncovered many differentially expressed genes involved in metabolic processes and growth and development. This work has created a better understanding of the genetic differences between hatchery and wild steelhead salmon. Brachypodium distachyon is a monocot grass important as a model for cereal crops and potential biofuels feedstocks. To better understand the genetic response of this plant to different environmental cues, a comprehensive assessment of the transcriptomic response was conducted under a variety of conditions including diurnal/circadian light/dark/temperature environments and different abiotic stress conditions. Using a whole-genome tiling DNA microarray, we identified that the majority of transcripts in Brachypodium exhibit a daily rhythm in their abundance that is conserved between rice and Brachypodium. We also identified numerous cis-regulatory elements dictating these rhythmic expression patterns. We also identified the genetic response to abiotic stresses such as salinity, drought, cold, heat, and high light. We uncovered a core set of genes which responds to all stresses, indicating a core stress response. A large number of transcription factors were uncovered as potential nodes for regulating the abiotic stress response in Brachypodium. Moreover, promoter elements that drive specific responses to discrete abiotic stresses were uncovered. Altogether, the transcriptome analyses in this work furthers our understandings of how particular organisms respond to environmental cues and better elucidates the relationship between genes and the environment. / Graduation date: 2012 / Access restricted to the OSU Community at author's request from Oct. 5, 2011 - April 5, 2012.