Structure, in its many forms, is a central theme in theoretical population ecology. At a mathematical level, it arises as nonuniformities in the topology of nonlinear dynamical systems. I investigate a mechanism wherein a chaotic time series can have episodes of nearly periodic dynamics interspersed with more 'typical' irregular dynamics. This phenomenon frequently appears in biological models, and may explain patterns of alternating biennial and irregular dynamics in measles epidemics. I investigate the interaction between spatial structure and density-dependent population regulation with a simple model of two logistic maps coupled by diffusive migration. I examine two different consequences of spatial structure: scale-dependent interactions ("nonlocal interactions") and spatial variation in resource quality ("environmental heterogeneity"). Nonlocal interactions allow three general dynamical regimes: in-phase, out-of-phase, and uncorrelated. With environmental heterogeneity, the dynamics of the total population size can be approximated by a logistic map with the mean growth parameter of the two patches; the dynamics within a single patch are often less regular. Adding environmental heterogeneity to non-local interactions has little qualitative effect on the dynamics when the differences between patches are small; when the differences are large, uncorrelated dynamics are most likely to be seen, and there are interesting consequences for the stability of source-sink systems. A third type of structure arises when individuals differ from one another. Accurate prediction of extinction risk in small populations requires that a distinction be made between demographic stochasticity (variation among individuals) and environmental stochasticity (variation among years or sites). I describe and evaluate two tests to determine whether all the variation in population survivorship can be explained by demographic stochasticity alone. Both tests have appropriate probabilities of type I error, unless the survival probability is very low or very high. Small amounts of environmental stochasticity are often not detected by the tests, but the hypothesis of demographic stochasticity alone is consistently rejected when environmental stochasticity is large. I also show how to factor out deterministic sources of variability, such as density-dependence. I illustrate these tests with data on a population of Acorn Woodpeckers.

Tallgrass prairie in North America has been severely degraded over the past century due to anthropogenic changes and is a subject of many restoration projects. Using these restoration projects, it is possible to examine potential drivers that influence community assembly. The environmental heterogeneity hypothesis provides a basis for enhanced diversity as function of resource partitioning and coexistence of potentially competing species. In essence, an area with higher levels of resource heterogeneity would be able to support a higher number of potentially competing species in contrast to an area with lower levels of resource heterogeneity (e.g. agricultural fields). The tallgrass prairie is naturally heterogeneous in abiotic resources such as soil depth and soil nitrogen, native prairie species both drive and exploit this heterogeneity and assemble a highly biodiverse community. Chapter 2 attempted to elucidate the effect of soil resource heterogeneity on plant community assembly, niche availability, and dimensionality. Chapter 3 attempted to examine the indirect influence of soil resources on aboveground Orthoptera herbivores. Both studies were conducted in a 16-year tallgrass prairie restoration experiment over a two-year period. There were no differences in plant community composition on a whole plot level. However, on a subplot level, shallow soil generally resulted in higher species richness and diversity. In contrast to previous studies, I found nitrogen addition increased forb richness and nitrogen reduction reduced forb diversity. As expected, the dominant grass Andropogon gerardii was positively influenced by high nitrogen regardless of soil depth. The multivariate analysis indicated the new species added to the experiment had unique trait spaces. Further analysis indicated niche availability and dimensionality were highest in treatments with nitrogen addition. This study suggests though fine scale spatial heterogeneity influences plant community composition, coarse scale spatial heterogeneity does not. This study also suggests that soil nitrogen may be a poor indicator of plant species diversity in the tallgrass prairie community. Orthoptera richness and biomass were higher in maximum heterogeneity treatments relative to control. The influence of high resource heterogeneity was highest on the richness of mixed-feeder grasshoppers and katydids. This effect, however, was inconsistent between years. Grass-feeder biomass was higher in the maximum heterogeneity treatment than control both years. This was attributed to nitrogen addition resulting in patches of higher quality forage in the maximum heterogeneity plots. Orthopterans are also influenced by the structural complexity of the plant community mediated by varying levels of soil resources. The maximum heterogeneity treatment contained higher variation in the cover and ANPP of a dominant grass, Andropogon gerardii. The positive relationship between plant richness and Orthoptera diversity suggests that maintaining plant richness in restored areas is important for maintaining diversity of higher trophic levels. The negative relationship between light interceptions and Orthoptera abundance suggests the dense vegetation from dominant tallgrass species may impede recruitment of some species. These results suggest suppression of dominant grasses can positively influence the plant community composition and Orthoptera herbivores. Understanding how soil resources influence plant community composition and higher trophic levels can aid our understanding of the community assembly process. Plant species benefited from higher variation in soil resources, particularly soil depth and soil nitrogen, while insect herbivores that depended on these plant species were also indirectly benefited. This study suggests soil heterogeneity is important for the assemblage of species on a multi-trophic level and this knowledge can assist land managers in restoration projects to achieve desired goals.

Rates of microbial reactions are important in understanding groundwater chemistry and bioremediation. In aquifers, microbial rates depend on physicochemical and biological factors and also on how groundwater transport impacts microbial reactions at pore-scale. I numerically simulate microbial acetate consumption in a porous medium, focusing on how physical heterogeneity of the medium impacts the rates. My model is a 3-D cube, which represents a portion of a sandy aquifer. Acetate is supplied by groundwater flow through the cube, and microbes live on randomly distributed grain surfaces by oxidizing acetate. I simulated microbial acetate oxidation under a range of groundwater velocity, acetate concentrations, spatial heterogeneity, and other physicochemical conditions. The results demonstrate a significant gap in microbial kinetics between the pore-scale and continuum model. Specifically, microbial rates are larger in porous media of greater heterogeneity. For this reason, I propose that microbial parameters should not be applied directly to field-scale biogeochemical modeling.

No description available.

Oligodendrocytes are the myelinating cells of the central nervous system (CNS), whose function is to optimise neuronal transmission and preserving axonal integrity. Oligodendrocytes are derived from a stem cell population, called oligodendrocyte progenitor cells (OPCs). Oligodendrocyte lineage cells (OLCs) have been implicated in the pathophysiology of various diseases including not only demyelinating diseases (eg. Multiple Sclerosis (MS) or Pelizaeus-Merzbacher disease (PMD)), but also psychiatric disorders (eg. schizophrenia or Rett syndrome (RTT)). Regardless of the type of disease, understanding the underlying fundamental biology of the oligodendrocyte lineage cells is pivotal to develop therapeutic strategies. In the mouse embryonic forebrain OPCs are generated in consecutive waves from distinct brain regions along a spatiotemporal gradient; with ventral OPCs emerging before dorsal OPCs. The developmentally distinct OPCs, and their progenies, persist in the brain throughout life. To investigate whether ventrally and dorsally derived OLCs fulfil different functions in the adult brain, dorsally derived OPCs were ablated in development using a \textit{Sox10}-driven diphtheria toxin fragment A (DTA) mouse model. As dorsally derived OPCs populate the cortex, locomotor coordination and cognition were investigated following dorsal OPC ablation. Mice ablated of the dorsal OPC population do not show a significant deficit in learning and attentional function. In contrast, ablated mice show an impaired locomotor coordination, while general vigilance, gait, balance and sensation are comparable to control groups. The locomotor coordination disabilities are a result of alterations of brain, not spinal cord homeostasis, as only a neglect able number of OLCs in the spinal cord are affected by the ablation model. In addition, no signs of neuronal cell death or chronic inflammatory response was detected in response to the ablation. As the oligodendrocyte numbers are similar between control and ablated animals, the locomotor coordination phenotype can also not be explained by reduced number of oligodendrocytes. However, clustering analysis following single-cell Drop-sequencing uncovered a heterogeneity of oligodendrocyte (OL) subpopulations in the motor cortex. Whilst some OL subpopulations are of mixed developmental origin, others are exclusively formed by either ventrally or dorsally derived OLs, arguing that dorsal oligodendrocyte subpopulations are crucial for homeostatic brain function. In the absence of dorsal OPCs, ventral OPCs are not capable of forming dorsal oligodendrocyte subpopulations in response to dorsal OPC ablation. In conclusion, my results indicate a functional heterogeneity of developmentally-distinct oligodendrocytes in physiological brain function.

The first two chapters study the effect of foreign lobbies on trade policy of a country which is a member of a Free Trade Agreement (FTA). They rely on a monopolistically competitive political economy model in which the government determines external tariffs endogenously. In the first paper the effect of foreign lobbying under the FTA is examined empirically using Canadian industry-level trade data that allow differentiating of lobby groups by the country of origin. The analysis suggests that the presence of foreign lobbying has a significant effect on the domestic trade policy: the presence of an organized lobbying group in an FTA partner country tends to raise trade barriers while an organized lobbying group of exporters from outside of the FTA is associated with less protection. The second paper analyses political viability of FTAs and their effect on the world trading system in the presence of lobbying by organized foreign interest groups. I show that the FTA in the presence of an organized lobby group in a prospective partner country may cause an increase in the level of protection against imports from third countries and impede trade with non-member countries. I also find that foreign lobby may encourage the local government to enter a welfare-reducing trade-diverting FTA. Finally, I show that the FTA increases the lobbying power of the organized lobby groups of the member countries, which can potentially obstruct the viability of welfare-improving multilateral trade liberalization. The last paper shows that the reason for a higher capital-labor ratio observed for exporting firms is a higher capital intensity of their production technology. Exporters are more productive, more likely to survive and, hence, more likely to repay loans. A higher repayment probability causes creditors to charge lower interest rate and reduces the marginal cost of the firm when a more capital-intensive technology is used. Here, a reduction in international trade costs stimulates exporting firms to use more efficient capital-intensive technologies, while non-exporters switch to less capital-intensive ones. This within-industry change in the composition of technologies reinforces the productivity advantage of exporters and contributes further to industry-wide productivity improvement. The results of model simulations highlight that to 10% of welfare and productivity gains of trade liberalization come from the adoption of new technologies by existing firms in the industry, thus amplifying the effect of resource reallocation from firms' entry and exit. / Arts, Faculty of / Vancouver School of Economics / Graduate

Antimicrobial resistance is a serious and imminent threat to human health, though its rise may be controlled with improved stewardship strategies that limit the emergence and spread of resistant strains. Motivated by theoretical models from population genetics and ecology, my M.Sc. experimentally evaluates how varying drug availability in either time or space impacts the prevalence of resistance in a population. By experimentally evolving Pseudomonas aeruginosa under different antibiotic selection regimes in vitro, I show that spatial, but not temporal, drug free refuges delay the fixation of resistance by promoting the coexistence of sensitive and resistant genotypes. Second, I establish that this polymorphism is underlain by a trade-off between resistance and growth rate in the absence of antibiotic that underpins the maintenance of diversity through negative frequency dependent selection. Third, I demonstrate that spatially varied drug selection cannot prevent the fixation of resistance because continued selection leads to the evolution of resistant types that pay smaller costs of resistance and gradually displace sensitive strains. These results provide insight into the fate of diversity under long-term selection and highlight the value of incorporating the principles of evolutionary ecology into antimicrobial resistance stewardship.

Pseudomonas fluorescens «switchers », souches évolués artificiellement au Rainey Lab, sont un système modèle pour les switch phénotypiques. Ces populations sont typiquement caractérisées par les fréquences de deux phénotypes alternatifs liés à la production d’une capsule d’acide colanique autour de la paroi cellulaire. Bien qu'on s’attende que telles fréquences soient définies d’une manière univoque par le génotype, elles varient au long de la croissance de la population, ce qui indique une possible dépendance des taux de transition à l’égard de la démographie. J’ai développé un modèle mathématique où les cellules sont représentées comme systèmes bistables contrôlés par une concentration intracellulaire et où les taux de transition dépendent de l’état de la croissance de la population.Le modèle reproduit quantitativement la dynamique de la composition phénotypique de la population (dépendante de l’histoire), et fournie des prédictions à propos de son quasi équilibre en phase exponentielle en fonction du taux de croissance de la population - prédictions ensuite qualitativement confirmées par les résultats de mon travail expérimental.Pour conclure, on ne peux pas caractériser une population croissante de « switchers » que par l’état asymptotique des fréquences de ses phénotypes alternatifs, puisque le switch est étroitement lié à la démographie.Dans une perspective évolutive, la persistance transgénérationnelle du phénotype, influencée par des concentrations intracellulaires, pourrait être à l’origine de l’émergence de stratégies comme le « bet-hedging ». / Pseudomonas fluorescens “switchers”, artificially evolved in Rainey Lab, are a model system for phenotypic switching.Populations can be characterized by the frequencies of two alternative states related tothe production of a colanic acid capsule around the cell wall. Expected to be at an equilibrium underpinned by the genetic background, such frequencies vary during population growth, hinting to a dependence of the switching rates on demography, and appear to be dependent on the history of the preculture. I thus developed a mathematical model with individual cells as bistable systems controlled by an intracellular concentration, where transition rates depend on the growth state of the population.The model quantitatively reproduces the history-dependent dynamics of the phenotypic composition of the population, and provides qualitative predictions on its quasi-steady state in exponential phase as a function of the growth rate — then corroborated by the results of my experimental work. I conclude that agrowing population of switching cells cannot be fully characterized only by the asymptotic steady state of the phenotypes’ frequencies,because phenotypic switching is inextricably intertwined with demography. From an evolutionary perspective, trans-generational inheritance of the phenotype mediated by internal concentrations may be at the basis of the emergence of bet-hedging-like strategies.

The presence of and interactions between structural defects, fluids, and trace elements during deformation play a vital role in the manner in which materials respond to an applied stress. Although the links between crystal defects and trace element mobility have been lying at the frontier of research in Earth sciences, the role of fluids and the underlying physico-chemical processes linking them remain poorly understood. Investigation of these nanometer scale processes requires a correlative approach combining high-spatial resolution analytical techniques. This thesis integrates novel 2D and 3D structural and geochemical mapping methods such as electron channeling contrast imaging, electron backscatter diffraction, scanning transmission electron microscopy (STEM) and atom probe tomography (APT) to interrogate the atomic structure and composition of geomaterials in an attempt to better understand long-standing questions in Earth sciences and build bridges between materials science and geoscience. The processes investigated in this thesis include: 1) the underlying diffusion processes that mobilize trace elements into deformation-induced nanostructures; 2) the mechanisms of trace element segregation associated with fluid inclusions; 3) the influence of fluid inclusions on the mobility of structural defects and trace element mobility; and 4) the initial stages of bubble nucleation in the presence of nanoscale chemical heterogeneities. Ultimately, this research interrogates the feedbacks between deformation and trace element diffusion processes, fundamentally investigating their impact on rheology. More specifically, the thesis investigates the influence of deformation and associated nanostructures on the remobilization of trace elements and, in turn, the influence of trace elements on the nucleation and mobility of nanostructures. The combined work successfully identified two diffusion mechanisms for deformation-induced trace element mobility, characterized fluid-inclusions in APT data, documented two processes that led to proposing a new fluid inclusion-induced hardening model, and documented direct evidence of bubble nucleation on the surface of nanoscale chemical heterogeneities. This work not only pushes the limits of high-spatial resolution analytical techniques including STEM and APT, but the results have significant transdisciplinary implications in the fields of geoscience, materials science, engineering, and analytical microscopy.

Advancements in Li-ion batteries are needed especially for the development of electric vehicles and stationary energy storage. Prior research has shown mesoscale variations in electrode electronic conductive properties, which can cause capacity loss and uneven electrochemical behavior of Li-ion batteries. A micro-four-line probe (μ4LP) was used to measure electronic conductivity and contact resistance over mm-length scales in that prior work. This work describes improvements to overcome the challenge of unreliable surface contact between theμ4LP and the sample. Ultimately a second generation flexible probe called the micro-radial-surface probe (μ4LP) was designed and produced. The test fixture was also optimized to obtain consistent contact with the new measurement probe and to perform measurements at a lower force. The μ4LP was then used to study the effect of heterogeneity on calendering, which is the compression of electrode films to obtain a uniform thickness and desired porosity. The thickness, electronic conductivity and contact resistance of two cathodes and one anode were measured before and after calendering. The the spatial standard deviation divided by the mean was used as a measure of heterogeneity. The results show variability in conductive properties increased for two of the three samples after calendering, despite the increased uniformity in thickness of the electrodes. This suggests that additional quality control metrics are needed besides thickness to be able to identify uneven degradation and produce longer lasting batteries.