Biological Sciences - Theses, Dissertations, and other Required Graduate Degree Essays

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Nutrient enrichment, trophic exchanges and feedback loops: effect of spawning salmon-derived nutrients on juvenile coho salmon

Date created: 
2014-07-11
Abstract: 

The movement of nutrients across ecosystem boundaries can affect recipient ecosystems at individual, population, and community levels. This is particularly the case when more productive systems subsidize less productive ones, where subsidies can sustain and enhance populations in nutrient-poor recipient environments. One prominent example of this is the annual migration of salmon from the marine environment into low-productivity freshwater streams for spawning. This thesis uses data collected from 47 near-pristine streams on the central coast of British Columbia to study spawning chum (Oncorhynchus keta) and pink (O. gorbuscha) salmon and the ecological implications of their nutrient subsidy, focusing on stream-rearing juvenile coho salmon (O. kisutch). While considering a broad suite of habitat characteristics, the strongest predictors of juvenile coho size and abundance were spawning chum and pink salmon abundance. Streams with more spawning chum salmon had larger coho, while streams with more spawning pink salmon had higher coho populations. Further, the evidence suggested the negative association between juvenile coho and their intraguild predators/competitors, sculpin (Cottus aleuticus and C. asper), may be reduced as more spawning salmon nutrients became available. Altogether, this thesis shows strong impacts of marine-derived nutrient subsidies to freshwater ecosystems at multiple ecological scales. In general, it provides insights into the ecological mechanisms by which species interact with their environments, the potential for nutrient subsidies to affect recipient populations through changing food supply and predator-prey dynamics, and the role of multi-trophic interactions in subsidized trophic cascades. In specific, this research improves our understanding of the potential positive feedback between different species of salmon while incorporating the importance of multiple habitat characteristics. This has the potential to inform conservation and ecosystem-based management, particularly in light of the drastic decline in spawning salmon abundance in northern Pacific regions.

Document type: 
Thesis
File(s): 
Senior supervisor: 
John Reynolds
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

The bird who kicked the wasp's nest: Red-throated Caracara predation, nesting and territorial behaviour

Date created: 
2014-07-10
Abstract: 

Red-throated Caracaras are enigmatic but seldom studied raptors of tropical American forests. They are known to prey on social wasps and exhibit cooperative breeding, but little quantitative data have been published. We investigated Red-throated Caracara nesting, predation and social behaviour in the field in French Guiana from 2008 to 2013. We closely studied two nests with automated camera systems and found a high level of cooperative behaviour among adults tending nests. Seven individuals were involved in bring prey to and guarding a nest in 2009. Our observations of caracaras nesting in bromeliads confirmed that the majority of their diet was comprised of the brood of social wasps, although they also brought millipedes and fruits to the nest. The social behaviour of the caracaras included intense territorial behaviour, including specific vocalizations and displays in response to conspecifics or playback of caracara calls. Caracaras also attacked conspecific decoys, and we observed them attacking members of other groups on two occasions in 2011. The caracaras provided their chicks with nests of a diverse assortment of wasp genera, including Polybia, Pseudopolybia, Leipomeles, Apoica and Parachartergus, and the proportional abundance of these taxa is not congruent with published studies on generic abundances. In addition, while army ants had previously been considered top predators of social wasps, we calculated that the caracaras, as specialist predators, could rival or exceed army ants as a mortality factor for social wasps. It had been hypothesized that these caracaras rely on a powerful chemical repellent to protect themselves from the stings of their defensive prey, but we found no evidence of such a repellent. We used a video recording arena to observe caracara predation behaviour on nests of various species of Polybia. We observed that the caracaras are indeed stung by some species of wasps, but the caracaras mount high-speed aerial strikes against such nests, knocking them to the ground or striking them repeatedly until the adult wasps depart in an absconding swarm. The caracaras exploit this absconding response when attacking highly defensive wasp species in order to minimize stings while obtaining the wasp brood.

Document type: 
Thesis
File(s): 
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Senior supervisor: 
Gerhard Gries
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Size-based insight into the structure and function of reef fish communities

Author: 
Date created: 
2014-07-15
Abstract: 

What would reef fish communities look like without humans? Effective ecosystem management and con- servation requires a clear understanding of community structure and the processes that drive it. Relatively undisturbed reef fish communities appear to be inverted biomass pyramids (IBPs) with greater biomass of large-bodied predatory fishes compared to smaller fishes at lower trophic-levels. However, the processes that might give rise to IBPs are subject to debate. In this thesis I show that biomass pyramids and size spectra are equivalent and interchangeable representations of community structure. Key constraints on the slopes of size spectra – particularly mean community predator-to-prey-mass ratio (PPMR) – also constrain the shapes of biomass pyramids, meaning that IBPs are unlikely for closed communities. There are surprisingly few quantitative descriptions of biomass pyramids, and PPMR has not been estimated on reefs. I undertook a detailed case-study and quantify fish community size-structure using underwater vi- sual surveys and empirically estimate PPMR using stable isotopes at a relatively undisturbed island chain in Haida Gwaii, BC. I observe an IBP, but the PPMR estimate suggests that the community should be a stack or bottom-heavy. There is 4-5 times more biomass at the largest body-sizes than would be expected given observed PPMR. I hypothesise that the most plausible explanation is energetic subsidies. Using the same fish assemblage I show how two foundational components of habitat complexity (substrate rugosity and kelp canopy characteristics) shape fish community size-structure. Higher kelp canopy cover and den- sity leads to more biomass across all size classes, whereas higher substrate rugosity boosts the biomass of smaller-bodied fishes and leads to a more even distribution of biomass across size classes. Finally, I step back to the global scale and estimate baseline biomass spectra for the world’s reef fishes, accounting for local ecological variation. Current reef fish biomass is less than half of the baseline expectation and 90% of the largest (> 1 kg), most functionally-important, individuals are absent. In addition to providing the first global description of how humans have shaped reef biomass pyramids, my thesis gives new insight into how size-based processes underlie the structure and function reef fish communities.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Nicholas Dulvy
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Why did the Carabid Cross the Fence?

Author: 
Date created: 
2014-08-14
Abstract: 

Physical barriers and biological control can be used to manage pests, but they have the potential to interfere with each other’s effectiveness. Exclusion fencing, which targets Delia radicum, could also create a barrier for poor-flying carabid beetles, polyphagous predators, from entering Brassica fields. I performed field and laboratory experiments to determine the permeability of exclusion fencing to the carabids Pterostichus melanarius and Bembidion lampros. The results show that the fence is permeable to both species, that as mesh size decreases, fence permeability decreases for B. lampros, and that B. lampros accumulates at the fence. A simulation model and cost-benefit analysis combined the results from the experiments with parameters from the literature to explore how carabids move across a field when a fence is present, and the fence’s cost to growers. Combining exclusion fence use with carabids and conservation biological control does not interfere with either tool’s effectiveness in controlling D. radicum.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Bernard Roitberg
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.P.M.

Comparative and Genetic Approaches to Placental Evolution and Disease

Date created: 
2014-07-14
Abstract: 

The placenta is an important locus of theory and empirical research in mammalian evolution, physiology, health and disease. Novel comparative approaches to the study of placentation hold great promise in bridging the gap between applied placental research and evolutionary theoretical biology, potentially providing insights into intractable medical conditions affecting the placenta in human beings. This thesis describes genetic and comparative approaches designed for the study of placentation, but which will also prove broadly useful in research at the intersection of human health and evolutionary biology. The thesis begins with a comprehensive investigation into the historical course of evolution of the eutherian placenta, with special focus on identifying the polarity of transformation of interhemal relations, fetal-maternal interdigitation and shape. A range of statistical approaches appear to concur on an early origin of invasive, hemochorial placentation and the existence of repeated independent transitions toward less invasive forms. Tests for positive selection, and assessment of positively selected genes for substitutions of major phenotypic effect, are used to identify genes involved in the evolution of spiral arteries at the origin of the great apes and in the evolution of reduced placental invasion in three independent branches of the euarchontogliran phylogeny. It is shown to be possible to prioritize such genes for investigation into their involvement in diseases of placental vasculature including preeclampsia. The thesis continues with elaboration and discussion of statistical models for the evolution of biological traits that are known to deviate from the neutral, gradualistic assumptions of standard approaches - such as independent contrasts and phylogenetic generalized least squares - that are based on a Brownian motion model of evolutionary change. First, I discuss the use of stable models of continuous character evolution and provide a methodology for estimating ancestral states and characterizing the evolutionary process operating on traits exhibiting occasional rapid bursts of change. Second, I discuss the incorporation of directional tendency into phylogenetically independent contrasts. Simulation studies and application to real biological datasets suggest that such methods may be superior under conditions that deviate markedly from Brownian motion.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Bernard Crespi
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Development of an in vivo plant-based screen for identifying pharmacological chaperones for treatment of human lysosomal storage diseases

Date created: 
2014-07-08
Abstract: 

Small-molecule- enzyme enhancement therapy has emerged as an attractive approach for the treatment of lysosomal storage diseases (LSDs), a broad group of genetic diseases caused by mutations in genes encoding lysosomal enzymes or proteins required for lysosomal function. Missense mutant lysosomal enzymes normally subjected to rapid disposal by ER-associated degradation (ERAD) can be stabilized by small molecule chaperones that increase residual enzyme activity largely by increasing the transport and maturation of the mutant enzyme. Mucopolysaccharidosis I (MPS I) and Gaucher disease were my research targets – two LSDs caused by a deficiency of alpha-L-iduronidase (IDUA) and β-glucocerebrosidase (GCase), respectively. My goals were two-fold: (1) To determine the proteostasis of a severely defective mutant lysosomal enzyme in plant cells. (2) To develop a plant-cell-based screening system to identify putative LSD therapeutics. For the former goal, post-ER trafficking of the severely malfolded L444P GCase protein, and some aspects of cellular homeostasis, were restored to different degrees by ERAD inhibitors and proteostasis regulators, which increased the steady-state levels of the mutant protein inside the plant cells and rescued a proportion of protein from proteolysis. For goal 2, I developed a plant-cell-screening tool for identifying putative small molecule therapeutics based on selecting for library molecules capable of enhancing the post-ER transport of missense mutant lysosomal enzymes. Since the recombinant variants were equipped with a signal peptide, and the expression cells - transgenic tobacco BY2 cells - possess no lysosomes, the assay was based on increased lysosomal enzyme activity in the secretion media. I first established the proof-of-principle for the assay (i.e. its selectivity and specificity) based on recombinant N370S GCase, and two characterized chaperones - ambroxol and N-(n-nonyl) deoxynojirimycin. Two IDUA mutant proteins that underlie MPS I disease (P533R- and R383H- IDUA), formed the basis of the plant-cell-based assay that was used to screen a library of 1,040 Food and Drug Administration-approved drugs. Downstream validation of the hits identified in the primary screening by secretion and heat denaturation assays resulted in the identification of a potential candidate molecule (‘X-372’) for P533R IDUA. Further development of this molecule may yield a therapeutic for MPS I disease.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Allison Kermode
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Theoretical and experimental studies on behavioral syndromes in aphids

Date created: 
2014-07-24
Abstract: 

Individuals’ behaviors can be correlated across time and contexts, in a phenomenon now known as behavioral syndromes. Using an experimental approach, I demonstrate that genetically identical pea aphids are highly repeatable in multiple behavioral traits, however these behaviors are uncorrelated. Then using a state variable model I show that asymmetries in size can maintain a hierarchy between least and most bold individuals in foraging intensity across development. However, individuals that complete compensatory growth show an inversion in the rank-order of foraging activity between early and late development (ie individuals that are the boldest early in life are less bold than their “timid” counterparts late in life). In conclusion, I demonstrate both theoretically and empirically that non-genetic differences are capable of explaining repeatability in the expression of a single behavior; however I found no evidence that non-genetic mechanisms can correlations between multiple behaviors.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Bernard Roitberg
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

The impact of nutrition on within and trans-generational disease resistance in the cabbage looper, Trichoplusia ni

Author: 
Date created: 
2014-07-30
Abstract: 

Parasites and pathogens are ubiquitous, and pose a threat to all living organisms. Investment in resistance mechanisms to fight parasite challenge can be costly, often resulting in trade-offs with other life-history traits. Host nutrition can alter the availability of resources to invest in resistance mechanisms and influence host-parasite interactions and their outcomes. I investigated the impact of nutrition on disease resistance in the cabbage looper, Trichoplusia ni. I assessed the role of dietary macronutrients on the expression of fitness costs exhibited by a T. ni strain that has evolved resistance to the bacterial pathogen, Bacillus thuringiensis (Bt). Reduced pupal weight and growth rate, which are fitness costs associated with Bt-resistance, resulted from reduced food intake rather than impaired macronutrient utilization. When given a choice, Bt-resistant T. ni self-composed a higher ratio of protein to carbohydrate (P:C ratio) than Bt-susceptible T. ni, allowing males to eliminate a fitness cost (reduced pupal weight), but not females. Next, I investigated the interaction between host nutrition and another key environmental factor, temperature, on the interaction between T. ni and two species of baculoviruses differing in host range (TnSNPV, narrow range; AcMNPV, broad range). Optimal performance of T. ni shifted to higher P:C ratios when challenged by either virus as survival increased with dietary protein content. This effect was strongly affected by temperature when challenged by AcMNPV but not TnSNPV. Virus performance was also differentially affected by the host’s environmental condition, such that AcMNPV had a broader peak of optimal performance (combined measure of host mortality and virus production) across environmental conditions than TnSNPV. Lastly, I examined the impact of nutritional stress on the ability of Bt-challenged T. ni to prime the immune system of their offspring. If parental T. ni experienced only nutritional stress or Bt-challenge, they transferred nutritional stress tolerance or immune priming to their offspring respectively. However, as surviving each stressor is costly, when experienced simultaneously a trade-off was observed where only immune priming was transferred. This study highlights the important influence of host nutrition on host resistance to pathogens, costs associated with resistance, and pathogen virulence and growth.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Jenny Cory
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Transgenerational effects of food quantity and quality on disease resistance in the western tent caterpillar, Malacosoma californicum pluviale

Author: 
Date created: 
2014-07-25
Abstract: 

Increasing population density may alter food quantity or quality. Dietary stressors can interact simultaneously and produce emergent fitness effects both intragenerationally and potentially transgenerationally, including changes in pathogen resistance. Western tent caterpillar (WTC) Malacosoma californicum pluviale populations undergo regular 6-11 year cycles; epizootics of nucleopolyhedrovirus (NPV) characterize population declines and may be triggered by density-related dietary changes. I tested the transgenerational interaction of three factors likely to be influenced in rising WTC populations. I manipulated foliage quantity, quality, and the presence of phylloplane bacteria provided to the parental generation and assessed NPV resistance and immunity in their offspring. Food limitation had strong impacts on life history traits of tent caterpillars. Somewhat unexpectedly, changes in foliage quality and ingestion of phylloplane bacteria had transgenerational effects on offspring, enhancing their NPV resistance and affecting expression of background pathogens. There was no evidence for increased disease susceptibility in offspring from combined parental stressors.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Jenny Cory
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Investigating the vector competence of the house fly (Musca domestica) for Campylobacter jejuni

Author: 
Date created: 
2014-07-11
Abstract: 

Campylobacteriosis is a severe gastroenteric disease in humans caused by the bacterium, Campylobacter jejuni, typically obtained through the ingestion of contaminated poultry products. Poultry facilities become contaminated through the introduction of pathogens, including C. jejuni, by the house fly, Musca domestica. This thesis investigates the vector competence of M. domestica for C. jejuni to determine if the bacteria survive house fly metamorphosis from larva to adult, and can multiply within adult flies to enhance transmission, and whether innate immune factors of the house fly can clear C. jejuni infections. We demonstrate that M. domestica mounts an effective innate immune response that prevents transmission of C. jejuni from larva to adult, and eliminates C. jejuni from adult house fly gastrointestinal tracts within hours. We propose that M. domestica serves as a mechanical vector, rather than as a true, amplifying, biological vector. These findings will help elucidate the elusive epidemiology of campylobacteriosis.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Carl Lowenberger
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.