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

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The speed of life in sharks and rays: methods, patterns, and data-poor applications

Date created: 
2017-04-11
Abstract: 

Since the theory of evolution by natural selection was first postulated, biologists have noted that life histories evolve following broad patterns across all organisms. Understanding the mechanisms causing these relationships is the central focus of life history theory; these insights can also be used to better estimate the biology and extinction risk of data-poor species. Sharks, rays, and chimaeras (class Chondrichthyes) are an ideal taxon to explore these relationships as they have evolved a broad range of life history strategies. In this thesis, I focus on two key time-related life history parameters that are often used as a measure of productivity: growth coefficient k, which is estimated from the von Bertalanffy growth function (VBGF), and maximum intrinsic rate of population increase rmax, estimated by simplifying the Euler-Lotka equation. I begin by clarifying two methodological problems regarding the estimation of growth and productivity. I first show that fixing the y-intercept in the VBGF, a common approach in chondrichthyan age and growth studies, often causes considerable bias in growth coefficient estimates, and recommend using the three-parameter VBGF instead. I then point out an important omission in a method commonly used for estimating r max in chondrichthyans and clarify the correct way to estimate it. Next I explore the effect of uncertainty on the estimation of r max and show that species with low annual reproductive outputs are bound to have very low productivities, thus focus should be placed into accurately estimating litter sizes, breeding intervals, and the variability of these traits. As an example of how these insights can be applied, I better estimate growth and productivity for a data sparse species of conservation concern, the Spinetail Devil Ray (Mobula japanica), and show it has a much lower somatic growth rate than previously thought and one of the lowest productivities among chondrichthyans. Finally, I show that productivity in chondrichthyans varies with temperature as well as depth, and that the scaling of this relationship changes with temperature according to the expectation from Bergman’s rule. My thesis demonstrates that simple insights from life history theory can further our knowledge on the broad patterns that shape the evolution of life histories we see today, which can be used to inform management of data-poor species.

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

Predictive cues and fitness consequences of breeding phenology

Author: 
Date created: 
2017-04-10
Abstract: 

Individual variation in the timing of breeding in birds has been strongly linked to the fecundity, and by extension fitness of the individual. Despite this important relationship, our understanding of the determinants of timing of breeding is unclear. Photoperiod determines a window of opportunity for breeding, but small-scale variation within this window still has major fitness consequences. This thesis explores potential cues that might account for variation in individual timing decisions, and possible consequences of timing on offspring and future broods. First we assess how pre-breeding male social cues and the development of tipulid larva (prey) might determine the female’s timing of egg-laying. While many lab studies have demonstrated that the presence of a male partner is necessary for female gonadal development, our 3-year field studies found no effect of male behaviour on female breeding phenology or performance. This suggests that male song may not be an important supplemental timing cue. Next we explore potential consequences of timing on chick quality and multiple brooding behaviour. We demonstrate that somatic and physiological traits are more developed in chicks from earlier nests (first broods). We also document that physiological maturity, in the form of hemoglobin concentration, is related to fledgling flight ability. Although we show that second brood chicks maintain the same trajectory of development just prior to fledging, they may pay a higher cost in the form of oxidative stress. Finally we document that multiple brooding behaviour is unrelated to timing in our highly synchronous population, and instead relates to individual quality. Comprehensively, this thesis suggests that male social cues may not be important cues determining timing of breeding, and that the consequences of timing on offspring include maturity at fledging and oxidative stress, but not multiple brooding in our system.

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

Sexual Communication in Yellowjackets (Hymenoptera: Vespidae)

Author: 
Date created: 
2017-04-11
Abstract: 

To determine if and how pheromones mediate sexual communication of yellowjackets [Dolichovespula arenaria, D. maculata, Vespula alascensis, V. pensylvanica, V. squamosa], I took three approaches: (1) In field trapping experiments, I baited traps with a virgin queen (gyne) or a male and tested for their ability to attract prospective mates. I found that only gynes of D. arenaria attracted males. (2) In laboratory Y-tube olfactometer experiments with D. arenaria, D. maculata and V. pensylvanica, I used sibling or non-sibling gynes as a test stimulus, and found that only D. maculata gynes attracted conspecific males, provided they were non-siblings. These results imply an olfactory-based mechanism of nestmate recognition and inbreeding avoidance. (3) I tested the hypothesis that cuticular hydrocarbons (CHCs) differentiate sex, caste, and nest membership. I found that each caste had specific CHC profiles. My data demonstrate the diversity and complexity of sexual communication in yellowjacket wasps, and inspire follow-up studies to identify the sex pheromones.

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

From forecasting vulnerabilities to assessing recovery: the utility of demographic models in addressing population declines

Date created: 
2017-04-13
Abstract: 

Curbing species’ decline driven by anthropogenic modifications to natural systems requires a deep understanding of how specific changes to biotic and abiotic processes affect populations. Individual life history stages may differ in their response to such changes, consequently buffering or accelerating population declines. I explore the concept of demographic compensation among life stages using stage-structured demographic models to improve predictions for two conservation challenges; 1) forecasting climate change impacts to amphibian populations in montane ecosystems, and 2) identifying the most effective life history targets for recovering declining amphibian populations. In Chapters 2 and 3, I use demographic data for the Cascades frog (Rana cascadae) at northern and southern range boundaries to parameterize stochastic matrix population models under current and future environmental conditions to evaluate how climate change affects population stability. I demonstrate that R. cascadae populations at the northern range boundary are stable, but that compounding negative effects of climate on early and late life history stages creates a demographic tipping point by the 2080’s. I find that counter to range shift predictions, the population growth rate for the southern population will change little in the face of climate change, and differences in population stability between northern and southern range limits are driven by contrasting responses to climate. Equally important to forecasting population vulnerability, is preventing extinction of declining populations. In Chapter 4, I use demographic models to elucidate recovery potential for declining populations of Oregon spotted frogs (Rana pretiosa) by evaluating the effectiveness of population supplementation at multiple life stages. I compare two supplementation strategies, head-starting early life stages and captive breeding, and find captive breeding up to two orders of magnitude more effective at reducing extinction probabilities than head-starting. In Chapter 5, I extend the utility of such models using formal decision analysis to evaluate tradeoffs between the effectiveness of conservation actions and their economic costs. I reveal that the supplementation of wild populations with captive bred larvae results in the largest reduction in extinction risk per dollar invested. In this thesis, I use demographic models to improve our predictions of species’ responses to climate change before declines occur, and conversely, advance the quantitative framework for recovering declining populations.

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

A role for insect availability in limiting populations of a threatened nightjar Antrostomus vociferous

Date created: 
2017-04-13
Abstract: 

Aerial insectivore birds, those that capture prey while in flight themselves, are the avian guild experiencing the steepest population declines in Canada. Although we lack long-term data on insect abundances, one potential cause of these declines could be a change in prey availability. Furthermore, some nocturnal insectivores, like nightjars, face the additional challenge of only foraging during twilight periods, or when adequate moonlight is available. In this thesis, I take a variety of approaches to test and inform predictions associated with possible drivers of population decline in a threatened nightjar, Eastern Whip-poor-will (Antrostomus vociferous). Whip-poor-will prefer open-canopy, or fragmented, forests that allow moonlight to penetrate the canopy, so I first tested whether an increase in forest area appeared to explain their population decline. In contrast to expectation, whip-poor-will presence was positively associated with forest area at a regional scale, and only a delayed effect of urban area explained disappearances. At a more local scale, however, whip-poor-will abundance was positively related to both presence of open-canopy forests, and insect abundance. At this local scale, insect abundance also influenced daily survival rates of chicks, and productivity was higher when hatching coincided with peaks in insect abundance. Next, I tracked migration using light-logging geolocation tags to identify the wintering range of individuals from across the northern portion of the breeding range. I found evidence of migratory stopover in the southeastern United States and wintering locations in Mexico and Central America, suggesting that both regions are potentially important for this population. Finally, I tested for diet change over the past century using nitrogen isotope ratios of museum specimen tissues. Whip-poor-will isotope profiles were consistent with a gradual shift to feeding on lower trophic-level prey for both breeding season grown feathers and winter grown claws. All of these results are consistent with the hypothesis that whip-poor-will populations are declining due to changes in prey abundance, but I caution that habitat and climatic conditions at locations used throughout the annual cycle could also be contributing to these population declines.

Document type: 
Thesis
File(s): 
Senior supervisor: 
David Green
Joseph Nocera
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Identification and characterization of Francisella tularensis proteins required for invasion and escape into non-phagocytic epithelial cells

Date created: 
2017-03-31
Abstract: 

The potential bioterror agent Francisella tularensis subspecies tularensis (F. tularensis) is an intracellular human pathogen and the causative agent of tularemia. As an invasive pathogen, Francisella invades host cells; occupies and escapes membrane bound vacuoles; replicates in the host cytosol; then initiates their release to infect other cells. Tularemia begins when bacteria invade the phagocytic and non-phagocytic cells of the host. While non-phagocytic cell colonization contributes significantly to disease, the process is poorly understood. In this thesis, I identify and characterize key proteins in the invasion and vacuole escape stages of the non-phagocytic cell infection process. In chapter 2, I evaluated Francisella in vitro cell culture infection models present in the literature side-by-side with the model our lab developed using the murine surrogate of F. tularensis, F. tularensis subspecies novicida (F. novicida) and murine cultured hepatocytes. I found compared to other models, our model most accurately reflected colonization levels seen in vivo. In chapter 3 and chapter 4, I investigated bacterial proteins involved in invasion and vacuole escape. I screened a F. novicida transposon mutant library using our infection model for microbes deficient in bacterial replication. Using bioinformatics, I searched for invasion-deficient transposon mutants inactivated in Francisella surface proteins to screen for proteins that could interact with the host cell surface. I then tested their ability to cause tularemia-induced mortality in mice. I showed that bacteria inactivated in two genes caused no disease in mice and protected mice as live-vaccines against a wild-type F. novicida challenge. One gene I identified as Francisella infectivity potentiator A (FipA). I presented evidence that FipA enables bacteria to escape the vacuole using both florescence and electron microscopy. The next gene I identified, characterized, and named Francisella virulence factor A (FvfA). I demonstrated that FvfA is a bacterial surface-exposed ligand that exploits host clathrin-mediated endocytosis for entry using functional assays and dot blots. Lastly, I crystallized FvfA and compared FvfA to its structural homolog, E. coli RcsF. Taken together, I described two virulence factors, FipA and FvfA, that are critical for the initial stages of the Francisella non-phagocytic cell infection process and consequently, tularemia-effected death.

Document type: 
Thesis
Senior supervisor: 
Julian Guttman
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Sialic acid metabolism in the opportunistic fungal pathogen, Aspergillus fumigatus

Author: 
Date created: 
2015-11-23
Abstract: 

My research investigated sialic acid metabolism in the opportunistic fungal pathogen, Aspergillus fumigatus. The sialic acid, N-acetylneuraminic acid (Neu5Ac), is a sugar found on fungal spore cell surface that mediates adhesion to host proteins and phagocytes. The aims of the thesis were to characterize a novel A. fumigatus exo-sialidase (AfS), and to clone and characterize putative A. fumigatus nucleotide sugar transporters (AfNSTs) to identify CMP-Neu5Ac or UDP-galactose transporters. The A. fumigatus sialidase gene was expressed in E. coli and crystallized; the crystal structure and Michaelis – Menten kinetic analysis revealed that the glycoside of another sialic acid, 2-keto-3-deoxynononic acid (KDN), was a better substrate for the enzyme than glycosides of Neu5Ac. This enzyme represents the first sialidase characterized from the Kingdom Fungi. To better understand why KDN is a better substrate for AfS than Neu5Ac, using the enzyme structure as a guide in conjunction with known sialidase structures, a point-mutation (R151L) was introduced in the substrate binding pocket to better accommodate glycans with terminal Neu5Ac. Activity of the R151L mutant was slightly enhanced toward Neu5Ac. Moreover, amino acid sequence comparisons revealed that this amino acid may be a hallmark of KDNases. In addition, I attempted to identify a CMP-sialic acid transporter in A. fumigatus, a type of nucleotide sugar transporter (NST). NSTs mediate nucleotide sugar transport into the endoplasmic reticulum and Golgi complex for subsequent addition to glycoproteins and glycolipids. STD-NMR analysis and 14C-transport assays were conducted to examine the substrate specificity of four putative A. fumigatus NSTs expressed in yeast. Two transporters (AfNST1 and AfNST5) bound UDP-glucose and UDP-galactose, and transported 14C-UDP-galactose. Epitope maps showed that the UDP-moiety anchored the nucleotide sugar and that sugar structure conferred specificity because not all UDP-sugars bound to the NSTs. No CMP-sialic acid transport was detected. Despite similarities in substrate preference between AfNST1 and AfNST5, growth and morphology of the corresponding knock-out mutants differed; only the Af∆NST5KO was compromised when grown on media containing cell wall stressors. Using lectins and flow cytometry, I found that the level of cell surface galactose was significantly reduced in both knockout strains as compared to the wild type; however, sialic acid density on conidia was significantly reduced only in the Af∆NST5KO mutant. This research demonstrates for the first time that NSTs are important for the integrity of the fungal cell and may represent novel targets for antifungal agents.

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

Population Dynamics of the Western Tent Caterpillar: The Roles of Fecundity, Disease and Temperature

Date created: 
2016-09-09
Abstract: 

Many populations of forest Lepidoptera exhibit regular periodic cycles in abundance. Explicit mechanisms for such dynamics however, remain a subject of debate in Ecology. I used annual field data (1977-2015) from a cyclical species of forest Lepidoptera native to southwestern B.C., the western tent caterpillar (Malacosoma californicum pluviale), to elucidate how fecundity, viral disease and temperature contribute to its dynamics. Using time-series analysis and relationships between lagged population density, disease prevalence and annual population growth rate, I demonstrated that cyclical dynamics can be generated. I then used AIC model selection to show that fecundity and lagged population density had the greatest contributions to annual population rate of increase, followed by disease prevalence and warmer spring temperatures during larval development. Using these factors, I constructed a population model capable of generating population cycles similar to those observed in the field. These results indicate that fecundity, density-dependent disease prevalence and temperature contribute significantly to the cyclical dynamics of these populations.

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

Mass mortality events of echinoderms: Global patterns and local consequences

Date created: 
2016-08-23
Abstract: 

Wildlife mass mortality events can have profound ecological consequences and may be becoming more frequent or severe due to climate change, anthropogenic factors or other stressors. Mortality events involving echinoderms are of particular concern because of the important role echinoderms play in structuring marine ecosystems. In this thesis I explore the local consequences of a widespread sea star mortality event, and investigate the global trends in echinoderm mass mortality events. I found that the mass mortality of the sunflower sea star Pycnopodia helianthoides, which began in the summer of 2013 as a result of a wasting syndrome, resulted in a trophic cascade involving urchins and kelp at the local scale (i.e., Howe Sound, BC). A global review of reports of echinoderm die-offs revealed that these events have not become more frequent or extensive since 1897. However, disease and climate change may be playing an increasing role. This study provides some of the first evidence of subtidal community shifts following sea star wasting syndrome, and highlights the need for consistent and comprehensive documentation of echinoderm population trends in the literature to increase our understanding of mass mortality events.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Dr. Isabelle Côté
Dr. Michael Hart
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Vibratory signalling in two spider species with contrasting web architectures

Author: 
Date created: 
2016-08-15
Abstract: 

Spiders provide a fascinating opportunity for the study of animal communication. Web-building spiders build their own signalling environments - the web is the medium that transmits vibrations from prey, predators and potential mates. However, we know little about how information is conveyed through different types of webs, or how spiders distinguish between different types of vibrations. In this thesis, I studied elements of vibratory communication in two species of spiders with contrasting web architecture: the western black widow, Latrodectus hesperus, which builds a tangle-web, and the hobo spider, Eratigena agrestis, which builds a funnel-web. In chapter 2, I document formerly undescribed life history traits of E. agrestis, and conclude that life history traits are robust to differential predator and competitor densities across two study sites in British Columbia. In chapter 3, I present hitherto lacking quantitative descriptions of courtship behaviours in L. hesperus, revealing that web reduction by males correlates with reduced female aggression, and that it may improve mating success of courting males. In chapter 4, I describe how vibration frequencies are transmitted through the webs of L. hesperus and E. agrestis. I found little difference in propagation efficiency between longitudinal and transverse vibrations and that in both species vibration transmission is more variable within webs than between webs, suggesting that specific frequencies play a minor role in signalling. In chapter 5, I tested whether male courtship produces vibratory signals that differ from prey cues. I analysed vibrations produced by courting males and by two types of prey (flies and crickets) on the webs of L. hesperus and E. agrestis, and also played back male and prey vibrations through the webs of L. hesperus. Male vibrations differ more from those of prey in L. hesperus than in E. agrestis. This finding supports the hypothesis that L. hesperus males, faced with aggressive females, produce vibrations that prevent them from being mistaken for prey. The low-amplitude vibrations caused by abdominal tremulations of L. hesperus males may be linked with lowered female aggression.

Document type: 
Thesis
File(s): 
Abdominal tremulation of black widow male
Walking, drumming and tapping of hobo spider male
Jerk of hobo spider male
Aggressive response of a black widow female to a male high-amplitude playback vibration
Senior supervisor: 
Gerhard Gries
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.