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

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Enhancing the growth and health of sockeye salmon (Oncorhynchus nerka) in land-based freshwater aquaculture

Author: 
Date created: 
2021-12-08
Abstract: 

The goal of this research was to provide data to assist in optimizing freshwater aquaculture practices for sockeye salmon (Oncorhynchus nerka), and specifically, for LSL a land-based, freshwater sockeye salmon farm. Thus, this study successfully conducted inaugural trials using 17 beta-estradiol waterborne treatments (200 μg/L, 400 μg/L and 800 μg/L) to feminize genetic males to develop an enhanced male population to achieve larger sized sockeye at slaughter. In addition, this study tested the effects of weekly netting stress over 100 days and revealed a significant reduction in body weight and length of juveniles, and a change in the abundance of three liver proteins involved in the immune-responsive gene regulation, protein processing and cytoskeletal structure organization. However, bacterial kidney disease prevalence, leukocyte count, hematocrit, and whole-body cortisol level were not affected. This research shows that mild physical stress does compromise growth in juvenile sockeye salmon and would restrict commercial production substantially.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Vicki Marlatt
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Functional roles of sea cucumbers in a coral reef-seagrass ecosystem

Author: 
Date created: 
2021-08-16
Abstract: 

Animals can mediate energy and material movement within a system, which can drive ecosystem function. Through excretion and egestion, animals can supply ammonium to nutrient-poor tropical marine systems, potentially altering primary productivity. My thesis explores how sea cucumber identity influences rates of ammonium excretion and bioturbation, and how this affects seagrass growth in The Bahamas. I quantified ammonium excretion and bioturbation rates in two species, Holothuria mexicana and Actinopyga agassizii, and found that H. mexicana excretes ammonium and bioturbates sediment at higher rates per-individual. I conducted a manipulative field experiment to test whether the differences I found between species translate to differences in seagrass productivity when one sea cucumber species is replaced by the other. I found that fish biomass was more important in predicting seagrass responses than sea cucumber identity or density, and that reef proximity and sampling day best predicted all seagrass responses. My research suggests that species-specific differences in bioturbation and ammonium excretion rates by sea cucumbers do not extrapolate at the ecosystem level. Thus, H. mexicana and A. agassizii may be functionally redundant, at least in terms of nutrient provisioning, in the patch reef-seagrass system I investigated in The Bahamas.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Isabelle Côté
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Assessment of biotransformation rates of organic compounds in mammals using in-vitro S9 bioassays

Author: 
Date created: 
2021-11-08
Abstract: 

The overall objective of this study was to develop an in vitro based screening approach to determine the biotransformation rate constants of neutral hydrophobic organic chemicals in rats from rat liver S9 bioassays, and to test this screening approach by comparing in-vitro predicted biotransformation rates to in-vivo measured biotransformation rates. The test chemicals used for this study were pyrene, benzo(a)pyrene, hexachlorocyclohexane-beta, methoxychlor, mono-n-butyl phthalate, and 4-n-nonylphenol. In-vitro biotransformation rate constants were successfully obtained for all test chemicals and extrapolated to whole organism biotransformation rate constants using various IVIVE models. All the model outputs (IVIVE & QSAR) were compared to one another using descriptive statistical analysis. Various statistical parameters imply that all IVIVE models are very similar in performance. This indicates that the IVIVE-b model and IVIVE-Krause & Goss model (blood flow not considered), which require fewer biological parameters, could be used instead of the IVIVE-ph and IVIVE-Krause & Goss model (blood flow considered) for bioaccumulation assessment. Additionally, the IVIVE models were shown to perform slightly better than the QSAR models, indicating that the IVIVE models might be a better tool for estimating biotransformation rate constants compare the QSAR models. However, due to the variability in the in-vivo data and only a few chemicals being tested, a definitive conclusion cannot be made regarding which model performs the best. Furthermore, the IVIVE and QSAR models could be further upgraded in the future and only time will tell which models are the best for predicting whole organism biotransformation rate constants in rats.

Document type: 
Graduating extended essay / Research project
File(s): 
Supervisor(s): 
Frank Gobas
Department: 
Science: Biological Sciences Department
Thesis type: 
(Project) M.E.T.

Managing emerging diseases of organic greenhouse vegetables: Interactions between vermicompost and biological control agents

Author: 
Date created: 
2021-05-07
Abstract: 

Biological control agents and composted materials, including vermicomposts and their water extracts, are used to suppress plant diseases in organic production systems, where fungicide use is limited. The past decade has seen a doubling in organic horticulture and a dramatic increase in vermicompost research. As disease suppression by vermicomposts has been inconsistent, research in this area requires standardization of methods, and compatibility with current biocontrol agents has not been assessed. I tested the disease suppressive abilities and microbial communities of five vermicomposts with differing characteristics, and developed Petri dish and growth chamber assays to examine compatibility with biocontrol agents. In vitro suppression of the pathogens Fusarium oxysporum f. sp. radicis-cucumerinum D.J. Vakalounakis (Forc), and Rhizoctonia solani J.G. Kühn, as well as disease suppression on cucumber and radish plants, respectively, was assessed using vermicomposts incorporated into sterilized substrate and using aerated vermicompost water extract. All vermicomposts provided significant pathogen suppression in vitro as well as plant disease suppression. The mechanism for pathogen suppression was negated by autoclaving. A range of responses between the biocontrol agents Bacillus subtilis (Ehrenberg) Cohn strain QST 713 (Rhapsody®) and Clonostachys rosea f. catenulata Samuels, Seifert, and Gams (syn, Gliocladium catenulatum) strain J1446 (Prestop®), and vermicomposts, was observed in vitro. I tested for interactions between these biocontrol agents and vermicomposts as an example of application of a biological control agent to a microbially competitive growth medium using a mixed effects model approach. Consistent antagonistic to neutral interactions in vitro, and a range of interactions from antagonistic to additive in planta, suggest that the interaction between a biocontrol agent and a competitive microbial milieu is not additive. The testing strategies investigated provide an efficient screen of vermicomposts for compatibility with existing biocontrol agents, and of biocontrol agent efficacy in a competitive environment. With improved and consistent testing methods, vermicompost can be a reliable approach for plant disease management in organic agriculture.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Zamir Punja
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Foraging ecology of the Northern Goshawk in coastal British Columbia

Author: 
Date created: 
2021-07-21
Abstract: 

Effective wildlife conservation requires understanding diet composition and its consequences for population demography. I measured the diet of an at-risk population of Northern Goshawks (Accipiter gentilis) in southwestern British Columbia during two breeding seasons using pellets, prey remains, and nest cameras. I compared diet composition across two ecological zones and assessed the impact of dietary diversity and specialization on goshawk productivity. Goshawks consumed 33 different species but primarily consumed pine squirrels (Tamiascuirus spp.), which composed 14-61% of dietary biomass, depending on source. Diet composition differed slightly between the coastal and transition zones. I also conducted a pilot study of goshawk breeding season movement using GPS-UHF transmitters. Male goshawks used more space and travelled further from the nest than female goshawks. While I found no correlation between dietary diversity or specialization on pine squirrels and goshawk productivity, the abundance of this key prey species may affect goshawk productivity and space use.

Document type: 
Thesis
File(s): 
Supervisor(s): 
David Green
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

A systematic analysis of iron and iglr genes’ function in axon guidance within the ventral nerve cord of Caenorhabditis elegans

Author: 
Date created: 
2021-07-27
Abstract: 

For the nervous system to develop properly, axons must connect neurons into networks by navigating to their target destinations. A large proportion of genes containing extracellular Leucine-Rich Repeats (eLRRs) function in neurodevelopment, including in axon guidance. The objective of this thesis is to identify novel eLRR genes in the Caenorhabditis elegans’ lron and iglr gene families that function in axon guidance. Animals with mutations in these genes were observed with pan-neuronal and pioneer markers to identify mutations that induced axon guidance defects. Six mutants had significant axon guidance defects. In addition, iglr-2 mutants were found to have fasciculation defects in the left ventral nerve cord. lron-11 mutants had the most penetrant axon guidance defects. Therefore, lron-11 animals were further characterized with several inter and motor neuron markers and further axon guidance defects were identified. This research suggests that lron-11 and possibly other lron/iglr genes function as receptors in axon guidance.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Harald Hutter
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Assessing species- and population-level vulnerability to climate-driven phenological mismatch in Pacific salmon

Author: 
Date created: 
2021-04-19
Abstract: 

Climate change is shifting the timing of life-cycle events, or phenology, of species at different rates, reshuffling species interactions, and sometimes resulting in consumer-resource mismatches, which can impact consumer fitness, survival, and population growth. Indeed, the match/mismatch hypothesis posits that a temporal mismatch between a consumer and its resource during a critical life stage will decrease consumer survival. Migratory species such as Pacific salmon move through multiple environments, experiencing different rates of climate change, and share the migratory challenge of matching with temporally limited resources that shift through time and space. For emigrating juvenile salmon smolts, survival during the critical early marine life stage may depend on matching with peak prey availability upon ocean entrance. Here I examine the vulnerability of Pacific salmon to phenological mismatches during the early marine life stage. In Chapter 2, I use a large-scale synthesis to show unpredictable patterns in phenological change across populations of Pacific salmon, which result in seemingly random rates of phenological mismatch with marine prey. In Chapter 3, I use a unique dataset of individually marked steelhead trout smolts to examine both individual and cohort marine survival across 14 years, demonstrating that size, outmigration timing, and a phenological match between smolts and annual phenology of the cold-water zooplankton community, are important predictors of marine survival. Thus, some species and populations of Pacific salmon are being exposed to phenological mismatches which negatively impact survival. In Chapter 4, using an experimental approach, I develop relationships between body condition and either prolonged swim performance or survival. Finally, in Chapter 5, I found within- and across-population variation in body condition of wild sockeye salmon smolts before and after migration. Using a bioenergetic model and the relationship between Fulton’s condition factor and swim performance developed in Chapter 4, I predicted starvation resistance, that is, days to death, to demonstrate how body condition could be used as a proxy for sensitivity to starvation associated with phenological mismatch. Collectively, these studies demonstrate that salmon are resilient to infrequent phenological mismatches, but it is unclear how anthropogenic change will impact vulnerability into the future.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Jonathan Moore
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

The roles of ectotherm physiology and habitat use with changing water availability

Author: 
Date created: 
2021-04-20
Abstract: 

Environmental regimes are shifting with accelerating climate change, putting at risk species whose ecology has been shaped by pre-industrial climates. Both species physiology and habitat associations are central to many predictions of future climate risk. Here I focus on the role of water, both in terms of ectotherm physiology through water loss, and as habitat essential for many amphibian life histories. In Chapter 1, I explore whether amphibian and squamate thermal safety margins are mediated by species’ propensity for water loss. In Chapter 2, I combine estimates of species’ habitat use and the hydrologic suitability of wetland habitats to predict how drying from climate change may drive future habitat loss in alpine regions of the US Pacific Northwest. This work indicates that water loss has been critical to shaping species’ physiology, and that water availability as critical habitat is central to species’ persistence across alpine landscapes in the future.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Wendy Palen
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

The effects of sediment organic carbon and chemical residence time on the acute toxicity of sea lice chemotherapeutants to benthic invertebrates

Author: 
Date created: 
2021-03-25
Abstract: 

Chemotherapeutants are commonly used to manage sea lice outbreaks in salmonid aquaculture. Among the classes of chemotherapeutants used are avermectins; these tend to persist in the sediments underneath salmon farms and may directly impact nearby benthic fauna of marine ecosystems. The present study sought to determine how two environmental factors – namely, sediment organic carbon (OC) and chemical residence time – can modify the toxicity of emamectin benzoate (EB; formulation: Slice®) and ivermectin (IVM) in two species of benthic invertebrates: the amphipod Eohaustorius estuarius and the polychaete Neanthes virens. In both species, sediment OC significantly reduced toxicity, an effect that was more pronounced for IVM and combination exposures. Four months of chemical residence time reduced toxicity in E. estuarius but did not affect toxicity in N. virens. This research provided novel insight into the effects of two environmental factors that potentially impact avermectin toxicity in nontarget species underneath salmon farms.

Document type: 
Graduating extended essay / Research project
Supervisor(s): 
Chris Kennedy
Department: 
Science: Biological Sciences Department
Thesis type: 
(Project) M.E.T.

The allometry of oxygen supply and demand in the California Horn Shark, Heterodontus francisci

Author: 
Date created: 
2021-01-21
Abstract: 

The scaling relationship between metabolic rate and body mass is one of the most notable functional relationships in comparative physiology and macroecology. In aquatic ectotherms, the surface area of the gills is thought to be a major contributor to the allometric scaling patterns we see for metabolic rate, both within and across species. Here, I first examined the allometric relationship between oxygen supply (gill area) and consumption (metabolic rate) and found that the allometry of gill area was isometric and very similar to that of metabolic rate. Second, I tested the effects of three statistical analysis techniques for estimating maximum metabolic rate and found that a rolling regression model was the best candidate model across four fish species. Together, these results support the hypothesis that oxygen supply and demand are closely matched and suggest that a two-dimensional gill can overcome geometric constraints to increase at the same rate as the three-dimensional mass of an inactive organism. Additionally, they highlight the importance of statistical choices in producing comparable and reproducible estimates of metabolic rate across species.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Nicholas Dulvy
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.