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

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River network structuring of climate and landscape effects in salmon watersheds

Author: 
Date created: 
2019-01-09
Abstract: 

Climate change is altering historic patterns of temperature and precipitation worldwide with significant implications for the abiotic and biotic dynamics of river ecosystems. Flowing downhill, precipitation aggregates into creeks, streams and eventually rivers, forming a branching network over the landscape architecturally similar to the branches, limbs and trunk of a tree. Linking disparate locations, these river networks integrate the varied expressions of climate within a watershed. Thus, the river network offers a framework for understanding how spatial patterns of climate are organized and become manifest in rivers. By considering the river network's structuring of climate and landscape interactions, we might better understand how climate and land-use change impact river ecosystems and more clearly identify particularly vulnerable biota. In chapter 2, I examine how river networks dampen signals of climate change in hydrologic flow by integrating varied flow trends from upstream. I demonstrate that by integrating a diverse climate portfolio, the network accumulates changing flow regimes of different volatility, direction and magnitude, such that on average downstream climate change trends are moderated. In chapter 3, I consider the match-mismatch potential of juvenile salmon migrating towards the springtime zooplankton resource pulse in the estuary. I show that populations further from, and whose climate is more dissimilar to, the estuary, are more likely to miss the peak zooplankton bloom. These findings suggest migratory distance influences phenological mismatch risk among populations. My fourth chapter develops an unsupervised machine learning method for cleaning stream temperature data to facilitate big data studies. In chapter 5, I gathered temperature data at over 100 locations throughout a watershed the size of Ireland, over 4 years at 2-hour intervals resulting in over 1 million data points. These data informed a spatial stream network model that quantified how landscape features and river connectivity control seasonal temperature dynamics. These temperature dynamics across space and time revealed that different adult salmon migrations have very different exposures to warm temperatures. Collectively, these findings illustrate that river networks: 1. integrate and dampen signals of climate change, 2. structure phenological match-mismatch patterns and 3. organize thermal exposure potential of biota.

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

Non-lethal human-shark interactions and their ecological consequences

Date created: 
2018-10-31
Abstract: 

Collapses of predator populations, caused mainly by unsustainable fishing, have been documented in many marine ecosystems. Predators are thought to play critical roles in marine environments where, through direct predation and fear effects, they can shape demographic processes and community structure. My thesis focusses on the effects of two non-lethal anthropogenic impacts on sharks: prey depletion and shark provisioning tourism. Using stable isotopes and a time series of shark vertebrae, I first examine the historical isotope ecology of seven shark species from the southwest Indian Ocean. Two species with generalist diets showed no change over two decades in δ15N or δ13C signatures. Large individuals of five primarily piscivorous species exhibited isotope signatures that deviate from historical baselines, suggesting long-term changes in diet and/or foraging strategy. Next, I measure the effects of tourism-related provisioning on the trophic signatures and movement patterns of Caribbean reef sharks Carcharhinus perezi in the Bahamas. Combining stable isotope analyses, acoustic telemetry and direct observations, I show that individual sharks that are provisioned more frequently have elevated δ15N signatures, but similar residency and movement patterns to un-provisioned conspecifics, suggesting that their broader ecological roles are not affected by long-term provisioning. Finally, I use the gradient of shark abundance generated by provisioning for ecotourism to reveal the wider coral reef community corollaries of reef shark presence. Benthic community structure varied across this gradient, with less macroalgae and more turf algae at sites with more sharks. Herbivorous parrotfish were abundant but fed less selectively and consumed more macroalgae at sites with more sharks, suggesting that fear effects may drive the patterns observed. Teleost fish biomass was almost twice as high near the provisioning site than further away, a pattern driven by fisher avoidance of areas of more sharks. Effective shark conservation may thus deliver broad cascading benefits to coral reef communities. While most marine predator declines are due to direct fishing mortality, my thesis evokes additional mechanisms by which anthropogenic activities may drive change in predator populations and their communities.

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

The pollination ecology of highbush blueberry (Vaccinium corymbosum) in British Columbia

Author: 
Date created: 
2018-05-28
Abstract: 

Agricultural systems often support low beneficial insect diversity because they reduce habitat quality. Agricultural management increases landscape homogeneity resulting in low habitat and resource diversity. Crops that rely on wild pollinators for fruit production or predators and parasitoids for pest control may lose access to these services as the agroecosystem becomes increasingly managed. I used yield data from pollination experiments conducted over four years, along with insect surveys, to better understand the dynamics between insect communities in agroecosystems and their use of the agricultural landscape in highbush blueberry (Vaccinium corymbosum) in the Fraser Valley of southern British Columbia, Canada. Regional land use was identified as being an important component in structuring beneficial insect communities. Semi-natural habitat, such as pasture or fallow, was found to support greater abundances and diversity of all beneficial insects. Land use with greater disturbance, like conventional non-flowering agriculture, reduced pollinator species richness but increased the abundance of generalist predators. The differences between groups in their response to land use types might be driven by variability in access to resources (ex. floral resources or pest insects) in the larger agricultural landscape. However, surrounding landscape composition did not affect blueberry yield deficit, which was instead determined primarily by bumble bee visits and minimum daily temperatures. This finding highlights the importance of weather conducive to pollinator foraging for crop production. Despite the importance of bumble bees for reducing yield deficit, experimental introduction of two managed bumble bee species did not mitigate these deficits. Differences in bumble bee species characteristics associated with reproduction predicted pollen forager recruitment, which when coupled with differences in foraging preferences (blueberry pollen comprised 50% of pollen loads in one species, but less than 20% in the other and in managed honey bees) provides some insight into which managed species is best suited for further commercial development. My results highlight the complexity associated with predicting crop pollination levels and demonstrate how the impact of wild insects on production will vary with surrounding land-use, species characteristics, and abiotic factors. In crops highly reliant on wild pollinators, like highbush blueberry, understanding the needs of beneficial insects may allow farmers to modify practices to improve ecosystem services.

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

The role of adaptive behaviour in migratory counts of shorebirds

Author: 
Date created: 
2018-12-11
Abstract: 

Shorebird population status and trends are commonly generated from counts made at migratory stopovers, where large numbers are concentrated at few locations. Shorebirds migrate long distances, encountering changing and unpredictable conditions. The ability to respond with adjustments in behaviours such as site selection, timing and routing, is likely essential. In this thesis I examine how the adaptive behaviour of migrants affects the use of stopover sites, and hence how many shorebirds are counted. I develop a model of mortality-minimizing decisions made by southbound western sandpipers (Calidris mauri) moving through a landscape with large and small stopover sites. I use the model to simulate counts that would be observed under different scenarios, each leaving distinct `fingerprints' on the outcomes. These outcomes were compared to counts made over five years by citizen-scientists across the Salish Sea region. The results support the hypothesis that inter-annual variation in the passage timing of peregrine falcons (Falco peregrinus - the most important sandpiper predator) strongly affects the distribution of sandpipers across small and large stopover sites. Other scenarios appear less parsimonious. An analysis of data collected by the Atlantic Canada Shorebird Survey (2754 surveys, 1974 - 2015) reveals that semipalmated sandpipers (C. pusilla) have steadily shifted their stopover site usage toward larger sites. Surveys of the northbound passage of western sandpipers and dunlins (C. alpina) along the Pacific Flyway show that over recent decades (1985 - 2016), both species passage southern sites, but not northern sites earlier. Each of these approaches demonstrates that the behavioural response of shorebirds to landscape-level conditions affects counts strongly enough that the accuracy of estimated population trends can be poor. Caution should be exerted when using migratory counts to generate trends in populations.

Document type: 
Thesis
Senior supervisor: 
Ronald Ydenberg
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.

Multiple axon guidance pathways asymmetrically distribute axons in the ventral nerve cord of Caenorhabditis elegans

Author: 
Date created: 
2018-11-22
Abstract: 

Early during development neurons project small filamentous processes, axons and dendrites, that extend and eventually connect with other cells and tissues. These processes can grow over long distances and allow for transmission of information between cells. The proper functioning of our nervous system is dependent on these same processes correctly navigating to specific end targets. This is achieved through guidance cues in the environment which interact with receptors on the extending processes allowing them to be steered in the correct direction. Unfortunately, due to the high complexity of most vertebrate nervous systems our understanding of how axons and dendrites use these cues to navigate is still very limited. The aim of this thesis was to discover novel genes regulating axon guidance to shine additional light on how axons navigate during development. Normally axons of the ventral nerve cord in the nematode Caenorhabditis elegans are invariably sorted asymmetrically. Animals with mutations impacting function in individual axon guidance signaling pathways show no or only very low penetrance of disruption of VNC asymmetry. Here genetic screens successfully isolated four mutants in which asymmetry between major longitudinal axon tracts is disrupted. One of these four mutants include a novel allele of the gene col-99 which encodes a previously uncharacterized transmembrane collagen with vertebrate homologs. Detailed characterization of animals lacking COL-99 revealed widespread axon guidance defects impacting longitudinal and lateral axon navigation of a variety of neurons. Of the remaining three mutants two were found to be alleles of unc-52 and unc-34, both previously characterised for roles in axon guidance, while the final mutation remains unidentified. Disruption of any one signaling pathway does not lead to penetrant VNC asymmetry defects suggesting redundancy between parallel signaling pathways here. To better understand how signaling pathways of multiple guidance cues may converge to control guidance at choice points single mutants were crossed into a nid-1 null mutant background and VNC asymmetry phenotypes examined. Previously nid-1 was found to substantially enhance navigation defects of the VNC pioneering neuron AVG when crossed into mutants showing a low penetrance of AVG navigation defects. Double mutants with nid-1 saw defect penetrance significantly increase in several cases indicating parallel signaling pathways. Combination of mutants into triple and quadruple mutant strains showed that UNC-6, SAX-3, and COL-99 represent members of parallel signaling pathways acting redundantly to guide axons in establishment of asymmetry which in addition depends on basement membranes components, including EPI-1. Thus multiple axon guidance signaling pathways, acting in tandem, ensure correct guidance and segregation of axons at the anterior choice point of the VNC establishing VNC asymmetry.

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

The expression and regulation of lipid transport proteins in the desert locust, Schistocerca gregaria

Author: 
Date created: 
2018-11-19
Abstract: 

Lipids play a central role in insects, both for storage of nutrients and as an energy source during development and dispersal. Due to their low water solubility, special transport mechanisms are required for their efficient mobilization and utilization. In this thesis, I studied intra- and extracellular proteins involved in lipid transport in the desert locust, Schistocerca gregaria. Vitellogenins are very high-density lipoproteins produced by adult females and deposited into the developing eggs. Two different vitellogenins, named VG-A and VG-B, are expressed in locust fat body. Their complete cDNA transcripts of ~5.6 kb each have been sequenced, coding for two proteins of ~200 kDa each. VG-A and VG-B are co-expressed in similar amounts by mature females, commencing 11 days after adult eclosion, and continuing at high levels throughout the entire adult life. The expression of both proteins is dependent on the nuclear transcription factors Met or RXR, and knockdown of each of these proteins almost completely eliminates VG expression. A similar expression profile was observed in adult muscle for the cytosolic fatty acid binding protein FABP, albeit in both sexes. The direct knockdown of the strongly expressed FABP by RNA inference reduced its levels to less than 2% of what is normally found 3 weeks after adult eclosion. In a series of flight experiments, it was demonstrated that in the absence of FABP, insects are incapable of engaging in flight longer than 30 min; at this time, most carbohydrate resources have been depleted, and locusts normally switch to lipids as the sole fuel for muscle energy production. Short-term flight performance of FABP knockdown locusts was identical to control insects, suggesting that the lack of FABP does not interfere with carbohydrate metabolism. Moreover, the mobilization of lipids in the fat body and their transport by the major hemolymph lipoprotein lipophorin was indistinguishable from control animals. In contrast, knockdown of apolipophorin III, which is essential for lipid transport during flight, completely eliminated flight capability, even for short duration flights. Taken together, this thesis highlights the essential role of lipid transport proteins for locust reproduction and dispersal and identifies potential targets for insect control strategies.

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

Testing the ability of in-vitro depletion rates to assess the biotransformation rate and bioconcentration factor of hydrophobic chemicals in rainbow trout (Oncorhynchus mykiss)

Date created: 
2018-12-03
Abstract: 

The objective of this study was to test the ability of in-vitro biotransformation rates to predict in-vivo biotransformation rates and BCFs to ultimately improve chemical bioaccumulation assessment. In-vitro biotransformation rates of hydrophobic chemicals pyrene, methoxychlor, cyclohexyl salicylate, and 2,6 dimethyldecane were determined using a rainbow trout liver S9 preparation and then input into two in-vitro-in-vivo extrapolation (IVIVE) models to estimate in-vivo biotransformation rates (kMET) and modelled BCFs. Comparisons of in-vitro derived kMET values using both IVIVE models were in reasonable agreement when compared to in-vivo derived kMET values for pyrene and methoxychlor. Estimated BCFs from this study for pyrene, methoxychlor, and cyclohexyl salicylate were also in good agreement with estimated BCFs from previous studies using in-vitro biotransformation rates as inputs to IVIVE models, but were significantly higher compared to empirical BCFs. This indicates the potential usefulness of in-vitro biotransformation assays and IVIVE models for estimating kMET and BCFs, however kMET values from IVIVE models and BCF estimates should only be considered a conservative estimate at this time due to the uncertainty (i.e. extrahepatic metabolism) associated with these models and the further work required to fine-tune these models.

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

Application of the Blue Mussel (Mytilus edulis) as an indicator of microplastic pollution within the Salish Sea

Date created: 
2018-11-27
Abstract: 

Plastic polymers less than 5 mm in diameter, called microplastics (MPs), are an emerging contaminant of concern impacting marine organisms globally. The blue mussel (Mytilus edulis) is a prominent bioindicator used to quantify the accumulation of lipophilic contaminants to assess the health of marine environments. For this reason, blue mussels were utilized to establish baseline MP abundances in British Columbia (BC) and assess the practicality of using mussels as indicators of MP pollution. Mussels (n = ~15, 000) were placed in cages at 11 locations within the Strait of Georgia and southern BC waters in the winter of 2017. Mussels were sampled on Day 0, Day 30 and Day 60 post deployment and MP abundances quantified. For all sites combined, a total of 336 suspected microplastics (SMPs) were identified in 171 mussels, resulting in an average of 1.96 (0.13 SE) SMPs per mussel. After correcting for contamination and standardizing for weight, mean SMP abundances averaged 0.43 (0.06 SE) CSMP/GWW (gram wet weight). 91% of the SMPs enumerated were microfibers. A two-factor complete randomized design analysis of variance revealed that mean CSMP/GWW differed significantly over the 60-day period between the 11 sites (p = 0.0003), however, only mussels at the T60 – Powell River site had significantly more CSMPs/GWW. Furthering this, Fourier Transform Infrared Spectroscopy identified a total of 11 of 66 SMP particles (17%) as plastic. A complimentary exposure experiment was conducted in the spring of 2018 to assess particle fate post mussel filtration. Using a combination of polymer types and sizes, mussels were exposed to three environmentally relevant concentrations of MPs. Pseudofaeces, faeces and whole mussels were examined for MPs 24-hours post exposure. While whole mussels had significantly more MPs than pseudofaeces and faeces (p<0.01; mean proportions ranged from 46-68%, 2-4%, 3-8%, respectively) our results confirmed that MPs were both rejected prior to, and eliminated post digestion, suggesting that blue mussels might be a poor indicator of MP pollution. If plastic loads continue to increase as theorized, however, it is probable that the ability of blue mussels to reject and eliminate MPs efficiently will be impacted.

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

Sub-lethal effects of clothianidin on early life stage sockeye salmon (Oncorhynchus nerka)

Author: 
Date created: 
2018-11-19
Abstract: 

One of the contaminants possibly contributing to declining sockeye salmon (Oncorhynchus nerka) in the Fraser River is pesticides. In this 4-month study, the effects of environmentally relevant concentrations of waterborne clothianidin (0.15, 1.5, 15 and 150 μg/L) on embryonic, alevin and early swim-up fry sockeye salmon derived from four unique genetic crosses of the Pitt River, BC stock were investigated. There were no significant effects of clothianidin on survival, hatching, growth or deformities, although genetic variation significantly affected these endpoints. Clothianidin caused a significant 4.7-fold increase in whole body 17β-estradiol levels in swim-up fry after exposure to 0.15 µg/L, but no effects were observed on testosterone levels. These results indicate additional examination of clothianidin and its effects on salmonid gonad development and the reproductive endocrine axis in general, is warranted.

Document type: 
Graduating extended essay / Research project
File(s): 
Senior supervisor: 
Vicki Marlatt
Department: 
Science: Biological Sciences Department
Thesis type: 
(Project) M.E.T.

Development of micro-propagation in bigleaf maple (Acer macrophyllum) and screening for early markers preceding figured wood formation

Author: 
Date created: 
2018-09-20
Abstract: 

Some bigleaf maple (Acer macrophyllum) trees develop defects during wood formation that result in attractive ‘wavy figure’ patterns in the wood. This wood commands a high price and is used primarily for making musical instruments and decorative products. While the underlying causes of these defects are unknown, the large extent and homogeneity of the defects in many individuals suggest an underlying genetic basis. Typically, available living material from cut trees is limited. To propagate trees from a limited amount of source material, we have developed an in vitro procedure that combines (i) cutting of shoot apices to break apical dominance with (ii) hormone treatment to induce shoot multiplication from lateral buds. This procedure can be repeated as needed for propagation, followed by root induction to generate bigleaf maple plants. It is not assured that clones of figured wood trees will develop figure patterns, and harvested trees typically do not show figure patterns in their 10–15 first growth rings. Hence, we have begun searching for potential early anatomical and/or chemical differences between young clones from non-figured and figured trees. Pyrolysis Molecular Beam Mass Spectroscopy analysis suggests that the content of two unknown cell wall components, m/z_69 and m/z_298, differ between non-figured wood and figured wood tree clones. The basis for this difference remains unknown. Taken together, we have developed the first micro-propagation procedure for bigleaf maple and also identified potential markers of early chemical differences between tested clones of figured and non-figured wood trees.

Document type: 
Thesis
File(s): 
Senior supervisor: 
Dr. Jim Mattsson
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.