Graduate Theses & Dissertations


Spatial Dynamics of Wind Pollination in Broadleaf Cattail (Typha latifolia)
Natural populations of flowering plants rarely have perfectly uniform distributions, so trends in pollen dispersal should affect the size of the pollination neighbourhood and influence mating opportunities. Here I used spatial analysis to determine the size of the pollination neighbourhood in a stand of the herbaceous, wind-pollinated plant (Typha latifolia; broad-leaved cattail) by evaluating patterns of pollen production and seed set by individual cattail shoots. I found a positive correlation between pollen production and seed set among near-neighbour shoots (i.e., within 4 m2 patches of the stand; Pearson's r = 0.235, p < 0.05, df = 77) that was not driven by a correlation between these variables within inflorescences (Pearson's r = 0.052, p > 0.45, df = 203). I also detected significant spatial autocorrelations in seed set over short distances (up to ~ 5 m) and a significant cross-correlation between pollen production and seed set over distances of < 1 m indicating that the majority of pollination events involve short distances. Patterns of pollen availability were simulated to explore the shape of the pollen dispersal curve. Simulated pollen availability fit actual patterns of seed set only under assumptions of highly restricted pollen dispersal. Together, these findings indicate that even though Typha latifolia produces copious amounts of pollen, the vast majority of pollen dispersal was highly localized to distances of ~ 1 m. Moreover, although Typha latifolia is self-compatible and has been described as largely selfing, my results are more consistent with the importance of pollen transfer between nearby inflorescences. Therefore, realized selfing rates of Typha latifolia should largely depend on the clonal structure of populations. Author Keywords: clonal structure, correlogram, dispersal curves, pollination, spatial analysis, Typha latifolia
Expression and characterization of cytochrome b5 from Giardia lamblia
Giardia lamblia is an intestinal parasite found globally in freshwater systems that is responsible for endemic outbreaks of infectious diarrhea. As a unicellular parasite that lacks mitochondria, a respiratory chain and lives in the anaerobic environment of its host's intestine, Giardia was assumed for decades to lack heme proteins. However, its genome encodes several putative heme proteins, including three with sequence similarity to the cytochrome b5 family, referred to as Giardia cytochromes b5 (gCYTb5). Recombinant expression of one of these genes (gCYTb5-I), results in a protein (17-kDa) that is isolated with noncovalently bound heme. Resonance Raman and UV-visible spectra of gCYTb5-I in oxidized and reduced states resemble those of microsomal cytochrome b5, while sequence alignment and homology modelling supports a structure in which a pair of invariant histidine residues act as axial ligands to the heme iron. The reduction potential of gCYTb5-I measured by cyclic voltammetry is -165 mV vs the standard hydrogen electrode and is relatively low compared to those of other family members. The amino- and carboxy-terminal sequences that flank the central heme-binding core of the gCYTb5 are highly charged and do not occur in other family members. An 11-kDa core gCYTb5-I variant lacking these flanking sequences was also able to bind heme; however, we observe very poor expression of this truncated protein as compared to the full-length protein. Author Keywords: b-type cytochrome, cytochrome b5, electron transfer protein, Giardia intestinalis, heme/heam protein, spectroelectrochemistry
Soil Geochemistry and Normative Mineralogy across Canada
Soils play a crucial role in ecosystem functioning, for example, soil minerals provide important provisioning and regulate ecosystem services. This study used major soil oxides from the North American Soil Geochemical Landscapes Project (n=560) to assess elemental associations and infer soil minerals through exploratory data analysis and to determined quantitative soil mineralogy using a normative method, Analysis to Mineralogy (n=1170). Results showed elemental variability of oxides across the provinces of Canada and strong correlations occurred between elements indicative of soil mineral composition (e.g., Silicon and Aluminium). Principal component analysis inferred soil minerals from soil oxides trends on biplots and classified minerals, generally, as carbonates, silicates, and weathered secondary oxides. Spatial variability in minerals (quartz, plagioclase, potassium feldspar, chlorite, and muscovite) was related to the underlying bedrock geology. The use of Analysis to Mineralogy led to a reliable method of quantifying soil minerals at a large scale. Author Keywords: Analysis to Mineralogy, Exploratory data analysis, Normative procedures, North American Soil Geochemical Landscapes Project, Soil geochemistry, Soil mineralogy
Effect of SP600125 JNK Inhibitor on Cadmium-Treated Mouse Embryo Forelimb Bud Cells In Vitro
This study investigated the role of the JNK signaling pathway in cadmium-treated mouse embryo forelimb bud cells in vitro. Primary cultures of forelimb bud cells harvested at day 11 of gestation were pre-treated with JNK inhibitor SP600125, and incubated with or without CdCl2 for 15, 30, 60, 120 minutes and 24, 48 hours or 5 days. Endpoints of toxicity were measured through cell differentiation by Alcian Blue Assay and phosphorylation of JNK proteins by Western blot. The results demonstrated that, in the cell differentiation assay, inhibiting JNK activation by 20 μM SP600125 causes an enhanced toxic effect in limb cells and inhibits cell differentiation, whereas 2 μM decreases differentiated nodule numbers under both cadmium stress and normal conditions. In conclusion, the JNK pathway has an essential role in the differentiation processes of limb bud cells in normal growth conditions. Author Keywords: Cadmium, Cell Signaling, JNK, Limbs, Mouse Embryo, Teratology
Cytokinin biosynthesis, signaling and translocation during the formation of tumors in the Ustilago maydis-Zea mays pathosystem
Cytokinins (CKs) are hormones that promote cell division. During the formation of tumors in the Ustilago maydis-Zea mays pathosystem, the levels of CKs are elevated. Although CK levels are increased, the origins of these CKs have not been determined and it is unclear as to whether they promote the formation of tumors. To determine this, we measured the CK levels, identified CK biosynthetic genes as well as CK signaling genes and measured the transcript levels during pathogenesis. By correlating the transcript levels to the CK levels, our results suggest that increased biosynthesis and signaling of CKs occur in both organisms. The increase in CK biosynthesis by the pathosystem could lead to an increase in CK signaling via CK translocation and promote tumor formation. Taken together, these suggest that CK biosynthesis, signaling and translocation play a significant role during the formation of tumors in the Ustilago maydis-Zea mays pathosystem. Author Keywords: Biosynthesis, Cytokinins, Signaling, Translocation, Ustilago maydis, Zea mays
Calving site selection and fidelity in a restored elk (Cervus elaphus) herd in Bancroft, Ontario, Canada
ABSTRACT Calving site selection and fidelity in a restored elk (Cervus elaphus) herd in Bancroft Ontario, Canada. Michael R. Allan Parturition site selection by ungulates is believed to be influenced by forage abundance and concealment from predators. In 2011 and 2012, I used vaginal implant transmitters and movements to identify calving sites for 23 GPS collared elk (Cervus elaphus) from a restored herd. I tested the hypothesis that maternal elk used sites with higher forage and denser concealment compared to pre-calving sites at micro and macrohabitat levels. I detected no significant microhabitat differences from direct measurements of vegetation. At the macrohabitat scale, based on proximity of landcover classes, mean distances to hardwood forests was significantly less for calving (153 m) than pre-calving sites (198 m). Site fidelity is hypothesized to offer security in terms of familiarity to an area. I tested the hypothesis that females demonstrated fidelity to their previous year's location during pre-partum, parturition, post partum, breeding and winter periods. Elk were more philopatric during parturition and post partum than during breeding. Compared to winter elk were more philopatric during pre-partum, parturition and post-partum periods. Expressed as distance between consecutive-year calving locations, site fidelity varied with 27% of females exhibiting high (<1 km), 18% moderate and 55% (>2.9 km) low fidelity. I measured nearest-neighbour distances at calving time, exploring the hypothesis that females distance themselves from conspecifics. Elk increased the average distances to collared conspecifics during parturition; however, sample sizes were small. This strategy might influence calving site selection. Rapid movement prior to parturition, low site fidelity and spacing-out of females during parturition appear to be strategies to minimize predator risk and detection. Little evidence of selection for vegetation structure suggests this may not be limiting to these elk. Author Keywords: calving, elk, fidelity, movement, parturition, selection
Comparative Evaluation of Effective Population Size Genetic Estimation Methods in Wild Brook Trout (Salvelinus fontinalis) Populations
Effective population size (Ne) is a key concept in population genetics, evolutionary biology and conservation biology that describes an important facet of genetic diversity and the capacity of populations to respond to future evolutionary pressures. The importance of Ne in management and conservation of wild populations encouraged the development of numerous genetic estimators which rely on a variety of methods. Despite the number and diversity of available Ne methods, however, tests of estimator performance have largely relied on simulations, with relatively few tests based on empirical data. I used well-studied wild populations of brook trout (Salvelinus fontinalis) in Algonquin Park, Ontario as a model system to assess the comparative performance of multiple Ne estimation methods and programs, comparing the resultant Ne estimates against demographic population size estimates. As a first step, the genetic diversity and ancestry of wild brook trout populations was determined using 14 microsatellite loci. Genetic structure of brook trout populations showed variable contributions from historical supplemental stocking and also identified localized gene pools within and between watersheds, reflecting variable levels of connectivity and gene flow. Once the genetic ancestry and connectivity of populations had been resolved, single sample (point) and two samples (temporal) genetic estimators were used to estimate Ne of populations with pure native ancestry. Values obtained from genetic estimators utilizing both methods were variable within as well as among populations. Single sample (point) estimators were variable within individual populations, but substantially less than was observed among the temporal methods. The ratios of Ne to the estimated demographic population size (N) in small populations were substantially higher than in larger populations. Variation among estimates obtained from the different methods reflects varying assumptions that underlay the estimation algorithms. This research further investigated the effect of sampling effort and number of microsatellite loci used on Ne values obtained using the linkage disequilibrium (LD) estimation method. Ne estimates varied substantially among values generated from subsets of loci and genotyped individuals, highlighting the necessity for proper sampling design for efforts aiming to measure Ne. Despite the variation observed among and within estimation methods, the Ne concept is a valuable for the conservation and management of both exploited and endangered species. Author Keywords: Brook Trout, Effective population size, Genetic Diversity, Genetic Structure
Shorebird Stopover Ecology and Environmental Change at James Bay, Ontario, Canada
I examined how shorebirds respond to environmental change at a key subarctic migratory bird stopover site, the southwestern coast of James Bay, Ontario, Canada. First, I investigated if the morphology of sandpipers using James Bay during southbound migration has changed compared to 40 years prior. I found shorter, more convex and maneuverable wings for sandpipers in the present-day compared to the historical monitoring period, which supports the hypothesis that wing length change is driven by increases in predation risk. Secondly, I assessed the relationship between migration distance, body condition, and shorebird stopover and migratory decisions. Species that travelled farther distances from James Bay to wintering areas migrated with more characteristics of a time-minimizing migration strategy whereas species that travelled shorter distances migrated with energy minimizing strategies. Body condition impacted length of stay, wind selectivity at departure, groundspeeds, and probability of stopover and detection in North America after departing James Bay. Thirdly, I examined annual variation in dry/wet conditions at James Bay and found that shorebirds had lower body mass in years with moderate drought. In the present-day, drought resulted in lower invertebrate abundance and refuelling rates of shorebirds during stopover, which led to shorter stopover duration for juveniles and a higher probability of stopover outside of James Bay for all groups except white-rumped sandpiper. Finally, I estimated the relative importance of intertidal salt marsh and flat habitats to the diets of small shorebirds and found that semipalmated and white-rumped sandpiper (Calidris pusilla and C. fuscicollis) and semipalmated plover (Charadrius semipalmatus) diets consist of ~ 40 – 75% prey from intertidal marsh habitats, the highest documented in the Western Hemisphere for each species. My research shows that James Bay is of high importance to white-rumped sandpipers, which are unlikely to stop in North America after departing James Bay en route to southern South America. Additionally, intertidal salt marsh habitats (and Diptera larvae) appear particularly important for small shorebirds in the region. My thesis shows that changing environmental conditions, such as droughts, can affect shorebird refuelling and stopover strategies. Author Keywords: body condition, diet, environmental change, migration, ornithology, stopover ecology
Genomic architecture of artificially and sexually selected traits in white-tailed deer (Odocoileus virginianus)
Understanding the complex genomic architecture underlying quantitative traits can provide valuable insight for the conservation and management of wildlife. Despite improvements in sequencing technologies, few empirical studies have identified quantitative trait loci (QTL) via whole genome sequencing in free-ranging mammal populations outside a few well-studied systems. This thesis uses high-depth whole genome pooled re-sequencing to characterize the molecular basis of the natural variation observed in two sexually selected, heritable traits in white-tailed deer (Odocoileus virginianus, WTD). Specifically, sampled individuals representing the phenotypic extremes from an island population of WTD for antler and body size traits. Our results showed a largely homogenous genome between extreme phenotypes for each trait, with many highly differentiated regions throughout the genome, indicative of a quantitative model for polygenic traits. We identified and validated several potential QTL of putatively small-to-moderate effect for each trait, and discuss the potential for real-world application to conservation and management. Author Keywords: evolution, extreme phenotypes, genetics, genomics, quantitative traits, sexual selection
Effects of Invasive Wetland Macrophytes on Habitat Selection by Turtles
Invasive species that alter habitats can have significant impacts on wildlife. The invasive graminoids Phragmites australis (Cav.) Trin. ex Steud, hereafter Phragmites, and Typha × glauca Godr. are rapidly spreading into North American wetlands, replacing native vegetation. Invasive Phragmites is considered a potential threat to several species-at-risk (SAR), including some turtle species. My study wetland contained large stands of Phragmites, as well as Typha spp. (including invasive T. × glauca) that have similar structural traits to Phragmites. To explore the hypothesis that Phragmites and Typha spp. do not provide suitable habitat for turtles, I tested the prediction that turtles avoid Phragmites- and Typha-dominated habitats. I used VHF-GPS transmitters to follow Blanding’s turtles (Emydoidea blandingii, n = 14) and spotted turtles (Clemmys guttata, n = 12). I found that both turtle species did not avoid Phragmites- or Typha-dominated habitats when choosing a home range, or while moving within their home range. I also tested whether the microhabitat selection of Blanding’s turtles and spotted turtles is affected by shoot density of Phragmites, Typha spp., or both. I compared shoot densities of Phragmites and Typha spp. in 4 m2 plots, from locations used by tracked turtles with paired, random locations in these turtles’ home ranges. For both turtle species, the densities of Phragmites and Typha shoots were comparable between used and random locations within the home ranges (generalized linear mixed model; p > 0.05). The use of Phragmites- and Typha-dominated habitats by Blanding’s turtles and spotted turtles suggests that these habitats do not automatically constitute “unsuitable habitats” for turtles. Phragmites and Typha spp. (especially T. × glauca) can replace preferred habitats of some turtle species, and the control of these invasive macrophytes can help to preserve habitat heterogeneity. However, the presence of SAR turtles in Phragmites and Typha spp. stands should inform risk-assessments for invasive plant species control methods that include mechanical rolling of stands, where heavy machinery might encounter turtles. Author Keywords: Blanding’s turtles, compositional analysis, habitat selection, Phragmites australis, spotted turtles, Typha x glauca
origin and ecological function of an ion inducing anti-predator behaviour in Lithobates tadpoles
Chemical cues are used commonly by prey to identify predation risk in aquatic environments. Previous work has indicated that negatively-charged ions of m/z 501 are possibly a kairomone that induces anti-predator responses in tadpoles. This thesis found that this ion species: (i) is produced by injured tadpoles; (ii) exhibits increased spectral intensity with higher tadpole biomass; and (iii) is not produced by starved predators. These results refute the hypothesis that the ion is a kairomone, and rather support its role as an alarm cue released from tadpoles. High resolution mass spectrometry (HR-MS) revealed a unique elemental composition for [M-H]-, m/z 501.2886, of C26H45O7S-. Collision induced dissociation (CID) of ion m/z 501 formed product ions of m/z 97 and m/z 80, HSO4- and SO3-, respectively, indicating the presence of sulfate. Green frog (Lithobates clamitans) tadpoles exposed to m/z 501, and an industrial analogue, sodium dodecyl sulphate (NaC12H25O4S), exhibited similar anti-predator responses, thereby suggesting the potential role of organic sulfate as a tadpole behavioural alterant. Author Keywords: Alarm cue, Amphibian, Chemical Ecology, Mass spectrometry, Predator-prey interactions
Phosphorus forms and response to changes in pH in acid-sensitive soils on the Precambrian Shield
Catchment soil acidification has been suggested as a possible mechanism for reducing phosphorus (P) loading to surface waters in North America and northern Europe, but much of the research that has been conducted regarding P immobilization in pH manipulated soils has been performed at high P concentrations (> 130 μM). This study investigated how soil acidity was related to P fractionation and P sorption at environmentally relevant P concentrations to evaluate the potential influence of long term changes in soil pH on P release to surface waters. Total phosphorus (TP) concentrations declined between 1980 and 2000 in many lakes and streams in central Ontario; over the same time period forest soils in this region became more acidic. Soils were collected from 18 soil pits at three forested catchments with similar bedrock geology but varying TP export loads. The soil pH at the 18 study soil pits spanned the historic soil pH range, allowing for `space for time' comparison of soil P factions. Soils were analysed by horizon for P fractions via Hedley P fractionation. Batch P sorption experiments were performed on selected B-horizon soils at varied solution pH. Soil P fractions varied by horizon but were comparable among the three catchments, with only apatite (PHCl) differing significantly across catchments. Contrary to expectation, both soluble and labile P showed negative relationships with pH in some horizons. Mineral soils were able to sorb almost all (> 90 %) of the P in solution at environmentally relevant P concentrations (4.5 - 45.2 μM). Phosphorus sorption at environmentally relevant P concentrations was unrelated to solution pH but at high P concentration there was a positive relationship between P sorption and solution pH, suggesting a P concentration dependant P sorption mechanism. Phosphorus budgets indicate that P is accumulating within catchments, suggesting that P is being immobilized in the terrestrial environment. An alternative hypothesis, which attempts to explain both the decline in stream TP export and terrestrial P accumulation, is discussed. The results from this study suggest that acidification induced P sorption in upland soils are not a contributing factor to decreases in stream TP concentration in the study catchments. Author Keywords: central Ontario, Hedley fractionation, phosphorus, podzols, soil acidification, sorption


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