Graduate Theses & Dissertations


Detectability and its role in understanding upland sandpiper (Bartramia longicauda) occurence in the fragmented landscape of southern Ontario
Upland Sandpipers (Bartramia longicauda), like many grassland birds, are undergoing population decline in parts of their range. Habitat fragmentation and change have been hypothesized as potential causes of decline. I used citizen-science occurrence data from Wildlife Preservation Canada’s Adopt-A-Shrike Loggerhead Shrike (Lanius ludovicianus) program in conjunction with validation surveys, using similar point-count methods, to examine detectability and determine if landscape level habitat features could predict occupancy of Upland Sandpipers in Southern Ontario. In a single season detectability study, I used Wildlife Preservation Canada’s survey protocol to determine detectability in sites that were known to be occupied. Detectability was low, with six surveys necessary to ensure detection using a duration of at least 18 minutes early in the breeding season. The proportion of open habitat did not affect detection on the landscape. Using a larger spatial and temporal scale, with five years of citizen-science data, I showed that Annual Crop Inventory data could not effectively predict Upland Sandpiper occupancy. Model uncertainty could be attributed to survey protocol and life history traits of the Upland Sandpiper, suggesting that appropriate survey methods be derived a priori for maximizing the potential of citizen-science data for robust analyses. Author Keywords: Bartramia longicauda, citizen-science, detection, landscape, occupancy, Ontario
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
Habitat selection by sympatric Canada lynx (Lynx canadensis) and bobcat (Lynx rufus)
Range expansion by the bobcat (Lynx rufus) may be contributing to range contraction by the Canada lynx (Lynx canadensis), but interactions between them are not well understood. To investigate the potential for competition, I conducted a literature review of hierarchical habitat selection by these two species. I determined that the lynx and the bobcat select different resources at the first and second orders, and that the fourth order is under-studied compared to higher orders. I therefore conducted a snow-tracking study of fine-scale habitat selection by lynx and bobcat in an area of sympatry in northern Ontario. I found that the two species selected similar resources at the fourth order, but appeared to be allopatric at the level of the home range. These results suggest that competition is unlikely to occur between lynx and bobcat, and other factors should be considered as more probable causes of the lynx range contraction. Author Keywords: Bobcat, Canada lynx, Competition, Habitat selection, Scale, Snow tracking
Risk of Mortality for the Semipalmated Plover (Charadrius semipalmatus) Throughout Its Life Cycle
Three long-term mark and recapture/resight data sets of individually marked Semipalmated Plovers (Charadrius semipalmatus) were analyzed using Cormack-Jolly- Seber models. Data came from two breeding populations (Churchill, Manitoba, Canada, n=982, and Egg Island, Alaska, USA, n=84) and one overwintering population (Cumberland Island, Georgia, USA, n=62). For Alaska and Georgia, time-invariant models were best-supported, giving annual survival estimates of 0.67 (95%C.I.: 0.58- 0.76) and 0.59 (95%C.I.: 0.49-0.67) respectively. Data from Manitoba supported a timedependent model: survival estimates varied from 1.00 to 0.36, with lowest estimates from recent years, supporting observations of local population decline. Seasonal survival analysis of the Georgia population indicated lower mortality during winter (monthly Φoverwinter: 0.959, 95%CI: 0.871-0.988; for 6 month period Φoverwinter: 0.780 (0.440-0.929)) than during combined breeding and migratory periods (monthly ΦBreeding+Migration: 0.879 (0.825-0.918); for 8 month ΦBreeding+Migration: 0356 (0.215-0.504)). I recommend, based on high resight rates, continued monitoring of survival of wintering populations, to determine potential range-wide population declines. Keywords: survival, longevity, mortality, shorebird, overwinter, breeding, migration, life cycle Author Keywords: life cycle, longevity, mortality, non-breeding, shorebird, survival
Hybridization dynamics in cattails (Typha spp.,) in northeastern North America
Interspecific hybridization is an important evolutionary process which can contribute to the invasiveness of species complexes. In this dissertation I used the hybridizing species complex of cattails (Typha spp., Typhaceae) to explore some of the processes that could contribute to hybridization rates. Cattails in northeastern North America comprise the native T. latifolia, the non-native T. angustifolia, and their fertile hybrid, T. × glauca. First, I examined whether these taxa segregate by water depth as habitat segregation may be associated with lower incidence of hybridization. I found that these taxa occupy similar water depths and therefore that habitat segregation by water depth does not promote mating isolation among these taxa. I then compared pollen dispersal patterns between progenitor species as pollen dispersal can also influence rates of hybrid formation. Each progenitor exhibits localized pollen dispersal, and the maternal parent of first generation hybrids captures more conspecific than heterospecific pollen; both of which should lead to reduced hybrid formation. I then conducted controlled crosses using all three Typha taxa to quantify hybrid fertility and to parameterize a fertility model to predict how mating compatibilities should affect the composition of cattail stands. I found that highly asymmetric formation of hybrids and backcrosses and reduced hybrid fertility should favour the maintenance of T. latifolia under certain conditions. Finally, I used a population genetics approach to characterize genetic diversity and structure of Typha in northeastern North America to determine the extent to which broad-scale processes such as gene flow influence site-level processes. I concluded that hybrids are most often created within sites or introduced in small numbers rather than exhibiting broad-scale dispersal. This suggests that local processes are more important drivers of hybrid success than landscape-scale processes which would be expected to limit the spread of the hybrid. Though my findings indicate some barriers to hybridization in these Typha taxa, hybrid cattail dominates much of northeastern North America. My results therefore show that incomplete barriers to hybridization may not be sufficient to prevent the continued dominance of hybrids and that active management of invasive hybrids may be required to limit their spread. Author Keywords: fertility model, genetic structure, Hybridization, invasive species, niche segregation, pollen dispersal
Enduring Attack
Numerous prey taxa employ defensive postures for protection against attack by predators. Defensive postures mitigate predation risk at various stages of the predator-prey sequence, including through crypsis, mimicry, thanatosis, aposematism, and deflection. In terrestrial salamanders, defensive postures may be aposematic, or deflect attacks away from vital body parts and towards the tail, however the extent to which these strategies act exclusively or synergistically remains poorly understood. Herein I demonstrate a novel approach to study the function of salamander defensive postures through experimental manipulation of predator response to antipredator behaviour in a natural field setting. I deployed 1600 clay salamander prey on Pelee Island, Ontario, manipulating prey size (small, large) and posture (resting, defensive) and documented attack rates across three predator types to further assess the effect of prey body size and predator type on antipredator efficacy. My research suggests that irrespective of prey body size, defensive posture does not function through aposematism, but rather acts to deflect predator attacks to the tail, which is commonly noxious and expendable in terrestrial salamanders. An intriguing possibility is that this behaviour facilitates taste-rejection by predators. Overall, my research should further contribute to our understanding of the importance and potential evolutionary significance of defensive posturing in Ambystoma salamanders, and more broadly, on the determinants of prey vulnerability to predation. I also briefly discuss the implications of my results to the conservation of Ambystoma populations on Pelee Island. Author Keywords: Anti-predator behaviour, Aposematism, Attack deflection, Predator avoidance, Small-mouthed salamander, Taste-rejection
De novo transcriptome assembly, functional annotation, and SNP discovery in North American flying squirrels (genus Glaucomys)
Introgressive hybridization between northern (Glaucomys sabrinus) and southern flying squirrels (G. volans) has been observed in some areas of Canada and the USA. However, existing molecular markers lack the resolution to discriminate late-generation introgressants and describe the extent to which hybridization influences the Glaucomys gene pool. I report the first North American flying squirrel (genus Glaucomys) functionally annotated de novo transcriptome assembly with a set of 146,621 high-quality, annotated putative species-diagnostic SNP markers. RNA-sequences were obtained from two northern flying squirrels and two southern flying squirrels sampled from Ontario, Canada. I reconstructed 702,228 Glaucomys transcripts using 193,323,120 sequence read-pairs, and captured sequence homologies, protein domains, and gene function classifications. These genomic resources can be used to increase the resolution of molecular techniques used to examine the dynamics of the Glaucomys hybrid zone. Author Keywords: annotation, de novo transcriptome, flying squirrels, high-throughput sequencing, hybridization, single nucleotide polymorphisms
New Interpretations from Old Data
Range contractions and expansions are important ecological concepts for species management decisions. These decisions relate not only to rare and endangered species but to common and invasive species as well. The development of the broad spatiotemporal extent models that are helpful in examining range fluctuations can be challenging given the lack of data expansive enough to cover the time periods and geographic extents needed to fit the models. Archival records such as museum databases and harvest data can provide the spatiotemporal extent needed but present statistical challenges given they represent presence-only location information. In this thesis, I used maximum entropy and Bayesian hierarchical occupancy algorithms fitted with archival presence-only records to develop spatiotemporal models covering broad spatial and temporal extents for snowshoe hare and Canada lynx. These two algorithm types are well suited for presence-only data records and can be adapted to include biological and physical processes, thus improving the ecological realism of the models. Using these modelling methods, I found the extent of occurrence (EOO) and area of occupancy (AOO) varied greatly over time and space for both snowshoe hare and Canada lynx, suggesting that management decisions for these species should include consideration of these variations. While the presence-only data were appropriate for model development and understanding changing values in EOO and AOO, it sometimes lacked the locational accuracy and precision needed to create fine scale ecological analyses, thus resulting in somewhat coarse but potentially relevant conclusions. Author Keywords: Area of occupancy, Bayesian hierarchical models, Canada lynx, Extent of occurrence, Presence-only data, Snowshoe hare
Time to adapt
To better understand species’ resilience to climate change and implement solutions, we must conserve environments that maintain standing adaptive genetic variation and the potential generation of new beneficial alleles. Coding trinucleotide repeats (cTNRs) providing high-pace adaptive capabilities via high rates of mutation are ideal targets for mitigating the decline of species at risk by characterizing adaptively significant populations. Ultimately, adaptive genetic information will inform the protection of biological diversity below the species level (i.e., “Evolutionarily Significant Units” or “ESUs”). This dissertation investigates cTNRs within candidate genes to determine their prevalence and influence under selection in North American mammals. First, I evaluated the potential for somatic mosaicism in Canada lynx (Lynx canadensis), and found that tissue-specific mosaicism does not confound cTNR genotyping success in lynx. Second, I assessed a selection of clock gene cTNRs across characterized mammals and found that these repeats are abundant and highly variable in length and purity. I also identified preliminary signatures of selection in 3 clock gene cTNRs in 3 pairs of congeneric North American mammal species, highlighting the importance of cTNRs for understanding the evolution and adaptation of wild populations. I further evaluated the influence of selection on the NR1D1 cTNR within Canada lynx sampled across Canada using environmental correlation, where I estimated the variation in NR1D1 cTNR alleles explained by environmental and spatial variables after removing the effects of neutral population structure. Although most variation was explained by neutral structure, environment and spatial patterns in eastern lynx populations significantly explained some of the variation in NR1D1 alleles. To examine the role of island populations in the generation and distribution of adaptive genetic variation, I used 14 neutral microsatellites and a dinucleotide repeat within a gene linked to mammalian body size, IGF-1, and found that both genetic drift and natural selection influence the observed genetic diversity of insular lynx. Finally, I estimated the divergence dates of peripheral lynx populations and made recommendations towards the conservation of Canada lynx; high levels of genetic differentiation coupled with post-glacial colonization histories and patterns of divergence at cTNR loci suggest at least 4 ESUs for Canada lynx across their range. Author Keywords: adaptation, Canada lynx, candidate genes, coding trinucleotide repeats, evolution, natural selection
Island Syndrome and Stress Physiology of Mice in the Genus Peromyscus
Biological differences between island and mainland conspecifics have been well studied, but few studies have addressed differences in stress physiology. Stressors, such as predation and competition for resources, cause the release of glucocorticoids (GCs). Characteristics of island wildlife, called “island syndrome”, are attributed to low levels of predators and competitors. I tested the hypothesis that island syndrome includes differences in GC levels between island and mainland rodents using two approaches; first, using white-footed mice (Peromyscus leucopus) from a near-shore archipelago (Thousand Islands, Ontario) and the nearby mainland; second, using study-skins of deer mice (Peromyscus maniculatus) from two archipelagos offshore of Vancouver Island, British Columbia. White-footed mice in the near-shore archipelago did not show characteristics of island syndrome, or changes in GC levels (feces and hair); however deer mice from both archipelagos in British Columbia were heavier and had lower hair GCs for their size than Vancouver Island mice. Author Keywords: Glucocorticoids, Island rule, Island syndrome, Peromyscus, Stress physiology
Assessing Canada Lynx Dispersal Across an Elevation Barrier
Mountain ranges are often thought to restrict movement of wildlife, yet previous studies evaluating the role of the Rocky Mountains as a dispersal barrier for Canada lynx (Lynx canadensis) have been contradictory. Our study uses neutral microsatellite loci to evaluate the role of the Rocky Mountains as a barrier to gene flow for lynx. Although lynx exhibited low genetic differentiation, we detected a limited effect of the mountains. Furthermore, we inferred the role played by landscape variables in gene flow (genetic differentiation predicted by landscape resistance). Limited gene flow most strongly related to resistance from physical factors (low snow cover and elevation), rather than other topographic and ecological factors (high terrain roughness, low forest cover, low habitat suitability, and geographic distance). Structural connectivity was a relatively poor predictor of functional connectivity. Overall, the Rockies represent an area of reasonably high functional connectivity for lynx, with limited resistance to gene flow. Author Keywords: Canada lynx, connectivity, gene flow, genetic structure, landscape genetics, Rocky mountains
Functional Genetic Diversity in American Mink (Neovison vison)
The release of domestic organisms to the wild is considered a threat to biodiversity because the introduction of domestic genes through interbreeding can negatively impact wild conspecifics via outbreeding and local extinction. In North America, captive American mink (Neovison vison) are frequently escaping into the wild, yet the impact of these events on the functional genetic diversity of wild mink populations is unclear. I characterized domestic and wild mink in Ontario at 17 trinucleotide microsatellites located in functional genes thought to be associated with traits affected by domestication. I found low functional genetic diversity, as only 4 of 17 genes were variable and of those four there was little evidence of allele frequency differences between domestic and wild mink. Using redundancy analysis and a spatial analysis of principal components on the four variable loci (AR, ATN1, IGF-1, and TOB1) I found no evidence to suggest domestic release events are affecting functional genetic diversity of free-ranging mink at the set of markers assessed. Author Keywords: American mink, domestication, functional gene, introgression, Neovison vison


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