Graduate Theses & Dissertations

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Making eDNA count
Environmental DNA (eDNA) is rapidly becoming an established method for the detection of species in aquatic systems and has been suggested as a promising tool to estimate species abundance. However, the strength of the relationship between eDNA concentrations and taxon abundance (density/biomass) can vary widely between species. I investigated the relationship between eDNA concentration and species abundance using two common and closely-related amphibians in eastern North America, the wood frog (Rana sylvatica) and northern leopard frog (Rana pipiens). I manipulated tadpole density in 80 L mesocosms and documented the relationship between tadpole density, biomass, and eDNA concentration. Species were comparable in biomass but differed in the amount of detectible genetic material produced; density and biomass were the superior abundance metric correlated with eDNA concentration for wood frogs and leopard frogs, respectively. However, increases in eDNA concentration reflected increasing tadpole biomass, therefore biomass is likely a better metric of abundance than density. Overall my findings support that eDNA concentration can be used as an index of species abundance, but that species-specific calibration may be needed before eDNA concentration can be effectively translated to an abundance metric. Future research should refine our understanding of how biotic and abiotic factors influence eDNA production, degradation, and recovery across species, before the method can receive widespread use as a monitoring tool in natural settings. Author Keywords: abundance estimates, environmental DNA, mesocosm, Rana pipiens, Rana sylvatica
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
Research and development of synthetic materials for presumptive testing in bloodstain pattern analysis
Chemical presumptive tests are used as the primary detection method for latent bloodstain evidence. This work focuses on developing a forensic blood substitute which mimics whole blood reactivity to a luminol solution commonly used in presumptive testing. Designing safe and accessible materials that mimic relevant properties of blood is a recognized research need in forensic science. Understanding the whole blood dynamics related to reactivity with presumptive testing chemicals is important for developing accurate analogues. Provided in this thesis is a quantitative and qualitative characterization of photoemission from the reaction of a luminol solution to ovine blood. Luminol reactivity of a horseradish peroxidase encapsulated sol-gel polymer was validated against this ovine blood standard. This material, the luminol-reactive forensic blood substitute, is a key deliverable of this research. An optimized protocol for implementing this technology as a reagent control test, and as a secondary school chemistry experiment are presented. This thesis outlines the research and development of a forensic blood substitute as it relates to presumptive testing in bloodstain pattern analysis. Author Keywords: bloodstain pattern analysis, forensic science, luminol, presumptive testing, secondary school education, sol-gel chemistry
Frog Virus 3
Understanding the maintenance and spread of invasive diseases is critical in evaluating threats to biodiversity and how to best minimize their impact, which can by done by monitoring disease occurrences across time and space. I sought to apply existing and upcoming molecular tools to assess fluctuations in both presence and strain variation of frog virus 3 (FV3), a species of Ranavirus, across Canadian waterbodies. I explored the temporal patterns and spatial distribution of ranavirus presence across multiple months and seasons using environmental DNA techniques. Results indicate that ranavirus was present in approximately 72.5% of waterbodies sampled on a fine geographical scale (<10km between sites, 7,150 km2), with higher detection rates in later summer months than earlier. I then explored the sequence variability at the major capsid protein gene (MCP) and putative virulence gene (vIF-2α) of FV3 samples from Ontario, Alberta, and the Northwest Territories, with the premise of understanding pathogen movement across the landscape. However, a lack of genetic diversity was found across regions, likely due to a lack of informative variation at the chosen genetic markers or lack of mutation. Instead, I found a novel FV3-like ranavirus and evidence for a recombinant between FV3 and a ranavirus of another lineage. This thesis provides a deeper understanding into the spatio-temporal distribution of FV3, with an idea of how widespread and threatening ranaviruses are to amphibian diversity. Keywords: ranavirus, frog virus 3, amphibians, environmental DNA, phylogenetics, wildlife disease, disease surveillance, major capsid protein, vIF-2α Author Keywords: amphibians, environmental DNA, frog virus 3, phylogenetics, ranavirus, wildlife disease
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
Assessment of an adult lake sturgeon translocation (Acipenser fulvescens) reintroduction effort in a fragmented river system
North American freshwater fishes are declining rapidly due to habitat fragmentation, degradation, and loss. In some cases, translocations can be used to reverse local extirpations by releasing species in suitable habitats that are no longer naturally accessible. Lake sturgeon (Acipenser fulvescens) experienced historical overharvest across their distribution, leading to endangered species listings and subsequent protection and recovery efforts. Despite harvest and habitat protections, many populations do not appear to be recovering, which has been attributed to habitat alteration and fragmentation by dams. In 2002, 51 adult lake sturgeon from the Mattagami River, Ontario, Canada were translocated 340 km upstream to a fragmented 35 km stretch of the river between two hydroelectric generating stations, where sturgeon were considered extirpated. This study assessed the translocation effort using telemetry (movement), demographics and genetic data. Within the first year, a portion of the radio-tagged translocated individuals dispersed out of the release area, and released radio-tagged individuals used different areas than individuals radio-tagged ten years later. Catches of juvenile lake sturgeon have increased over time, with 150 juveniles caught within the duration of this study. The reintroduced population had similar genetic diversity as the source population, with a marked reduction in effective population size (Ne). The results indicate that the reintroduction effort was successful, with evidence of successful spawning and the presence of juvenile lake sturgeon within the reintroduction site. Overall, the results suggest adult translocations may be a useful tool for re-establishing other extirpated lake sturgeon populations. Author Keywords: conservation, endangered species, lake sturgeon, reintroduction, telemetry, translocation
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
Ground-truthing effective population size estimators using long-term population data from inland salmonid populations
Effective population size (Ne) is a foundational concept in conservation biology, in part due to its relationship to the adaptive potential of populations. Although Ne is often estimated for wild populations, it is rarely calibrated against actual population estimates (Nc) other than to produce Ne/Nc ratios. This project used demographic and genetic data for from two intensively-studied populations of lake trout (Salvelinus namaycush) in Ontario’s Experimental Lake Area (ELA) as baseline data for evaluating the performance of multiple Ne estimators. Several temporal and single-time (point) genetic methods of estimating Ne were compared against demographic Ne estimates and known population data, as well as variation and consistency within and among Ne estimators. Changes in genetic Ne estimates over time were also compared to changes in demographic structure and fluctuating census estimates, including the effect of an experimentally manipulated population bottleneck on demographic and genetic Ne estimates during population reduction and recovery. Sampling years that included the most pre-, during and post-bottleneck data revealed the lowest estimates using temporal estimators (Ne = 16 to 18) despite pre- and post-bottleneck census estimates of 591 and 565. Estimation of Ne had increasingly tighter confidence intervals as sample sizes approached the actual number of breeding individuals in each population. Performance differences among the tested estimators highlight their potential biases and reliance on different assumptions, illustrating their potential value and caveats for assessing adaptive potential of wild populations. Author Keywords: Effective Population Size, Experimental Lakes Area, Fish Population Assessment, Lake Trout, Population Demographics, Population Genetics
Social discrimination by female polar bears (Ursus maritimus) when accompanied by dependent offspring during the ice-free season in southern and western Hudson Bay and James Bay
Polar bears are generally described as solitary, but features of their life cycles and habitats regularly necessitate interaction. Effective conspecific assessment, including accurate recognition and discrimination, likely confers benefits, especially to females accompanied by dependent young. Individuals in the Southern (SH) and Western (WH) Hudson Bay subpopulations are ideal for studying polar bear social behaviours because of the prolonged high densities of the ice-free season. First, I looked outside family groups to model their fine scale sociospatial organization on land. Capture locations were more likely to correspond to family groups when there were fewer neighbouring bears, when a greater proportion of neighbours were female, and when the focal individual and neighbours were significantly related. Second, I looked within the family group to assess offspring recognition. Of 288 offspring in 207 family groups captured in the SH subpopulation from 1999 through 2013, only one case of adoption (of a singleton) was observed. Author Keywords: Adoption, Kin Recognition, Logistic Regression, Maternity Analysis, Social Discrimination, Sociospatial
Temperature effects on the routine metabolic rates of brook trout (Salvelinus fontinalis) eggs, alevin and fry
Early developmental stages of cold-adapted ectotherms such as brook trout (Salvelinus fontinalis) are at risk of mortality with increasing water temperatures because of their sensitivity to changes in their environment. I studied the mass and routine metabolic rate (RMR) of wild-origin brook trout eggs, alevin and young fry reared at normal (5°C) and elevated (9°C) temperatures for the duration of the study or at mismatched temperatures. This setup determined if preconditioning acclimation for one temperature benefits or hinders the organism later in life. Three levels of biological organization (ancestry, population, family) were studied using Akaike’s Information Criterion (AIC) to identify models that best accounted for variation in the data. Family, mass and temperature were most important in predicting body mass and mass-adjusted RMR, although population and ancestral-level differences were also detected at some life stages. Strong variation in body mass and mass-adjusted RMR among families may indicate adaptive potential within brook trout populations to respond to increases in water temperature with climate change. Author Keywords: Acclimation, AIC, Brook trout (Salvelinus fontinalis), Environmental matching, Routine metabolic rate, Temperature
successful invader in expansion
Researchers have shown increasing interest in biological invasions for the associated ecological and economic impacts as well as for the opportunities they offer to study the mechanisms that induce range expansion in novel environments. I investigated the strategies exhibited by invasive species that facilitate range expansion. Invasive populations exhibit shifts in life-history strategy that may enable appropriate responses to novel biotic and abiotic factors encountered during range expansion. The spatio-temporal scales at which these shifts occur are largely unexplored. Furthermore, it is not known whether the observed dynamic shifts represent a consistent biological response of a given species to range shifts, or whether the shifts are affected by the abiotic characteristics of the new systems. I examined the life-history responses of female round gobies Neogobius melanastomus across fine and coarser spatial scales behind the expansion front and investigated whether invasive populations encountering different environmental conditions (Ontario vs France) exhibited similar life-history shifts. In both study systems, I found an increase in reproductive investment at invasion fronts compared to longer established areas at coarse and fine scales. The results suggest a similar response to range shifts, or a common invasion strategy independent of environmental conditions experienced, and highlight the dynamic nature of an invasive population’s life history behind the invasion front. The second part of my research focused on the development of an appropriate eDNA method for detecting invasive species at early stages of invasion to enable early detection and rapid management response. I developed a simple, inexpensive device for collecting water samples at selected depths for eDNA analysis, including near the substrate where eDNA concentration of benthic species is likely elevated. I also developed a protocol to optimise DNA extraction from water samples that contain elevated concentration of inhibiters, in particular near-bottom samples. Paired testing of eDNA and conventional surveys was used to monitor round goby expansion along its invasion pathway. Round gobies were detected in more sites with eDNA, permitting earlier, more accurate, upstream detection of the expansion front. My study demonstrated the accuracy and the power of using eDNA survey method to locate invasion fronts. Author Keywords: Age-specific reproductive investment, DNA extraction, Energy allocation, Fecundity, Invasion front, Range expansion

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