Genetics

Populations have long been delineated by physical barriers that appear to limit reproduction, yet increasingly genetic analysis reveal these delineations to be inaccurate. The eastern and mid-continent populations of sandhill cranes are expanding ranges which is leading to convergence and warrants investigation of the genetic structure between the two populations. Obtaining blood or tissue samples for population genetics analysis can be costly, logistically challenging, and may require permits as well as potential risk to the study species. Non-invasively collected genetic samples overcome these challenges, but present challenges in terms of obtaining high quality DNA for analysis. Therefore, methods that optimize the quality of non-invasive samples are necessary. In the following thesis, I examined factors affecting DNA quality and quantity obtained from shed feathers and examined population differentiation between eastern and mid-continent sandhill cranes. I found shed feathers are robust to environmental factors, but feather size should be prioritized to increase DNA quantity and quality. Further, I found little differentiation between eastern and mid-continent populations with evidence of high migration and isolation-by-distance. Thus, the two populations are not genetically discrete. I recommend future population models incorporate migration between populations to enhance our ability to successfully manage and reach conservation objectives.

Author Keywords: feathers, genetic differentiation, non-invasive DNA, population genetics, population management, sandhill crane (Antigone canadensis)

Species ranges are changing and the rate at which the climate is warming is faster than anything previously seen in the past, consequently species will need to adapt quickly, track the climate or perish. Cold adapted terrestrial species are the most vulnerable, because they are limited by the availability of land at the cold edge of their range. This means that many alpine, boreal and polar species essentially have nowhere to go as the climate warms. Habitat generalists are widely distributed across the globe and are highly adaptable to anthropogenic change. Our future biodiversity may only consist of several habitat generalists. The Canada lynx (Lynx canadensis) is a boreal species that has limited range expansion potential at the cold end of its range and its range has already contracted by 40%. The lynx has nowhere to go as climate warming progresses in this current century. Therefore, understanding the causes of its range contraction could enlighten us on conservation and management strategies that we might undertake as climate warms. My analyses indicated that the Canada lynx seems to have tracked the habitat that it is adapted to in more northern homogenous boreal forests and the bobcat (Lynx rufus), a habitat generalist, has simply replaced it in the south.

Author Keywords: Anthropogenic Change, Competition, Connectivity, Lynx canadensis, Lynx rufus, Range change

Assessments of the adaptive potential of natural populations are essential for understanding and predicting responses to environmental stressors like climate change and infectious disease. The range of stressors species face in a human-dominated landscape, often have contrasting effects. White-tailed deer (Odocoileus virginianus, deer) are expanding in the northern part of their range following decreasing winter severity and increasing forage availability, caused by climate change. Chronic wasting disease (CWD), a prion disease affecting cervids, is likewise expanding and represents a major threat to deer and other cervids We obtained tissue samples from free-ranging deer across their native range in Ontario, Canada which has yet to detect CWD in wild populations of cervids. High throughput sequencing was used to assess neutral genomic variation and variation in the gene responsible for the protein that misfolds into prions when deer contract CWD, known as the PRNP gene. Neutral variation revealed a high number of rare alleles and no population structure, consistent with an expanding population of deer. Functional genetic variation revealed that the frequencies of variants associated to CWD susceptibility and disease progression were evenly distributed across the landscape and the frequencies were consistent with deer populations not infected with CWD. These findings suggest that an observable shift in PRNP allele frequencies likely coincides with the start of a novel CWD epidemic. Sustained surveillance of genomic and genetic variation can be a useful tool for CWD-free regions where deer are managed for ecological and economic benefits.

Author Keywords: Canadian wildlife, population genetics, prion, PRNP, RADseq, ungulate

Wild populations are notoriously difficult to study due to confounding stochastic variables. This thesis tackles two components of investigating wild populations. The first examines the use of niche modeling to quantify macro-scale predator-prey relationships in canid populations across eastern North America, while the second examines range-wide molecular structure in Canada lynx. The goal of the first chapter is to quantify niche characteristics in a Canis hybrid zone of C. lupus, C. lycaon, and C. latrans to better understand the ecological differentiation of these species, and to assess the impacts of incorporating biotic interactions into species distribution models. The goal of the second chapter is to determine if DNA methylation, an epigenetic marker that modifies the structure of DNA, can be used to differentiate populations, and might be a signature of local adaptation. Our results indicated that canids across the hybrid zone in eastern North America exhibit low levels of genetic and ecological differentiation, and that the importance of biotic interactions are largely lost at large spatial scales. We also identified cryptic structure in methylation patterns in Canada lynx populations, which suggest signatures of local adaptation, and indicate the utility of DNA methylation as a marker for investigating adaptive divergence.

Author Keywords: Ecological Epigenetics, Ecological Genetics, SDM

In Canada, eastern flowering dogwood (Cornus florida L.) is an endangered tree that occurs only in the Carolinian forest of southern Ontario. Threats to this species include habitat fragmentation and the fungal pathogen dogwood anthracnose (Discula destructiva). I conducted a population genetic analysis using seven nuclear microsatellite markers to determine if fragmented populations are genetically isolated from one another and have low levels of genetic diversity. Genetic comparisons suggest on-going dispersal among sites and relatively high genetic diversity within most sites; however, smaller populations and younger trees were less genetically diverse. I also used linear mixed effects models to assess potential relationships between several ecological variables and the prevalence of dogwood anthracnose. Disease severity was higher in trees on shallow slopes and in larger trees; the latter also had higher likelihood of infection. Insights from this study will be important to incorporate into future management strategies.

Author Keywords: Cornus florida, Discula destructiva, dogwood anthracnose, Eastern flowering dogwood, endangered, population genetics

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

Identifying the biotic and abiotic factors that influence individual reproductive fitness under natural conditions is essential for understanding important aspects of a species' evolutionary biology and ecology, population dynamics, and life-history evolution. Using next generation sequencing technology, I developed five microsatellite multiplex reactions suitable for conducting large scale parentage analysis of smallmouth bass, Micropterus dolomieu, and used molecular pedigree reconstruction techniques to characterize the genetic mating system and mate selection in adult smallmouth bass nesting in Lake Opeongo, Ontario, Canada. I used multivariate spatial autocorrelation analysis to indirectly infer the occurrence and extent of natal philopatry among spawning adults, to assess the strength and direction of sex-bias in natal dispersal patterns, and to evaluate the degree of nest site fidelity and breeding dispersal of spawning adults. I also evaluated how differences in littoral zone water temperature caused by wind-induced seiche events influence the relative reproductive success of spawning adults. Lastly, I provide a synopsis of potential future research aimed at further exploring factors that influence the reproductive fitness of smallmouth bass in Lake Opeongo. This information will contribute to our understanding of the factors regulating smallmouth bass populations, and provide insight into the factors controlling the variance in individual reproductive success and thus recruitment dynamics in this species.

Author Keywords: Dispersal, Fitness, Mate selection, Mating systems, Philopatry

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

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

Environmental DNA (eDNA) metabarcoding targets sequences with interspecific

variation that can be amplified using universal primers allowing simultaneous detection

of multiple species from environmental samples. I developed novel primers for three

barcodes commonly used to identify plant species, and compared amplification success

for aquatic plant DNA against pre-existing primers. Control eDNA samples of 45 plant

species showed that species-level identification was highest for novel matK and preexisting

ITS2 primers (42% each); remaining primers each identified between 24% and

33% of species. Novel matK, rbcL, and pre-existing ITS2 primers combined identified

88% of aquatic species. The novel matK primers identified the largest number of species

from eDNA collected from the Black River, Ontario; 21 aquatic plant species were

identified using all primers. This study showed that eDNA metabarcoding allows for

simultaneous detection of aquatic plants including invasive species and species-at-risk,

thereby providing a biodiversity assessment tool with a variety of applications.

Author Keywords: aquatic plants, biodiversity, bioinformatics, environmental DNA (eDNA), high-throughput sequencing, metabarcoding