Biology

Since the mid-Pleistocene, evolutionary histories of North American species were shaped by extreme climatic oscillations involving major range and habitat shifts at a rapid pace. The peopling of the continent and the subsequent human colonisation waves created further pressures affecting North American faunal and plant populations. Cervidae (deer family) are a diverse group which arrived in North America approximately 5 million years ago, and is represented on the continent by several extant species. The overarching aim of my thesis is to understand how North America's dynamic history shaped the evolutionary trajectory of the region's Cervidae species. In Chapter 2, I investigated the speciation and hybridisation history of the sister species white-tailed (Odocoileus virginianus) and mule deer (Odocoileus hemionus) using whole genome data of individuals from across their ranges, including zones of sympatry and allopatry. I found negligible patterns of ancient gene-flow suggesting white-tailed and mule deer divergence occurred via drift and their hybridisation is the result of secondary contact. In Chapter 3, I furthered our understanding of the Odocoileus species pair evolutionary history through explicit demographic inference and selection analyses. I used deer samples from across North America and found strong signals of climate- and human-induced population declines. Particularly, this work highlights the impact of European settlers and patterns of conservation concerns for mule deer. For Chapter 4, I clarified the phylogenetic relationship of a contentious taxon, Torontoceros hypogaeus, that went extinct during the late Pleistocene extinction event. I analysed 11k years old DNA of the single specimen representing the species, performed phylogenetic and divergence analyses, and found it belongs to the Odocoileus genus as Odocoileus (Torontoceros) hypogaeus which should be included in North America's late Pleistocene extinction list. Finally, in Chapter 5, I investigated genetic diversity over time in five North American Cervidae using contemporary and ancient DNA. I found patterns of change in genetic diversity that are consistent with known dispersal and demographic histories of our target species. Altogether, my thesis provides valuable insight into the evolutionary history of Northern American Cervidae, and on how they have been impacted by the continent's dynamic past.

Author Keywords: Cervidae, Demographic history, Extinction, Human impact, Hybridisation, Speciation genomics

Mutations in the CLN7 (MFSD8) gene, causes CLN7 disease, a subtype of neuronal ceroid lipofuscinosis. MFSD8 is a lysosomal transmembrane protein that transports chloride across membranes. Experimentation regarding Dictyostelium discoideum revealed that mfsd8 deficiency altered lysosomal enzyme activity. During starvation, the aggregation of mfsd8¬¬- cells was delayed, and cells formed more mounds that were smaller in size, phenotypes that were attributed to reduced cell-substrate adhesion and altered lysosomal enzymatic activities. This study examines the possible transcriptomic and secretomic basis for these phenotypes. This work generated new datasets for examining the effect of mfsd8 loss on the transcriptome and secretome. The validity of these datasets was supported by use of western blotting and RT-PCR along with a set of assays probing relevant biological processes. Together these results elucidate the biological mechanisms behind the observed phenotypes and lay the foundation for future studies to further study the cellular role of MFSD8.

Author Keywords: Battens disease, CLN7, Dictyostelium discoideum, MFSD8, Secretome, Transcriptome

DNA methylation (DNAm) is a useful indicator of phenotypic expression and diversity, and can potentially inform adaptations to environmental changes. This thesis uses epigenetic techniques to investigate the mechanisms underlying phenotypic variation in white-tailed deer, black bear, and mountain goat, with a particular focus on age and body size. In the second chapter, we aimed to contribute to wildlife monitoring by developing epigenetic clocks, or predictive models of age, and diagnostic markers of age class and sex. In the third chapter, we aimed to investigate the involvement of DNAm in body size variation of white-tailed deer by developing a model predictive of hindfoot length, and by identifying CpGs and genes that may be involved in hindfoot length variation. My results indicate that DNAm is an effective predictive marker of various phenotypes in these North American large mammals, and that epigenetic methods offer valuable insights for managing human impacts on wildlife.

Author Keywords: Age, Body Size, DNA Methylation, Epigenetics, Phenotypes, Population Genetics

The Lesser Yellowlegs (Tringa flavipes) is a steeply declining shorebird that breeds across boreal North America. I studied nest survival in Anchorage, Alaska, USA and Churchill, Manitoba, Canada and nest site selection factors in Churchill. Nests were monitored at each site and daily nest survival rates (DSR) were calculated based on a maximum likelihood approach. Overall nest survival was ~63% for Anchorage (lcl–ucl = 0.450–0.773, n=49) and ~28% (lcl–ucl = 0.113–0.481, n=26) for Churchill. Earlier initiation dates, warmer mid-incubation temperatures and lower temperature variability during nesting were linked with higher DSR. I tested nest site selection at territorial and microhabitat scales using multiple logistic regression to compare nest sites with random points. Lesser Yellowlegs selected territories further from water and, at the microhabitat scale, taller shrubs. Projected climate-related shifts in weather and habitat will likely present both benefits and challenges to Lesser Yellowlegs.

Keywords: Lesser Yellowlegs, Tringa flavipes, shorebird, nest survival, nest success, nesting habitat, breeding habitat, boreal, sub-arctic, climate change, Anchorage, Alaska, Churchill, Manitoba

Author Keywords: boreal, breeding habitat, Lesser Yellowlegs, nest survival, shorebird, Tringa flavipes

Globally, fledglings of more than 50 seabird species are vulnerable to stranding in human settlements near their colonies as they leave their nests for the first time. This phenomenon has been attributed to attraction toward and disorientation by artificial light at night (ALAN). Grassroots rescue programs find more birds in illuminated locations than in dark ones, but it is unclear to what extent this pattern is driven by seabird versus rescuer behaviour. I studied behavioural responses to ALAN in stranding-prone Atlantic puffin (Fratercula arctica) and Leach's storm-petrel (Hydrobates leucorhous) fledglings and investigated detection probabilities of 3D-printed puffin fledgling decoys by rescuers. I hypothesized that seabird strandings are due to attraction toward ALAN; that post-stranding behaviour varies with taxon and lighting conditions; and that post-stranding behaviour (e.g., concealment) and lighting conditions drive variance in detection probability of stranded seabirds by rescuers. To address my first hypothesis, I alternately illuminated two beaches near a Newfoundland puffin colony and found significantly more puffin fledglings stranded when the beaches were illuminated than when they were dark, supporting the light attraction hypothesis. Stranded puffins similarly moved toward light over darkness in a Y-maze choice experiment and were less active under LED light than in darkness or under high-pressure sodium light, demonstrating a preference toward certain light conditions post-stranding. In contrast, storm-petrels predominantly avoided lit conditions in a Y-maze and were less active in darkness than under light. Further, when provided with a place to hide, more than half of storm-petrels concealed themselves when in light conditions versus none in darkness. To test my third hypothesis, I deployed puffin decoys and found that rescuers detected them more easily in higher light levels, in less concealed locations, and with increased search effort. My results support historical deductions that seabird fledgling strandings are caused by attraction toward artificial light but demonstrate that post-stranding behavioural responses to ALAN depend on species and light type, which may in turn affect detection probability by rescuers.

Author Keywords: artificial light, atlantic puffin, charadriiform, Leach's storm-petrel, light attraction, procellariiform

Climate change affects birds' reproductive ecology by altering breeding timing, distribution, and habitat suitability. Snowmelt patterns complicate these changes affecting habitat availability and suitability for birds and their arthropod prey. Snow varies as a function of both large-scale climate patterns and local-scale topography. I used elevational gradients as a proxy for local- scale snow impacts, investigating how elevation affects arthropod abundance, and nest placement, initiation, fate, and habitat for Lapland Longspur (Calcarius lapponicus) and Semipalmated Sandpiper (Calidris pusilla) north of Baker Lake, Nunavut. I found and monitored nests over multiple breeding seasons and used pitfall traps and conducted vegetation surveys. Results show that elevation significantly affects arthropod biomass and nest placement, but not nest initiation or success. Both species preferentially nested at lower elevations with higher arthropod biomass. Thus, birds in the central Arctic choose nesting sites at lower elevations with better food availability rather than higher elevations with earlier snowmelt.

Author Keywords: Arctic, arthropod biomass, Lapland Longspur, nest site selection, nest success, Semipalmated Sandpiper

Animal migrations are ubiquitous and one of the most threatened ecological processes globally. Because of the multifaceted nature of migration – seasonal movements between home ranges – it can be difficult to tease apart the underlying mechanisms influencing this behaviour. It is necessary to understand these mechanisms, not only to deepen our fundamental understanding of migration in animals, but also because migrations in many species are vulnerable to environmental change. In Chapter 2, I first systematically identify the broad proximate drivers of migration and offer generalities across vertebrate taxa. I quantitatively reviewed 45 studies and extracted 132 observations of effect sizes for internal and external proximate drivers that influenced migration propensity. Through this meta-analysis, I found that internal and external drivers had a medium and large effect, respectively, on migration propensity. Predator abundance and predation risk had a large effect on migration propensity, as did individual behaviour. Of the studies that examined genetic divergence between migrant and resident populations, 64% found some genetic divergence between groups. In Chapter 3, I explore the genetic basis for migration and identified genes associated with migration direction from pooled genome-wide scans on a population of 233 migrating female mule deer (Odocoileus hemionus) where I identified genomic regions including FITM1, a gene linked to the formation of lipids, and DPPA3, a gene linked to epigenetic modifications of the maternal line. These results are consistent with the underlying genetic basis for a migratory trait which contributes to the additive genetic variance influencing migratory behaviours and can affect the adaptive potential of a species. Finally, in Chapter 4 I used a pedigree-free quantitative genetic approach to estimate heritability and sources of environmental variation in migration distance, timing, and movement rate of the same population of mule deer. I found low heritability for broad patterns of migration timing, and greater variation in heritability for behaviours during migration, with low heritability for distance and duration and high heritability for movement rate along the route. Insights into the genetic and environmental sources of variation for migration are critical both for the eco-evolutionary dynamics of migration behaviour, and for the conservation of species whose migrations may be vulnerable to environmental change. My thesis reveals that broad patterns of migration are driven largely by environmental effects while within these broad patterns, migration behaviour is driven to a measurable degree by genetic variation.

Author Keywords: heritability, migration, Odocoileus hemionus, reduced representation sequencing, whole genome sequencing

Measuring biodiversity has become increasingly complex as biologists and ecologists have gradually learned more about how biotic systems are structured and interact. Given the wide range of tools, techniques and approaches now in use to quantify biological diversity, it is useful to consider different "dimensions of diversity" to classify these measurements and provide context for their interpretation. Even within the genetic dimension of diversity alone, recent improvements in theory, technology, and statistics has generated several approaches which can provide distinct insights into natural systems. In this thesis, I use multiple "axes of diversity" to subdivide the dimension of genetic diversity to better understand a complex ecological system - the unisexual Ambystoma complex on Pelee Island, Ontario. By focusing on the genomotype axis, I found that the composition of local unisexual Ambystoma assemblages generally reflects the current relative abundance of the local sexual host populations. This suggests that sexual hosts can be thought of as a keystone species for the complex not only because they are required for unisexual Ambystoma to reproduce, but also because their relative abundance governs the composition of entire unisexual Ambystoma assemblages. Comparatively, when assessing the lineage axis of genetic diversity, unisexual Ambystoma assemblage diversity patterns primarily reflected historic landscape structure, and spatial patterns of increased lineage richness were linked to areas where both potential hosts were locally available (currently or historically). Thus, while both of the investigated axes of diversity are forms of genetic diversity, each revealed distinct factors that have shaped contemporary diversity patterns across the landscape operating at different spatial and temporal scales. Critically, our understanding of complex ecological systems is likely to be broadened by including additional axes of diversity (e.g., allelic, loci, or chromosomal structure axes), and such investigations are not limited to clonal hybrid systems. Overall, this work illustrates the importance of combining insights from distinct conceptual and analytical toolkits to generate a comprehensive understanding of the factors which have shaped the patterns of diversity we observe today.

Author Keywords: Biological diversity, Dimensions of diversity, Ecological genetics, Metacommunity ecology, Unisexual Ambystoma

Wildlife translocation programs are widely employed as a strategy to reintroduce extirpated species into regions they once inhabited but no longer do. Reintroduction programs can be successful at re-establishing extirpated populations and also provide unique opportunities to study post-reintroduction population dynamics and behavioural ecology. The wild turkey (Meleagris gallopavo) is a forest generalist species that, prior to European colonization, inhabited much of the Carolinian zone in Ontario. This species was hunted to extirpation in the early 1900's and reintroduced in the mid-1980's through a series of wildlife trade agreements and coordinated trap and transfer efforts. Ontario's contemporary populations are seemingly thriving, with wild turkey harvest permitted in many regions of the province. However, given this species history of extirpation, understanding the size, distribution, and behavioural ecology of Ontario's reintroduced population of wild turkeys is essential to their long-term persistence in the province. We captured and radio-tagged 77 wild turkeys over four years in Peterborough, Ontario and studied their movement, sociality, and habitat preferences. My findings indicate that Ontario may contain relatively high densities of this species when compared with other parts of their range. My analyses also elucidated interesting aspects of this species habitat selection patterns within an anthropogenic landscape, in addition to novel findings surrounding wild turkey sociality and genetic structure.

Author Keywords: behaviour, genetics, Ontario, reintroduction, wild turkey, wildlife management

On many farms, stone and wooden field borders define field sizes. These are commonly perceived as land lost to production and refuges for pests and disease, causing such fences and hedges to be removed to create larger fields for increased productivity; this process has eliminated trees and shrubs that provide habitat along these fencerows. This research explores the alignment of agricultural productivity and wildlife conservation, proposing that species such as feral apples may serve as direct economic resources for producers and act to protect such remaining fences and hedges. This study focused on farms in the Dummer Moraine, which have small fields, adventive hedges on rock piles and rail fences. Using field size analysis, apple frequencies and apple jelly tasting, the research demonstrates that feral apples could provide economic incentive for keeping these hedges intact, offering a practical mechanism for their conservation, benefiting both biodiversity and farm productivity.

KEYWORDS: biodiversity conservation, farm gate sales, fencerows, feral apples, hedges, linear forests

Author Keywords: biodiversity conservation, farm gate sales, fencerows, feral apples, hedges, linear forests