Conservation biology

Similar to other shorebird trends around the world, the Piping Plover population (Charadrius melodus circumcinctus) is projected to decline if concerted conservation efforts are relaxed. To date, there is insufficient understanding of the connection between habitat type, prey abundance, and chick behaviour of the Piping Plover breeding population in Ontario. The aim of my thesis was to gain knowledge about prey abundance at recent and historic breeding locations, understanding how habitat influences prey abundance and chick behaviour across the Piping Plover breeding range in Ontario's Great Lakes. The objective of my first study was to understand prey abundance across the breeding region Great Lakes of Ontario from 2018-2019, including occupied and unoccupied sites, and to quantify variation among habitats and periods of reproduction. To evaluate resources, I sampled 17 locations to compare prey abundance using invertebrate traps (n= 3,507). Sampling took place over the reproductive periods of nest initiation, post-hatch, and fledging and in four habitat types of shoreline, wrack, berm, and back dune. Occupied breeding sites had higher prey abundances, and different assemblages of invertebrate prey than unoccupied sites. Additionally, breeding sites had higher prey abundance during nest initiation and supported higher amounts of prey in shoreline and wrack habitat. The objective of my second study was to understand how habitat types influence chick behaviour. To evaluate behaviour-habitat trends, instantaneous chick observations were recorded at the four nest sites from the post-hatch to fledging stages. In total there were 23 fledged chicks that we observed across the two years. Chicks in this study spent 60.9% of their time foraging, 11.9% of the time displaying alert behaviour, 21.4% of their time resting or being brooded, and 5.9% of their time preening. Chicks spent a large proportion of time foraging in the shoreline, resting in the back dune, and alert in berm habitat. The frequency of these alert, defensive behaviours differed among sites, with Sauble Beach chicks spending more time in defensive behaviours compared to other sites. I concluded that in both nesting and brood-rearing periods, habitat is selected non-randomly by adult and young Piping Plovers to maximize access to invertebrate prey for growth and survival. Access by chicks to the most productive habitats should be considered in local management decisions.

Author Keywords: chick behaviour, endangered, Great Lakes Region, habitat, Piping Plovers, prey abundance

I implemented three hayfield management regimens in southern Ontario (a typical schedule at the farmer`s discretion, a delayed first harvest after July 14, and an early first harvest before June 1 with 65 days before second harvest), and evaluated the costs/benefits to farmers regarding hay quality and feasibility, and to Bobolinks (Dolichonyx oryzivorus) regarding reproductive activity and phenology. Typical management resulted in little to no Bobolink reproductive success, and early harvested sites were not (re)colonized. On delayed harvest sites Bobolinks experienced high reproductive success, but hay quality fell below ideal protein levels for most cattle before harvest. I also examined the habitat features Bobolinks use as the basis for establishing territories and associations between Bobolink territory size and habitat quality. I compared vegetation structure, patch size, and prey abundance between small and large territories. Small territories typically occurred on smaller fields with more preferred vegetation characteristics and greater prey abundance.

Author Keywords: agro-ecosystem, Bobolink, Dolichonyx oryzivorus, grassland birds, hayfield management

Site fidelity is the behaviour of individuals to return to the same location; for female woodland caribou it may reflect reproductive success and depend on habitat quality. I investigated the influence of landscape and disturbance conditions on fidelity among three populations in Manitoba and Ontario, Canada. Habitat classifications were based on Forest Resource Inventory (FRI) and Landsat TM landcover maps. A total of 261 sites were ground-truthed to determine mapping accuracy. An amalgamated map incorporating FRI and Landsat TM data was estimated from field measurements to have an overall accuracy of 69.0%. Site fidelity was expressed as the distance between consecutive-year locations of individuals and was investigated during five week-long periods representing calving, early and late post-calving, winter, and breeding. Site fidelity was strongest during the post-calving seasons and weakest during the winter. Habitat had little influence on site fidelity in all seasons, excepting winter, even under highly disturbed conditions, suggesting maintenance of fidelity may be a maladaptive trait. Individual variation proved a strong predictor and cursory mapping indicated that caribou may return to sites visited two or more years earlier. Conservation management and policy should recognize that site fidelity may represent an ecological trap.

Author Keywords: calving, disturbance, habitat, movement, Rangifer tarandus caribou, site fidelity

Current major issues in conservation biology include habitat loss, fragmentation and population over-exploitation. Animals can respond to landscape change through behavioural flexibility, allowing individuals to persist in disturbed landscapes. Individual behaviour has only recently been explicitly included in population models. Carnivores may be sensitive to changing landscapes due to their wide-ranging behaviour, low densities and reproductive rates. Canada lynx (Lynx canadensis) is a primary predator of snowshoe hares (Lepus americanus). Both species range throughout the boreal forests of North America, however lynx are declining in the southern range periphery. In this dissertation, I developed new insights into the effects of habitat loss and fragmentation on lynx. In Chapter 2, I created a habitat suitability model for lynx in Ontario and examined occurrence patterns across 2 regions to determine if habitat selection is flexible when different amounts of habitat are available. Although lynx avoided areas with <30% suitable habitat where suitable land cover is abundant, I found that they have flexible habitat selection patterns where suitable land cover is rare and occurred in low habitat areas. In Chapter 3, I investigated the effects of dispersal plasticity on occupancy patterns using a spatially explicit individual-based model. I showed that flexible dispersers, capable of crossing inhospitable matrix, had higher densities and a lower risk of patch extinction. In contrast, inflexible dispersers (unable to cross inhospitable matrix), were most limited by landscape connectivity, resulting in a high extinction risk in isolated patches. I developed three predictions to be explored with empirical data; (1) dispersal plasticity affects estimates of functional connectivity; (2) variation in dispersal behaviour increases the resilience of patchy populations; and (3) dispersal behaviour promotes non-random distribution of phenotypes. Finally, in Chapter 4, I examined the consequences of anthropogenic harvest on naturally cycling populations. I found that harvest mortality can exacerbate the effects of habitat fragmentation, especially when lynx densities are low. Dynamic harvest regimes maintained lynx densities and cycle dynamics while reducing the risk of population extinction. These results suggest that lynx display some flexibility to changing landscapes and that the metapopulation structure is more resilient to increasing habitat loss and fragmentation than previously understood. Future studies should focus on determining a threshold of connectivity necessary for population persistence and examining the effects of habitat loss on the fecundity of lynx.

Author Keywords: Fluctuating Populations, Habitat Fragmentation, Landscape Ecology, Occupancy Dynamics, Population Ecology, Spatially Explicit Population Models

Pacific Rim National Park Reserve's 16 km of coastal beaches attract many thousands of people and shorebirds every year. To identify locations where shorebirds concentrate and determine the impact of human activity and habitat characteristics on shorebirds, I conducted shorebird and visitor surveys at 20 beach sectors during fall migration in 2011 to 2013 and spring migration in 2012 and 2013. The probability of shorebird presence decreased with increasing number of people at a beach sector. The time that shorebirds spent at a sector increased with increasing sector width. Close proximity to people increased the proportion of time shorebirds spent moving while shorebirds spent more time moving and less time foraging on wider beaches than on narrower ones. My findings suggest that placing restrictions on beach access and fast moving activities (e.g., running) may be necessary to reduce shorebird disturbance at Pacific Rim and similar stopover areas.

Author Keywords: habitat use, human disturbance, predation risk, prey availability, shorebird, stopover

Climate change has had numerous impacts on species' distributions by shifting suitable habitat to higher latitudes and elevations. These shifts pose new challenges to biodiversity management, in particular translocations, where suitable habitat is considered crucial for the reintroduced population. De-extinction is a new conservation tool, similar to reintroduction, except that the proposed candidates are extinct. However, this novel tool will be faced with similar problems from anthropogenic change, as are typical translocation efforts. Using ecological niche modelling, I measured suitability changes at translocation sites for several Holarctic mammal species under various climate change scenarios, and compared changes between release sites located in the southern, core, and northern regions of the species' historic range. I demonstrate that past translocations located in the southern regions of species' ranges will have a substantial decline in environmental suitability, whereas core and northern sites exhibited the reverse trend. In addition, lower percentages (< 50% in certain scenarios) of southern sites fall above the minimal suitability threshold for current and long-term species occurrence. Furthermore, I demonstrate that three popular de-extinction candidate species have experienced changes in habitat suitability in their historic range, owing to climate change and increased land conversion. Additionally, substantial increase in potentially suitable space is projected beyond the range-limits for all three species, which could raise concerns for native wildlife if de-extinct species are successfully established. In general, this thesis provides insight for how the selection of translocation sites can be more adaptable to continued climate change, and marks perhaps the first rigorous attempt to assess the potential for species de-extinction given contemporary and predicted changes in land use and climate.

Author Keywords: climate change, de-extinction, ecological niche models, MaxEnt, reintroduction, translocation

The objective of this thesis is to better understand the demography and habitat selection of Newfoundland caribou. Chapter 1 provides a general introduction of elements of population ecology and behavioural ecology discussed in the thesis. In Chapter 2, I examine the causes of long-term fluctuations among caribou herds. My findings indicate that winter severity and density-dependent degradation of summer range quality offer partial explanations for the observed patterns of population change. In Chapter 3, I investigate the influence of climate, predation and density-dependence on cause-specific neonate survival. I found that when caribou populations are in a period of increase, predation from coyotes and bears is most strongly influenced by the abiotic conditions that precede calving. However, when populations begin to decline, weather conditions during calving also influenced survival. I build on this analysis in Chapter 4 by determining the influence of climate change on the interplay between predation risk and neonate survival. I found that the relative equilibrium between bears and coyotes may not persist in the future as risk from coyotes could increase due to climate change. In Chapter 5, I investigate the relationships in niche overlap between caribou and their predators and how this may influence differential predation risk by affecting encounter rates. For coyotes, seasonal changes in niche overlap mirrored variation in caribou calf risk, but had less association with the rate of encounter with calves. In contrast, changes in niche overlap during the calving season for black bears had little association with these parameters. In Chapter 6, I examine broad-level habitat selection of caribou to study trade-offs between predator avoidance and foraging during the calving season. The results suggest that caribou movements are oriented towards increased access to foraging and the reduction of encounter risk with bears, and to a lesser extent, coyotes. Finally, I synthesize the major findings from this thesis and their relevance to caribou conservation in Chapter 7, to infer that Newfoundland caribou decline is ultimately driven by extrinsic and intrinsic elements related to density-dependence. Reduction in neonate survival emerged from nutritionally-stressed caribou females producing calves with lower survival.

Author Keywords: Behavioural ecology, Black bear (Ursus americanus), Coyote (Canis latrans), Population ecology, Predator-prey interactions, Woodland caribou (Rangifer tarandus)

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

Detecting relevant and meaningful patterns from the complex, interconnected network of relationships between organisms and their environment is a primary objective of ecology. Ecological patterns occur across multiple scales of space and time. In this dissertation, I examine aspects of environmental structure that influence a species' distribution and are expressed in that species' population dynamics. I compare the morphology of the five-lined skink (Plestiodon fasciatus) near its high latitude range limits with a lower latitude population and evaluate the economics of their behaviour in the context of its reproductive strategy. I tested the conformity of this species to biogeographical rules postulated by MacArthur, Bergmann, and Rensch. Spatial ecology was investigated in the context of the environmental potential for polygamy proposed by Emlen and Oring (1977) The five-lined skink, Plestiodon fasciatus, conformed to these biogeographic rules. Specifically, abiotic factors were the primary limiting factors affecting distribution at the high latitude range limits of the species; body size was larger in high latitude populations; and the degree of sexual size dimorphism was greater at high latitude than at low latitude. Spatial ecology at the individual scale was influenced by sites with suitable thermal conditions which facilitate the polygynandrous mating system documented in P. fasciatus in high latitude populations. My results confirm the importance of microsites with suitable thermal profiles as key habitat for ectothermic vertebrates at high latitudes. The influence of temperature as a limiting abiotic factor is expressed in population density, body size, spatial ecology, and reproductive strategy of P. fasciatus. Conservation and restoration of high latitude populations of ectothermic vertebrates should focus on ensuring thermal requirements of the species of concern are met before other factors are addressed, as temperature is likely the single most important limiting factor at high latitude range limits.

Author Keywords: biogeography, lizard, Plestiodon fasciatus, range limits, sexual size dimorphism, spatial ecology

Many rare and elusive species have low detection probabilities, thereby imposing unique challenges to monitoring and conservation. Here, we assess the detection probability of the Eastern Massasauga (Sistrurus catenatus) in contrast to a more common and conspicuous species, the Eastern Gartersnake (Thamnophis sirtalis). We found that patterns of detection probability differed between species, wherein S. catenatus was detected less often and under a more specific set of sampling conditions. Correspondingly, detection trials with S. catenatus found a high non-detection rate, while detection trials with artificial models suggest that regional differences in detection probability are driven by variation in population density and habitat use. Our results suggest that current monitoring efforts are not sufficient, and that S. catenatus is frequently undetected. Accordingly, we highlight the importance of species-specific monitoring protocols when monitoring rare and elusive species, and recommend a multi-faceted approach that estimates detection probability and identifies species-specific challenges to monitoring.

Author Keywords: detection probability, elusive species, monitoring programs, non-detection, S. catenatus, snakes