Wildlife conservation

While the harvest of mammals is monitored in each jurisdiction across Canada and the USA, there has been no analysis of this wild harvest at a continental scale across North America. The recreational wild harvest of large mammals varies geographically across North America, and I hypothesized that this variation is influenced by both anthropogenic and other environmental factors on the landscape. I tested this hypothesis using annual harvest tallies collected by Conservation Visions Inc. for mammals for each state, provincial, and territorial jurisdiction in Canada and the USA. I built multiple additive models of the harvest, in one harvest year, 2015 – 2016, to test for landscape gradients that explain the variation in harvest levels for seven large mammal species: white-tailed deer (Odocoileus virginianus), black bear (Ursus americanus), bighorn sheep (Ovis canadensis), elk (Cervus canadensis), mule deer (Odocoileus hemionus), pronghorn (Antilocapra americana), and moose (Alces alces). I built these models from a suite of nine putative predictor variables that comprised landcover, human footprint, and evapotranspiration. For all large mammal species except for pronghorn, anthropogenic influence had a positive effect on the wild harvest density, consistent with the idea that the proximity of human populations and roads are important for fostering wild harvest activity by providing hunters access to hunting areas. The harvest of white-tailed deer, elk, and pronghorn were negatively affected by vegetation structure, urbanization, and primary productivity, respectively. Understanding the recreational wild harvest at a broad-spatial scale provides a unique perspective of the North American model of wildlife conservation and spurs future comparative analyses of the wild harvest across spatial scales.

Author Keywords: Anthropogenic Influence, Hunting, Large Mammals, Primary Productivity, Vegetation Structure, Wild Harvest

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

Resources and risk are in constant flux and an organism's ability to manage change may improve their likelihood of persistence. I examined intra-seasonal variation in nest-site selection and survival of a declining wetland bird, the Black Tern (Chlidonias niger surinamensis). I modelled nest site occupancy and survival of early and late-nesting birds as a function of static and dynamic factors. Early-nesting birds selected nest sites based on the degree and direction of habitat change that occurred over the nesting cycle, while late-nesting birds selected sites based on static conditions near the time of nest-site selection. Nest age had the strongest influence on daily survival rate for both early and late-nesting birds, but the shape of this relationship showed intra-seasonal differences. Additionally, early-season survival improved slightly with increasing vegetation coverage and distance between conspecific nests, while late-season survival increased with clutch size. My results suggest that intra-seasonal variation in nest-site selection and survival is driven by changing habitat conditions and predator behavior.

Author Keywords: Black Tern, Chlidonias niger surinamensis, daily survival rate, intra-seasonal variation, nest-site selection

Drivers of North American Barn Swallow population declines are not well understood, but foraging habitat loss is thought to be a contributing factor. Determining patterns of habitat use is challenging for swallows because they move rapidly but are too small to carry GPS tags. We showed that automated radio-telemetry could be used to track the movements of swallows with enough accuracy (median error 250 m) to monitor local habitat use. We then combined information on breeding Barn Swallows habitat use, land cover, aerial insect abundance, and fledging success to test for a link between foraging habitat quality and reproductive success. Foraging activity was concentrated within 600 m of nest sites and varied with land cover; however, responses to land cover were not consistent across birds. Aerial insects were most abundant near wetlands and least abundant near open water and over cropland. Consistent with a link between foraging habitat and reproductive success, nests in barns with more wetland and less open water within 1 km, and with less field area within 2 km occupied by row crops, on average fledged more young swallows.

Author Keywords: aerial insectivores, automated telemetry, habitat use, land cover, movement, nest success

Pastures and hayfields provide surrogate habitat for many declining grassland birds. Understanding agricultural land use dynamics and habitat quality can impact conservation of grassland species. I investigated 1) patterns of land use change in protected and unprotected sites in relationship to Bobolink occurrence in Carden, Ontario, Canada and 2) whether continuous grazing at lowmoderate cattle densities provided suitable breeding habitat, using both real and artificial nests. I replicated the 2001-2005 Ontario Breeding Bird Atlas to evaluate site habitat changes and Bobolink population trends. In continuously grazed pastures and late-cut hayfields, I monitored Bobolink abundance and reproductive success and modeled daily survival rate of nests using habitat management, vegetation structure, and prey availability. Results indicated that Bobolink have declined by -15.3% since 2001 in Carden; losses were explained almost entirely by changes from suitable breeding habitat (e.g. hayfields) to tilled land or by the colonization of shrubs. For pastures, stocking densities of ≤ 1Animal Units/ha did not negatively impact Bobolink. Year and caterpillar biomass, and vegetation height were the strongest predictors of nesting success in pastures and hayfields, respectively. Focus on the preservation of suitable habitat on the breeding grounds and management on small-scale beef farms can contribute to conservation action for this declining species.

Author Keywords: agricultural management, avian ecology, Bobolink, continuous grazing, grassland birds, nest success

Barn Swallow (Hirundo rustica) populations have declined in North America over the past 40 years and they are listed as Threatened in Ontario, Canada. Changes in the food supply have been hypothesized as a potential cause of this population decline. I used DNA barcoding to investigate the diet and food supply of Barn Swallows and to determine if the food supply affects their reproductive performance. In two breeding seasons, I monitored nests, collected fecal samples, and monitored prey availability by collecting insects from the habitat surrounding breeding sites using Malaise traps. I used DNA barcoding to identify insect specimens collected from the habitat and to identify prey items from Barn Swallow nestling fecal samples. I found that Barn Swallow nestlings were fed a very broad range of prey items but were fed larger prey items more frequently. Prey availability was not related to the timing of reproduction, the number of nests at a breeding site, or the reproductive output of individual nests. This study provides information on the diet composition of Barn Swallows in North America and suggests that food limitation during the breeding season may not be a major factor in their population decline.

Author Keywords: aerial insectivore, diet, DNA barcoding, Hirundo rustica, metabarcoding, reproductive success

Chimney swifts are listed as Threatened nationally and in many provinces within Canada due to rapid population declines. I examined large-scale spatial variation in the maximum size of chimney swift roosts at the northern edge of their range to identify where larger roosts occur. I used multi-sourced data collected across Ontario and Quebec between 1998 and 2013. I found that larger roosts were found at more northerly latitudes, and that very large roosts (>1000 birds) only occurred north of 45°. I also investigated fine-scale patterns of chimney swift positioning inside one of the largest roosts in Ontario. Using digitally recorded images, I calculated the angular position of swifts inside the roost relative to ambient and roost temperature. I found that swifts showed a strong preference for clinging to the south facing wall and clustered more when ambient air temperature was warmer. Thus, huddling in swifts provides additional or alternate benefits, other than serving purely to reduce costs of thermoregulation at low ambient temperatures. This research contributes to the understanding of chimney swift roosting ecology and identifies large roosting sites that should be retained for conservation.

Author Keywords: chimney swift, communal roosting, conservation, group size, social thermoregulation, species-at-risk

Environmental DNA (eDNA) detection uses species-specific markers to screen DNA from bulk samples, such as water, to infer species presence. This study involved the development and testing of species-specific markers for four freshwater pearly mussels (Unionidae). The markers were applied to water samples from intensively sampled mussel monitoring sites to compare species detections from eDNA with established sampling method detections. Target species were detected using eDNA at all sites where they had previously been detected by quadrat sampling. This paired design demonstrated that eDNA detection was at least as sensitive as quadrat sampling and that high species specificity can be achieved even when designing against many sympatric unionids. Detection failures can impede species conservation efforts and occupancy estimates; eDNA sampling could improve our knowledge of species distributions and site occupancy through increased sampling sensitivity and coverage.

Author Keywords: conservation genetics, cytochrome oxidase subunit I (COI), environmental DNA (eDNA), quantitative PCR (qPCR), species at risk (SAR)

Around the world, many populations of migratory shorebirds appear to be declining. Conservation strategies to reverse declining trends rely on, among other information, a firm understanding of breeding ground population dynamics. From 2010 to 2014, I studied a breeding population of Dunlin (Calidris alpina hudsonia) near Churchill, Manitoba using mark-recapture methods. I found that females were significantly larger than males. I subsequently developed an equation based on morphological features that successfully classified 87.1% of females and 92.6% of males, sexed using molecular techniques. Using program MARK, I quantified the annual apparent survival of adults (± SE) within the breeding population (0.82 ± 0.063 for males, 0.73 ± 0.12 for females). Transient adults made up a significant percentage of the female population (32%, P = 0.011), but non-significant in the male population (12%, P > 0.05). Re-sight rate was high for both sexes, and ranged from 0.86-0.90 per year. Sex, year, and nest initiation date were the factors that had the greatest influence on annual returns. There was no significant difference in mean inter-annual nest site distance between sexes (male: 82.01 ± 13.42 m, female: 208.38 ± 55.88 m, P > 0.05). The high survival estimates obtained in this study suggest that the breeding population is stable and may not be contributing to suspected population declines within the subspecies.

Author Keywords: demography, discriminant function analysis, mark-recapture, sexual size dimorphism, survival

Identifying the population origin of aquaculture-reared caviar is crucial for both conservation and management strategies of farmed fish but could also facilitate international trade of a CITES regulated product. Shortnose sturgeon (Acipenser brevirostrum) is the main source of caviar production in Atlantic Canada, from Breviro Caviar Inc. aquaculture facility. Shortnose sturgeon are also listed as a species-at-risk under the Species At Risk Act. Currently there is no genetic method for delineating wild from aquaculture-reared caviar. By targeting the mitochondrial genome (mitogenome) using novel long-range PCR primers and next-generation sequencing (NGS) methods we have successfully sequenced the full mitogenome of 37 shortnose sturgeon. The purpose of this study was to increase the resolution of diagnostic variation among populations and to validate Canadian aquaculture-reared stock from wild US populations.

Results provided a previously unobserved novel control region haplotype in high frequency within both the aquaculture-reared and Saint John River wild sample sets. Similar frequencies were observed with whole mitogenome haplotypes. Diagnostic mitochondrial lineage found in high frequency within the captive Breviro Caviar Inc. population has the potential to allow caviar product from Breviro Caviar Inc. to be distinguished from protected US shortnose sturgeon populations. The application of full mitogenomic characterization provides the potential to further resolve differences between aquaculture and natural Canadian shortnose sturgeon stocks, US/Canadian populations and to contribute to future conservation strategies. Future research identifying signatures of selection on the mitogenome between captive and wild populations and across latitudinal gradients found within the species range. These novel methods have produced a proof-of-concept to provide a "farm-to-fork" validation and ecobrand of Breviro Caviar Inc. product and its aquaculture origin to support importation into US caviar markets.

Author Keywords: aquaculture, mitogenome, next-generation sequencing, species-at-risk, sturgeon