Understanding the impacts of both natural and anthropogenic landscape features on genetic diversity, population structure and connectivity has important implications for conservation of species living in fragmented environments. Here, I combine population genetic data, detailed land cover information, and computer simulations to explore how landscape shapes genetic structure across two regional populations of the threatened eastern massasauga rattlesnake (Sistrurus catenatus catenatus) in Ontario, Canada: one along the eastern shores of Georgian Bay and the other largely confined to the northern half of the Bruce Peninsula. First I used spatial Bayesian assignment to quantify the genetic population structure within each regional population. I found marked subpopulation structure within eastern Georgian Bay with differentiation of island and mainland snakes, a north-south split within the mainland coinciding with the town of Parry Sound, and evidence of further subdivision within the cluster of snakes north of Parry Sound. In contrast I found no population subdivision within the mainland of the Bruce Peninsula, but genetic distinction of mainland and island snakes. Next, I identified the landscape features that shape spatial genetic structure within regional populations. In eastern Georgian Bay I found local variation in the effect of landscape on populations. North of Parry Sound I found no effect of landscape on inter-individual genetic differentiation, but a strong pattern of isolation-by-distance. In contrast I found that both open water and roads restrict gene flow of snakes south of Parry Sound. I found no evidence of isolation-by-distance or that landscape shape genetic structure within the Bruce Peninsula. Finally I used individual-based, spatially explicit simulations to identify the lag-time associated with the detection of contemporary landscape feature effects on genetic structure of massasaugas, and explore the consequences of using spatially correlated land cover elements in landscape genetic analyses. I found that the genetic consequences of roads could be detected within 2-12 generations when population sizes were small or juvenile dispersal was low. However, I also found that roads could be spuriously identified as impediments to gene flow when spatially correlated features such as water are included in genetic models. / Thesis (Master, Biology) -- Queen's University, 2011-10-14 15:06:35.956

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Utilizing environmental DNA (eDNA) for the detection of species in the field is a potentially cost-effective and time-saving technology that may be useful in understanding the distribution and abundance of threatened or endangered species such as the Eastern Massasauga (Sistrurus catenatus). I describe the development of an eDNA assay for the species and evaluate its ability to detect eDNA in laboratory and field conditions. In the field samples, I also investigated the potential for abiotic conditions to influence eDNA detection. Species-specific primers and probe were designed to amplify a 152 bp segment of the massasauga COI gene. Target eDNA could be detected in samples containing as little as 100 copies of target DNA/μL. Water samples collected from laboratory housed snakes indicated that eDNA can be detected in water 56 days after massasauga removal. Field samples were taken from crayfish burrows, known overwintering habitat for the species, from four sites that vary in snake use as ascertained by traditional visual surveys. Of the 60 burrows sampled, seven had a positive detection for massasauga eDNA with no difference in detection rate between DNA extracted from burrow water and burrow sediment. Occupancy models fitted to burrow water indicated that larger amounts of total DNA in a sample may increase the probability of detection of a massasauga eDNA. Large confidence intervals in site occupancy (ѱ) and burrow detection (Θ) values suggest that a larger sample size is needed for more reliable occupancy models. Abiotic conditions within crayfish burrows varied among sites but correlation with eDNA detection was not supported. Estimates of qPCR detection within a burrow with eDNA (ρ) suggest that up to 10 qPCR replicates per burrow sample may be necessary. Further studies need to examine eDNA degradation in the field, improve upon the limit of detection, and sample a larger number of sites for eDNA sampling to be a stand-alone survey method for Eastern Massasaugas.

Over the 21st century, climate change and wetland habitat loss will pose major threats to the Eastern Massasauga (Sistrurus catenatus), a federally threatened and Great Lakes region endemic rattlesnake. I collected capture-recapture data from sites across the range and modeled the effect of climatic variables on growth rate and asymptotic size. I found that high snow residence time was associated with larger asymptotic sizes but slower growth, while high spring precipitation increased growth rate. I then projected future growth and size under different carbon emission scenarios. Given the threat posed by successional encroachment of woody vegetation, I used spatially explicit capture-recapture models to examine the effects of landscape characteristics and phenology on the spatial distribution of density for a population in Michigan. I found highest density in areas close to a stream and with low vegetation intensity, which can inform prescribed burn programs and give additional insights into life history.