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

Amentotaxus is an ancient lineage of gymnosperm genus. Based on the Tertiary fossil evidence, the ancient lineage was once widespread in the Northern Hemisphere but range contraction in Pleistocene and Holocene. Currently, the distributional range is restricted to southwestern China, Vietnam and Taiwan. In this study, the 15 polymorphic microsatellite primers were designed from A. formosana H. L. Li, and were used these primers for genetic research of species level and population level. In species level, we tested the transferability and polymorphism in four species, A. argotaenia (Hance) Pilger, A. formosana H. L. Li, A. poilanei (Ferr&#x00E9; & Rouane) D.K. Ferguson and A. yunnanensis H. L. Li were evaluated. In population level, we evaluate the genetic variation and genetic structure on two habitats including Mt. Chachayalaisham and Jinshueiying for the delimited of relevant genetic units and to establish useful conservation strategies. In species level, the 15 microsatellite primers had 100% successfully amplified fragments in these three species, also showing high polymorphisms (PIC=0.25-0.61). In population level, the genetic diversity analysis in the two population of A. formosana show that expected and observed heterozygosities were ranged from 0.52 to 0.60 and 0.28 to 0.36, respectively. In addition, 15 loci were deviated from Hardy-Weinberg equilibrium (P<0.001) and the inbreeding coefficient were displayed positive (FIS=0.48368; P <0.05), revealing the genetic fixation causing by inbreeding. The analysis of molecular variance (AMOVA) revealed that high genetic variation with population (83.85% and 52.39%), and also showed high levels of population differentiation (FST =0.10972-0.16155; P <0.05). IMa revealed low migration rate (1.13¡Ñ10-6-1.15¡Ñ10-4), also showed small effective population size (Cha: 77.36-1830.67; Jin: 21.41-506.67) and large ancestral population size (10496.8-248424.17), inferring the A. formosana undergo significant population declined. Using Bayesian clustering algorithms and Markov chain Monte Carlo (MCMC) iterations to distinct genetic units and make assignments in the programs SAMOVA¡BSTRUCTURE and INSTRUCT, the best clustering was occurred at K=2, and found 11 and 9 distinct genetic groups in Mt. Chachayalaisham and Jinshueiying based on GENELAND analysis, respectively. We correlated the distinct genetic units and the age structures to evaluate the individuals with unique genotype for seed source to maintain the maximum genetic diversity of A. formosana.

Understanding the events and processes responsible for patterns of within species diversity, provides insight into major evolutionary themes like adaptation, species distributions, and ultimately speciation itself. Here, I combine ecological, genetic and spatial perspectives to evaluate the roles that both historical and contemporary factors have played in shaping the population structure and genetic variation of foxsnakes (Pantherophis gloydi). First, I determine the likely impact of habitat loss on population distribution, through radio-telemetry (32 individuals) at two locations varying in habitat patch size. As predicted, individuals had similar habitat use patterns, but restricted movements to patches of suitable habitat at the more disturbed site. Also, occurrence records spread across a fragmented region were non-randomly distributed and located close to patches of usable habitat, suggesting habitat distribution limits population distribution. Next, I combined habitat suitability modeling with population genetics (589 individuals, 12 microsatellite loci) to infer how foxsnakes disperse through a mosaic of natural and altered landscape features. Boundary regions between genetic clusters were comprised of low suitability habitat (e.g. agricultural fields). Island populations were grouped into a single genetic cluster suggesting open water presents less of a barrier than non-suitable terrestrial habitat. Isolation by distance models had a stronger correlation with genetic data when including resistance values derived from habitat suitability maps, suggesting habitat degradation limits dispersal for foxsnakes. At larger temporal and spatial scales I quantified patterns of genetic diversity and population structure using mitochondrial (101 cytochrome b sequences) and microsatellite (816 individuals, 12 loci) DNA and used Approximate Bayesian computation to test competing models of demographic history. Supporting my predictions, I found models with populations which have undergone population size drops and splitting events continually had more support than models with small founding populations expanding to stable populations. Based on timing, the most likely cause was the cooling of temperatures and infilling of deciduous forest since the Hypisthermal. On a smaller scale, evidence suggested anthropogenic habitat loss has caused further decline and fragmentation. Mitochondrial DNA structure did not correspond to fragmented populations and the majority of foxsnakes had an identical haplotype, suggesting a past bottleneck or selective sweep. / Thesis (Ph.D, Biology) -- Queen's University, 2011-01-11 10:40:52.476