The use of genetic evidence to facilitate management outcomes for species of conservation or cultural concern can benefit from broadening the scope of inquiry. These efforts can include not only multiple geographic and genomic scales but also other academic disciplines and ways of knowing, which can identify unconventional drivers of genetic patterns. Genetic patterns revealed through such a broad approach can provide key information to managers regarding population differentiation, viability, isolation, and adaptive capacity, and can be incorporated into long-term precautionary management plans at local and regional scales. In this dissertation, I addressed several applied questions using multi-scale, interdisciplinary, and community-led approaches. The dramatic variation in habitat types and resource distribution in British Columbia, especially along the coastal to interior ecotone, allowed for investigation of potential genetic differentiation, landscape resistance, and local adaptation in two wide-ranging, omnivores. Grizzly bears (Ursus arctos) and black bears (Ursus americanus) in the area now known as British Columbia (BC) also hold high cultural value. Additionally, bears and people have been cohabitating and sharing resources on this landscape for millennia, prompting investigations of how this relationship and shared landscape might have shaped both. This relationship is reflected in Indigenous-led long term bear monitoring on the central coast of BC by the Nuxalk, Haíɫzaqv, Kitasoo/Xai’xais, Gitga’at, and Wuikinuxv First Nations. In the bear system of the central coast and larger BC there are management opportunities for the integration of local and regional monitoring, intergovernmental collaboration, and using genetic data to re-assert Indigenous-led management goals. Finally, given that black bear populations of the area contain a single genetic variant responsible for creating white phase or Spirit bear individuals, relevant genetic evidence that can be considered in the management of bears in BC ranges from a single genetic variant to genome-wide investigations of local adaptation across the coastal to interior ecotone. In my first data-driven chapter (Chapter 2), I used microsatellite markers to examine the pattern of genetic structure and its potential drivers among grizzly bears on the central coast of BC. We incorporated potential landscape resistance factors informed by relevant literature. Also recognizing the dramatic changes in Indigenous settlement density following European colonization and the potential for genetic markers to reflect historical patterns, we estimated resistance surfaces reflective of both pre and post colonization periods. Although no resistance surface explained a consequential proportion of genetic differentiation, we found a significant spatial overlap between Indigenous language families and the three bear genetic groups. We suspect that this pattern reflects a similar response of bears and people to unknown resource and geographic discontinuities across the landscape. This work contributes to the emerging intersection of landscape genetic and biocultural scholarship that includes non-traditional landscape factors at multiple temporal scales and considers parallel responses of wildlife and people to the landscapes they share. Additionally, given that current Provincially-designated management unit boundaries misalign to spatial patterns shown by genetic groups this research contributes detailed and actionable management implications. In Chapter 3, I used similar genetic methods to identify patterns of genetic differentiation for black bears of the central coast. In contrast with the three genetic groups of grizzly bears, we found eight genetic groups of black bears at a similar scale. This pattern likely reflects the differences in home range sizes and foraging ecology between these species. We also identified groups with low genetic diversity, with two of these groups containing high frequencies of the Spirit bear allele. We additionally found that wide waterways corresponded to genetic differentiation between groups and areas of lower than average estimated migration. We provide management recommendations based on these results that focus on balancing sufficient gene flow to ensure long-term viability of isolated and genetically depauperate genetic groups with ensuring that the rare Spirit bear variant is not swamped by an influx of genetic material. With this work, we show that linear landscape features other than roads (i.e. waterways) can provide resistance to even highly mobile species and that more gene flow is not always optimal for all scales of genetic conservation. In my third data chapter (4), I broadened the investigation of grizzly bear genetic differentiation from the scale of the central coast used in Chapter 2 to the ecotone spanning coastal and interior BC. Using whole genome resequencing, we additionally expanded the scale of genetic data to identify potential signatures of local adaptation. We found two broad-scale genetic groups corresponding to coastal and interior populations admixed along valleys that bisect the North to South Coast Mountain Range. We additionally identified potential signatures of local adaptation in genes associated with growth, development of muscle and bone, and immunity in the coastal genetic group, as well as those related to DNA repair and growth inhibition in the interior group. The functions of these candidate genes broadly align with morphological differences observed between larger coastal bears with consistent access to salmon and smaller interior bears with intermittent access to protein resources and exposure to more extreme environmental conditions. In a management context, this work highlights vulnerabilities to rapid environmental or resource changes in potentially locally adapted populations, and supports management efforts to protect connectivity via valleys that bisect the Coast Mountain Range. Finally, I summarize and discuss the conceptual and management contributions of this work and opportunities for future research (Chapter 5; dissertation conclusion). I highlight the contribution of Indigenous stewardship partners and their traditional and local ecological knowledge in defining, shaping, and expanding the scope of this dissertation, as well as applying management- relevant results. Our research methods and findings support the inclusivity of broad scientific and non-scientific communities and knowledge in genetic research and the application of genetic research to local management. / Graduate / 2022-09-14

Gene flow dictates a broad range of ecological and evolutionary processes. Understanding the factors mediating magnitude and direction of gene flow is crucial for interpreting patterns of genetic diversity and for answering many kinds of biological questions. Recent advances at the interface of population genetics and GIS technology have expanded our perspective of the geographic and physical features influencing gene flow and, in turn, shaping genetic structure of populations. I investigated the effect of surface-level trade winds on genetic structure and gene flow in two species of phyllostomid bats in the Bahamas and Greater Antilles: Erophylla sezekorni (the buffy flower bat) and Macrotus waterhousii (Waterhouse's leaf-nosed bat). Bayesian Clustering Analysis revealed that all islands sampled represent independent genetic populations for M. waterhousii but not for E. sezekorni. Samples from 13 islands (spanning E. sezekorni?s range) clustered into five genetic populations and revealed the existence of two main clades (eastern: Hispaniola and Puerto Rico; western: Cuba, Jamaica, and Bahamas). To test the hypothesis that surface-level trade winds mediate gene flow in this system, I generated measures of effective distance between islands using anisotropic cost modeling based on wind data from the National Climactic Data Center. Both species exhibited significant isolation by distance with geographical distance and some of the measures of effective distance, but effective distance did not provide increased explanatory power in predicting distribution of genetic diversity. The IBDGEO slope was steeper for E. sezekorni than M. waterhousii, suggesting greater dispersal ability in the former species. According to Maximum Likelihood analysis, a majority (80%) of gene flow between genetic populations was asymmetric in both species. The degree of asymmetric gene flow between populations was not explained by the degree of asymmetry in effective distance or island area, indicating an unknown mechanism driving asymmetric gene flow. More information about the ecology of these taxa is required to understand the incidence of asymmetric gene flow in this system. The results of this study suggest that gene flow among islands is highly restricted for M. waterhousii and that this species deserves greater taxonomic attention and conservation concern.

No description available.

Understanding the ecological and evolutionary processes responsible for shaping patterns of genetic variation in natural populations is a long-standing goal in molecular ecology. Although an extensive number of recent studies focus on patterns and processes throughout tropical rain forest ecosystems, substantially less effort has been placed on tropical dry forests (TDFs); a habitat known to harbour a large percentage of Earth’s diversity. In this thesis I use leaf-toed geckos of the genus Phyllodactylus to understand both the historical and contemporary processes influencing diversification throughout Mexico’s TDFs. In Chapter 2 I isolate and characterize microsatellite markers for the gecko P. tuberculosus. Chapter 3 uses these loci to conduct a landscape genetic analysis of the species near Alamos, Sonora. I find that the inclusion of landscape variables explains more genetic variance versus Euclidean distance alone. Chapter 4 examines the evolutionary history of the P. tuberculosus group throughout western Mexico. Results suggest that habitat and climate shifts during the Miocene and Pleistocene were important divers of diversification. Chapter 5 uses microsatellite and mtDNA markers to compare historical and contemporary demographic parameters in P. tuberculosus. I find evidence for low historical gene flow and high female philopatry, recent reductions in population sizes, and higher correlations between landscape and contemporary gene flow versus historical gene flow and mtDNA divergence. In Chapter 6 I examine the biogeographic and taxonomic consequences of the dynamic history of Baja California. My phylogenetic results provide evidence for a trans-peninsular seaway in the Isthmus of La Paz region and suggests that P. xanti nocticolus warrants species status. My results also suggest the possibility of a seaway near the Loreto area that needs to be evaluated further. By combining multiple molecular marker-types and analytical methods, this thesis adds to our understanding of diversification processes throughout the threatened Mexican TDF.

Understanding the ecological and evolutionary processes responsible for shaping patterns of genetic variation in natural populations is a long-standing goal in molecular ecology. Although an extensive number of recent studies focus on patterns and processes throughout tropical rain forest ecosystems, substantially less effort has been placed on tropical dry forests (TDFs); a habitat known to harbour a large percentage of Earth’s diversity. In this thesis I use leaf-toed geckos of the genus Phyllodactylus to understand both the historical and contemporary processes influencing diversification throughout Mexico’s TDFs. In Chapter 2 I isolate and characterize microsatellite markers for the gecko P. tuberculosus. Chapter 3 uses these loci to conduct a landscape genetic analysis of the species near Alamos, Sonora. I find that the inclusion of landscape variables explains more genetic variance versus Euclidean distance alone. Chapter 4 examines the evolutionary history of the P. tuberculosus group throughout western Mexico. Results suggest that habitat and climate shifts during the Miocene and Pleistocene were important divers of diversification. Chapter 5 uses microsatellite and mtDNA markers to compare historical and contemporary demographic parameters in P. tuberculosus. I find evidence for low historical gene flow and high female philopatry, recent reductions in population sizes, and higher correlations between landscape and contemporary gene flow versus historical gene flow and mtDNA divergence. In Chapter 6 I examine the biogeographic and taxonomic consequences of the dynamic history of Baja California. My phylogenetic results provide evidence for a trans-peninsular seaway in the Isthmus of La Paz region and suggests that P. xanti nocticolus warrants species status. My results also suggest the possibility of a seaway near the Loreto area that needs to be evaluated further. By combining multiple molecular marker-types and analytical methods, this thesis adds to our understanding of diversification processes throughout the threatened Mexican TDF.

Landscape genetics is an emerging field that seeks to understand how specific landscape features and microevolutionary processes such as gene flow, genetic drift, and selection interact to shape the amount and spatial distribution of genetic variation. This study explores, through agent based simulations, how the specific mating and social system of tamarin primates (genus Saguinus) influences population genetic structure and patterns of relatedness within and among groups of this primate species, which might affect the ability of landscape genetic studies to detect the effects of fragmentation on gene flow. I use a spatially-explicit agent-based population genetics simulation model (GENESYS) configured to reflect the particular social system of tamarin monkeys (i.e. small group size, limited numbers of breeders per group, frequent twin births, and short dispersal distances) to assess whether the isolation by distance model of genetic differentiation expected in an unfragmented landscape can be distinguished from the isolation by barrier model expected in a fragmented landscape. GENESYS allows a user to explore the effects of social structure and landscape features on the population genetic structure of social animals, such as primates. I simulated two different landscapes containing an otherwise equivalent population of tamarins. In the first setup I simulated a homogeneous landscape unconstrained by any barriers to gene flow, while for the second setup, a barrier to gene flow restricted dispersal from one half of the landscape to the other. I found that the particular mating system of tamarin results in the rapid genetic differentiation of its social groups and consequently its populations. Social groups in the continuous landscape indeed revealed an isolation by distance pattern, while social groups on the fragmented landscape yielded instead an isolation by barrier model, where the barrier rather than geographic distance per se influenced the spatial genetic structure of the population. The results from this study suggest that features of the tamarin social system influence population genetic structure, which could affect the ability of landscape genetic studies to detect the effects of fragmentation on gene flow. To more fully address that issue, future studies should focus on a range of different primate social systems. / text

Patterns of genetic diversity in natural systems are influenced by landscape heterogeneity over spatial and temporal scales. Certain natural or anthropogenic landscape features may facilitate or impede organism dispersal and subsequent gene flow. Characterizing the geographical distribution of genetic diversity and identifying the factors contributing to population genetic structure is imperative for maintaining functional connectivity between isolated populations across a fragmented landscape. In this study, I combined genetic data and high-resolution land cover information to investigate patterns of population genetic structure in the threatened eastern hog-nosed snake (Heterodon platirhinos) at its northern range limit in Ontario, Canada. First, using putatively neutral microsatellite markers, I found evidence of genetic differentiation between two geographically disjunct regional populations: in the Carolinian region of southwestern Ontario, and along the eastern shoreline of Georgian Bay. Spatial and non-spatial Bayesian clustering algorithms also detected population genetic structure within each regional population. I found evidence of weak structure within Georgian Bay, roughly corresponding to regions north and south of Parry Sound. A genetic cluster at Wasaga Beach, located at the southern terminus of Georgian Bay, was highly differentiated from other populations, despite its geographic proximity to Georgian Bay. Excess homozygosity and reduced allelic diversity in Wasaga Beach compared to other sampled populations imply a population bottleneck event. Secondly, I inferred the role of landscape features on eastern hog-nosed snake dispersal and subsequent gene flow in the Georgian Bay regional population. Using techniques derived from electrical circuit theory, I estimated pairwise resistance distances between individuals by assigning costs to landscape features that are predicted to impede hog-nosed snake movement: open water, wetland, settlement and agriculture, and roads. Landscape features did not influence genetic structure within Wasaga Beach. However, I found weak evidence for an effect of landscape features, particularly open water and roads, on gene flow in eastern Georgian Bay. This study is the first to examine potential factors driving population genetic structure of eastern hog-nosed snakes and provides an empirical foundation for future tests of demographic models and spatially explicit simulations of gene flow. / Thesis (Master, Biology) -- Queen's University, 2012-10-30 11:58:05.094

A large proportion of the earth's surface is dedicated to food production, and agriculture is widely acknowledged to influence local biodiversity via habitat loss and degradation. Landscape genetics is an emerging field which can provide detailed understanding of how wildlife populations are influenced by landscape configuration and composition but the approach is yet to be fully integrated with agroecology. When addressing landscape genetics questions, small mammals may provide insight; they may act as model organisms, they are abundant, they are relatively easy to sample and they may have important ecological roles within arable ecosystems. This thesis merged the study of arable landscapes, landscape genetics and small mammals, to develop what is known about the landscape genetics of wild species in this dynamic habitat type. To decide upon a study organism, small mammals were surveyed at an example arable field site. Wood mice (Apodemus sylvaticus) were found to be the most abundant species and a microsatellite marker multiplex was developed for genotyping individuals. Two aspects of their landscape genetics in arable habitat were investigated. First, the possibility of temporal patterns in fine scale genetic structure of arable populations was explored, since this had not been investigated previously. Next, inter-population genetic differentiation was examined to determine whether arable habitat acted as a barrier to gene flow for this species. At the fine scale, three genetically distinct clusters of wood mice were identified and temporal variation in the spatial pattern was confirmed. There was no evidence that arable habitat acted as a barrier to gene flow for this species in comparison to populations in urban habitat, which showed significant differentiation. It is hoped that the landscape genetic insights provided by this thesis will encourage greater momentum for conducting landscape genetics studies in agricultural habitat.

Influenza causes thousands of illnesses and deaths annually in the United States. In part, this is a product of rapid changes in influenza genetics, resulting in different variants than a previous season. Influenza virus traverses landscapes by infecting susceptible hosts, thus allowing seasonal influenza to move great distances due to the mobility of humans who occupy diverse natural, social, and built environments. Using H3N2 influenza viral sequences from Minnesota in the 2012-2013 influenza season we explored relationships between the diversity of influenza genetics and the environments in which humans live. Landscape genetic methods were used to test for relationships between genetic diversity of influenza viruses with different concepts of distance separating the viruses in time and space. Additional analyses were used to identify relationships between influenza genetic evolution and socio-environmental characteristics of Minnesota zip code tabulation areas (ZCTAs) where those viruses were isolated. Influenza hospitalization data in Minnesota ZCTAs was also analyzed with spatial and statistical methods to compare differences and similarities between environmental features driving influenza genetic evolution and influenza morbidity. Findings indicated a complex genetic landscape with few significant correlations between genetic distance and other distance concepts. Elderly populations and populations without health insurance were found to be drivers of H3 hospitalizations. The synthesis of information from theses analyses can be used to inform our overall understanding of influenza diffusion and will allow for more targeted and effective public health prevention strategies.

With a case fatality rate higher than the 1918 Spanish Flu pandemic, H5N1 highly pathogenic avian influenza represents a threat to global public health. Efforts to identify locations with the greatest potential for pandemic emergence, as well as how the virus is spreading, may help minimize this threat. First detected in Egypt in 2006, H5N1 viruses have resulted in the deaths of millions of birds in both commercial and backyard poultry flocks, and more than 350 human infections, the most of any country, have been confirmed. Human outbreaks have been so far constrained by poor viral adaptation to non-avian hosts. There are two evolutionary mechanisms by which the H5N1 avian influenza virus could acquire pandemic potential: 1) via reassortment as a result of coinfection with another subtype (such as low pathogenic avian influenza H9N2); and/or 2) via antigenic drift and the accumulation of randomly occurring genetic changes found to improve viral fitness, herein called key substitutions (KS). Both mechanisms were investigated using geospatial methods including ecological niche modeling and hot spot analyses to predict locations with elevated potential for pandemic emergence. Using ecological niche modeling environmental, behavioral, and population characteristics of H5N1 and H9N2 niches within Egypt were identified, with niches differing markedly by subtype. Niche estimates were combined using raster overlay to estimate co-infection potential, with known occurrences used for validation. Co-infection was successfully predicted with high accuracy (area under the receiver operating characteristic (ROC) curve (AUC) 0.991). 41 distinct KS in H5N1 were detected in Egyptian isolates, including 17 not previously reported in Egypt. Phenotypic consequences of detected KS were varied, but the majority have been implicated in improving mammalian host adaptation and increasing virulence. Statistically significant spatial clustering of high KS rates was detected in the northwestern portion of the Nile River delta in the governorates of Alexandria and Beheira. To investigate how the virus spreads between poultry farms, landscape genetics techniques were employed. Viral genetic sequences were evaluated using phylogenetics to determine viral relatedness between samples, then distance models representing competing diffusion mechanisms were created using road networks and a least-cost path model designed to approximate wild waterbird travel using niche modeling and circuit theory. Spatial correlations were evaluated using Mantel tests, Mantel correlograms, and multiple regression of distance matrices within causal modeling and relative support frameworks. Samples from backyard farms were most strongly correlated with least cost path distances, implicating wild bird diffusion, while samples from commercial farms were most strongly correlated with road network distances, implicating human-mediated diffusion. Results were largely consistent across gene segments. Identifying areas at risk of co-infection can help target spaces for increased surveillance. Similarly, detecting spatial hot spots of KS highlight areas of concern for pandemic emergence from antigenic drift. Demonstration of different diffusion mechanisms by farm type should inform both surveillance and biosecurity practices. Knowledge of where to focus intervention efforts, both spatially and strategically, allows limited public health resources to be targeted most effectively. By detecting where in the country pandemic influenza is likely to emerge and identifying how the virus is spreading between farms, this work contributes to efforts to predict and prevent the next influenza pandemic.