Manseau, Micheline

Globally, wildlife populations are experiencing increasing rates of range loss, population decline, and extinction. Caribou (Rangifer tarandus) have experienced dramatic declines in both range and population size across Canada over the past century. Boreal caribou (R. t. caribou), one of twelve Designatable Units, have lost approximately half of their historic range in the last 150 years, particularly along the southern edge of their distribution. Despite this northward contraction, some populations have persisted at the trailing range edge, over 150 km south of the boreal continuous range (BCR) in Ontario, along the coast and near-shore islands of Lake Superior. Better understanding the population structure and evolutionary history of caribou in the Lake Superior range (LSR) could help to inform conservation and management actions, such as the delineation of conservation or management units or translocations between populations. In this thesis, I use whole genome sequences from boreal, eastern migratory and barren-ground caribou sampled in Manitoba, Ontario, and Quebec to investigate evolutionary history and population structure. I discovered that the LSR caribou form a distinct group but also some evidence of gene flow with the BCR. Notably, caribou from the LSR demonstrated relatively high levels of inbreeding (measured as Runs of Homozygosity; ROH) and genetic drift, which may contribute to the differentiation observed between caribou occupying the two ranges. Despite inbreeding, the LSR caribou retained Heterozygosity Rich Regions (HRR). I found genomic structure among caribou populations from the LSR and BCR but found these two ranges had similar demographic histories. My analyses indicate that the LSR caribou display distinct genomic characteristics but share ancestry with the BCR, with historical gene flow between these two ranges. Collectively, this dissertation characterizes the population structure and evolutionary history of caribou from the southernmost range in Ontario, providing key insights for the conservation and management of these small and isolated populations.

Understanding genetic structure, connectivity, and movement of a species iscritical to management and conservation. Genetic network approaches allow the analysis of genetic information with flexibility and few prior assumptions. In chapter one, I tested the ability of individual-based genetic networks to detect fine-scale structure and connectivity in relation to sampling efforts. My findings revealed individual-based genetic networks can detect fine-scale genetic structure of caribou when using 15 highly variable microsatellite loci. Sampling levels less than 50% of the estimated population size resulted in highly disconnected networks which did not allow for accurate structure analysis; however community detection algorithms were robust in grouping closely related individuals despite low sampling. In chapter two, I used individual-based and population-based genetic networks to investigate structure, connectivity, and movement of caribou across a large study area in Western Canada. A community detection algorithm partitioned the population-based genetic network at multiple spatial scales which uncovered patterns of hierarchical genetic structure and highlighted patterns of gene flow. The hierarchical population structure results aligned with the known distribution of different caribou Designatable Units (DUs) and additional structure was found within each DU. Furthermore, individual-based networks that were constructed with a subset of samples from the Mackenzie Mountains region of the Northwest Territories revealed patterns of long-distance movement and high connectivity across the region.

Author Keywords: Biological Conservation, Caribou, Community Detection, Connectivity, Genetic Networks, Structure

Variation in habitat quality and disturbance levels can strongly influence a species' distribution, leading to spatial variation in population density and influencing population dynamics. It is therefore critical to understand how density can lead to variability in demographic responses for effective conservation and recovery of species. My dissertation illustrates how density and spatial familial networks can be integrated together to gain a better understanding of the influence of density on population dynamics of boreal caribou. First, I created an analytical framework to assess results from empirical studies to inform spatially-explicit capture-recapture sampling design, using both simulated and empirical data from noninvasive genetic sampling of several boreal caribou populations in Alberta, Canada, which varied in range size and estimated population density. Analysis of the empirical data indicated that reduced sampling intensity had a greater impact on density estimates in smaller ranges, and the best sampling designs did not differ with estimated population density but differed between large and small population ranges. Secondly, I used parent-offspring relationships to construct familial networks of boreal caribou in Saskatchewan, Canada to inform recovery efforts. Using network measures, I assessed the contribution of individual caribou to the population with several centrality measures and then determined which measures were best suited to inform on the population demographic structure. I found substantial differences in the centrality of individuals in different local areas, highlighting the importance of analyzing familial networks at different spatial scales. The network revealed that boreal caribou in Saskatchewan form a complex, interconnected familial network. These results identified individuals presenting different fitness levels, short- and long-distance dispersing ability across the range, and can be used in support of population monitoring and recovery efforts. Finally, I used a spatial capture-recapture analytical framework with covariates to estimate spatial density of boreal woodland caribou across the Saskatchewan Boreal Plains, and then reconstructed parent-offspring relationships to create a familial network of caribou and determined whether spatial density influenced sex-specific network centrality, dispersal distance, individual reproductive success, and the pregnancy status of females. I show that caribou densitygreatly varied across the landscape and was primarily affected by landscape composition and fragmentation, and density had sex-specific influences on dispersal distance, reproductive success, and network centrality. The high density areas reflected good-quality caribou habitat, and the decreased dispersal rates and female reproductive output suggest that these remnant patches of habitat may be influencing demographic responses of caribou.

Author Keywords: boreal caribou, density, familial networks, population dynamics, rangifer tarandus caribou, spatial capture-recapture

Sex-specific genetic structure is a commonly observed pattern among vertebrate species. Facing differential selective pressures, individuals may adopt sex-specific life historical traits that ultimately shape genetic variation among populations. Although differential dispersal dynamics are commonly detected in the literature, few studies have investigated the potential effect of sex-specific functional connectivity on genetic structure. The recent uses of Graph Theory in landscape genetics have demonstrated network capacities to describe complex system behaviors where network topology intuitively represents genetic interaction among sub-units. By implementing a sex-specific network approach, our results suggest that Sex-Specific Graphs (SSG) are sensitive to differential male and female dispersal dynamics of a fisher (Martes pennanti) metapopulation in southern Ontario. Our analyses based on SSG topologies supported the hypothesis of male-biased dispersal. Furthermore, we demonstrated that the effect of the landscape, identified at the population-level, could be partitioned among sex-specific strata. We found that female connectivity was negatively affected by snow depth, while being neutral for males. Our findings underlined the potential of conducting sex-specific analysis by identifying landscape elements that promotes or impedes functional connectivity of wildlife populations, which sometimes remains cryptic when studied at the population level. We propose that SSG approach would be applicable to other vagile species where differential sex-specific processes are expected to occur.

Author Keywords: genetic structure, Landscape Genetics, Martes pennanti, Population Graph, sex-biased dispersal, Sex-Specific Graphs