Wilson, Paul J.

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

Maintaining functional connectivity among wildlife populations is important to ensure genetic diversity and evolutionary potential of declining populations, particularly when managing species at risk. The Boreal Designatable Unit (DU) of woodland caribou (Rangifer tarandus caribou) in Ontario, Manitoba, and Saskatchewan has declined in southern portions of the range because of increased human activities and has been identified as 'threatened' by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). In this dissertation, I used ten microsatellite DNA markers primarily from winter-collected fecal samples to delineate genetic structure of boreal caribou in declining portions of the range and increase understanding of the potential influence of the non-threatened Eastern Migratory DU of woodland caribou on genetic differentiation. Eastern migratory caribou are characterized by large home ranges compared to boreal caribou and migrate seasonally into portions of the Boreal DU range. A regional- and local-scale analysis using the spatial Bayesian clustering algorithm in program TESS delineated four regional clusters and 11 local clusters, with the majority of local clusters occurring along the southern periphery of the range. One of those clusters in Ontario corresponded spatially with the seasonal overlap of boreal and eastern migratory caribou and was characterized by substantial admixture, suggesting that the two DUs could be interbreeding. Next, I decoupled the impacts of historical and contemporary processes on genetic structure and found that historical processes were an important factor contributing to genetic differentiation, which may be a result of historical patterns of isolation by distance or different ancestry. Moreover, I found evidence of introgression from a currently unsampled population in northern Ontario, presumably barren-ground caribou (R. t. groenlandicus). Finally, because our analysis suggested recent processes were also responsible for genetic structure, I used a landscape genetics analysis to identify factors affecting contemporary genetic structure. Water bodies, anthropogenic disturbance, and mobility differences between the two DUs were important factors describing caribou genetic differentiation. This study provides insights on where conservation and management of caribou herds should be prioritized in threatened portions of the boreal caribou range and may have implications for future delineation of evolutionarily significant units.

Author Keywords: boreal forest, genetic structure, landscape genetics, microsatellite DNA, Rangifer tarandus, woodland caribou

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