Graduate Theses & Dissertations


Comparative phylogeography in conservation biology
Phylogeographic histories of taxa around the Great Lakes region in North America are relevant to a range of ongoing issues including conservation management and biological invasions. In this thesis I investigated the comparative phylogeographic histories of plant species with disjunct distributions and plant species with continuous distributions around the Great Lakes region; this is a very dynamic geographic area with relatively recent colonisation histories that have been influenced by a range of factors including postglacial landscape modifications, and more recently, human-mediated dispersion. I first characterized four species that have disjunct populations in the Great Lakes region: (Bartonia paniculata subsp. paniculata, Empetrum nigrum, Sporobolus heterolepis, and Carex richardsonii). Through comparisons of core and disjunct populations, I found that a range of historical processes have resulted in two broad scenarios: in the first scenario, genetically distinct disjunct and core populations diverged prior to the last glacial cycle, and in the second scenario more recent vicariant events have resulted in genetically similar core and disjunct populations. The former scenario has important implications for conservation management. I then characterized the Typha species complex (T. latifolia, T. angustifolia, T. x glauca), which collectively represent species with continuous distributions. Recent microevolutionary processes, including hybridization, introgression, and intercontinental dispersal, obscure the phylogeographic patterns and complicate the evolutionary history of Typha spp. around the Great Lakes region, and have resulted in the growing dominance of non-native lineages. A broader geographical comparison of Typha spp. lineages from around the world identified repeated cryptic dispersal and long-distant movement as important phylogeographic influences. This research has demonstrated that comparisons of regional and global evolutionary histories can provide insight into historical and contemporary processes useful for management decisions in conservation biology and invasive species. Author Keywords: chloroplast DNA, conservation genetics, disjunct populations, invasive species, phylogeography, postglacial recolonisation
Elemental Variation in Daphnia
Environmental variation can affect consumer trait expression and alter ecological and evolutionary dynamics in natural populations. However, although dietary nutrient content can vary by an order of magnitude in natural ecosystems, intra-specific differences in consumer responses to food quality have not been thoroughly investigated. Therefore, the purpose of my dissertation was to examine the influence of dietary nutrition and other environmental factors on consumer phenotypic variation using the freshwater cladoceran Daphnia. I conducted a series of complementary laboratory and field studies where I examined the effects of dietary phosphorus (P) content and additional biological/environmental variables (multi-elemental limitation, genetic variation, and temperature) on daphnid life-history, biochemistry, body elemental composition, and population growth. In general, phenotypic expression within a species varied significantly in response to all experimental variables, but the relative influence of each was highly context dependent. In my first chapter, I found that dietary P content and environmental calcium (Ca) concentrations both altered Daphnia body Ca:P ratios and growth rates of individuals and affected intrinsic rates of increase at the population level. However, food quality appeared to have a much larger effect on trait expression, and body Ca:P ratios were highly sensitive to other forms of dietary nutrient limitation. Next, I documented significant quantitative genetic variation and phenotypic plasticity in daphnid P content, growth, and P use efficiency of field collected animals grown across dietary P gradients. Trait expression was also influenced by genotype X diet interactions suggesting that consumer responses to dietary nutrient limitation can be heritable and may be adaptive in different nutrient environments. Finally, I found that temperature appeared to override food quality effects and decouple P metabolism in natural Daphnia populations, but total biomass production was affected by both dietary P content and temperature, depending on the nutrient content of the lake. Overall, my dissertation shows that consumer responses to nutrient limitation can vary significantly within a species and that changes in trait expression may be modified by other environmental variables. These results should be incorporated into existing stoichiometric models and used to investigate the eco-evolutionary consequences of consumer phenotypic variation in response to nutritional stress. Author Keywords: ecological stoichiometry, evolution, life-history, nutrient limitation, nutrient metabolism, zooplankton
Sex-Specific Graphs
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
Testing for Interspecific Hybridization and a Latitudinal Cline Within the Clock Gene Per1 of the Deer Mouse (Peromyscus maniculatus) and the White-Footed Mouse (Peromyscus leucopus)
The recent northward expansion of the white-footed mouse (Peromyscus leucopus) in response to climatic changes provides a natural experiment to explore potential adaptive genetic variation within the clock gene Per1 in Peromyscus undergoing latitudinal shifts, as well as, the possibility of hybridization and introgression related to novel secondary contact with its sister species the deer mouse (Peromyscus maniculatus). Because clock genes influence the timing of behaviors critical for survival, variations in genotype may reflect an organism’s ability to persist in different environments. Hybridization followed by introgression may increase the adaptive potential of a species by quickly generating adaptive variation through novel genetic recombination or by the transfer of species-specific alleles that have evolved in response to certain environments. In chapter 2, I used microsatellite and mtDNA markers to test for hybridization and introgression between P. maniculatus and P. leucopus and found that interbreeding is occurring at a low frequency (<1%). In chapter 3, I tested for a latitudinal cline in a polyglycine repeat located within the Per1 gene of Peromyscus and discovered a putative cline in the Per1-142 and Per1-157 allele of P. leucopus and P. maniculatus, respectively. Chapter 4, further expands upon these findings, limitations, and the lack of evidence supporting introgression at the Per1 locus. Despite this lack of evidence, it is possible that novel hybridization has or could lead to adaptive introgression of other genes, allowing for the exchange of adaptive alleles or traits that could be advantageous for range expansion and adaption to future environmental changes. Author Keywords: Clock genes, Hybridization, Latitudinal gradient, Per1, Peromyscus, Range Expansion
Adaptive Genetic Markers Reveal the Biological Significance and Evolutionary History of Woodland Caribou (Rangifer tarandus caribou) Ecotypes
Migratory and sedentary ecotypes are phenotypic distinctions of woodland caribou. I explored whether I could distinguish between these ecotypes in Manitoba and Ontario using genetic signatures of adaptive differentiation. I anticipated that signatures of selection would indicate genetic structure and permit ecotype assignment of individuals. Cytochrome-b, a functional portion of the mitochondrial genome, was tested for evidence of adaptation using Tajima’s D and by comparing variations in protein physiology. Woodland caribou ecotypes were compared for evidence of contemporary adaptive differentiation in relation to mitochondrial lineages. Trinucleotide repeats were also tested for differential selection between ecotypes and used to assign individuals to genetic clusters. Evidence of adaptive variation in the mitochondrial genome suggests woodland caribou ecotypes of Manitoba and Ontario corresponded with an abundance of functional variation. Woodland caribou ecotypes coincide with genetic clusters, and there is evidence of adaptive differentiation between migratory caribou and certain sedentary populations. Previous studies have not described adaptive variation in caribou using the methods applied in this study. Adaptive differences between caribou ecotypes suggest selection may contribute to the persistence of ecotypes and provides new genetic tools for population assessment. Author Keywords: Adaptation, Cytochrome-B, Ecotype, RANGIFER TARANDUS CARIBOU, Selection, TRINUCLEOTIDE REPEAT
Long-Term Population Dynamics of an Unexploited Lacustrine Brook Trout (Salvelinus fontinalis) Population
Long-term studies of demographic processes such as survival and abundance conducted in unexploited systems provide unique insight into the natural population ecology of fish, but are rarely available. I used historical tagging records of a sanctuary population of brook trout (Salvelinus fontinalis) in Algonquin Park, Ontario to investigate long-term population dynamics in an unexploited population. Adult brook trout in Mykiss Lake (23.5ha) were surveyed and tagged biannually (May and October) between 1990 and 2004. Open-population capture-mark-recapture models were used to test the importance of time, size, sex and season on estimates of apparent survival and abundance. Seasonal population growth and recruitment were estimated and compared with large-scale climate indices. Time-dependent survival and abundance estimates fluctuated, with distinct periods of increase. Population growth and recruitment were positively correlated with summer NAO and ENSO values, whereas survival was negatively correlated. Seasonally, larger individuals experienced higher apparent survival during winter and decreased survival during summer. These findings provide valuable insights into the natural demography of unexploited brook trout populations, and should help inform sustainable management of inland fisheries. Author Keywords: capture-mark-recapture, long-term, population dynamics, Salvelinus fontinalis, seasonal variation, survival
Conservation genetics of Redside Dace (Clinostomus elongatus)
Recent range reductions of endangered species have been linked to urban development, increased agricultural activities, and introduction of non-native species. I used Redside Dace (Clinostomus elongatus) as a focal species to examine the utility of novel monitoring approaches, and to understand historical and contemporary processes that have influenced their present distribution. I tested the efficacy of environmental DNA (eDNA) to detect Redside Dace, and showed that eDNA was more sensitive for detecting species presence than traditional electrofishing. Parameters such as season, number of replicates, and spatial versus temporal sampling need to be accounted for when designing an eDNA monitoring program, as they influence detection effectiveness and power. I also assessed the species’ phylogeographic structure using both mitochondrial and microsatellite DNA analysis. The data from the microsatellite markers indicate that Redside Dace populations are genetically structured, with the exception of several populations from the Allegheny River basin. Combined sequence data from three mitochondrial genes (cytochrome b, ATPase 6 and ATPase 8) indicated that Redside Dace persisted within three Mississippian refugia during the last glaciation. Secondary contact between two lineages was indicated by both mitochondrial and microsatellite data. The combined results from the eDNA and conservation genetics studies can be used to inform Redside Dace recovery efforts, and provide a template for similar efforts for other aquatic endangered species. Author Keywords: eDNA, endangered, genetics, phylogeography
Genetic diversity and differentiation of Ontario’s recolonizing fishers (Pekania pennanti)
Fishers (Pekania pennanti) were extirpated from many parts of Ontario in the early 20th century, but as of the early 2000s the species had recolonized most of its historical range. While the primary population genetic structure of fishers in central and eastern Ontario has not changed drastically over the past ten years, we did find evidence of increased secondary structure and a reduction in northward movement from southeastern Ontario, a site of recent immigration from the Adirondacks in northern New York. This may be indicative of a reduction in density and thus in density-dependent migration, or it may be a consequence of the population reaching equilibrium following a period of rapid expansion associated with recolonization. We also observed no variation within central and eastern Ontario at 14 of 15 candidate functional loci we screened, suggesting possible directional or stabilizing selection and a lack of adaptive potential. Author Keywords: fisher, functional genes, Ontario, Pekania pennanti, population genetics, recolonization
Habitat loss and fragmentation can disrupt population connectivity, resulting in small, isolated populations and low genetic variability. Understanding connectivity patterns in space and time is critical in conservation and management planning, especially for wide-ranging species in northern latitudes where habitats are becoming increasingly fragmented. Wolverines (Gulo gulo) share similar life history traits observed in large-sized carnivores, and their low resiliency to disturbances limits wolverine persistence in modified or fragmented landscapes - making them a good indicator species for habitat connectivity. In this thesis, I used neutral microsatellite and mitochondrial DNA markers to investigate genetic connectivity patterns of wolverines for different temporal and spatial scales. Population genetic analyses of individuals from North America suggested wolverines west of James Bay in Canada are structured into two contemporary genetic clusters: an extant cluster at the eastern periphery of Manitoba and Ontario, and a northwestern core cluster. Haplotypic composition, however, suggested longstanding differences between the extant eastern periphery and northwestern core clusters. Phylogeographic analyses across the wolverine's Holarctic distribution supported a postglacial expansion from a glacial refugium near Beringia. Although Approximate Bayesian computations suggested a west-to-east stepping-stone divergence pattern across North America, a mismatch distribution indicated a historic bottleneck event approximately 400 generations ago likely influenced present-day patterns of haplotype distribution. I also used an individual-based genetic distance measure to identify landscape features potentially influencing pairwise genetic distances of wolverines in Manitoba and Ontario. Road density and mean spring snow cover were positively associated with genetic distances. Road density was associated with female genetic distance, while spring snow cover variance was associated with male genetic distance. My findings suggest that northward expanding anthropogenic disturbances have the potential to affect genetic connectivity. Overall, my findings suggest that (1) peripheral populations can harbour genetic variants not observed in core populations - increasing species genetic diversity; (2) historic bottlenecks can alter the genetic signature of glacial refugia, resulting in a disjunct distribution of unique genetic variants among contemporary populations; (3) increased temporal resolution of the individual-based genetic distance measure can help identify landscape features associated with genetic connectivity within a population, which may disrupt landscape connectivity. Author Keywords: conservation genetics, Holarctic species, landscape genetics, peripheral population, phylogeography, wolverine
Ecological and morphological traits that affect the fitness and dispersal potential of Iberian pumpkinseed (Lepomis gibbosus)
The Pumpkinseed (Lepomis gibbosus) is a sunfish that is endemic to eastern portions of Canada and the United States. During the late 19th century, the species was introduced into Europe, and it is now present in over 28 countries. Previous attempts to determine the characteristics that can predict the spread of non-indigenous species have been largely unsuccessful, but new evidence suggests that phenotypic plasticity may help to explain the dispersal and range expansion of some organisms. Experimental comparisons on lower-order taxa have revealed that populations from areas outside of their native range are capable of exhibiting stronger levels of phenotypic plasticity than counterparts from their source of origin. Using Pumpkinseed, I conducted the first native/non- native comparison of phenotypic plasticity in a vertebrate. Progeny from adult Pumpkinseed collected in Ontario, Canada and the Iberian Peninsula (Spain) were reared under variable water velocities, habitat type and competitive pressures, three ecological factors that may affect the dispersal potential of fishes introduced into novel aquatic systems. Differences in phenotypic plasticity, assessed from a morphological perspective, were compared among populations using a traditional distance-based approach. All populations exhibited divergent morphological traits that appeared to be inherited over successive generations. In each experiment, all populations responded to environmental change by developing internal and external morphological forms that, in related taxa, enhance and facilitate foraging and navigation; however, non-native populations always exhibited an overall lower level of phenotypic plasticity. Pumpkinseed from non-native areas may have exhibited a reduction in phenotypic plasticity because of population-based differences. Nevertheless, all Pumpkinseed populations studied were capable of exhibiting phenotypic plasticity to novel environmental conditions, and develop morphological characteristics that may enhance fitness and dispersal in perturbed areas. Author Keywords: Invasive species, Morphology, Phenotypic plasticity, Pumpkinseed sunfish, Reaction norm
Understanding Historical and Contemporary Gene Flow Patterns of Ontario Black Bears
Consequences of habitat loss and fragmentation include smaller effective population sizes and decreased genetic diversity, factors that can undermine the long-term viability of large carnivores that were historically continuously distributed. I evaluated the historical and contemporary genetic structure and diversity of American black bears (Ursus americanus) in Ontario, where bear habitat is largely contiguous, except for southern regions that experience strong anthropogenic pressures. My objectives were to understand gene flow patterns in a natural system still largely reflective of pre-European settlement to provide context for the extent of genetic diversity loss in southern populations fragmented by anthropogenic influences. Phylogeographic analyses suggested that Ontario black bears belong to a widespread "continental" genetic group that further divides into 2 subgroups, likely reflecting separate recolonization routes around the Great Lakes following the Last Glacial Maximum. Population genetic analyses based on individual genotypes showed that Ontario black bears are structured into 3 contemporary genetic clusters. Two clusters, located in the Northwest (NW) and Southeast (SE), are geographically vast and genetically diverse. The third cluster is less diverse, and spatially restricted to the Bruce Peninsula (BP). Microsatellite analyses revealed that the NW and SE clusters are weakly differentiated from each other relative to mitochondrial DNA findings, suggesting male-biased dispersal and isolation by distance across the province. I also conducted simulations to assess competing hypotheses that could explain the reduced genetic diversity on the BP, which supported a combination of low migration and recent demographic bottlenecks. I showed that management actions to increase genetic variation in BP black bears could include restoring landscape connectivity between BP and SE; however, the irreversible human footprint in the area makes regular translocations from SE individuals a more practical alternative. Overall, my work suggests that: 1) historical genetic processes in Ontario black bears were likely predominated by isolation by distance, 2) large mammalian carnivores such as black bears can become isolated and experience reduced diversity in only a few generations, and 3) maintaining connectivity in regions under increased anthropogenic pressures could prevent populations from becoming small and geographically and genetically isolated, and should be a priority for conserving healthy populations. Author Keywords: American black bear, carnivore, conservation genetics, Ontario, phylogeography, population genetics
Selection on functional genes across a flying squirrel (genus Glaucomys) hybrid zone
While hybridization between distinct taxa can have undesirable implications, it can also result in increased genetic variability and potentially, the exchange of adaptive genes or traits. Adaptive variation acquired through introgressive hybridization may be particularly advantageous for species facing rapid environmental change. I investigated a novel, climate change-induced hybrid zone between two flying squirrel species: the southern (Glaucomys volans) and northern (G. sabrinus) flying squirrel. I was interested in the occurrence of hybridization and introgression, the type of selective pressures maintaining the hybrid zone and the potential for adaptive introgression. I found relatively low hybridization and introgression frequencies (1.7% and 2.9% of the population, respectively) and no evidence of selection on hybrids or backcrosses in particular environments. I conclude that the data are more consistent with a hybrid zone maintained by endogenous (environment-independent) selection. I tested for adaptive introgression using two functional genes: IGF-1 and CLOCK. I documented intermediate functional allele frequencies in backcrosses compared to parental populations, suggesting the alleles do not confer fitness advantages in backcrosses. Despite lack of evidence for current adaptive introgression, genetic admixture between G. volans and G. sabrinus may provide adaptive potential should these species face more rapid or drastic environmental change in the future. Author Keywords: adaptive introgression, flying squirrel, Glaucomys sabrinus, Glaucomys volans, hybridization, introgression


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