Graduate Theses & Dissertations

Comparative Evaluation of Effective Population Size Genetic Estimation Methods in Wild Brook Trout (Salvelinus fontinalis) Populations
Effective population size (Ne) is a key concept in population genetics, evolutionary biology and conservation biology that describes an important facet of genetic diversity and the capacity of populations to respond to future evolutionary pressures. The importance of Ne in management and conservation of wild populations encouraged the development of numerous genetic estimators which rely on a variety of methods. Despite the number and diversity of available Ne methods, however, tests of estimator performance have largely relied on simulations, with relatively few tests based on empirical data. I used well-studied wild populations of brook trout (Salvelinus fontinalis) in Algonquin Park, Ontario as a model system to assess the comparative performance of multiple Ne estimation methods and programs, comparing the resultant Ne estimates against demographic population size estimates. As a first step, the genetic diversity and ancestry of wild brook trout populations was determined using 14 microsatellite loci. Genetic structure of brook trout populations showed variable contributions from historical supplemental stocking and also identified localized gene pools within and between watersheds, reflecting variable levels of connectivity and gene flow. Once the genetic ancestry and connectivity of populations had been resolved, single sample (point) and two samples (temporal) genetic estimators were used to estimate Ne of populations with pure native ancestry. Values obtained from genetic estimators utilizing both methods were variable within as well as among populations. Single sample (point) estimators were variable within individual populations, but substantially less than was observed among the temporal methods. The ratios of Ne to the estimated demographic population size (N) in small populations were substantially higher than in larger populations. Variation among estimates obtained from the different methods reflects varying assumptions that underlay the estimation algorithms. This research further investigated the effect of sampling effort and number of microsatellite loci used on Ne values obtained using the linkage disequilibrium (LD) estimation method. Ne estimates varied substantially among values generated from subsets of loci and genotyped individuals, highlighting the necessity for proper sampling design for efforts aiming to measure Ne. Despite the variation observed among and within estimation methods, the Ne concept is a valuable for the conservation and management of both exploited and endangered species. Author Keywords: Brook Trout, Effective population size, Genetic Diversity, Genetic Structure
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
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
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
Development of genetic profiles for paternity analysis and individual identification of the North Atlantic right whale (Eubalaena glacialis)
The endangered North Atlantic right whale (Eubalaena glacialis) has been internationally protected from whaling since 1935 but recovery has been slow compared to the southern right whale (Eubalaena australis) due to anthropogenic mortalities and poor reproduction. Prey availability, genetic variability, and alleles of genes associated with reproductive dysfunction have been hypothesized to contribute to low calf production. The North Atlantic Right Whale DNA Bank and Database contains 1168 samples from 603 individuals. I added 115 new genetic profiles to the database which now contains profiles for 81% of individuals alive since 1980. Paternity assignments using these profiles resulted in 62% of sampled calves being assigned a father and only 38% of candidate males being assigned a paternity. This may suggest false exclusion due to genotyping errors or the existence of an unknown group of males. The use of the DNA database allowed for the identification of 10 deceased individuals which has implications for identifying cause of death and reducing mortalities. However, genetic identification is dependent on the time of post-mortem sample collection which influences DNA quantity and quality. An assessment for variations in methylenetetrahydrofolate reductase, a candidate gene associated with reproductive dysfunction, revealed six females heterozygous for a synonymous A/T variant in exon four which may influence reproductive success through changes in enzyme production, conformation or activity. Author Keywords: Eubalaena glacialis, Forensic Identification, Genetic Profiling, North Atlantic Right Whale, Paternity, Reproductive Dysfunction
Understanding the establishment of Typha spp. in North America using population genetics and common garden studies
There are three cattail (Typha) taxa in Canada: T. latifolia (native), T. angustifolia (introduced), and their hybrid T. x glauca. The latter is invasive in regions around the Laurentian Great Lakes, and I investigated the potential role that commercial suppliers may be playing in the introduction of non-native Typha by comparing genotypes of North American, European, and commercially available plants. I found that Ontario garden centres are importing both hybrids and non-native lineages of T. angustifolia into Canada, but was unable to identify the provenance of T. latifolia. I also investigated the possibility that the hybrid cattail leaf litter shade and leachate influences germination and early growth of the parental species of the hybrids. Using three common garden experiments, I found that T. x glauca leaf litter suppresses germination rates of the three taxa. In the early seedling growth experiment, plant performance varied by taxa, and for the competition experiment there were no intra- or interspecific competition or treatment effects on the performance of plants. Overall, my research identified a potential mechanism allowing T. x glauca to dominate wetlands, and also shows that non-native lineages are being introduced into Canada through commercial trade Author Keywords: Competition, Germination, Non-native lineages, Plant nurseries, Seedling Growth, Typha spp.
Detection of four at-risk freshwater pearly mussel species (Bivalvia
Environmental DNA (eDNA) detection uses species-specific markers to screen DNA from bulk samples, such as water, to infer species presence. This study involved the development and testing of species-specific markers for four freshwater pearly mussels (Unionidae). The markers were applied to water samples from intensively sampled mussel monitoring sites to compare species detections from eDNA with established sampling method detections. Target species were detected using eDNA at all sites where they had previously been detected by quadrat sampling. This paired design demonstrated that eDNA detection was at least as sensitive as quadrat sampling and that high species specificity can be achieved even when designing against many sympatric unionids. Detection failures can impede species conservation efforts and occupancy estimates; eDNA sampling could improve our knowledge of species distributions and site occupancy through increased sampling sensitivity and coverage. Author Keywords: conservation genetics, cytochrome oxidase subunit I (COI), environmental DNA (eDNA), quantitative PCR (qPCR), species at risk (SAR)
Evaluating Environmental DNA (eDNA) Detection of Invasive Water Soldier (Stratiotes Aloides)
In 2008, the first North American water soldier (Stratiotes aloides) population was discovered in the Trent River, Ontario. Water soldier is an invasive aquatic plant with sharp, serrated leaves that has the potential to spread rapidly through dispersed vegetative fragments. Although it is too late to prevent water soldier establishment in the Trent River, its local distribution remains limited. In this study, environmental DNA (eDNA) was explored as a potential tool for early detection of water soldier. Species-specific markers were designed from chloroplast DNA regions matK and rbcL, and a qPCR assay with rbcL primers yielded the most sensitive detection of water soldier eDNA. Positive detections were obtained from six of 40 sampling locations, of which five were collected in Seymour Lake, an area with large patches of water soldier. As water soldier plants were known to be present at these sites, high eDNA concentrations were expected. The sixth positive detection from Trent Lock 5 (50 km downstream of Lake Seymour) was unexpected as it was obtained at a site with no water soldier sightings. This is one of the first studies to demonstrate the effectiveness of eDNA detection from aquatic plants. Author Keywords: aquatic plant, eDNA, environmental DNA, invasive species, Stratiotes aloides, water soldier
Ground-truthing effective population size estimators using long-term population data from inland salmonid populations
Effective population size (Ne) is a foundational concept in conservation biology, in part due to its relationship to the adaptive potential of populations. Although Ne is often estimated for wild populations, it is rarely calibrated against actual population estimates (Nc) other than to produce Ne/Nc ratios. This project used demographic and genetic data for from two intensively-studied populations of lake trout (Salvelinus namaycush) in Ontario’s Experimental Lake Area (ELA) as baseline data for evaluating the performance of multiple Ne estimators. Several temporal and single-time (point) genetic methods of estimating Ne were compared against demographic Ne estimates and known population data, as well as variation and consistency within and among Ne estimators. Changes in genetic Ne estimates over time were also compared to changes in demographic structure and fluctuating census estimates, including the effect of an experimentally manipulated population bottleneck on demographic and genetic Ne estimates during population reduction and recovery. Sampling years that included the most pre-, during and post-bottleneck data revealed the lowest estimates using temporal estimators (Ne = 16 to 18) despite pre- and post-bottleneck census estimates of 591 and 565. Estimation of Ne had increasingly tighter confidence intervals as sample sizes approached the actual number of breeding individuals in each population. Performance differences among the tested estimators highlight their potential biases and reliance on different assumptions, illustrating their potential value and caveats for assessing adaptive potential of wild populations. Author Keywords: Effective Population Size, Experimental Lakes Area, Fish Population Assessment, Lake Trout, Population Demographics, Population Genetics
De novo transcriptome assembly, functional annotation, and SNP discovery in North American flying squirrels (genus Glaucomys)
Introgressive hybridization between northern (Glaucomys sabrinus) and southern flying squirrels (G. volans) has been observed in some areas of Canada and the USA. However, existing molecular markers lack the resolution to discriminate late-generation introgressants and describe the extent to which hybridization influences the Glaucomys gene pool. I report the first North American flying squirrel (genus Glaucomys) functionally annotated de novo transcriptome assembly with a set of 146,621 high-quality, annotated putative species-diagnostic SNP markers. RNA-sequences were obtained from two northern flying squirrels and two southern flying squirrels sampled from Ontario, Canada. I reconstructed 702,228 Glaucomys transcripts using 193,323,120 sequence read-pairs, and captured sequence homologies, protein domains, and gene function classifications. These genomic resources can be used to increase the resolution of molecular techniques used to examine the dynamics of the Glaucomys hybrid zone. Author Keywords: annotation, de novo transcriptome, flying squirrels, high-throughput sequencing, hybridization, single nucleotide polymorphisms
Hybridization dynamics in cattails (Typha spp.,) in northeastern North America
Interspecific hybridization is an important evolutionary process which can contribute to the invasiveness of species complexes. In this dissertation I used the hybridizing species complex of cattails (Typha spp., Typhaceae) to explore some of the processes that could contribute to hybridization rates. Cattails in northeastern North America comprise the native T. latifolia, the non-native T. angustifolia, and their fertile hybrid, T. × glauca. First, I examined whether these taxa segregate by water depth as habitat segregation may be associated with lower incidence of hybridization. I found that these taxa occupy similar water depths and therefore that habitat segregation by water depth does not promote mating isolation among these taxa. I then compared pollen dispersal patterns between progenitor species as pollen dispersal can also influence rates of hybrid formation. Each progenitor exhibits localized pollen dispersal, and the maternal parent of first generation hybrids captures more conspecific than heterospecific pollen; both of which should lead to reduced hybrid formation. I then conducted controlled crosses using all three Typha taxa to quantify hybrid fertility and to parameterize a fertility model to predict how mating compatibilities should affect the composition of cattail stands. I found that highly asymmetric formation of hybrids and backcrosses and reduced hybrid fertility should favour the maintenance of T. latifolia under certain conditions. Finally, I used a population genetics approach to characterize genetic diversity and structure of Typha in northeastern North America to determine the extent to which broad-scale processes such as gene flow influence site-level processes. I concluded that hybrids are most often created within sites or introduced in small numbers rather than exhibiting broad-scale dispersal. This suggests that local processes are more important drivers of hybrid success than landscape-scale processes which would be expected to limit the spread of the hybrid. Though my findings indicate some barriers to hybridization in these Typha taxa, hybrid cattail dominates much of northeastern North America. My results therefore show that incomplete barriers to hybridization may not be sufficient to prevent the continued dominance of hybrids and that active management of invasive hybrids may be required to limit their spread. Author Keywords: fertility model, genetic structure, Hybridization, invasive species, niche segregation, pollen dispersal

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