Despite long-term study, the mechanism explaining the parapatric distribution of two Australian reptile ticks species, Bothriocroton hydrosauri and Amblyomma limbatum, is not understood. This project aimed to use molecular genetic data to investigate aspects of the population biology of these two tick species, such as population structure and dispersal, to gain further insights into the cause and maintenance of this parapatric boundary. I developed and subsequently tested for Mendelian inheritance a suite of B. hydrosauri and A. limbatum species-specific microsatellites markers. Pedigree analysis showed one B. hydrosauri locus and all of the A. limbatum loci to be inherited in a non-Mendelian manner. Thus I could not investigate A. limbatum population structure and focused solely on B. hydrosauri. The first part of this study tested predictions of a model formulated to explain B. hydrosauri transmission dynamics. The “ripple” model, based on detailed ecological and behavioural data on B. hydrosauri and Tiliqua rugosa, B. hydrosauri’s most common host, predicts higher relatedness among larvae than among nymphs or adults on a host, and significant spatial autocorrelation in larvae extending further than for the later life stages. The model also predicts that adult ticks are likely to encounter related partners and that this will generate inbreeding within the population. I tested those predictions using nine microsatellite loci on a sample of 848 ticks (464 larvae, 140 nymphs and 244 adults) collected from 98 T. rugosa hosts at the northern edge of B. hydrosauri’s distribution range. My data did support all of the predictions of the “ripple” model and indicated that the dynamics of transmission among hosts play an important role in parasite population structure. The second part of this project focused on investigating the population genetic structure of B. hydrosauri at the edge of its geographic range and testing the predictions of a population model derived to explain B. hydrosauri’s parapatric boundary with A. limbatum. The “ridge and trough” model suggested the tick population was organised spatially into a series of “ridges” where tick density was high and “troughs” where it was low. Genetically, the expectation was to find clusters of more closely related individuals associated with the ridges. Cluster analysis of microsatellite allele frequencies and analysis of molecular variance of mitochondrial haplotype frequencies revealed the presence of four genetic clusters within a sample of 244 B. hydrosauri adults. As the highly genetically divergent clusters had overlapping distributions, and in some cases were syntopic, the genetic population structure predicted for these ticks by the “ridge and trough” model was not observed. Several explanations were considered for the observed B. hydrosauri genetic population structure, but syntopy of the clusters suggested that assortative mating is the most likely. I speculated that the clusters have formed in allopatry, when the environment was extremely heterogeneous, such that the ticks (and their hosts) were confined to isolated patches of high-quality habitat. Given sufficient time, this could have resulted in reproductive incompatibility between ticks occupying different patches. The population structure I uncovered indicates subsequent secondary recontact of divergent groups. Although my study allowed for a better understanding of B. hydrosauri biology and population structure, the reasons for the parapatric distributions of B. hydrosauri and A. limbatum are still unclear. Further research should focus on investigating the population genetic structure of A. limbatum at the edge of its range, as well as on performing a larger-scale study of B. hydrosauri population genetic structure and a more detailed investigation of the applicability of the “ridge and trough” model to this tick species. Moreover, it will be useful to inspect the population structure of both these species within the centers of their ranges and compare these findings with population structure found at the edge of the range.

Population structure, gene flow and dispersal are some of the most commonly estimated population parameters in population genetics, evolutionary biology and conservation genetics. The primary aim of thesis is to test the precision and accuracy of genetic estimates of population structure, gene flow and dispersal. The controlled replicated Drosophila melanogaster experiments of known effective population size (Ne = 14.3) and dispersal rate (m = 0.0025 - 0.04) all adhered to Wright??s demographic island model. Three statistical approaches were empirically tested: 1) the conversion of population structure to gene flow using FST, RST, SHUA and PhiST ; 2) the private alleles method to estimate gene flow; 3) a Bayesian assignment method to estimate dispersal (BAYESASS 1.2). Even in the best-case scenario, almost all current methods except SHUA significantly underestimate population structure, and consequently overestimate gene flow and dispersal when applied to real populations. It was crucial to ensure that the manipulated rate of gene flow was correctly defined. This led to three supporting investigations of hybrid performance, inversion polymorphisms and effective population size. The hybrid performance investigation demonstrated that the manipulated rate of gene flow had not been unexpectedly inflated by hybrid vigour or reduced by breakdown. These experiments also demonstrated that close inbreeding is not a necessary precondition for hybrid vigour or breakdown, which is important for conservation strategies involving induced dispersal. The investigation of inversion polymorphisms ensured that the manipulated rate of gene flow was not affected by selection on inverted regions. The effective population size investigation used a temporal estimation method to confirm that the Ne was accurately predicted by an N:Ne ratio of 0.286. Additionally this experiment showed that the single-sample estimation methods implemented by ONeSAMP or LDNE resulted in downwardly biased estimates of Ne in structured populations. In conclusion these results call into question the confidence that biologists may have in some of the most widely used molecular tools in conservation biology.

Association mapping (AM), based on linkage disequilibrium, is a complementary strategy to traditional quantitative trait loci (QTL) mapping for describing associations between genotypes and phenotypes in crop plants. Yellow endosperm colour, an important quality trait in durum wheat (<i>Triticum turgidum L. var. durum</i>), was studied to determine the potential of AM to (1) identify previously reported QTL using a genome wide scan and (2) to determine allelic association of the phytoene synthase 1 (Psy1) gene using a candidate gene analysis. At present, a number of QTL for endosperm colour have been identified, and phytoene synthase, the initial enzyme of the carotenoid biosynthetic pathway, has been associated with QTL on the group 7 chromosomes which are considered to play a significant role in expression of yellow pigment concentration. CIE 1976 b*, a light reflectance measurement, and water-saturated butanol extracted pigments were assessed on a collection of 93 elite accessions from a variety of geographic origins, and genotyped with 245 markers. Population structure was assessed using genetic distance and Bayesian model based approaches, identifying five sub-populations consistent with breeding origin and pedigree. Association analysis identified significant associations with yellow endosperm colour on all chromosomes, including several previously identified QTL as well as new regions for genomic dissection. Pairwise LD mapping of Psy1-B1 and Psy1-A1 located the genes to chromosomes 7B and 7A respectively, to regions which have previously been identified for yellow pigment concentration QTL. The results of this study indicate that AM can be used to complement traditional QTL mapping techniques, and identify novel QTL for further study.

<p>Habitat fragmentation and anthropogenic development influence the level of isolation and security in and around protected habitats affecting wolf movements and the distribution and abundance of their prey. In light of recent concern about the ecology of animals in protected areas, I initiated a research project to investigate the molecular and foraging ecology of grey wolves in and around Prince Albert National Park (PANP), Saskatchewan. <p>Estimates of genetic diversity and population structure can be used as surrogates to detect effects of habitat degradation on wolves. Genetic diversity was high in these populations relative to other North American wolf populations. My results suggest that wolves in central Saskatchewan form a panmictic population, however there is some evidence showing partial isolation of one group of wolves within PANP. I speculate that the level of human activity such as road networks, hunting, and trapping act as dispersal impediments to this isolated group. Further, the genetic homogenization, indicating high population turnover, of wolf groups that use the periphery and adjacent areas of PANP may also contribute to the observed genetic subdivision. The partially isolated NW group, characterized by slightly lower diversity indices, low migration rates, and higher levels of allele fixation, indicated this group was a more stable social unit comprised of more related individuals.</p><p>Knowledge of wolf food habits and how they change over time is a fundamental component to understanding wolf ecology. Using scat analysis I evaluated wolf foraging ecology by calculating indices of occurrence/faeces (OF) and percent prey biomass contribution: white tailed deer contributed 43% and 33% respectively to wolf diet; elk (33%, 50%), moose (7%, 14%), beaver (5%, 2%), and snowshoe hare (2%, <1%). I found no evidence of livestock depredation nor did wolves prey on bison or caribou. There were no differences in OF indices between years. Prey selectivity was apparent in both years with wolves selecting elk and avoiding beaver. A diversity of ungulate prey are readily available to wolves in this system; however, scat analysis and tests for prey selection indicate a preference for elk. I presume this is a choice made to balance risk with profitability of food items in concordance with optimal foraging theory.</p><p>I examined trophic relationships between the grey wolf and 18 mammalian species from the boreal forest of central Saskatchewan, Canada, using ä13C and ä15N stable isotope values measured in hair samples. Variance in isotope values for wolves and other carnivores was investigated as a proxy for dietary variation. IsoSource, an isotopic source partitioning model, quantified the relative proportions of 5 most likely prey items in the diets of wolves.</p><p>I compared these results with investigations of faecal contents using percent biomass contributions of prey items in wolf diet. I found no difference between percent biomass measures and mean percent contributions derived from IsoSource. Despite social foraging, my results indicate highly variable diets among individual wolves and I discuss this in terms of boreal wolf ecology.

<p>Habitat fragmentation and anthropogenic development influence the level of isolation and security in and around protected habitats affecting wolf movements and the distribution and abundance of their prey. In light of recent concern about the ecology of animals in protected areas, I initiated a research project to investigate the molecular and foraging ecology of grey wolves in and around Prince Albert National Park (PANP), Saskatchewan. <p>Estimates of genetic diversity and population structure can be used as surrogates to detect effects of habitat degradation on wolves. Genetic diversity was high in these populations relative to other North American wolf populations. My results suggest that wolves in central Saskatchewan form a panmictic population, however there is some evidence showing partial isolation of one group of wolves within PANP. I speculate that the level of human activity such as road networks, hunting, and trapping act as dispersal impediments to this isolated group. Further, the genetic homogenization, indicating high population turnover, of wolf groups that use the periphery and adjacent areas of PANP may also contribute to the observed genetic subdivision. The partially isolated NW group, characterized by slightly lower diversity indices, low migration rates, and higher levels of allele fixation, indicated this group was a more stable social unit comprised of more related individuals.</p><p>Knowledge of wolf food habits and how they change over time is a fundamental component to understanding wolf ecology. Using scat analysis I evaluated wolf foraging ecology by calculating indices of occurrence/faeces (OF) and percent prey biomass contribution: white tailed deer contributed 43% and 33% respectively to wolf diet; elk (33%, 50%), moose (7%, 14%), beaver (5%, 2%), and snowshoe hare (2%, <1%). I found no evidence of livestock depredation nor did wolves prey on bison or caribou. There were no differences in OF indices between years. Prey selectivity was apparent in both years with wolves selecting elk and avoiding beaver. A diversity of ungulate prey are readily available to wolves in this system; however, scat analysis and tests for prey selection indicate a preference for elk. I presume this is a choice made to balance risk with profitability of food items in concordance with optimal foraging theory.</p><p>I examined trophic relationships between the grey wolf and 18 mammalian species from the boreal forest of central Saskatchewan, Canada, using ä13C and ä15N stable isotope values measured in hair samples. Variance in isotope values for wolves and other carnivores was investigated as a proxy for dietary variation. IsoSource, an isotopic source partitioning model, quantified the relative proportions of 5 most likely prey items in the diets of wolves.</p><p>I compared these results with investigations of faecal contents using percent biomass contributions of prey items in wolf diet. I found no difference between percent biomass measures and mean percent contributions derived from IsoSource. Despite social foraging, my results indicate highly variable diets among individual wolves and I discuss this in terms of boreal wolf ecology.

Association mapping (AM), based on linkage disequilibrium, is a complementary strategy to traditional quantitative trait loci (QTL) mapping for describing associations between genotypes and phenotypes in crop plants. Yellow endosperm colour, an important quality trait in durum wheat (<i>Triticum turgidum L. var. durum</i>), was studied to determine the potential of AM to (1) identify previously reported QTL using a genome wide scan and (2) to determine allelic association of the phytoene synthase 1 (Psy1) gene using a candidate gene analysis. At present, a number of QTL for endosperm colour have been identified, and phytoene synthase, the initial enzyme of the carotenoid biosynthetic pathway, has been associated with QTL on the group 7 chromosomes which are considered to play a significant role in expression of yellow pigment concentration. CIE 1976 b*, a light reflectance measurement, and water-saturated butanol extracted pigments were assessed on a collection of 93 elite accessions from a variety of geographic origins, and genotyped with 245 markers. Population structure was assessed using genetic distance and Bayesian model based approaches, identifying five sub-populations consistent with breeding origin and pedigree. Association analysis identified significant associations with yellow endosperm colour on all chromosomes, including several previously identified QTL as well as new regions for genomic dissection. Pairwise LD mapping of Psy1-B1 and Psy1-A1 located the genes to chromosomes 7B and 7A respectively, to regions which have previously been identified for yellow pigment concentration QTL. The results of this study indicate that AM can be used to complement traditional QTL mapping techniques, and identify novel QTL for further study.

Little is known about the population structure and genetic variability of blackfin tuna despite catch increases over the past 25 years. In this thesis, levels of genetic variation contained in 323bp of the mitochondrial DNA (mtDNA) control region-I (CR-I) and in six microsatellite loci were characterized for two regions: the Gulf of Mexico (GoM) and the Northwest Atlantic. Large amounts of mtDNA diversity (h>0.99; =0.047) were observed in both regions. Mismatch distribution analysis of the CR-I sequence data, using a mutation rate of 1.6% Ma-1for scombroid fishes, indicate blackfin tuna underwent population expansion about 1.4 Ma, a timeline concordant with the expansion of other tunas and billfishes. Estimates of female effective population size were very large at 7.8 million and 12.8 million individuals for the NW Atlantic and the GoM, respectively. Both mtDNA and six microsatellite loci were used to determine blackfin tuna population structure. Microsatellite and mtDNA AMOVAs revealed significant differentiation (msat st=0.01, p=0.006 and mtDNA st=0.01, p=0.049) between the GoM and the NW Atlantic samples. Migration estimates using mtDNA data indicate that twice as many females enter the NW Atlantic from the GoM (346 individuals/generation) than the opposite direction (150 individuals/generation). Migration estimates using microsatellite data were substantially smaller, with the Gulf receiving 7 individuals/generation and the NW Atlantic 4 individuals/generation. Finally, low levels of genetic differentiation using microsatellite data have been reported in other highly abundant marine fishes, which have been attributed to homoplasy in allele size. To test this hypothesis, the allele frequency distributions of blackfin and yellowfin tuna at six microsatellite loci were compared. The distances between species were surprisingly small (Da=4.0%, (delta mu)squared=1.08), with a large degree of similarity in frequency distributions at four loci. The comparison of bigeye tuna at two microsatellite loci revealed additional inter-specific similarities. A mutation rate for these loci was estimated by modifying an equation used to estimate time since divergence. Microsatellites in tunas appear to evolve at a rate (4.3x10-7 Ma-1) that is two orders of magnitude slower than other fishes (1x10-5 Ma-1). Accordingly, microsatellite allele size similarities are plesiomorphic and not due to homoplasy.

Understanding how anthropogenic activity impacts the health and viability of wildlife populations is one of the most important tasks of environmental biology. A key concern related to bi-products of human activity is the accumulation of environmental pollutants within aquatic environments. Pollutants such as endocrine disruptors and heavy metals have the potential to impact both human and wildlife populations in contaminated areas. While much research has focused on how these compounds impact natural selection processes, such as viability and reproduction, their effect on sexual selection processes is not as clear. The goal of this dissertation was to address how environmental contaminants impact sexual selection processes in a sex-role reversed pipefish and evaluate how these effects may impact long-term population viability. Here we show that short periods of exposure to environmentally relevant concentrations of a synthetic estrogen result in male pipefish with female-like secondary sexual traits. While these males are capable of reproduction, exposed males are discriminated against by females in mate choice tests. In natural populations, this type of discrimination could reduce male mating opportunities, potentially reducing their reproductive success. In an additional component of this dissertation, it was discovered that pipefish populations around Mobile Bay, specifically Weeks Bay, are currently being exposed to significantly elevated levels of mercury. These populations are genetically distinct from coastal populations but moderate levels of gene flow occur among sites, and gene flow between contaminated and non-contaminated population may be influencing how environmental contaminants are impacting genetic diversity and population viability. In the case of endocrine disruptors, migration between contaminated and non-contaminated sites may negatively impact population viability. Morphological traits induced with exposure to contaminants may be maintained for extended periods of time, therefore, the effect the exposed phenotype has on mating dynamics and sexual selection could be carried to non-contaminated sites if exposed individuals move to new populations. On the other hand, immigration of individuals from non-contaminated sites into contaminated areas may help maintain genetic diversity within exposed populations. In conclusion, the work presented in this dissertation shows that the presence of environmental toxins can significantly impact sexual selection processes, which in turn can have profound effects on the viability and future evolutionary trajectory of populations. Future work in this area should not only address how these toxins impact individual fitness, but should also address how population structure may be influencing the severity of these compounds on natural populations.

Genetic analyses of two endangered species of mammals in the Lower Keys of Florida (Lower Keys marsh rabbit, LKMR, Sylvilagus palustris hefneri; silver rice rat, SRR, Oryzomys palustris natator) were performed to evaluate the genetic structure of their populations. Mitochondrial sequence data (control region; 763 base pairs (bp), LKMR; 788 bp, SRR) were used to explore patterns of genetic variation within and among island populations in both species. Analysis of the SRR also included 8 polymorphic nuclear microsatellite loci (9 to 16 alleles). Phylogenetic analyses of mitochondrial sequence data for both species revealed two main lineages corresponding to eastern and western localities, with high levels of genetic structuring (LKMR FST = 0.982, SRR ΦST = 0.916). The two species differed in the level of sequence divergence between eastern and western populations (LKMR, 19 bp; SRR 4 bp). In addition to an overall similar pattern of genetic subdivision, populations of both species possessed low levels of mtDNA variation (haplotypic diversity in the LKMR = 66.1%, SRR = 58.6%). Microsatellite analyses of the SRR revealed subdivision between eastern and western regions. Although less pronounced than the structure observed in mtDNA, the overall pattern was still apparent. Additional examination of divergence between mainland and Lower Keys rice rats revealed a genetic division that indicated a lack of recent gene exchange between the regions (i.e. no shared haplotypes, the presence of private alleles, and distinctive separation in numerous analyses). Although this degree of division does not warrant species designation, the levels and patterns of divergence, both morphological and genetic, do suggest genetic isolation of mainland and island forms. This fact, along with restricted gene flow between the Lower Keys and the Everglades, suggests that the SRR is on an evolutionary trajectory separate from its mainland counterparts and validates its identification as a separate subspecies, Oryzomys palustris natator. Finally, the genetic division between eastern and western populations of the SRR and LKMR suggests that populations of both species in these two regions of the Lower Keys should be treated as separate management units, especially when considering the enhancement of populations via translocations.

Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We used 47,506 single-nucleotide polymorphisms (SNPs) to investigate cattle population history. Cattle are descendants of two independently domesticated lineages, taurine and indicine, that diverged 200,000 or more years ago. We found that New World cattle breeds, as well as many related breeds of cattle in southern Europe, exhibit ancestry from both the taurine and indicine lineages. Although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. We extended these analyses to compare timing of admixture in several breeds of taurine-indicine hybrid origin. We developed a metric, scaled block size (SBS), that uses the unrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient admixture. By comparing test individuals to standards with known recent hybrid ancestry, we were able to differentiate individuals of recent hybrid origin from other admixed individuals using the SBS metric. We genotyped SNP loci using the bovine 50K SNP panel. The selection of sites to include in SNP analyses can influence inferences from the data, especially when particular populations are used to select the array of polymorphic sites. To test the impact of this bias on the inference of population genetic parameters, we used empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We compared the inference of population histories for simulated data sets across different ascertainment conditions using F[subscript ST] and principal components analysis (PCA). Ascertainment bias that results in an over-representation of within-group polymorphism decreases estimates of F[subscript ST] between groups. Geographically biased selection of polymorphic SNPs changes the weighting of principal component axes and can bias inferences about proportions of admixture and population histories using PCA. By combining empirical and simulated data, we were able to both test methods for inferring population histories from genomic SNP data and apply these methods to practical problems. / text