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The main thrust of this thesis was to characterize P.falciparum genetic diversity in northern Ghana. To do this, I used simple techniques to purify P. falciparum DNA from clinical samples across a rural setting for whole-genome sequencing. The goal was to provide a framework for exploring host-parasite genetic interactions. Utilizing Illumina deep sequencing data for 277 isolates I analyzed P. falciparum genetic diversity and described within-host diversity across this area. I observed random mating (ie no population structure) in the local parasite population, and a high genetic diversity indicative of high out-crossing. Moreover, when I aggregated my data with similar published data from Burkina Faso and Mali (sites ≈500km apart), no population structure was evident. In contrast, sites sampled in Cambodia and Thailand (≈ 800km apart) were found to have greater population structure and high potential for inbreeding. This may be driven by differences in transmission intensity between the sites sampled in West Africa and southeast Asia. To demonstrate the utility of deep sequencing data, I focused on the genomic regions of pfdhfr, pfdhps and pfcrt, known to be under antimalarial drug selection. I surveyed the full diversity of point mutations already characterized in these genes and discovered previously unknown variants. However, in order to provide a means to follow up on new variants or interesting candidate regions in large clinical samples with limited parasite DNA, I assessed the Sequenom iPLEX platform for high-throughput genotyping of P. falciparum polymorphisms. This necessitated developing a method appropriate for assigning genotypes in haploid genome mixtures common in natural infections. Finally, I used this method to type host and parasite markers in a case-control sample set from this region for exploring host-parasite genetic interactions. I found that children who have the sickle-cell trait and carry parasites that have pfdhfr resistant alleles lose their protection against severe malaria as compared to children who have normal haemoglobin and are infected with parasites with these resistant alleles.

Doctor of Philosophy / Department of Plant Pathology / Christopher R. Little / Understanding the genetic structure of fungal pathogens enables the prediction of evolutionary forces that drive pathogen evolution, which assists informed decision-making regarding disease management. The genetic structure of Fusarium thapsinum and F. andiyazi, two important pathogens that cause grain mold and stalk rot of sorghum (Sorghum bicolor), are little understood. The genetic structure and pathogenicity of a F. thapsinum population from sorghum in Kansas were evaluated with amplified fragment length polymorphisms (AFLPs), vegetative compatibility groups (VCGs), sexual cross-fertility, and seedling pathogenicity. Two sympatric populations and a genetically intermediate "hybrid" group were identified in Kansas. Seedling pathogenicity of strains ranged from non-pathogenic to pathogenic, which may be partially attributable to genetic variability in the F. thapsinum populations. Genetic relatedness between populations of F. thapsinum from sorghum in Kansas, Australia, Thailand, and three African countries (Cameroon, Mali, and Uganda) were evaluated with AFLP markers and sexual crosses. Genetic diversity was high in all locations, but female fertility is very low. These results are consistent with the hypothesis that both sexual and asexual modes of reproduction are important components of the life cycle of F. thapsinum in these populations. More strains from Kansas and Africa were available for analysis than from Australia and Thailand, so the Kansas and Africa populations dominated the genetic structure observed. The two smaller populations from Australia and Thailand were more closely related to the Kansas population than they were to the African population. The three non-African populations contained information from the African population and from other, as yet unidentified, source population(s). Identifying the population(s) from which this genetic diversity originated is an important unanswered question. Stalk rot of sorghum was evaluated by inoculating stalk rot sensitive and stalk rot resistant sorghum lines with six genetically diverse F. thapsinum strains from Kansas under field and greenhouse conditions. One susceptible line (Tx7000) and two resistant lines (SC599 and BTx399) were evaluated in the field but only Tx7000 and SC599 were evaluated in the greenhouse. Disease severity was measured by major lesion length and the number of nodes crossed by the lesion. There were differences in aggressiveness amongst the F. thapsinum strains in both the greenhouse and field evaluations. This study provides the first evidence for differences in stalk rot aggressiveness amongst F. thapsinum strains and highlights the importance of challenging germplasm with well-characterized strains that represent the genetic spectrum of the entire population. The genetic diversity within F. andiyazi populations and some closely related strains was evaluated with AFLP markers. Phylogenetic and STRUCTURE analyses of the AFLP markers grouped the 81 F. andiyazi strains into three distinct clusters. The clusters were not based on the geographic origin of the strains. These results indicate the presence of at least one and possibly two undescribed sister taxa of F. andiyazi. More work is needed to further characterize these sister species of F. andiyazi and to understand their role in sorghum pathogenicity. There is genetic variation in global populations of F. thapsinum and the observed variation could be associated with variation in both seedling and adult plant pathogenicity. The study of F. andiyazi populations validated the need to properly identify and characterize Fusarium spp. associated with sorghum from different regions of the world.

The management of genomic diversity is important within breeding programs and is primarily achieved through controlling the rate of inbreeding. A failure to adequately manage the rate of inbreeding will result in an increased risk of the expression of lethal recessive mutations, inbreeding depression and losses in genetic variance, thereby restricting long-term genetic progress. Each research chapter within this thesis used real data collected from a commercial pig breeding operation to examine a key area of research regarding the management of genomic diversity. The first research chapter examined the selection outcomes from the practical application of Optimal Contributions (OC). These outcomes were examined to determine their alignment with the current theories regarding selection, particularly as to the extent by which selection decisions were influenced by estimated Mendelian sampling terms. This assessment was conducted for the initial selection of individuals as parents, which parents went on to provide a long-term contribution and the magnitude of these contributions. OC was shown to have shifted breeding decisions more closely in alignment with the estimated Mendelian sampling terms. The second research chapter used genomic data to assess the adequacy of the pedigree-based approach for managing diversity during selection. This approach assumes the infinitesimal model with all loci neutral and no impact from selection per se on heterozygosity. Using genomic information, the observed loss of heterozygosity at each marker was compared to the loss of heterozygosity expected from the pedigree-based relationships. Regional disparities between the observed and expected losses in heterozygosity were detected, which were potentially attributable to selection. Runs of homozygosity and the pairwise linkage disequilibrium between markers were also examined within these regions. Regions showing disparity were found to contain well validated quantitative trait loci for important traits. The third research chapter sought to provide a genomic solution to the shortcomings of the pedigree-based approach for quantifying relatedness, identified above. A methodology was devised for tracing identity by descent (IBD) at each allelic position over five ancestral generations, following phasing and imputation of the genomic data. A comparison was made between the inbreeding expected from the pedigree relationships and that observed from the identity by descent of genomic information. In the population studied it was not currently feasible to derive a relationship matrix based exclusively on observed IBD. The fourth research chapter used imputed genomic information to identify haplotypes which had a putative lethal recessive effect. Haplotypes which were never observed in the homozygous form, either in the population or in the offspring produced between carriers, were classified as candidate haplotypes. The top candidates on each chromosome were then examined for a reduction in the total number born when two carriers were mated together. A total of six putative lethal recessive haplotypes were detected relating to at least four putative lethal recessive mutations, where one homozygote was absent and the size of the reduction in litter size matched that expected for a lethal recessive effect. The research chapters contained within this thesis demonstrate the important role that genomics can have in managing inbreeding in addition to generating genetic gain. Genomics is able to provide a more accurate prediction of the Mendelian sampling term, better quantify the relatedness between individuals and detect lethal recessive effects.

Begonia is one of the ten largest plant genera and is found throughout the tropics. I have used Begonia section Gireoudia to study the genetics underlying vegetative diversity in tropical herbaceous plants. Section Gireoudia is a large Central American group. The section is remarkably diverse in morphology and habitat preference. It ranges from wet rainforests to seasonally dry forests. I have investigated variation in morphological, anatomical and ecophysiological differences for 21 species in Begonia section Gireoudia. Based on the observed variation, species in Begonia section Gireoudia form a complex and unique group that stands out from currently analysed taxa in the global scale of variation on the basis of leaf function and resource use strategy traits as well as their peculiar leaf anatomy. Traits directly related to leaf function such as photosynthesis and stomatal conductance has very low values which overlap with those of CAM and aquatic plants. Values for traits indicative of resource use such as leaf mass area (LMA) and leaf dry matter content (LDMC) are also very low in Begonia when compared with the values observed globally. The trait- trait correlations across the species in section Gireoudia were also investigated and revealed patterns in micromorphology and ecophysiology. Some of the traits measured are correlated with each other in apparently straightforward, well charaterised biological relationships e.g., the variation among Begonia species in stomatal conductance and net assimilation rate are positively correlated. On the other hand, the linkage of high Amass with high Nmass which is in large part the result of a direct causal relationship, has been observed at the global scale but this relationship is not significant in Begonia section Gireoudia. I examined B. plebeja and B. conchifolia, two very closely related though ecologically divergent species from Meso-America, in more detail. I detected significant differences between the species for a number of phenotypic variables which may be related to their habitat preferences. This suggested that environmental conditions have driven divergent evolution of phenotypic traits for these two species. Using a mapping population generated from hybrids between these two species I was able to examine the genetic basis of these differences. This revealed that although some traits (such as anthocyanin accumulation) appear to be under simple genetic control, most of the variation between species has complex genetic inheritance patterns. I used QTL analysis to identify significant QTLs for 20 physiological, anatomical and morphological traits which varied between these two species. Leaf shape traits appear to be largely influenced by a few loci of large effect, making these good potential targets for further analysis. The study also identified clusters of coincident QTLs for different correlated traits identifying pleiotropic genes or suites of linked loci.

Helianthus eggertii (Asteraceae) is a federally threatened sunflower species that typically grows between open woods and barrens. This species has both sexual and asexual modes of reproduction, which can influence the amount of genetic diversity present within and among populations. Maintaining genetic diversity is one of the primary objectives in managing threatened species or populations. Fire and population size may influence genetic diversity. Two Inter-Simple Sequence Repeat Markers (873 and MAO) were used to characterize many important genetic parameters of 17 populations in 2003 and four populations in 2004. This information was used to assess the effectiveness of different conservation management strategies. The main objectives of this project were to determine whether: 1) larger populations of Helianthus eggertii have a higher genetic diversity within populations than smaller populations 2) fire or other management strategies influence genetic diversity of populations 3) sexually derived progeny of H. eggertii have greater genetic diversity than mixed reproduction in parent populations assuming some degree of clonal reproduction. This study found that there is higher mean genetic diversity in larger populations, though not significant. Genetic diversity showed no difference in populations that are frequently burned than in populations that are not burned. However, there tends to be an increase in genetic diversity in some populations immediately after a fire event. The seed population studied had a higher genetic diversity. Genetic diversity is high at both Mammoth Cave National Park (.5246) and Arnold Engineering and Development Center(.4555). The high genetic diversity observed suggests that while clones may exist in a population, seedling establishment is actively putting new genetically diverse individuals in a population. These results show that the current management strategies being used are suitable for protecting this species.

Native prairie grasses of western Canada have the potential for development as turf and forage grass cultivars for semiarid environments. Nuttall’s salt-meadow, or alkali grass (Puccinellia nuttalliana (Shultes) Hitchc.), is a native grass species in North America well known for its salt tolerance. Little information is available about the genetic diversity of natural populations of this species. Understanding the genetic diversity of this species is a prerequisite for developing populations for forage or turf use in western Canada. The objectives of this study were to assess the variation in agronomic/morphological characters and AFLP markers of collections of Puccinellia and identify promising populations and genotypes for turf and forage utilization. A four replicate randomized complete block field nursery of twenty-four collections from western Canada was established in 2010. Plant height, tiller number, crown diameter, dry matter yield, seed yield, and leaf related characters were measured for each collection in the summers of 2011 and 2012. Considerable phenotypic variation was detected among and within the twenty-four populations. Promising populations and genotypes were identified with respect to their superior turf and forage related characteristics. The amplified fragment length polymorphism (AFLP) technique was used to assess the comparative genetic diversity of the collections. Five AFLP primer pairs were employed to screen 15 genotypes from each population, and 185 polymorphic AFLP bands were scored for each sample. Their frequencies of occurrence ranged from 0.02 to 0.99 with a mean of 0.61. The analysis of molecular variance revealed more than 96% of the total AFLP variation resided within populations. Populations were not highly differentiated with only 4% of the total AFLP variation residing among populations. A Mantel test revealed a significant but low correlation between genetic and geographic distances (r=0.293; P=0.024) and non-significant correlation between genetic and phenotypic distances (r=0.070; P=0.282). Implications for P. nuttalliana conservation, germplasm sampling, and cultivar development are discussed.

Incorporating molecular genetic data into management decisions would provide fisheries managers with new tools to identify the magnitude of population structure, metapopulation dynamics, at risk populations, and possible genetic interactions between species, so that management strategies could be tailored to better support long-term viability of species and populations. Alewife (Alosa pseudoharengus) and Blueback Herring (Alosa aestivalis) are two closely related anadromous clupeid fishes native to the Atlantic coast of North America. Current management strategies for these two species, collectively known as river herring, take no account of stock structure or even the distinction between the two species. Using 12 neutral microsatellite loci, I examined at multiple spatial scales the patterns of population structure and genetic differentiation for river herring, with particular reference to comparisons of population structure in the U.S., where extensive stocking has occurred, and Canada, where there has been no stocking. Results suggested strong population structure within the Canadian portion of the range and weaker population structure in the U.S. portion. Highly significant genetic isolation by distance (IBD) for parts of the range unaffected by stocking provided evidence of natal homing and limited dispersal. The differing IBD results obtained in three Canadian regions may reflect differences in historical biogeographical factors and contemporary dispersal patterns among regions. Very weak differentiation and an absence of significant IBD for American stocked populations provided evidence that stocking has reduced genetic differentiation between populations in the U.S. portion of the range, except for two divergent stocked populations that appeared to have resisted homogenization. Evidence of recent population bottlenecks were identified in both U.S. and Canadian populations. The genetic structure of Blueback Herring populations appeared to be similar to that seen in Alewife. When sampled in the same river, Alewife and Blueback Herring were strongly differentiated, although hybrids of the two species were detected. Evidence of genetic impacts of stocking, regional variation in patterns of population structure and complex genetic interactions between the species suggest that current management strategies should be re-evaluated.