The objective of this thesis was to assess the diversity and community structure of fungi in a forest plot in Ontario using a variety of field sampling and analytical methods. Three broad questions were addressed: 1) How do different measures affect the resulting view of fungal diversity? 2) Do fruiting bodies and soil rDNA sampling detect the same phylogenetic and ecological groups of Agaricomycotina? 3) Will additional rDNA sampling resolve the phylogenetic position of unclassified fungal sequences recovered from environmental sampling? Generally, richness, abundance, and phylogenetic diversity (PD) correspond and identify the same dominant fungal groups in the study site, although in different proportions. Clades with longer branch lengths tend to comprise a larger proportion of diversity when assessed using PD. Three phylogenetic-based comparisons were found to be variable in their ability to detect significant differences. Generally, the Unifrac significance measure (Lozupone et al., 2006) is the most conservative, followed by the P-test (Martin, 2002), and Libshuff library comparison (Singleton et al., 2001) with our dataset. Fruiting body collections and rDNA sampling recover largely different assemblages of fungi at the species level; however, both methods identify the same taxonomic groups at the genus-order level as well as ectomycorrhizal fungi as the dominant functional type of Agaricomycotina. This work also shows that the Soil Clone Group I (SCGI) clade is widespread in soils of diverse origins and represents a novel subphylum of Ascomycota.

Though molecular phylogenetics has been very successful in reconstructing the evolutionary history of species, some phylogenies, particularly those involving ancient events, have proven difficult to resolve. One approach to improving the resolution of deep phylogenies is to increase the amount of data by including multiple genes assembled from public sequence databases. Using modern phylogenetic methods and abundant computing power, the vast amount of sequence data available in public databases can be brought to bear on difficult phylogenetic problems. In this thesis I outline the motivation for assembling large multigene datasets and lay out the obstacles associated with doing so. I discuss the various methods by which these obstacles can be overcome and describe a bioinformatics solution, TaxMan, that can be used to rapidly assemble very large datasets of aligned genes in a largely automated fashion. I also explain the design and features of TaxMan from a biological standpoint and present the results of benchmarking studies. I illustrate the use of TaxMan to assemble large multigene datasets for two groups of taxa – the subphylum Chelicerata and the superphylum Lophotrochozoa. Chelicerata is a diverse group of arthropods with an uncertain phylogeny. When a set of mitochondrial genes is used to analyse the relationships between the chelicerate orders, the conclusions are highly dependent upon the evolutionary model used and are affected by the presence of systematic compsitional bias in mitochondrial genomes. Lophotrochozoa is a recently-proposed group of protostome phyla. A number of distinct phylogenetic hypotheses concerning the relationships between lophotrochozoan phyla have been proposed. I compare the phylogenetic conclusions given by analysis of nuclear and mitochondrial protein-coding and rRNA genes to evaluate support for some of these hypotheses.

The biology of the sub-aquatic lichen, Dermatocarpon luridum, was investigated. This lichen is sparsely distributed within the temperate climatic zones around the world, colonizing rock along watercourses that regularly experience water level fluctuations. Specimens collected from Canada and Austria were cultured using standard growth media. Brightfield microscopy was used for algal species identification, while fungal ITS, algal ITS and algal actin gene sequences were used for phylogenetic and population genetic evaluation. Results were: 1) axenic cultures of the photobiont were successful, while those of the mycobiont were not successful; 2) Diplosphaera chodatii is the photobiont associated with D. luridum var. luridum and allies, suggesting algal sharing between mycobiont species; 3) genetic diversity is high, and gene flow was high within local populations, but low between continental populations. Diplosphaera chodatii may be a keystone species contributing to the survival of D. luridum var. luridum along with other sub-aquatic, aquatic and terrestrial lichens.

Accurate identification of pathogens and vectors is essential in epidemiological studies of mosquito-borne pathogens. However, the members of the communis and punctor complexes are difficult to distinguish because they are highly cryptic species, with little to no species-specific morphological characters. The objective of this thesis is to develop molecular tools, including RFLP and DNA barcoding using cytochrome oxidase I (COI), internal transcribed spacer 2 (ITS2) and the intron of ribosomal protein S12 (RPS12) to facilitate identification of the members of these two complexes in Manitoba. A distinct interspecific distance for COI was found between the members of the communis complex included here, and diagnostic RFLP profiles were developed for Oc. communis and Oc. churchillensis. Relatively low average interspecific genetic distances using COI, ITS2 and RPS12 were observed between the members of the punctor complex, indicates no discernable boundaries between these species based on DNA barcoding.

Understanding the ecological and evolutionary processes responsible for shaping patterns of genetic variation in natural populations is a long-standing goal in molecular ecology. Although an extensive number of recent studies focus on patterns and processes throughout tropical rain forest ecosystems, substantially less effort has been placed on tropical dry forests (TDFs); a habitat known to harbour a large percentage of Earth’s diversity. In this thesis I use leaf-toed geckos of the genus Phyllodactylus to understand both the historical and contemporary processes influencing diversification throughout Mexico’s TDFs. In Chapter 2 I isolate and characterize microsatellite markers for the gecko P. tuberculosus. Chapter 3 uses these loci to conduct a landscape genetic analysis of the species near Alamos, Sonora. I find that the inclusion of landscape variables explains more genetic variance versus Euclidean distance alone. Chapter 4 examines the evolutionary history of the P. tuberculosus group throughout western Mexico. Results suggest that habitat and climate shifts during the Miocene and Pleistocene were important divers of diversification. Chapter 5 uses microsatellite and mtDNA markers to compare historical and contemporary demographic parameters in P. tuberculosus. I find evidence for low historical gene flow and high female philopatry, recent reductions in population sizes, and higher correlations between landscape and contemporary gene flow versus historical gene flow and mtDNA divergence. In Chapter 6 I examine the biogeographic and taxonomic consequences of the dynamic history of Baja California. My phylogenetic results provide evidence for a trans-peninsular seaway in the Isthmus of La Paz region and suggests that P. xanti nocticolus warrants species status. My results also suggest the possibility of a seaway near the Loreto area that needs to be evaluated further. By combining multiple molecular marker-types and analytical methods, this thesis adds to our understanding of diversification processes throughout the threatened Mexican TDF.

Unraveling the relationships between organisms and patterns of diversity is a central goal of evolutionary biology, pursuant to the aim of reconstructing the history of life. I constructed a hypothesis for species relationships in the shorebird suborder Scolopaci, and mapped onto this framework behavioural and life-history traits to infer their evolutionary history. Relationships were well-resolved and well-supported, although reliable resolution of certain nodes will require additional, independent sources of information. We estimated the Scolopaci ancestor to be monogamous, and care-giving through fledging, but ancestral breeding location and migration distance reconstructions were equivocal. Tests for correlations between parental care and other traits to explain extant species’ trait diversity show that, contrary to previous reports, evolution of Scolopaci diversity was a complex process that cannot be explained by individual character correlations. This study provides important insights into Scolopaci and shorebird evolutionary history, and the general practice of inferring past processes from phylogenetic hypotheses.

Understanding the ecological and evolutionary processes responsible for shaping patterns of genetic variation in natural populations is a long-standing goal in molecular ecology. Although an extensive number of recent studies focus on patterns and processes throughout tropical rain forest ecosystems, substantially less effort has been placed on tropical dry forests (TDFs); a habitat known to harbour a large percentage of Earth’s diversity. In this thesis I use leaf-toed geckos of the genus Phyllodactylus to understand both the historical and contemporary processes influencing diversification throughout Mexico’s TDFs. In Chapter 2 I isolate and characterize microsatellite markers for the gecko P. tuberculosus. Chapter 3 uses these loci to conduct a landscape genetic analysis of the species near Alamos, Sonora. I find that the inclusion of landscape variables explains more genetic variance versus Euclidean distance alone. Chapter 4 examines the evolutionary history of the P. tuberculosus group throughout western Mexico. Results suggest that habitat and climate shifts during the Miocene and Pleistocene were important divers of diversification. Chapter 5 uses microsatellite and mtDNA markers to compare historical and contemporary demographic parameters in P. tuberculosus. I find evidence for low historical gene flow and high female philopatry, recent reductions in population sizes, and higher correlations between landscape and contemporary gene flow versus historical gene flow and mtDNA divergence. In Chapter 6 I examine the biogeographic and taxonomic consequences of the dynamic history of Baja California. My phylogenetic results provide evidence for a trans-peninsular seaway in the Isthmus of La Paz region and suggests that P. xanti nocticolus warrants species status. My results also suggest the possibility of a seaway near the Loreto area that needs to be evaluated further. By combining multiple molecular marker-types and analytical methods, this thesis adds to our understanding of diversification processes throughout the threatened Mexican TDF.

Unraveling the relationships between organisms and patterns of diversity is a central goal of evolutionary biology, pursuant to the aim of reconstructing the history of life. I constructed a hypothesis for species relationships in the shorebird suborder Scolopaci, and mapped onto this framework behavioural and life-history traits to infer their evolutionary history. Relationships were well-resolved and well-supported, although reliable resolution of certain nodes will require additional, independent sources of information. We estimated the Scolopaci ancestor to be monogamous, and care-giving through fledging, but ancestral breeding location and migration distance reconstructions were equivocal. Tests for correlations between parental care and other traits to explain extant species’ trait diversity show that, contrary to previous reports, evolution of Scolopaci diversity was a complex process that cannot be explained by individual character correlations. This study provides important insights into Scolopaci and shorebird evolutionary history, and the general practice of inferring past processes from phylogenetic hypotheses.

In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. Inferring this underlying tree is challenging. We investigate some curious cases in which different methods like Maximum Parsimony, Maximum Likelihood and distance-based methods lead to different trees. Moreover, we state that in some cases, ancestral sequences can be more reliably reconstructed when some of the leaves of the tree are ignored - even if these leaves are close to the root. While all these findings show problems inherent to either the assumed model or the applied method, sometimes an inaccurate tree reconstruction is simply due to insufficient data. This is particularly problematic when a rapid divergence event occurred in the distant past. We analyze an idealized form of this problem and determine a tight lower bound on the growth rate for the sequence length required to resolve the tree (independent of any particular branch length). Finally, we investigate the problem of intermediates in the fossil record. The extent of ‘gaps’ (missing transitional stages) has been used to argue against gradual evolution from a common ancestor. We take an analytical approach and demonstrate why, under certain sampling conditions, we may not expect intermediates to be found.

Canine tick-borne diseases are an emerging problem within Australia and throughout the world. This thesis investigates Babesia gibsoni and Anaplasma platys infections in dogs in Australia and also explores the evolutionary relationships and taxonomy of the canine piroplasm species and the members of the order Piroplasmida. A nested PCR-RFLP assay was developed for the detection and differentiation of the canine piroplasm species and was found to have a high detection limit, capable of detecting a 2.7 x 10-7 % parasitaemia or the equivalent of 1.2 molecules of target DNA. Detection of piroplasm DNA applied to Whatman FTA“ classic cards using nested-PCR was found to have a lower detection limit than when using DNA extracted from whole blood but higher than IsoCode‘ Stix or QIAamp extraction from filter paper based techniques. The nested PCR-RFLP assay was further evaluated for the detection of B. gibsoni infection in dogs being exported from Australia to New Zealand and compared to the current screening methods, the Immunofluorescent Antibody Test (IFAT) and microscopy. Of 235 dogs screened, 11 were IFAT positive, 1 was microscopy positive and 3 were PCR positive for B. gibsoni, highlighting the discordance that exists between various detection techniques. Replacing microscopic examination of blood smears with PCR-RFLP is suggested for screening dogs entering New Zealand, in addition to revising the current IFAT cut-off titre to minimize false positive results. The first case of B. gibsoni in New South Wales is also reported. A study was also conducted to further investigate the recent discovery of B. gibsoni in Australia and the association of this infection with American Pit Bull Terriers in an epidemiological study. Both American Pit Bull Terriers (n = 100) and other dog breeds (n = 51) were screened for B. gibsoni using IFAT and PCR-RFLP. A questionnaire was also completed by each dog owner regarding thethe husbandry and habits these dogs. Fourteen dogs were positive for B. gibsoni using IFAT and/or PCR-RFLP and all were American Pit Bull Terriers. Dogs that were male and/or were bitten by or were biters of other American Pit Bull Terriers were statistically more likely to be B. gibsoni positive, thus suggesting that blood-to-blood transmission may contribute to the spread of this disease. Experimental B. gibsoni infections were established in vivo to investigate the efficacy of combined atovaquone and azithromycin therapy and to determine the detection limits of PCR, IFAT and microscopy during various stages of infection. While atovaquone and azithromycin produced a reduction in circulating parasite levels, it did not cause total eradication, and possible drug resistance also developed in one dog. PCR was found to be most useful in detecting early and acute stage infections, while IFAT was most useful during chronic and acute infections. Microscopy is suggested to be only useful for detecting acute stage infections. This study also describes the detection of B. gibsoni in tissue samples during chronic infection for the first time, suggesting possible sequestration of this parasite. Anaplasma platys has also only recently been reported in Australia and the distribution, molecular-charcterisation, pathogenesis, co-infection with Babesia canis vogeli and treatment of infection with doxycycline were investigated. For the first time, A. platys is reported in Western Australia, Queensland and Victoria, with each isolate found to be genetically identical on the basis of the 16S rRNA gene. No correlation could be established between A. platys infection and the development of clinical signs or pathogenesis and definitive treatment using doxycycline could not be determined. Isolates of canine piroplasms from various geographical locations worldwide (n = 46), including Australia were characterised on the basis of multiple gene loci to explore the distribution, genetic variation and possible phylogeographical relationships of these species. Separate genotypes of B. canis vogeli, B. canis canis and B. gibsoni are suggested and may be correlated to different geographical origins. Characterization of B. canis vogeli, B. canis canis and B. canis rossi on the basis of the HSP 70 gene and B. gibsoni on the basis of the ITS 1, 5.8S rRNA gene and ITS 2 is described for the first time. Elevation of each of the B. canis subspecies, with the exclusion of B. canis presentii, to separate species is also proposed. The current paraphyly and taxonomic confusion associated with the members of the order Piroplasmida led to a review of the phylogenetic and taxonomic status of this group of organisms. Phylogenetic relationships are determined using 18S rRNA gene, 5.8S rRNA gene, HSP 70 gene and combined loci analyses. Rearrangement of the Piroplasmida into three families, including the new family Piroplasmiidae is proposed, in addition to the establishment of two new genera, the Piroplasma (Patton, 1895) and the Achromaticus (Dionisi, 1899). Other proposed schemes of classification and the limitations of phenotypic characteristics in taxonomic classification within the Piroplasmida are also discussed.