The recent call to reconstruct a detailed picture of the tree of life for all organisms has forever changed the field of molecular phylogenetics. Sequencing technology has improved to the point that scientics can now routinely sequence complete plastid/mitochondrial genomes and thus, vast amounts of data can be used to reconstruct phylogenies. These data are accumulating in DNA sequence repositories, such as GenBank, where everyone can benefit from the vast growth of information. The trend of generating genomic-region rich datasets has far outpaced the expasion of datasets by sampling a broader array of taxa. We show here that expanding a dataset both by increasing genomic regions and species sampled using GenBank data, despite the inherent missing DNA that comes with GenBank data, can provide a robust phylogeny for the plant order Caryophyllales (angiosperms). We also investigate the utility of trnK intron in phylogeny reconstruction at relativley deep evolutionary history (the caryophyllid order) by comparing it with rapidly evolving matK. We show that trnK intron is comparable to matK in terms of the proportion of variable sites, parsimony informative sites, the distribution of those sites among rate classes, and phylogenetic informativness across the history of the order. This is especailly useful since trnK intron is often sequenced concurrently with matK which saves on time and resources by increasing the phylogenetic utility of a single genomic region (rapidly evolving matK/trnK). Finally, we show that the inclusion of RNA edited sites in datasets for phylogeny reconstruction did not appear to impact resolution or support in the Gnetales indicating that edited sites in such low proportions do not need to be a consideration when building datasets. We also propose an alternate start codon for matK in Ephedra based on the presense of a 38 base pair indel in several species that otherwise result in pre-mature stop codons, and present 20 RNA edited sites in two Zamiaceae and three Pinaceae species. / Ph. D.

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<p>Previous studies have found that DNA flanking low-complexity regions (LCRs) have an increased substitution rate. Here, the substitution rate was confirmed to increase in the vicinity of LCRs in several primate species, including humans. This effect was also found within human sequences from the 1000 Genomes Project. A strong correlation was found between average substitution rate per site and distance from the LCR, as well as between the proportion of genes with gaps in the alignment at each site and distance from the LCR. Along with substitution rates, dN/dS ratios were also determined for each site, and the proportion of sites undergoing negative selection was found to have a negative relationship with distance from the LCR.</p> <p>Low-complexity regions in proteins often form and extend through the gain or loss of repeated units, a process that is dependent on the presence of a relatively pure string of repeats. Any interruption should disrupt the mechanisms of LCR extension and contraction, inhibiting LCR formation. Despite this, several examples have been found of LCR-coding DNA which are interrupted by introns. While many of these LCRs may be the result of two shorter LCRs forming on opposite sides of an intron, shuffling the order of exons showed that more intron-interrupted LCRs exist than would be expected to occur randomly. Another possible explanation for this phenomenon is the apparent movement of either the LCRs or introns, possibly through recombination or the appearance of new splice sites through the gain of repeat units.</p> / Master of Science (MSc)

Lhx genes are a sub-family of Hox genes that play important roles in animal development. In Caenorhabditis elegans there are seven Lhx genes, including the founding family member lin-11. The lin-11 gene is necessary for the specification of neuronal and reproductive tissues. My thesis work has involved understanding the mechanism of lin-11 regulation and its function in these tissues. To this end, I addressed two distinct but complementary questions, one of which focused on how transcriptional regulation of lin-11 occurs and the second on the role of LIN-11 protein domains/regions. My work on the transcriptional regulation has uncovered important roles of two of the largest lin-11 introns, intron 3 and intron 7. These introns promote lin-11 expression in non-overlapping sets of amphid neurons. Based on gene expression patterns and behavioural assays, intron 3 is capable of restoring lin-11 function in lin-11(n389 ) null mutant allele. Comparison of intron 3-driven reporter expression in the neuronal cell types between C. elegans and C. briggsae has revealed cis and trans evolutionary changes in lin-11 regulation between the two species. Functional dissection of the introns in C. elegans has led to the identification of three distinct non-overlapping enhancers, each specific for a single amphid neuron, i.e., RIC, AIZ, and AVG. I have also identified four transcription factors, SKN-1, CEH-6, CRH-1, and CES-1, that act through these enhancers to regulate neuronal expression of lin-11. Furthermore, I have characterized the function of the LIM domains and a proline-rich (PRR) C-terminus region of LIN-11 in the specification of neuronal and reproductive tissues. My work shows that while the LIM domains are required for LIN-11 function in these tissues, the PRR region is dispensable. I have also examined the functional conservation of lin-11 domains using two other Lhx genes, Drosophila melanogaster (dLim1) and Mus musculus (Lhx1 ), and found that both of these genes were able to rescue lin-11 defects. Together, my work has significantly advanced our understanding of transcriptional regulation of lin-11, the importance of LIM domains in tissue formation, and functional conservation of Lhx genes across phyla. / Thesis / Doctor of Philosophy (PhD)

Agaricus bisporus, le champignon de Paris, est un basidiomycète saprophytenaturellement présent dans la litière de cyprès (Cupressus macrocarpa). Il possède différentsmodes de reproduction. Pour étudier leur rôle dans la dynamique spatio-temporelle et l’évolutionde la diversité génétique au cours du temps, des dispositifs expérimentaux ont été mis en place.Dix souches sauvages d’Agaricus bisporus var. bisporus ont été sélectionnées, à partir de deuxpopulations françaises, sur leurs traits phénotypiques et génotypiques. L’étude de l’évolutionmoléculaire de leurs génomes a montré que, pour le génome mitochondrial, la mobilité desintrons de groupe I apparait comme la principale source de polymorphisme. Des taux desubstitution nucléotidique (nt) faibles ont été observés chez tous les types de séquencesmitochondriales (éléments mobiles, séquences géniques et inter géniques). Cette forteconservation, comparée avec les taux élevés de substitution nt des séquences nucléairessimilaires, contraste avec ce qui est généralement décrit dans l’évolution des séquencesfongiques. Des expériences de croisements entre sporocarpes et mycelia de souches sauvages ontété menées sur du compost, dans une chambre de culture, pour simuler l’implantation d’unepopulation naturelle. Pour les sporocarpes récoltés, les données montrent l’existence d’unphénomène parasexuel de Buller conduisant à des souches hybrides d’A. bisporus dans lachambre de culture et potentiellement dans la nature. Parallèlement, les mycelia de souchessauvages ont été introduits dans deux parcelles expérimentales de cyprès. L’analyse génotypiquedes sporocarpes récoltés la première année d’introduction n’a pas permis de mettre en évidencede souche hybride et les conditions climatiques de la seconde année n’ont pas permis d’obtenir defructification. Les dispositifs et outils mis au point doivent permettre un suivi génétique spatiotemporelde la population sur le long terme. / Agaricus bisporus, the button mushroom, is a saprophytic basidiomycete naturallyfound in cypress litter (Cupressus macrocarpa). It possesses different modes of reproduction. Tostudy their role in the spatio-temporal dynamics and in the evolution of the genetic diversity,experimental systems have been set up. Ten wild strains of Agaricus bisporus var. bisporus havebeen selected, from two french populations, on both phenotypic and genotypic traits. Themolecular evolution of their genomes has shown that, for the mitochondrial genome, group Iintron mobility was the main source of gene polymorphism. Low nucleotide (nt) substitutionrates were found in all types of mitochondrial sequences (mobile elements, genic and intergenicones). This stringent conservation of mitochondrial sequences, when compared with the high ntsubstitution rates of their nuclear counterparts, contrasts to what is widely accepted in fungalsequence evolution. Mating experiments between sporocarps and mycelia of wild strains wereconducted on compost in a room culture, to simulate the implantation of a natural population.Among the collected sporocarps, results indicate the occurrence of a parasexual Bullerphenomenon leading to hybrid strains of A. bisporus in room culture and putatively in the wild.In parallel, mycelia of the wild strains have been introduced in two experimental plots of cypress.Genotypic analysis of the sporocarps collected from these plots in the first year of introduction,failed to evidence a hybrid strain. The climatic conditions of the second year did not allowobtaining fruiting-bodies. The developed experimental systems and tools must allow a followingat the genetic level of the spatio-temporal evolution of the population.

This work presents a survey of blue-stain fungi found in Northwestern Ontario, characterization of a homing endonuclease gene within Grosmannia piceiperda and finally an examination of the introns and homing endonuclease genes found in the large ribosomal subunit gene in species of Ceratocystis; using molecular techniques and phylogenetic analysis, we studied the molecular evolution of these mobile genetic elements. The blue-stain fungi of Northwestern Ontario were identified based on phylogenic analysis of rDNA internal transcribed spacer region sequences. This data was supplemented with morphological characteristics of the fungal cultures. The second project was an examination of a LAGLIDADG homing endonuclease and its IC2 group I intron. This intron is uniquely positioned within the group I intron-encoded rps3 gene of the large subunit ribosomal RNA gene. The final chapter is an investigation of the large subunit ribosomal RNA gene in species of Ceratocystis. The 3’ segment of this gene contains several novel introns and homing endonuclease genes. There is also much diversity between strains despite their close relation on the rDNA internal transcribed spacer region phylogenetic tree. Further, our data also suggest that the single motif LAGLIDADG homing endonuclease of the rDNA mL1923 intron is likely to be an ancestor to other homing endonucleases in the area. The results of these studies demonstrate the role that these elements play in the genetic diversity observed in the blue-stain fungi.