This thesis presents a novel approach to reconstructing ancestral genomes of a number of descendant species related by a phylogeny. Traditional methods face challenges due to cycles of whole genome doubling followed by fractionation in plant lineages. In response, the thesis proposes a new approach that first accumulates a large number of candidate gene adjacencies specific to each ancestor in a phylogeny. A subset of these which to produces long ancestral contigs are chosen through maximum weight matching. The strategy results in more complete reconstructions than existing methods, and a number of quality measures are deployed to assess the results. The thesis also presents a new computational technique for estimating the ancestral monoploid number of chromosomes, involving a "g-mer" analysis to resolve a bias due to long contigs and gap statistics to estimate the number. The method is applied to a set of phylogenetically related descendant species, and the monoploid number is found to be 9 for all rosid and asterid orders. Additionally, the thesis demonstrates that this result is not an artifact of the method, by deriving a monoploid number of approximately 20 for the metazoan ancestor. The reconstructed ancestral genomes are functionally annotated and visualized through painting ancestral projections on descendant genomes and highlighting syntenic ancestor-descendant relationships. The proposed method is applied to genomes drawn from a broad range of plant orders. The Raccroche pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree, and constructs chromosomes by counting the frequencies of ancestral contig co-occurrence on the extant genomes, clustering these for each ancestor, and ordering them. Overall, this thesis presents a significant contribution to the field of ancestral genome reconstruction, offering a new approach that produces more complete reconstructions and provides valuable insights into the evolutionary process giving rise to the gene content and order of extant genomes.

Vegetation science, like any science, uses classification to organize knowledge about plants and plant communities. Classification is helpful for understanding how different plant communities relate to one another and their environments, for facilitating further studies of vegetation, and for conservation. To familiarize onself with vegetation of a large area, it is very convenient and efficient to begin with a few general units, such as plant orders rather than with many very detailed units, such as plant associations and subassociation. We offer such an approach and think that the information given in this series will be sufficient to assign any forested coastal community to one the orders or suborders. In spite of a history of vegetation studies in British Columbia, there has not yet been any attempt to develop a comprehensive hierarchical classification of plant communities for the province. As the culmination of fifty years of detailed surveys carried out by V.J. Krajina and his students, the Ecology Program Staff of the BC Forest Service, and other workers, we used tabular and multivariate analyses of 3,779 sample plots established in natural, old-growth, submontane, montane, and subalpine forest communities in coastal BC to develop a hierarchy of vegetation units according to the methods of biogeoclimatic ecosystem classification.