Abstract 189 9.1 Introduction 189

9.1.1 Organism, Gene and Genome 190 9.1.2 Taxonomy and Phylogeny Based on Organisms and Genes 190 9.1.3 Genomes as a Basis for Phylogenetic Inference 191

9.2 Methods 194 9.3 Results and Discussion 195 9.4 Envoi 202 Acknowledgment 203 References 203

The classification of organisms has value beyond taxonomy as it can reveal their natural relationships and evolutionary history. Morphological and physiological traits have largely given way to genetic characterization in determining phylogeny, though the gene might not always represent the organism. The problem goes beyond statistical concerns as real biological processes can muddle or shuffle inferred relationships. The collective of genes within a genome might better represent the organism if the goings-on of individual genes do no more than add unbiased noise to an otherwise resilient signal. We explore such genomebased phylogenic methods and find that genome trees largely resemble the standard small subunit ribosomal RNA (SSUrRNA) tree, suggesting that genomes are suitable proxies for the organisms that contain them.