is providing profound insight into the tree of life at all levels of divergence (Fig. 17.1A). It is thus not surprising that understanding phylogenetic relationships is a prevalent research goal among not only evolutionary biologists but also all scientists interested in the organization and function of the genome. New genome sequences and analysis methods are helping improve our understanding of phylogeny, and at the same time improved phylogenies and phylogenetic theory are generating a better understanding of genome evolution. Currently however, the level of genome sequencing for different branches of the tree of life is far from equivalent. Prokaryotic genome projects are abundant, mainly due to their small genome sizes, with >200 genomes already published and at least 500 currently in progress (www.genomesonline.org). In contrast, <300 eukaryotic genomes are either finished or in progress (www.genomesonline.org). Nevertheless, these data are starting to have a major impact on our understanding of eukaryotic evolution.
These new genomic data have informed our understanding of phylogenetic relationships, and the emerging consensus topologies are adding new insight to the small subunit ribosomal RNA phylogenies. For example, the topology of the ribosomal eukaryotic tree has been recently redrawn with the use of genomic signatures that place the root of all eukaryotic life between two newly uncovered major clades, Unikonts and Bikonts (Fig. 17.1A). Unikonts, which contain the heterotrophic groups Opisthokonta and the Amebozoa, share a derived three-gene fusion of enzymeencoding genes in the pyrimidine synthesis pathway (Stechmann and Cavalier-Smith, 2003), whereas Bikonts, which contain the remaining eukaryotic clades, share another derived gene fusion between dihydro folate reductase and thymidine synthase (Stechmann and Cavalier-Smith, 2002). All photosynthetic groups of primary and secondary plastid symbiotic origins are now thought to be within the Bikonts. Although the animal, fungal, and plant lineages are the most widely represented in terms of genome initiatives (Fig. 17.1B–D), it is significant that multiple protistan genome projects have also been initiated by the interest of diverse scientific communities, including parasitologists (Gardner et al., 2002), plant pathologists (Waugh et al., 2000), oceanographers (Armbrust et al., 2004), and evolutionary biologists (www.biology.uiowa.edu/workshop).
As more whole-genome projects are being completed, postgenomic biology is also providing insight into the function of biological systems by the use of new high-throughput bioanalytical methods, information technology, and computational modeling. This new revolution in biology has become known as systems biology (Hood, 2003). In addition to shifting approaches to biological research from reductionist strategies to pathway- and system-level strategies (Hartwell et al., 1999), another paradigm