is rapidly emerging, namely the use of phylogenetically based inference in systems biology. Before the genomic revolution, research questions were typically addressed within a single model organism, with only occasional comparative studies when similar information was available for another organism. These comparisons were made between distantly related taxa, and the evolutionary implications were rarely mentioned or taken into account. The increasing importance of comparative analysis is evident in the growing proportion of new prokaryotic genome projects that have been chosen primarily because of their phylogenetic relationship to model organisms, such as Escherichia coli and Bacillus subtilis and their corresponding related taxa. This same trend is occurring for eukaryotes. Some prominent examples are the multiple Saccharomyces genome projects and those of other ascomycote fungi, the several Plasmodium projects and other genome initiatives for apicomplexan taxa, the numerous Caenorhabditis and other nematode genome projects, the multiple Drosophila and arthropod genome projects, and the large number of primate and mammalian genome projects.

The sampling of the metazoan tree, and in particular of the chordate branch, was undertaken primarily due to the usefulness of the genomes in understanding human biology. However, this larger genomic dataset is already providing a powerful tool for comparative analysis and more accurate evolutionary inference. Deeper divergences in the Metazoan tree have become the target of major scrutiny due to the interest in comparative developmental genetics (Fig. 17.1B). Based on molecular phylogenies, the bilaterian phyla have been rearranged into three large clades, deuterostomes, lophotrochozoans, and ecdysozoans, these last two being sister taxa inside the protostome clade. At present, there is still debate regarding the placement of nematodes in the tree (i.e., the Ecdysozoa vs. Coelomata hypotheses) because analysis of genomic data currently challenges the placement of Caenorhabditis elegans as an ecdysozoan (Dopazo et al., 2004; Wolf et al., 2004).

In addition to the traditional developmental model organisms, genomes from unrepresented protostome (Annelida, Platyhelmintha, and Mollusca) and basal phyla are now being sequenced (Porifera, Placozoa, and Cnidaria) (www.jgi.doe.gov/sequencing/cspseqplans.html). Finally, another node in the tree of life that has gained recent interest is that of the choanoflagellates, a unicellular sister group to metazoans (King, 2004).