Abstract 171 8.1 Introduction 172 8.2 Red Algal and Green Plant Origins as a Case Study for Genomic Analyses 173 8.3 Do Genomic Studies Provide Clear Support for a Relationship between

Green Plants and Red Algae? 173 8.4 Do Mitochondrial Genome Investigations Support a Red-Green Relationship? 174 8.5 Molecular and Biochemical Processes as Shared-Derived Characters 176 8.6 Major Innovations in How the Genome Is Expressed 177 8.7 An Overhaul of RNA Polymerase II Transcription? 178 8.8 Control of the Cell Cycle and Cellular Differentiation 181 8.9 Homologies in the Mechanisms of Homeotic Development 182 8.10 Conclusions 183 Acknowledgment 184 References 184

The ongoing revolutions in biotechnology and genomics are producing an ever-growing body of molecular sequence data for comparative evolutionary study. As more and more genes become available from diverse organisms, trees constructed from sequence-based phylogenetic analyses hold the promise of strongly supported clades of major eukaryotic taxa, and thereby the hope of solving a number of long-standing controversies over ancient evolutionary relationships. This chapter examines some of the assumptions and potential problems inherent to broad-scale sequence-based phylogenetic analyses, particularly the potential for circularity when these analyses are used both to formulate and to test a given evolutionary hypothesis. In addition to direct sequence comparisons, enormous quantities of molecular information are generated from genomic studies, and evolutionary researchers face challenges in developing new methodologies that can complement and test the results of traditional phylogenetic investigations. The exploration of complex, multigenic and coadapted functional systems is one such approach. For example, differences have begun

to emerge among eukaryotes in mechanisms for controlling gene expression, the cell cycle and cellular differentiation during ontogenetic development. Such complicated systems, although not immediately apparent at the phenotypic level, are neither likely to be the result of evolutionary convergence nor are they easily lost once fully integrated into the molecular machinery of a given lineage. As such, they hold great promise as clearly defined, sharedderived characters that can be used to infer monophyletic relationships among major eukaryotic taxa.