Introduction

    The origin of the eukaryotic cell was a milestone in the evolution of life. Although eukaryotes use the same genetic code and metabolic processes as prokaryotes, eukaryotes' higher levels of organizational complexity has permitted the development of truly multicellular organisms. Without eukaryotes, the world would lack all mammals, birds, fish, invertebrates, mushrooms, plants, and complex single-celled organisms. Only the bacteria, or prokaryotes, would remain.

The nucleus is the defining character for which eukaryotes are named (eu = good or true, karyote = nut or kernel, as in nucleus). The nucleus is intimately connected with the origin of eukaryotes since a nucleus is present in all eukaryotes, but not in prokaryotes. As part of their cellular complexity, eukaryotes contain an extensive system of internal membranes that enclose the nucleus and define organelles. This compartmentalization has required a number of unique eukaryotic innovations.     Many questions concerning the prokaryotic origins of nuclear genes are presently incompletely understood, and current ideas concerning their origins are changing rapidly with the advent of completely sequenced genomes. The most widely known view holds that eukaryotes are derived from an evolutionary ancestor common to all Archaea. The eocyte view, favored by our lab and others, differs from this view in two ways. It posits that the Archaea are not a true (monophyletic) evolutionary group because a major hyperthermophilic group, the eocytes (crenarchaeotes), is phylogenetically closer to the eukaryotes. Second, it is becoming clear that many tree reconstruction artifacts, related to the difficulty of aligning RNA sequences and analyzing RNAs, make analysis of ribosomal sequences difficult and frequently unreliable.

    It is becoming increasingly evident that eukaryotic genomes have significant contributions from eubacteria. Even the mechanism by which the nucleus was formed may have involved an endosymbiosis between two prokaryotic organisms.