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We easily recognize trees, mushrooms, and insects as plants, fungi, and animals, respectively. But there is a dazzling assortment of other eukaryotic organisms—mostly microscopic—that do not fit into these three groups. Eukaryotes that are not plants, animals, or fungi have traditionally been called protists. But phylogenetic analyses reveal that many of the groups we commonly refer to as protists are not, in fact, closely related. Thus the term “protist” does not describe a monophyletic group, but is a convenience term for “all the eukaryotes that are not plants, animals, or fungi.”

The unique characteristics of the eukaryotic cell lead scientists to conclude that the eukaryotes are monophyletic, and that a single eukaryotic ancestor diversified into the many different protist lineages as well as giving rise to the plants, fungi, and animals. As we saw in Key Concept 25.1, eukaryotes are a specialized group of archaea that acquired a cell nucleus. The mitochondria and chloroplasts of eukaryotes, however, are clearly derived from bacterial lineages (see Figure 25.1).

Biologists have hypothesized that the origin of eukaryotes from a specialized archaean ancestor was followed by the endosymbioses with bacterial lineages that led to the origin of mitochondria and chloroplasts. Some biologists prefer to view the origin of eukaryotes as the fusion of lineages from the two prokaryote groups. This difference is largely a semantic one that hinges on the subjective point at which we deem the eukaryote lineage to have become definitively “eukaryotic.” In either case, we can make some reasonable inferences about the events that led to the evolution of a new cell type, bearing in mind that the environment underwent an enormous change—from low to high availability of free atmospheric oxygen—during the course of these events.