Suppose that you've been hired by a firm interested in using bacteria to clean up organic solvents found in toxic waste dumps. Your new employer is particularly interested in finding cells that are capable of breaking a molecule called benzene into less-toxic compounds. Where would you go to look for bacteria that can metabolize benzene as an energy or carbon source? How would you design an enrichment culture capable of isolating benzene-metabolizing species?

The traditional tree of life (shown above) presents the three domains as distinct, monophyletic lineages. However, other hypotheses propose different views on the relationships among the Archaea, Bacteria, and Eukarya. In particular, the two-domain hypothesis—or eocyte hypothesis—is emerging as a well-supported alternative to the three-domain hypothesis. The eocyte hypothesis, illustrated below, suggests that eukaryotes evolved from eocytes (also known as the Crenarchaeota—a major lineage of the Archaea). Resolving the relationships among these ancient lineages is difficult, but it has profound implications on our understanding of the origin of eukaryotic cells.

Early ideas on the classification of life recognized all organisms as belonging to one of two fundamental lineages—prokaryotes or eukaryotes. Is this view compatible with either of the hypotheses illustrated here? Explain.
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Key Concepts
Three-Domain Hypothesis
Two-Domain Hypothesis (Eocyte Hypothesis)
Prokaryotes vs. Eukaryotes
The traditional tree of life (shown above) presents the three domains as distinct, monophyletic lineages. However, other hypotheses propose different views on the relationships among the Archaea, Bacteria, and Eukarya. In particular, the two-domain hypothesis—or eocyte hypothesis—is emerging as a well-supported alternative to the three-domain hypothesis. The eocyte hypothesis, illustrated below, suggests that eukaryotes evolved from eocytes (also known as the Crenarchaeota—a major lineage of the Archaea). Resolving the relationships among these ancient lineages is difficult, but it has profound implications on our understanding of the origin of eukaryotic cells.
Why are Archaea considered a monophyletic group according to the three-domain hypothesis?
a. Because this group includes all organisms except eukaryotes.
b. Because this group includes an ancestral population and all of its descendants.
c. Because all members of this group lack membrane-bound organelles.
d. Because this group evolved after the origin of bacteria.
The traditional tree of life (shown above) presents the three domains as distinct, monophyletic lineages. However, other hypotheses propose different views on the relationships among the Archaea, Bacteria, and Eukarya. In particular, the two-domain hypothesis—or eocyte hypothesis—is emerging as a well-supported alternative to the three-domain hypothesis. The eocyte hypothesis, illustrated below, suggests that eukaryotes evolved from eocytes (also known as the Crenarchaeota—a major lineage of the Archaea). Resolving the relationships among these ancient lineages is difficult, but it has profound implications on our understanding of the origin of eukaryotic cells.
The Bacteria and Archaea both include microscopic prokaryotes that lack membrane-bound nuclei. What criteria have led to the classification of these two groups as separate domains?
The traditional tree of life (shown above) presents the three domains as distinct, monophyletic lineages. However, other hypotheses propose different views on the relationships among the Archaea, Bacteria, and Eukarya. In particular, the two-domain hypothesis—or eocyte hypothesis—is emerging as a well-supported alternative to the three-domain hypothesis. The eocyte hypothesis, illustrated below, suggests that eukaryotes evolved from eocytes (also known as the Crenarchaeota—a major lineage of the Archaea). Resolving the relationships among these ancient lineages is difficult, but it has profound implications on our understanding of the origin of eukaryotic cells.
Other hypotheses for the tree of life present the Archaea as the ancestors to all other organisms. Sketch a phylogenetic tree that presents Bacteria and Eukarya as more closely related to each other than to Archaea, and that has Archaea as a sister group to Bacteria and Eukarya.
The traditional tree of life (shown above) presents the three domains as distinct, monophyletic lineages. However, other hypotheses propose different views on the relationships among the Archaea, Bacteria, and Eukarya. In particular, the two-domain hypothesis—or eocyte hypothesis—is emerging as a well-supported alternative to the three-domain hypothesis. The eocyte hypothesis, illustrated below, suggests that eukaryotes evolved from eocytes (also known as the Crenarchaeota—a major lineage of the Archaea). Resolving the relationships among these ancient lineages is difficult, but it has profound implications on our understanding of the origin of eukaryotic cells.
Evaluate this statement: According to the two-domain hypothesis, all members of the domain Archaea are prokaryotes and therefore lack membrane-bound nuclei.
The traditional tree of life (shown above) presents the three domains as distinct, monophyletic lineages. However, other hypotheses propose different views on the relationships among the Archaea, Bacteria, and Eukarya. In particular, the two-domain hypothesis—or eocyte hypothesis—is emerging as a well-supported alternative to the three-domain hypothesis. The eocyte hypothesis, illustrated below, suggests that eukaryotes evolved from eocytes (also known as the Crenarchaeota—a major lineage of the Archaea). Resolving the relationships among these ancient lineages is difficult, but it has profound implications on our understanding of the origin of eukaryotic cells.
What other types of evidence or features might be used to ascertain whether the tree of life is best represented according to the three-domain or the eocyte hypothesis?
