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Life in its entirety constitutes one of the great intellectual achievements of the late twentieth century.
    The first thing to notice about the tree is that it contains three major limbs, termed domains by Woese. Two of the domains are unsurprising: the eukaryotes and the bacteria fall on distinct branches. The third, however, came as a shock when Woese and then postdoctoral fellow George Fox proposed it in 1977. The Archaea are prokaryotic in cell organization, and for many years the organisms on this branch had been thought of (when they were thought about at all) as metabolically unusual bacteria. But comparison of ribosomal RNA genes suggests that these microbes are fully as distinct from the conventional bacteria as bacteria are from eukaryotes. What’s more, the tree indicates that archaeans are actually more closely related to the eukaryotes than they are to bacteria. (In phylogenetic discourse, closeness of relationship reflects recency of common ancestry; it is a statement about genealogy, not similarity.)
    The complete genome (genetic information encoded in DNA) of the archaean Methanococcus janaschii was published in 1996, revealing that this microbe shares just 11–17 percent of its genes with bacteria whose genomes have been sequenced. More than 50 percent of its genes are unknown in either eukaryotes or bacteria, confirming that archaeans are distinctly different from organisms in the other two domains. Archaeans do, however, have some important characters in common with bacteria, such as (most obviously) prokaryotic cell organization, the molecular structure of the ribosome, and the arrangement of genes on a single circular chromosome. Equally, on the other hand, archaeans share attributes such as molecular details of DNA transcription and susceptibility to specific antibiotics with eukaryotes. And there are still other traits thatbacteria and eukaryotes share to the exclusion of Archaea—prominent among these is the nature of the cell membrane.

    Figure 2.1. The Tree of Life, a depiction of the genealogical relationships of living organisms, based on sequence comparisons of genes that code for RNA in the small subunit of the ribosomes found in all cells. Note the three principal branches, made up of Bacteria, Archaea, and Eucarya. Branch lengths indicate degree of difference among gene sequences; because genes can evolve at different rates, however, this does not necessarily translate into time. Bacterial groups with photosynthetic members are highlighted by clear boxes; methanogenic archeans fall within the shaded box. Heavy lines denote hyperthermophiles—groups of organisms that live at high temperatures. (Adapted from a depiction of the tree by Karl Stetter)
    How then do we tell who is more closely related to whom? Put another way, where do we place the root on this tree? A three-branched tree can’t be rooted by conventional means, and a bit more consideration of character distributions shows why. Features such as ATP or the genetic code that are shared by all three domains carry no information on genealogical relationships, but permit inferences about the nature of the last common ancestor of the three branches. In contrast, attributes such as cell wall composition that are distinct in each limb provide no information on either genealogy or ancestral features. Characters shared by two of the three domains would appear to offer better prospects for tree building, but such distributions can be explained equally well in several different ways. For example, if we assume that membranes composed of fatty acids were present in the last common ancestor, then we can posit that this trait was retained in bacteria and eukaryotes but replaced by isoprenoid-based membranes along the road to the Archaea. Alternatively, we can assume that membranes built from isoprenoids are ancestral, but were swapped for fatty-acid membranes in the common ancestor of bacteria and eukaryotes. Like the first alternative, this tree