Archaea as ...

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… the “missing link” between Bacteria and Eukarya

The Tree of Life, rooted, showing the Archaea as primitive relatives of the eukaryotes : Norm Pace

Despite the fact that all of life on Earth is alike in most ways, Bacteria and Eukarya do differ in significant ways. Traditionally, it is assumed that where Bacteria and Eukarya differ, the bacterial version is primitive, because Bacteria are generally simpler than are Eukarya. But simple and primitive are not synonymous, and so this is a bad assumption. What is need is a tie-breaker, an intermediate third distinct phylogenetic group, and the more primitive the better. Such intermediate groups are often called “missing links”; this term is a left-over of the pre-Darwinian “chain of being” view discussed in Chapter 2. If a trait is common to two of the three phylogenetic groups, then presumably it was also present in the common ancestor of those two groups. Because the last common ancestor is apparently on the branch between the Bacteria and Archaea/Eukarya, any trait common to Bacteria and either Archaea or Eukarya probably existed in the last common ancestor.

… a deep branch of Eukarya

In order to understand eukaryotic complexity, it would be useful to have a group of primitive organisms that diverged from the rest of the Eukarya early in their evolution. Properties shared by such organisms and more complex Eukarya, but not by Bacteria, would presumably represent the unique traits of the deep ancestor of Eukarya. If these organisms were also relatively simple, they could tell you a lot about the core functionalities of eukaryal cells, unobscured by all the bells and whistles that were added later in their evolutionary history. Where might you look for such an organism? As you can see from the rooted tree above, these organisms are already known - they are the Archaea. For this reason, the Archaea are often studied for their eukaryal-like processes that are simpler and easier to understand than the homologous counterparts in plants, animals or fungi. Examples include RNA polymerase (Archaea have a single RNA polymerase homologous to eukaryal RNA polymerase II), small nucleolar ribonucleoproteins (snoRNPs, involved in RNA modifications), and DNA packaging (Archaea have relatively simple nucleosomes). In addition, archaeal complexes are often easier systems to study using standard biophysical processes such as X-ray diffraction, because of the extreme stability of thermophilic or halophilic complexes.

... reflections of early life on Earth

The Archaea are, as a group, more primitive than are either the Bacteria or Eukaryotes. Primitive Archaea (e.g. Thermococcus, Pyrococcus) are similar to primitive Bacteria (e.g. Aquifex) in being thermophilic sulfur/hydrogen metabolizers, and so this is probably the general phenotype of the last common ancestor, and perhaps primitive life in general. Although modern Archaea are not the ancestors of other modern organisms, they probably do resemble in many ways these ancestral life forms. In may be that they haven't changed much because of their thermophilic environment - evolutionary drift in genes is much more constrained in thermophiles than in mesophiles, because their macromolecules are less tolerant of minor perturbations that are allowed in molecules than function at lower temperatures. For example, most single changes in an RNA-encoding gene will create a mismatch in the secondary structure of the RNA - no big deal for a mesophile, that can tolerate the defect with minimal decrease in fitness until a compensatory change occurs. But the mismatch is a big problem for a thermophile because of the thermal destabilization it causes, making it much less likely that a compensatory change will occur before the decrease in fitness leads to extinction.