Primitive thermophilic Bacteria

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These two phyla represent the best known of several small groups of organisms that are both primitive and deeply branching in the bacterial tree.

They are primitive in that they have changed less than other organisms since their common ancestry, at least in terms of 16S rRNA sequences; the distance from the common ancestor to the modern sequences is shorter for them than for other Bacteria. This does not mean that they are the ancestors of other Bacteria, or that they are any less complex.

They are deeply branching in that their branches connect to the bacterial tree closer to the root than do the other branches. This statement, that these groups are “deeply branching”, comes with two caveats. The first is that it presumes that the bacterial phyla represent distinct “kinds” of creatures regardless of how these phyla are related to one another, in the same way that animal phyla are different “kinds” (evidenced by differences in basic body plan) regardless of the details of how these phyla are related one to another. This is related to the difference between evolutionary rates and modes, and implies that each phylum emerged during a distinct transition. If this is not the case, then “deeply branching” becomes a relative term only; Aquifex and Thermotoga are deeply branching with respect to, for examples, the cyanobacteria, proteobacteria, or Gram-positive Bacteria, but E. coli could be viewed as a deeply-branching mesophile from the perspective of Aquifex and its relatives.

The second caveat to the view that these phyla are deeply branching comes from uncertainties inherent in phylogenetic trees, particularly as the result of unequal evolutionary rates. This can result in an artifact in trees known as “long branch attraction”, in which long branches (groups with higher evolutionary rates) are “pushed” toward each other as the result (in part) of underestimating the actual evolutionary distance between them. In the case of the bacterial tree, this may result in the artifactual clustering of the longer branches, excluding the shortest branches into the deeper parts of the tree. One observation in favor of this view is that as more and more diverse sequences are included in the bacterial tree, the more all of the bacterial phyla come closer to seeming to emerge from a single point of radiation.

Even with these caveats in mind, however, it does seem that the deepest branches of the bacterial tree are both thermophilic and primitive. The fact that they are primitive with respect to 16S rRNA sequences may represent only a lower tolerance at high temperatures for the transient non-Watson-Crick base pairs that are the inevitable intermediates of evolutionary change in RNA structures, and may not represent primitiveness in other features of these organisms.