Prokaryote Systematics: The Evolution of a Science

Prokaryote Systematics: The Evolution of a Science: "The most useful molecular chronometers actually are molecules like the ribosomal RNAs - molecules with universal, constant, and highly constrained functions that were established at early stages in evolution, functions that are not affected by changes in the organism's environment (except for changes in basic physical parameters such as intracellular pH and temperature). (A strong indicator of the constancy of rRNA function is the near constancy of the molecule's secondary structure within each of the primary kingdoms, and the approximate constancy that holds even between kingdoms [Gutell et al., 1985]). Because rRNAs are large molecules, they contain considerable information; their size also makes them less erratic chronometers than smaller molecules (Woese, 1987). Moreover, rRNAs are easy to isolate in relatively large quantities; they seem not to be subject to lateral gene transfer; and they can be sequenced directly (without resort to gene cloning).

The fact that a precisely functioning molecule such as RNA is under strict functional constraints is both an advantage and a disadvantage. The advantage lies in the constancy of the constraints on the various positions in the sequence and the fact that some positions change far more slowly than others; this last makes the molecule like a clock that includes both a second hand and a calendar—i.e., it can measure a wide range of time intervals. The disadvantage is that the stringent constraints lead to more (local) sequence convergence than otherwise, and the vast differential in rates at which positions change makes analysis more problematic than it would be for a uniform rate situation. (Another of its advantages would appear to be that RNA is a “nonlinear” chronometer and so is potentially capable of distinguishing rapidly vs. slowly evolving lineages, and, therefore, localizing the root of a tree without the need to resort to the use of outgroup sequences [Woese, 1987]).

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