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Molecular clocks and the tree of life

L.A. Moran lamoran at gpu.utcs.utoronto.ca
Sun Sep 15 07:55:46 EST 1991

The question of rates of molecular evolution is a vexing one. Are there 
really changes in the rate with time or in different lines? If the rate
of evolution is not constant then it is possible to argue that some living
organisms are more primitive than others.

As an example of the current problems consider the following diagram which
is discussed in a recent review in one of the most prestigious and popular
journals of molecular and cellular biology (-: (-:. Pace (1991) makes the 
claim that the archaebacteria are "primitive" organisms relative to species 
in the other two kingdoms because the rate of evolution of ribosomal RNA genes
in archaebacteria (A) is slower than the rate in eubacteria (B) or in
eukaryotes (E). Because archaebacteria are "primitive" he claims that the
common ancestor of all life was chemosynthetic and thermophilic, as are
many of the archaebacterial species.

      B                 E       Evolution of ribosomal RNA sequences in
      |                 |       the three kingdoms. The length of the
      |                 |       vertical lines represents the number 
      |                 |       differences (ie. nucleotide substitutions).
      |                 |       Thus there have been fewer changes in the
      |        A        |       line leading to archaebacteria (A) than
      |        |        |       in the lines leading to eubacteria (B)
      |        |        |       or eukaryotes (E).
      |        |        |
      |        ----------
      |             |
      |             |
      |             |
       common ancestor

I do not believe that Pace's data is correct. The archaebacteria may have
evolved at the same pace (pun indended) as the other groups. When other
genes are examined it is not obvious that the archaebacterial lines are
shorter. This could be an artifact of the ribosomal RNA sequences.

In addition I do not follow the logic of Pace's argument even if the diagram
is correct. It is just as logical to propose that the archaebacteria arose 
from a heterotrophic ancestor that lived in a temperate environment and that 
there was a slow down in the rate of evolution following this divergence. 

Furthermore, the logic used in Pace's argument is similar to that which gives
rise to the description of coelacanths as "fossil" organisms. In this case 
the observation is that one set of characteristics (external morphology) has 
not changed much in the past million years. The conclusion is that all other 
characteristics have also not changed. Therefore the fish is a "living fossil".
(The one characteristic in archaebacteria is the sequence of rRNA. Who knows
whether ALL characteristics have also evolved slowly?)

It may be true that the common ancestor lived in hot water and avoided oxygen
but there is no support for this hypothesis from molecular data (IMHO). 
I remain skeptical of conclusions that rely on the existance of differential
rates of evolution, especially when only one gene has been examined.

Laurence A. Moran (Larry)
Dept. of Biochemistry

Pace, N. R. (1991) Origin of Life - Facing Up to the Physical Setting
   Cell 65, 531-533. 

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