Punctuated equilibrium and molecular clocks?

Dr. Peter Gegenheimer PGegen at UKans.nolospamare.edu
Fri Sep 4 18:37:39 EST 1998

On Wed, 2 Sep 1998 15:16:45, Johnjoe McFadden <j.mcfadden at surrey.ac.uk> wrote:

> Punctuated equilibrium and molecular clocks?
> The punctuated equilibrium hypothesis of Gould and Eldridge, in which
> evolution is proposed to go through long periods of stasis interspersed
> with bursts of rapid evolution, is of course related to the fossil
> record. However, periods of rapid evolution should also leave their
> trace in molecular clocks. 
> Does the phylogenetic analysis of protein gene sequences suggest that
> their evolution has in some cases been episodic? I guess the evidence,
> if it existed, would come from comparison of sequence divergence of a
> protein like globin with a molecular clock sequence (e.g. ribosomal RNA)
> for the same group of species. Is their any evidence that over
> geological periods of time (measured by the clock sequence) the protein
> undergoes episodic bouts of evolution?

Punctuated equilibrium is almost certainly driven by large-scale genome and 
chromosome rearrangements which will not be reflected in the sequences of 
individual genes. Rather, it is the organization & spatial/temporal patterns of
gene expression which vary, driven perhaps by the relocation of epigeneitc 
regulation (e.g. DNA methylation or protein binding). As you can see, this is 
the hard-core McClintock line, and I think it will prove to be right. 

Sequences of core enzymes, such as rRNA (the catalytic component of the 
ribosome), cannot vary greatly over time without losing function. Sequences 
involved in developmental regulation and external form of an organism can vary 

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