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Molecular clock? [switch to Fixed Pitch Font to see the beautiful trees]

Andrew Rambaut andrew.rambaut at zoology.oxford.ac.uk
Mon Dec 8 11:08:56 EST 1997


>So what does the data say? Sometimes the RRT gives a positive result,
>but just as often it doesn't. For the clock to exist it should always
>give positive result. The clock doesn't exist.

Sorry to be pedantic but, actually a positive RRT rejects the clock.
Secondly, you are being extremely naive in your understanding of current
theory on the subject. Certainly the phrase 'clock' promotes 
misunderstanding
by suggesting a universal non-stochastic process i.e. clock-like. There 
are
many reasons why we might expect departures from a constant rate model of
molecular evolution particularly between divergent groups of animals, and
in genes under selective pressures. Even under neutral theories of 
molecular
evolution, we would expect differences in rate (generation time, etc.). 
This
is all well discussed in the recent literature. The clock is not a 
biological
dogma, just an observation that over time, genes tend to accumulate 
mutations 
and if one is careful and rigorous (particulaly in the estimation of 
confidence
intervals), one can use this observation to obtain estimates of times of 
divergence of homologous genes.

Andrew.

======================================================================
  Andrew Rambaut,             EMAIL - Andrew.Rambaut at zoology.ox.ac.uk
  Zoology Department,           WWW - http://evolve.zoo.ox.ac.uk/
  University of Oxford,         TEL - +44 1865 271272
  South Parks Road, Oxford, UK  FAX - +44 1865 271249
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