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Molecular systematics - is it all rubbish?

higgins at ebi.ac.uk higgins at ebi.ac.uk
Wed Jun 14 09:49:15 EST 1995

In article <3rldgd$f10 at studium.student.umu.se>, Agneta Guillemot <Agneta.Guillemot at historia.umu.se> writes:
> Most people have never conceived an original idea in their 
> entire life. There is no difference between the man on the 
> floor in a factory, a schoolteacher or a scientist at a 
> university. In a normal job you don't need original ideas. 
> But at the university you do. With the explosive increase 
> in research in different fields the problem becomes acute. 
> It is usually solved by inventing "new methods" i.e.  
> intellectual fashion. Molecular systematics is one of those 
> fashions.  
> It solves many problems in biological research. Just sequence  
> a gene in a few organisms, run the sequences through a computer,  
> out comes a parsimony tree, and you have material for an essay. 
> The material to work with is almost indefinite. From beetles to  
> hydras, from humans to algae, it just goes on and on. 
> But it is'nt koscher. Why? There is one vital factor that molecularr 
> systematicists never seem to take into account in their work:  
> Different species evolve at different rates at different times. 
> Evolution is'nt just a clockwork that goes on and on. What if,  
> for example, the taxa you want to exclude from a grouping of  
> organisms, that you have just discovered, have evolved much faster 
> at some previous time? It will be different, and you will jump 
> to the wrong conclusions.  
> Let's face it: Evolution in a species slows down and speeds up at 
> different times. Some species are left in the backwater, others 
> evolve fast in new evolutionary niches. There is no way of knowing 
> what happened when. The molecular clock does'nt exist! 

Ludvig: this is just hand-waving!!  All that matters with molecular
clocks is whether or not they exist.  Whether or not you THINK they
should exist (or wish that they did not) is not relevant.   When you
actually look at the data, the amazing thing about sequence evolution is
that it often is just "a clockwork that goes on and on".  You can
find systematic variation between organisms, proteins, organelles etc. etc.
with regard to how fast the sequences change but you can also find remarkable
degrees of constancy (within statistical errors).   Whether or not
the morphology changes in a similar manner is not relevant.  

Folks often then get angry and say "but why should there be a clock
in the first place"??  One answer comes from Kimura and the neutral theory
of evolution but that is a different can of nematodes (and annelids I
suppose).  Again, all that matters from the point of view of reconstructing
phylogenies and estimating divergence dates is what actually happened.

> There is only one school of systematics whose theorethical basis 
> is untouchable. It is of course cladistics. If you apply cladistic 
> methodology to sequence data you come to the right, unquestionable 
> conclusions. 

Amazing!!!!.... methods that guarantee the right answer???? ...... every time??
Wow, gimme some of that!!!!  And there I was thinking the reconstruction of
phylogenies from sequences was a tricky business.  

> Most molecular systematicists seem to ignore cladistics. 

Actually not true.  If by cladistics, you mean "use parsimony", the field
is pretty even in terms of what people use.  Some people even have the
audacity to try some different methods out, just in case it helps them
understand their data sets better.  If by cladistics, you mean using
cladistic logic as suggested by Hennig, this is also valuable and useful
and used by molecular tree makers.  

What about YOU??? Have you ignored
the entire literature on molecular evolution???  

> I hope this will change. 
> Thank you for your attention! 

You are welcome ;-}
Des Higgins

> Ludvig Mortberg

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