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Molecular systematics - is it all rubbish?

Joe Felsenstein joe at evolution.genetics.washington.edu
Thu Jun 15 19:36:21 EST 1995

In article <3rldgd$f10 at studium.student.umu.se>,
Ludvik Mortberg <Agneta.Guillemot at historia.umu.se> wrote:
(in newsgroup bionet.molbio.evolution).

>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! 
>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. Most molecular systematicists seem to ignore cladistics. 
>I hope this will change. 

The clock is better than you think, better the closer the relationship of
the species you study.  But let me address the more general issue.

Very few systematic methods in use depend on different lineages
evolving at the same rate.  Distance matrix methods don't assume it,
for the most part.  Likelihood methods don't assume it.  
Lake's "evolutionary parsimony" doesn't either.  And parsimony doesn't.

So this argument is a "straw man".

If by "cladistics" you mean parsimony, no, it doesn't always come to
"the right, unquestionable conclusions".  Some fellow in the late
1970's showed that it can be inconsistent, converging on the wrong
answer, under certain conditions.

If you mean using only states that you are sure are unique and
unreversed, well, those are generally not available. There may be some,
but their recognition is not a trivial question.

Joe Felsenstein         joe at genetics.washington.edu     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360

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