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"Logic of Cladistics"

Mike Zwick mezwick at ucdavis.edu
Sun Jun 12 21:53:04 EST 1994

In article <Cr8nAE.HHt at zoo.toronto.edu>, mes at zoo.toronto.edu (Mark Siddall)

> On this thread, and more pertinent to this group perhaps, I am increasingly
> concerned with a tendency to crank off sequences, fire them into some
> phylogenetic software like PHYLIP, PAUP, MEGA or Hennig86 without
> full understanding of what's going on.  The argument can be made that
> it is an awkward, if not dangerous, thing to simply pump out a
> parsimony tree, a Fitch-Margoliash distance tree, a UPGMA, and whatever
> and publish them all side by side. There appears to be in some arenas
> a fundemental ignoring of the issues, as though phylogenetic investigation
> was so-much recipe work.  It is not.  There are issues that need to be
> addressed by all practitioners in their analyses regarding multiple
> trees, assumptions, defensibility of a chosen approach, and so much
> more...
> Just a thought.
> Mark

And furthermore, I don't really think it is just a problem of DNA sequence
data.  How much do we really know about the evolution of one's favorite
taxonomically informative morphological character?  I would guess probably
less than the evolution of DNA sequences (especially coding sequences where
alignment is not a problem).  Fundamentally, when people make tree from DNA
sequences, they are making hidden assumptions about how molecular evolution
proceeds.  I think the same probably holds true for morphological

mike zwick
mezwick at ucdavis.edu
Department of Ecology and Evolution
Center for Population Biology

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