"Logic of Cladistics"

Stephen W. Schaeffer sws4 at psu.edu
Sun Jun 12 15:07:25 EST 1994


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

>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...

    Here's a thought problem, suppose one could sequence the entire genome 
for one's favorite group of organism's,  make reasonable alignments of all 
the data, and had a computer large enough to handle any phylogenetic 
analysis that you pleased to conduct.  Would the resulting tree(s) yield the 
'true' species phylogeny?  I think that phenetic and cladistic methods would 
generate a tree, but the meaning would be hard to interpret.



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