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.
