In article <Cr8nAE.HHt at zoo.toronto.edu>, mes at zoo.toronto.edu (Mark Siddall)
wrote:
> 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
characters.
--
mike zwick
mezwick at ucdavis.edu
Department of Ecology and Evolution
Center for Population Biology
