In article <sws4.3.2DFB6AFD at psu.edu> sws4 at psu.edu (Stephen W. Schaeffer) writes:
>> 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.
No, it would not neccessarily be the 'true' tree. It would definitely be the
best tree based on sequence data. Follow-up questions would be what do
morphological data tell you? What does trasnversional weight tell you?
What about changing the code into amino acids? what about proteins'
tertiary structure like helices and sheets? And on and on.
Besides, bases can only change into 3 alternatives. The fourth change
is guaranteed to be misleading.
This does not mean the results are hard to interpret. It does mean that
the interpretation must be undertaken with great care and thought. It
should mean sleepless nights and intellectual trauma.
Mark E. Siddall "I don't mind a parasite...
mes at vims.edu I object to a cut-rate one"
Virginia Inst. Marine Sci. - Rick
Gloucester Point, VA, 23062