Re: Parsimony

["Thomas R. Holtz, Jr." <th81@umail.umd.edu>]

Stan Friesen wrote:

>I would prefer to treat such "nearly most parsimonious" cladograms on the
>same footing as the single most parsimonious one.  They should either all
>be reported, or some sort of consensus cladogram should be generated from
>them.  Unfortunately most of the cldogram generating programs I have access
>to cannot deal with this - they can only make consensus cldograms from sets
>of *equally* parsimonious cladograms. [I simply cannot get "the set of
>cladograms within N steps of most parsimonious" out of any software I can
>get runnning on my home system].

PAUP can do this.  One option: find the number of steps in the most
parsimonious tree(s), then click on the option "Save all trees of length:"
and input a number one, two, five, or whatever larger.

Also, on the "Exhaustive Search" option, you can get a histogram of the
spread of tree lengths as one of the standard option.

>Will somebody give me a grant for developing a test for statistical
>significance in step count differences? :-)

Try checking out the journals Systematic Biology or Cladistics for general
discussions of this sort.  There is a VAST body of literature on theory and
practice of phylogenetic methodology, of which very few dino fans (or
professionals) are aware.

Thomas R. Holtz, Jr.
Vertebrate Paleontologist     Webpage: http://www.geol.umd.edu
Dept. of Geology              Email:th81@umail.umd.edu
University of Maryland        Phone:301-405-4084
College Park, MD  20742       Fax:  301-314-9661

"There are some who call me...  Tim."
-- Tim the Enchanter, "Monty Python and the Holy Grail"
---------- subtitle --[Monty Python ik den Holy Grailen]

"Tim?!?  They called me TIM?!?!"
-- Tom the Paleontologist, on seeing "The Ultimate Guide to T. rex" :-)