[Fwd: Re: Probabilities on Phylogenetic Trees]

Curtis Clark jcclark at CSUPOMONA.EDU
Mon Sep 15 20:28:07 CDT 1997


At 04:31 PM 9/15/97 -0500, Byron Adams wrote:
>>At 02:15 PM 9/15/97 -0700, Richard Zander wrote:
>>> A series of cladograms,
>>>each depending on the one previous to establish a correct outgroup, is a
>>>house of cards.
>
>Curtis Clark wrote:
>
>>An outgroup is not necessary to form a cladogram, only to root it.
>
>        I think what you meant to say was that an outgroup is not necessary
>to form, but only to root a _phenogram_ or _dendrogram_.  Assuming one uses
>cladistic treebuilding methodology, by definition an outgroup is required
>(in order to establish character polarity) and the resulting tree is a
>cladogram.

See Clark, Curtis and Daniel J. Curran. 1986. Outgroup analysis, homoplasy,
and global parsimony: A response to Maddison, Donoghue, and Maddison. Syst.
Zool. 35:150-154.

>I don't think many would argue with me that these (unrooted
>phenograms/dendrograms) are not the same thing as cladograms.  Nor would
>they argue that somebody who can arbitrarily polarize characters _sans_
>outgroup comparison is actually doing cladistics.

Of course not, but the point of our 1986 paper was that rooting the tree is
algorithmically independent of finding the shortest tree, and that there
are good reasons to keep them separate. The "series of cladograms"
postulated by Richard is unnecessary and counterproductive.


------------------------------------------------------------------------
Curtis Clark                 http://www.intranet.csupomona.edu/~jcclark/
Biological Sciences Department                     Voice: (909) 869-4062
California State Polytechnic University, Pomona    FAX:   (909) 869-4078
Pomona CA 91768-4032  USA                          jcclark at csupomona.edu




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