Assumptions in Computing phylogenies

[Stanley Friesen]

At 09:25 AM 2/29/00 +0000, Hans Holm wrote:
>SF>Actually, properly done, cladistic analysis *determines* which
>SF>characters are innovations and which are retentions.

>.. In my humble understanding it is vice versa.
>The biologist or linguist decides which features are retentions vs.
>innovations, and the cladistic algorithm computes the 'optimal' tree.

Actually, the initial "assignments" of status for a character as derived or
ancestral are purely for ease of encoding, and have no real impact on the
final result.  In the final analysis it is the placement of the characters
relative to the root that matters. Thus one has to have some means of
placing the root independent of the researcher's judgement of the relative
advancement of the characters.

I have this on very good authority - from people who do cladistic analysis
for a living, such as the paleontologist Dr. Holtz.

[I suppose one could *tentatively* place the root at the link with the
highest count of ancestral characters per the researcher's judgement, but
this would be considered weak evidence, at best].

> See
>my parallel mail for a textbook on the topic.
>But perhaps it is a misunderstanding.

I think it is.  When encoding the characters, the researcher usually
assigns numeric codes in the expected order of derivation from the most
"primitive".  But once the tree is actually derived, position of the
character on the tree takes precedence over this initial encoding.

Dr. Holtz is VERY insistent on that.

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May the peace of God be with you.         sarima at ix.netcom.com