Linked or associated characters

[Robert Mesibov]

One thing that's always puzzled me about character analysis, say in
cladistics, is how you tell whether two characters are independent, or
instead are linked or associated.

By "linked" I mean inseparably paired in a developmental program or a
metabolic pathway, so that when character A is in state 1, character B is
invariably in state 2. By "associated" I mean that if an organism has A=1,
it's heavily selected to have B=2. It theoretically could have A=1 and B=4,
but this would be functionally a bad move and the 1/4 forms get eliminated
before we see them.

It's easy enough to tell that A and B are independent if you can find
organisms showing A=1 B=2; A=1, B=4; A=3 B=2; and A=3 B=4. But it seems to
me that this would be a relatively rare situation, and I sometimes see
analyses (mainly of invertebrate morphological characters, since those are
the papers I read) in which the characters listed seem to me to be ones
which are likely to be linked in development.

What happens when an analysis is based on part on non-independent
characters? How do the outputs of the different phylogenetic software
programs vary as you "dilute" the information content of the taxon-character
matrix by adding more and more non-independent characters?

Please note that I ask these questions as a cladistic and
numerical-taxonomic ignoramus, so if there's a basic reference I can be
directed to, I'd be grateful for the citation. (Nothing I've looked at so
far deals with these questions).
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Dr Robert Mesibov
Honorary Research Associate, Queen Victoria Museum and Art Gallery
and School of Zoology, University of Tasmania
Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
(03) 6437 1195

Tasmanian Multipedes
http://www.qvmag.tas.gov.au/zoology/multipedes/mulintro.html
Spatial data basics for Tasmania
http://www.geog.utas.edu.au/censis/locations/index.html
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