In article <3q8oem$2us_001 at is.co.za>, neil at gecko.biol.wits.ac.za (Neil
> I'm having a debate with some colleagues about cladistics and character
> independence, and I would like to hear the opinion of readers of this group.
>> I think it's clear that one cannot treat RFLPs as caldistic character data
> due to the non-independence of fragment lengths (add one cut site between two
> others, and you loose one long fragment and gain two shorter ones).
Non-independence doesn't mean that the data cannot have cladistic structure.
It is perhaps better to think of this non-independence as characters that
have been weighted more than they should have been, rather than characters
that cannot be analyzed with cladistic methods. The same applies to other
molecular examples, such as rRNA sites that are part of stems and might
evolve with compensatory substitutions. The "bad" weighting may or may
not confound the attempts to estimate branching patterns. It depends on
the balance between synapomorphies due to history versus those due
Doug Eernisse <DEernisse at fullerton.edu>
Dept. Biological Science MH282
California State University
Fullerton, CA 92634