More on the 'cladistics' of sequences

[Richard.Zander at MOBOT.ORG]

-----Original Message-----
From: Richard Jensen [mailto:rjensen at SAINTMARYS.EDU]
Sent: Monday, June 07, 2004 8:36 AM
To: TAXACOM at LISTSERV.NHM.KU.EDU
Subject: Re: [TAXACOM] More on the 'cladistics' of sequences

So, then, how does one objectively determine which characters represent
"potential" synapomorphies and which do not?  It seems to me that, in an
objective approach, one must assume that all characters represent potential
synapomorphies.  The analysis then provides information about which
characters
represent synapomorphies and which reflect homoplasy.  And, what do you do
with
the characters that were not included as potential synapomorphies?  Chances
are
many of them will not fit the tree in question.

[[R.Z.]]: Seems to me that all characters should be assumed to be
parallelisms. Then apply the model (all analytic procedures, apparently, are
model-based), and see if you can come up with something other than a star
that rejects the null of parallelism. This is done with a phylogenetics
program (e.g. PAUP, Max. Likelihood, MrBayes) and a reliability measure
(e.g. nonparametric bootstrap, posterior probability).

______________________
Richard H. Zander
Bryology Group
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