More on the 'cladistics' of sequences

Richard.Zander at MOBOT.ORG Richard.Zander at MOBOT.ORG
Mon Jun 7 08:56:19 CDT 2004

-----Original Message-----
From: Richard Jensen [mailto:rjensen at SAINTMARYS.EDU]
Sent: Monday, June 07, 2004 8:36 AM
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
represent synapomorphies and which reflect homoplasy.  And, what do you do
the characters that were not included as potential synapomorphies?  Chances
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
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299
richard.zander at <mailto:richard.zander at>
Voice: 314-577-5180
Fax: 314-577-9595
Bryophyte Volumes of Flora of North America:
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