FW: Re: [TAXACOM] More on the 'cladistics' of sequences

[John Grehan]

-----Original Message-----
From: John Grehan 
Sent: Monday, June 07, 2004 2:52 PM
To: 'Richard.Zander at MOBOT.ORG'
Subject: RE: Re: [TAXACOM] More on the 'cladistics' of sequences

I seem to have no problem with either approach - potential synapomorphy
or parallelism. 

As for the outgroup - I have not problem with this being an issue. I've
mentioned before that the outgroup being used for orangutans is at least
all other primates. I presume that for a comparable character array for
DNA sequences one would have to have an identical character sequence
present in all species outside the great apes for each gene sequence
being used within the great apes. Does anyone know if this been shown to
be the case for any genes used into hominid systematics?

John Grehan

-----Original Message-----
From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU] On
Behalf Of Richard.Zander at MOBOT.ORG
Sent: Monday, June 07, 2004 9:56 AM
To: TAXACOM at LISTSERV.NHM.KU.EDU
Subject: Re: [TAXACOM] More on the 'cladistics' of sequences

-----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
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