[Taxacom] cladistics (was: clique analysis in textbooks)

[Richard Zander]

A voice of reason. No Nikes needed.

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Anthony Gill
Sent: Thursday, August 18, 2011 9:28 PM
To: Barry Roth
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] cladistics (was: clique analysis in textbooks)

I've been very reluctant to weigh in on this thread as I fear that it
will
lead to endless debate with people that have already made their minds
up.
However, I thought I should weigh in on a few points (then run like
hell, so
I don't have to waste more time on it):

1) John's methods are not outlandish. In fact I would say that his
criteria
are the norm among fish morphologists. He has made a selection of
characters
that he feels he can justify as potential synapomorphies (using criteria
defined by Hennig, among others), in so doing, excluding characters that
(from his initial experimental design - i.e., with a defined ingroup)
are
known to be homoplastic. He has not excluded characters that might
produce
conflicting relationships within his ingroup. His goal is to test which
of
the characters of choice are congruent and what relationships they
imply.
Whether optimization (parsimony) is an appropriate method of analysis is
another matter. It seems that some in this thread would rather John
sampled
ALL characters (whatever that means), include outgroups as ingroups
(again,
whatever that means), and place his faith in a computer algorithm that
requires no scholarly appraisal of the characters a priori. As far as
I'm
concerned, that's a phenetic approach, at least in spirit. I fail to see
how
it has anything to do with cladistics.

2) It may well be professional suicide to engage in 3ia, but that in
itself
doesn't mean it is an incorrect approach. 3ia is not simply another
method
of analysis, but rather a method of viewing the original data. When
characters are reduced to the minimal relationships (3 item statements)
they
imply, it does not matter whether you analyse the 3 item statements with
compatibility or parsimony analysis ... you will get the same results.
What
you will not get, however, is an endless shifting of optimal results
(each
with a different interpretation of character evidence) as taxa are added
or
subtracted from the data sets.

3. Although the issue title suggests that the essays are only concerned
with
molecular versus morphological data, some of the debate on optimization
and
3ia was played out in several papers in a recent issue of Zootaxa (
http://www.mapress.com/zootaxa/list/2011/2946.html).

Now to go get my running shoes.

Tony