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

[Anthony Gill]

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



On Fri, Aug 19, 2011 at 12:15 PM, Barry Roth <barry_roth at yahoo.com> wrote:

> Perhaps I missed it, but at any time has the complete morphological
> character/taxon matrix been posted here, such that any of us with an
> interest in method and outcome could analyze it by our own chosen means?  I
> don't mean a selection of characters that John Grehan or anyone else has
> chosen based on any criterion, but rather the assembled data that form the
> ground and starting point of any analysis.  Obviously, assembling such an
> array took a lot of scholarship, which deserves thanks and respect (not to
> mention credit whenever it's cited, formally or informally).  If that matrix
> is contained within a publication discussed (and which I in my sluggishness
> have failed to call up and read), I'd be grateful for a pointer to it.  The
> discussion of method here has become so ponderous, with each contributor
> sometimes seeming to speak with his/her own unique vocabulary, that I
> despair of getting anything further out of it.  But I'm still curious about
> the
>  case in point, and (1) what would happen if we each applied our own
> methods -- algorithmic or seat-of-the-pants -- to it; (2) how sensitive the
> results would be to, e.g., different settings in PAUP; and (3) just how
> robust either or the two (no, wait, there's three) competing statements of
> relationship is.
>
> Barry
> .._ at v
>
> From: Pierre Deleporte <pierre.deleporte at univ-rennes1.fr>
> To: taxacom at mailman.nhm.ku.edu
> Sent: Thursday, August 18, 2011 6:40 PM
> Subject: Re: [Taxacom] cladistics (was: clique analysis in textbooks)
>
> Le 17/08/2011 14:41, John Grehan wrote:
> > Pierre speaks, of course, authoritatively on such matters,
>  _______________________________________________
>
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom archive going back to 1992 may be searched with either of these
> methods:
>
> (1) by visiting http://taxacom.markmail.org
>
> (2) a Google search specified as:  site:
> mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>



-- 
Dr Anthony C. Gill
Natural History Curator
A12 Macleay Museum
University of Sydney
NSW 2006
Australia.

E-mail:  anthony.c.gill at sydney.edu.au