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

[John Grehan]

The data used in the orangutan study is available and can be analyzed by any clustering procedure one chooses to prefer.

To me the veracity of claimed character states is something that has been largely overlooked in human origins studies. The same characters get recycled in one study after another (so they come out with the same or similar results) even though the original documentation of many characters is hairy to say the least. 

In the Lehtonen et al reply we go to the original sources of the character state assertions and in quite a few cases we could not find anything in the original literature that supported the claimed character states. I have either missed something obvious and I am going to be very much embarrassed down he line, or my findings are correct which would make me wonder why the authors never noticed the discrepancies in the first place.

John Grehan

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Barry Roth
Sent: Thursday, August 18, 2011 10:16 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] cladistics (was: clique analysis in textbooks)

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,
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