[Taxacom] To clade or not to clade

Régine Vignes-Lebbe vignes at ccr.jussieu.fr
Wed May 24 08:30:38 CDT 2006


My opinion is that, of course, maximum parsimony is a clustering method.
This type of method (clustering) is (for me) defined by the common
objective to construct, from a set of "objects" (I choose deliberately a
general term), a classificatory structure (which is a set of clusters on
the "objects", with properties depending of the type of classification
structure : partition, hierarchy, pseudo hierarchy ...). The optimized
criteria are numerous and define multiple different methods (like
maximum parsimony), and the context we apply the method gives to the
result a biological meaning.

Régine Vignes Lebbe
-----------------------------------------------------------------------------
Régine Vignes Lebbe, Professeur
Laboratoire Informatique & Systématique (UMR 5143)
Equipe Systématique, Recherche Informatique et Structuration des
cladogrammes
Escalier B, 2eme étage
Université Pierre et Marie Curie
12 rue Cuvier, 75005 Paris
Tel : 01 44 27 65 21 (ou 65 22)
Fax : 01 44 27 65 60
http://lis.snv.jussieu.fr
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Richard Zander wrote:
> I went to a meeting of the Classification Society and took the pre-meeting cluster analysis tutorial. At question time, I asked the guys running the tutorial (the then president of the Society, and Pierre Legendre) if they thought maximum parsimony was a clustering technique.
> 
> They looked at each other disconcertedly, mumbled, then allowed as how, yes, it was. I did get the feeling that they were indulging in some hegemonizing, but they have a point. Cladograms are not ultrametric, but certainly cluster. Given the many kinds of cluster analysis (compare k-means), why not?
> 
> ******************************
> Richard H. Zander
> Missouri Botanical Garden
> PO Box 299
> St. Louis, MO 63166-0299 USA
> richard.zander at mobot.org
> Web sites: http://www.mobot.org/plantscience/resbot/
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> -----Original Message-----
> From: Barry Roth [mailto:barry_roth at yahoo.com] 
> Sent: Tuesday, May 23, 2006 11:49 PM
> To: TAXACOM
> Subject: [Taxacom] To clade or not to clade
> 
> I have heard (and used) it in discussions with pals and colleagues -- generally in situations where the rules of formal syntax and diction were, er, relaxed.  But it is a good word ("taxon A clades with taxon B in this cladistic analysis"), on the model of "taxon C clusters with taxon D in this cluster analysis."  Cladistic analysis is not a clustering procedure, so it is incorrect to use the verb "to cluster" in that context.  I also like the word (did I coin it, or just dream that I did?) "concladal" -- meaning, obviously, "belonging to the same clade."  It follows the model of "congeneric" and "confamilial" but without attribution of any particular taxonomic rank.
>    
>   Barry Roth
> 
> Don.Colless at csiro.au wrote:
>   
> Dear Ken,
> 
> You have, I think, just created linguistic history. I'm not aware of any previous use of the verb "to clade". As Dr Johnson might have said "A good word, Sir".
> 
> Don Colless,
> Div of Entomology, CSIRO,
> GPO Box 1700,
> Canberra. 2601.
> Email: don.colless at csiro.au
> Tuz li munz est miens envirun
> 
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