[Taxacom] To clade or not to clade

Richard Jensen rjensen at saintmarys.edu
Wed May 24 07:39:15 CDT 2006


I agree with Pierre, Richard and others who recognize maximum parsimony and other tree building algorithms as methods of cluster analysis.  They are, after all, grouping procedures.  However, I believe that most cladists (and, perhaps most systematists), prefer to use clade rather than cluster to refer to the groups that appear in the tree.  Cluster is probably overly burdened with its identity with "phenetic" analyses to be considered for use in describing phylogenetic trees.  That said, I review many papers in which the authors refer to the groups in phylogenetic trees as clusters and, occasionally, refer to the groups in UPGMA trees (regardless of the data used) as
clades.

Note that Everitt [who has produced a couple of books dealing with cluster analysis and numerical (mathematical) taxonomy] treats maximum parsimony separately from cluster analysis.  Perhaps one reason for this is that in maximum parsimony analyses, hypothetical entities (the nodes) are proposed to assist in building the tree.  Such entities do not play a role in what most recognize as "clustering" methods.

Dick J

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
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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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--
Richard J. Jensen              | tel: 574-284-4674
Department of Biology      | fax: 574-284-4716
Saint Mary's College         | e-mail: rjensen at saintmarys.edu
Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen







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