[Taxacom] Ageism and classification

[Richard Jensen]

Well. I don't know....

Cluster analysis, when SAHN techniques are employed, will produce 
phenograms, tree-like (but unrooted) diagrams that reflect the nested 
structure of the data (if such structure exists). The fact that two 
groups are nested together, and a third group occurs outside them, 
should not be interpreted as evidence of phylogenetic or evolutionary 
relationships, except under certain conditions, as Don Colless has 
noted. Other clustering techniques, e.g., k-means, do not produce 
tree-like diagrams.

It should be well-known that proponents of phenetic classification never 
intended that their classifications be viewed as phylogenetic 
classifications. However, because of the rather odd fact that 
phylogenetically closely related taxa often are, by virtually any 
measure of overall similarity, similar, the results of phenetic analyses 
may be a good first approximation of phylogeny.

Evolution may not produce clusters, but it may produce taxa that, when 
examined and analyzed by a method such as cluster analysis, cluster 
together.

Cheers,

Dick J

Richard Jensen, Professor
Department of Biology
Saint Mary’s College
Notre Dame, IN 46556
Tel: 574-284-4674



Richard Zander wrote:
>  
>
> A Web-based science encyclopedia:
>
> http://science.jrank.org/
>
> has an article by Peter A. Ensminger:
>
> http://science.jrank.org/pages/6711/Taxonomy.html
>
> which says in part:
>
>  
>
> "Evolutionary taxonomy can be considered a mixture of phenetics and
> cladistics. It classifies organisms partly according to their
> evolutionary branching pattern and partly according to the overall
> morphological similarity. Evolutionary taxonomy is basically the method
> used by the early evolutionary taxonomists and is also called classical
> taxonomy. The major limitation of evolutionary taxonomy is that it
> requires a highly arbitrary judgment about how much information to use
> for overall similarity and how much information about branching pattern
> to use. This judgment is always highly subjective, and makes
> evolutionary taxonomy a very poor method of classification, albeit one
> that survives in the hands of certain older taxonomists."
>
>  
>
> Anent "older taxonomists" let's discuss tree-thinking. In "Mathematical
> Taxonomy" by N. Jardin & R. Sibson, 1971, John Wiley, New York, on page
> 150 it says: "Prima facie the case for using numerical methods of
> automatic classification to construct taxonomic hierarchies for all
> kinds of organisms can be made to appear quite strong. The case rests
> upon the following assumptions. First, the purely phenetic approach to
> taxonomy must be accepted. Secondly, it must be assumed that automatic
> classification based upon an adequate selection of populations and
> attributes can be guaranteed to produce optimal phenetic
> classification." 
>
>  
>
> This is from 1971. What are the results of phenetic cluster analysis?
> Trees. Parsimony analysis also generates trees through a nonultrametric
> method based on a simple model of evolution of traits), and I have it on
> good authority (Pierre Legendre, pers. comm.) that parsimony analysis
> really is cluster analysis. Cluster analysis, whether phenetic or
> phylogenetic or even MCMC Bayesian, produces trees and does not identify
> ancestors. 
>
>  
>
> Evolution does not act by clustering. It acts by descent with
> modification of one biological entity (identifiable at some degree of
> resolution) into another. Paraphyly is one method of identifying an
> ancestor at some degree of resolution. 
>
>  
>
> "Automatic classification" by clustering methods to create trees as
> hierarchical sister-groups has been around since the late 1960's and is
> now at least 40 years old. Clustering methods with morphology and
> molecular data are valuable in investigating evolution, but more
> information may be had about evolution than that obtained from
> clustering methods and presented to us in classification via holophyly. 
>
>  
>
> I think it is time for students to confront their doddering geezer or
> geezette professors of phylogenetics with a paradigm change that calls
> for an eclectic approach to evolutionary content in classification, and
> reject holophyly (and other automatic or judgment-free aspects of
> phylogenetics) in favor of recognition of paraphyly and autophyletic
> products of descent with modification based on reasoned and seasoned
> judgment of all available information about evolution.
>
>  
>
> *****************************
> Richard H. Zander 
> Voice: 314-577-0276
> 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/
> and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> Non-post deliveries to:
> Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110
> *****************************
>
>  
>
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