[Taxacom] burn out (was: classification of Class Rosopsida)

Tue Apr 14 15:23:52 CDT 2009

Richard,
you say: "If we combine the names into one to enforce holophyly, then 
the cladogram retains the relationship information but the 
classification does not."
How exactly does a phylogenetic classification lose that information 
(vs. one that allows paraphyly)? In my view, you actually gain the 
information that group A (your autophyletic group) is derived from group 
B (the paraphyletic group) if you make A a subgroup of B (a phylogenetic 
classification). You do not have that information if you classify both A 
and B in the same rank (allowing paraphyly).

You also say: "The relationship information in the cladogram, however, 
does not include the unique evolutionary traits of the autophyletic 
taxon since these were either not in the data set to begin with or were 
eliminated as autapomorphies after generation of the cladogram." You can 
perfectly have autapomorphies included in a data matrix to be analized 
cladistically; they just won't affect the resulting groups. And if your 
autophyletic taxon is a group of species, then those traits are no 
longer autapomorphies but potential synapomorphies and will not be taken 
out of the matrix anyway.

And, as an aside, the Alpha Taxonomy wikipedia article you cite says 
that it "focuses more on the species end of that spectrum (e.g., 
classifying organisms [specimens] into species groups, and classifying 
those into genera, rather than determining the higher-level 
relationships between families or orders)." Not that it matters that 
much; "alpha taxonomy" also has different meanings for different people. 
In my (admittedly strict) view, even when you describe a new genus, you 
are no longer in the realm of alpha taxonomy (because you are advancing 
a hypothesis that the species in that genus are more closely related 
between themselves than to other organisms, either phylogenetically or 
by some other criterion).

Mario

Richard Zander wrote:
> Mario:
>
> A paraphyletic group in a classification is so because it was found to
> be paraphyletic in a cladogram. If we keep different names for the
> paraphyletic group and the autophyletic taxon (that which makes the
> group paraphyletic if recognized at a proper level to flag its unique
> evolutionary qualities), then we have different names in the
> classification. If we combine the names into one to enforce holophyly,
> then the cladogram retains the relationship information but the
> classification does not. The relationship information in the cladogram,
> however, does not include the unique evolutionary traits of the
> autophyletic taxon since these were either not in the data set to begin
> with or were eliminated as autapomorphies after generation of the
> cladogram. Thus, classification (names for things) and cladograms
> (sister-group relationships) and evolution (ancestor-descendant
> relationships) are intertwined, and there is information available in
> systematic analyses about all three. All such information should be
> preserved, since all contribute to science. 
>
> Some of the logical fallacies you detect may be just different
> definitions of terms or different assumptions or just misunderstandings.
> Also, I'm quite an advocate of paraconsistency. Depends on results, you
> know. :)
>
> No, I do not want static classifications, or expect them. I just do not
> want artificial (holophyletic) classifications passed off as wonderful
> products of a new paradigm in evolutionary science (analysis of
> sister-group relationships). It's not a paradigm, it's just a method of
> inferring sister-group relationships, which are not the be-all and
> end-all of evolution as applied to systematics.
>
> Alpha taxonomy is not just describing species. See
> http://en.wikipedia.org/wiki/Alpha_taxonomy
> We also describe higher taxa.
>
> Oh, and I'm also a phylogeneticist, just like you, in that I treasure
> information about sister-group relationships generated by any clustering
> method, including parsimony. I think, however, that classification
> should preserve ancestor-descendant relationships, too, and thus rather
> style myself an evolutionary taxonomist. See
> http://en.wikipedia.org/wiki/Evolutionary_taxonomy 
>
>
> *****************************
> 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
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> *****************************
>
>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Mario Blanco
> Sent: Tuesday, April 14, 2009 11:14 AM
> To: TAXACOM
> Subject: Re: [Taxacom] burn out (was: classification of Class Rosopsida)
>
> Richard,
> I pointed out logical fallacies in your statements, which you use to
> support your view that paraphyletic classifications are inherently
> better than phylogenetic ones.
>
> You say that "alpha taxonomy [taxonomists?] has the best grip on
> evolution-generated groupings". This is necessarily a subjective
> statement, because it depends on what you consider "best". Seems to me
> that what you consider best are unchangeable classifications set only by
> alpha taxonomists.
>
> However, classifications have been constantly modified over time, not
> just by molecular phylogeneticists; also by people using cladistic
> methods with morphological traits, and for an even longer time,
> exclusively by "alpha" taxonomists using no particular method of
> analysis. Not to mention that, by definition, alpha taxonomy focuses on
> species-level issues, not higher level classifications. You mean
> traditional systematists, which many taxonomists are.
>
> Besides, many taxonomists are also phylogeneticists (molecular or not),
> or routinely collaborate with them; thus the distinction you want to
> make is not clear at all.
>
> I still cannot understand the logic in your statement that phylogenetic
> classifications eliminate information on ancestor-descendant
> relationships. You always have to refer to a cladogram or some other
> type of evolutionary diagram to visualize these relationships. How does
> a paraphyletic classification have more of this information? A
> classification is just a series of names of taxa and associated ranks. 
> You cannot see that one group descended from another just by looking at
> a list of names in a paraphyletic classification.
>
> Mario
>
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