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

[Richard Zander]

Okay. Again, Mario. 

You ask: How exactly does a phylogenetic classification lose that
information (vs. one that allows paraphyly)?

Reply: Sometimes you lose the information, sometimes you only make the
information less important. 1. Lump an autophyletic family into another
family without making provision as a subfamily or tribe and the genera
are scattered, maybe listed alphabetically, among the genera of the
other family, and the information is not flagged as important in the
classification. 2. Do the same but leave the autophyletic family as a
subfamily or tribe signals that the autophyletic taxa is about as
important evolutionarily as the other subfamilies or tribes, being
simply a sister-group; but actually it is more important if you take its
unique evolutionary traits into account by flagging the group as a
separate family in the classification. Lump a family into a genus and it
becomes a subgenus at best, doubtless a rare extreme.

No, you can't tell the difference in the classification between (1) taxa
with higher level names because of evolutionarily important unique
traits or (2) because they are sister taxa at a particular level. But if
you have cladograms and taxon trees to accompany the classification,
then you can. Otherwise much, perhaps most, evolutionary information is
lost. Sister-group relationships, remember, are indirect indicators of
evolution, but ancestor-descendant relationships are direct indicators
of evolution.

Well, heck, sure, autapomorphic traits are future synapomorphic traits
for future speciation. Just another reason to recognize autophyletic
taxa in classification.

You say "... 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)."

Reply: My realm is greater than your realm, Mario. My hypothesis is that
the species in a genus are not only more closely related to each other
than to species in other genera via sister-group relationships, but that
they also comprise a taxon tree of ancestor-descendant relationships
(ignoring reticulation here).

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Richard H. Zander 
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Missouri Botanical Garden
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richard.zander at mobot.org
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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 3:24 PM
To: TAXACOM
Subject: Re: [Taxacom] burn out (was: classification of Class Rosopsida)

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