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Re: Dinosaur FAQ #9 (Hold on now!)




Mike,
Sorry I missed that post----I would have certainly answered it. Your criticisms may apply to the traditional Linnean System, but they do not apply to my modification of the Linnean System (i.e. The Kinman System).
The only difference is that I would tend to use plus signs instead of minus signs (when necessary). The traditional (paraphyletic) Synapsida is simply Pelycosauriformes + Therapsiformes. The clade Synapsida is *very* simply Reptilea 1, which as my book shows is the above two orders + the marker {{Mammalea}}. Clade Cyanodontia would be something like Therapsiformes 13+, and therefore your Cyanodontia-Theria would be my Therapsiformes 13+ plus Mammalea 1-10. I'm not sure such a paraphyletic group would be used much, but a modified Linnean System can handle it if the need arises.
The really major difference is that phylogenetic taxonomy formally names an enormous number of taxa. I have gone the other direction, reducing formal taxa to only Phylum, Class, Order, Family, Genus, Species (eliminating all "formal" intermediate taxa). So my system is much more flexible than the traditional Linnean System, with fewer formal taxa (and a WHOLE lot fewer than PT taxonomy). This makes it far more practical for non-systematists, who can usually just ignore the coding (details of relationship) and have a very stable and relatively uncomplicated, utilitarian classification. And it doesn't strip away the "divergence" component of traditional classifications.
Therefore, I cannot see how you can justify the use of phylogenetic taxonomy, which has few advantages over a modified Linnean system, and PT has some terrible disadvantages, such as: (1) hierarchical instability, (2) a huge multiplicity of names (many which will turn out to be invalid), and admit it or not (3) even an enormous number of ranks-----cladists don't always label them as ranks, but indented classifications are ranked whether you name the ranks or not. And all these disadvantages will be exacerbated by the PhyloCode as workers rush in to establish priority for their favorite names (with their names attached as the author).
The disadvantages of strict PT are so great (as Benton has written in his recent review) that it seems far more prudent to modify the Linnean System instead, for a variety of reasons.
------Ken Kinman
********************************************************
From: "T. Mike Keesey" <tmk@dinosauricon.com>
Reply-To: tmk@dinosauricon.com
To: -Dinosaur Mailing List- <dinosaur@usc.edu>
Subject: Re: Dinosaur FAQ #9
Date: Sat, 10 Feb 2001 17:02:45 -0500 (EST)

On Sat, 10 Feb 2001, Ken Kinman wrote:

> And cladistics to me has two distinct aspects or components: (1)
> cladistic analysis, which has revolutionized biological systematics; and (2)
> cladistic (a.k.a. "phylogenetic") taxonomy. I embrace the latter only to
> the extent that it is useful, but in it strictest form (the elimination of
> all paraphyletic groups), it cannot produce classifications that are (in the
> long run) stable, useful, or natural. This is because strictly phylogenetic
> taxonomy attempts to only reflect phylogeny, and strips classifications of
> an important phenetic component (often referred to as divergence). And a
> classification with only the phylogenetic component cannot be fully natural,
> useful, or stable. (I think I hear some booes and hisses, so will stop
> there).


I posted a brief essay to sci.bio.paleontology and sci.bio.systematics
title "Supierority [_sic_] of Phylogenetic Taxonomy for Terming
Paraphyletic Groups". I was rather surprised when Ken Kinman, or anyone
else for that matter, didn't respond to it.

Although (as the title suggests) this is about the utility of PT when it
comes to paraphyletic groups, you can easily see how it could be
interpreted as PT being superior with regards to representing divergence
as well.

(NOTE: This is probably getting a bit off topic -- this discussion should
probably move to sci.bio.systematics, the PhyloCode mailing list, some
other forum, or personal e-mail.)

Here is the essay as originally posted:

Under the traditional system, official recognition of a paraphyletic taxon
bars certain other paraphyletic taxa from being recognized, as well as
barring certain clades from being recognized. For example, if we choose to
recognize Subclass Synapsida as (Clade Synapsida - Mammalia), then we are
prevented from recognizing many other paraphyletic taxa (e.g., Clade
Synapsida - Theria), or (Clade Cynodontia - Eutheria), etc.), as well as
many clades (e.g. Clade Synapsida, Clade Cynodontia, etc.)

This is, in essence, unfair. Why should any particular paraphyletic group
be designated at the expense of designating certain clades and other
paraphyletic groups? It's true that in the phylogenetic system there are
named and unnamed clades, but naming a clade does not specifically exclude
another clade from being named.

Under the phylogenetic system, every paraphyletic group of equal degree of
paraphyly has equal opportunity. Every singly paraphyletic group can be
termed using the formula "non-b A" (provided clades A and B are named, and
every clade does have the chance to be named). Every doubly paraphyletic
group can be termed by "non-b, non-c A". If you want to go beyond doubly
paraphyletic, you might want to a) question the utility of the group, b)
use the term "basal A", or c) use an alternate description based on the
criterion you are using (e.g., "ectothermic Amniota" or "Mesozoic
Archosauria").

Phylogenetic taxonomy does not do away with paraphyletic groups.
Instead, it offers a more precise and flexible convention for naming them.
I can speak of not only non-mammalian Synapsida (=Subclass Synapsida), but
non-therian Synapsida (i.e., oviparous Synapsida), non-eutherian
Synapsida, non-therian Cynodontia, non-cynodontian Therapsida,
non-therapsid Amniota, non-chiropteran Mammalia -- the only limit is the
number of named clades (and more can always be named if deemed necessary).
Furthermore, each of these terms is explicitly defined (non-therian
Synapsida boils down to Clade(_Homo_ <-- _Passeres_) - Clade(_Homo_ +
_Macropus_), or some equivalent formula).

It is my opinion that it does nto really matter if paraphyletic groups are
"natural" or not -- if you want to discuss them, you should have a way to
discuss them. And I believe phylogenetic taxonomy offers the best system.

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