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Re: Question(s) about Cladistics and PhyloCode



----- Original Message -----
From: "Jeff Leach" <leachjeff2@hotmail.com>
Sent: Thursday, April 20, 2006 9:54 AM

This isn't really the proper list for these question, so if anyone knows of
some relevant articles or list(s) can you point me in the right direction.

On the PhyloCode page http://www.ohiou.edu/phylocode there are instructions for joining the PhyloCode mailing list. Before that, however, read the entire thing -- it takes just an evening.


1. If I understand correctly under PhyloCode clade definitions don't change
(A node can move around on a tree but its definition is always the same).

Yes.

My question is - are not clade definitions based only on
extinct taxa in a state of flux?

I gather you haven't understood what "definition" means in phylogenetic nomenclature.


Definition: Clause that explains where in the tree of life to find the first (oldest) member of a clade. For example: "Dinosauria = the most recent common ancestor of *Tyrannosaurus rex* and *Triceratops horridus*, and all of its descendants". Is not supposed to change.
Diagnosis: List of characters that the first member of a clade had (according to a cladogram) and its ancestors lacked. Often called "definition" in earlier times. Changes every time our knowledge advances.
Contents: The members of the clade. Change occasionally as our knowledge advances (depending on how carefully the definition was made).


As an example: a paper defines a taxon as a finite number of character
states,

No, that's a diagnosis, not a definition.

a cladistic analysis is done and a tree is printed in an article. So
we have a tree were every node is clearly defined.

I think you mean "diagnosed" again.

Now a few years later a new article is published and it adds a few
character states to the previous list, a new analysis done, and the new
tree is nearly identical to the previous one except for the new taxon as
a terminal node at the top of the tree. None of the clade definitions have
changed except for the additions of new characters. We have the same
clades but they now how more precise definition.

They have more precise diagnoses now. Their names keep their definitions; and in your example the contents have not changed except for the addition of the new taxon.


2. Is it really wise to declare taxa based on scrappy remains nomia dubia
because they lack a single unique derived character even before we have
stabil (or at least somewhat exhaustive) definitions of the taxa they most
closely resemble?

This has recently been discussed on this list. :-) Archives: http://dml.cmnh.org


I recently read an article were three taxa were declared nomia dubia
eventhough their closest suspected relative lacks a modern description.

IMHO this was probably too hasty.

While the results of the article were formally correct under the rules of
cladistics and the present knowledge of the clade (really a more inclusive
clade),

Cladistics is not at all concerned with names. It is phylogenetics, not nomenclature.


the taxa might need to be reinstated when the knowledge of the
clade improves.

The names might need to, yes. I'm sure we'll see sooner or later.