Re: Question(s) about Cladistics and PhyloCode

[David Marjanovic <david.marjanovic@gmx.at>]

----- 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.