Question(s) about Cladistics and PhyloCode

[mike@miketaylor.org.uk (Mike Taylor)]

Jeff Leach writes:
 > 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.
 > 
 > 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).

Correct.  (And this is not just a property of the PhyloCode, but of
all phylogenetic definitions ... for example, those in *ahem* Taylor
and Naish 2005, which explicitly do not follow the PhyloCode's
recommendations.)

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

Yes.  But then, so is _everything_ based only on extinct taxa.  (Or
extant taxa, for that matter :-)

Everyone agrees that stabilityt is A Good Thing: we don't want
nomenclature to shift under our feet.  The great division among
taxonomists is whether stability of content or of definition is more
important.

The old "Linnaean" approach was that stability of content was
paramount: taxa were defined either by explicit enumeration of the
included genera and species, or by "key apomorphies" (e.g., if it has
feathers, it's a bird).  The problem with that approach is that new
discoveries (such as feathered compsognathids) change the extent of
the group, and may well result in its becoming paraphyletic.

The new "phylogenetic" approach is that stability of definition is
more important than stability of content.  A group such as Aves
(birds) is _defined_ to be (for example) all descendants of the most
recent common ancestor of _Archaeopteryx_ and the common sparrow; then
individual genera, species or indeed specimens are included or
excluded depending only on the phylogenetic hypothesis.  The upside to
this is that you don't then have to call _Sinosauropteryx_ a bird just
because it has feathers, when it's phylogenetically distant from what
we normally think of as birds.  The downside is that the content
changes with phylogenetic hypothesis: for example, if a new analysis
recovers tyrannosaurids closer to modern birds than to
_Archaeopteryx_, then we have to say that _T. rex_ is a bird.

You pays your money and you takes your choice.

 > As an example: a paper defines a taxon as a finite number of
 > character states, a cladistic analysis is done and a tree is
 > printed in an article. So we have a tree were every node is clearly
 > defined.

Yes, but "clearly defined" is not the same thing as "strongly
supported", and neither of those is the same thing as "probably
correct".

 > 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.

Well, yes.  This is _good_, isn't it?  Not only do the definitions
remain stable (as they must, by their very nature), but the content
also remains stable as far as possible.  Everyone wins.

 > 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?

No.  Hopefully, no-one does that.

 > I recently read an article were three taxa were declared nomia
 > dubia eventhough their closest suspected relative lacks a modern
 > description.  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), the taxa might need to
 > be reinstated when the knowledge of the clade improves.

Sorry, I don't follow that at all.

 _/|_    ___________________________________________________________________
/o ) \/  Mike Taylor  <mike@miketaylor.org.uk>  http://www.miketaylor.org.uk
)_v__/\  "Never ruin an apology with an excuse" -- Kimberly Johnson.