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Re: "Phylogenetic Definitions and Nomenclature..."

A few comments on recent postings about the theropod taxonomy paper:

1) We don't have reprints for the paper yet... should be a month or so?
Best way to get one is to snail mail Padian, me, or Tom a reprint request
with your snail mail address on it.  Personally, I am an absent minded grad
student and often lose e-mail requests for papers.  Having a hard copy
glaring at me from my desktop is easier to remember.

2) There are no well established rules for phylogenetic taxonomy yet;
DeQueiroz, Gauthier, and others are working on a new code but I know next
to nothing about its progress or contents.  PT is still in its early stages
-- expect controversy and confusion.

3) In our paper we prefer to avoid definitions that include >2 taxa,
because the more taxa you introduce into a definition, the less stable the
definition is.  This is especially true for polytomies (or weakly supported
clades), which are obviously unstable in their own right, and are commonly
the groups chosen for multitaxon definitions.  We do value taxonomic
stability even if it is often a wild goose chase or just plain ignorance,
that's why we avoid such unstable definitions.  It may be better just to
avoid defining such taxa until their relationships are straightened out.
As we advocate in the paper, names should be defined mainly for well
supported clades, and a PT for a clade is only as stable as the phylogeny
("consensus" or otherwise) it's based on.  That's just how we prefer it, we
aren't writing the rules here, but we are making suggestions.

4) In many cases we've followed Sereno's practice of using more inclusive
clade names in our definitions, e.g. Tetanurae as "all *neotheropods* more
closely related to Neornithes than to _Ceratosaurus_".  Play around with a
few cladograms' topologies and you'll see how this can promote stability,
especially in the case of some vagrant taxa such as the arctometatarsalian
triumvirate.  Granted, stability is a relative thing and it will seldom
keep everyone happy.  There is no optimal solution that I can see, until
relationships are firmly established, if ever.

5) To be honest there are some errors/inconsistencies in the paper but
these will be worked out eventually.  As Tom has already posted, we expect
controversy over our uses of names for abelisaur subclades, Avetheropoda,
Aves, Ornithurae, and Neornithes especially.  As there are no clear rules,
and priority is what you want it to be, expect things to change.  We saw a
lot of confusion in the literature on uses of certain clades (especially
stems being confused as equivalent to nodes) and set out to rectify that.
I don't think we were delusional enough to think that our paper would solve
everything.  :)

6) On priority: As I recall it, our concept of priority changed from the
initial drafts of the paper to its final version.  We became more strict
near the end, and I think it's safe to say that the three of us agree that
PT priority should be based on explicit phylogenetic definitions only, as
other authors have endorsed.  However, as consensus and stability of
meaning are desirable, exceptions may have to be made.  Taxonomy is, has
always been, and may always be mutable.  The "Aves vs. Neornithes" issue
will be the most contentious, and perhaps that's unfortunate.  Whatever the
new code eventually manifests itself as, it will have guidelines for
redefining taxa to maintain stability and consensus.  Until then, there are
no real rules.

7) Eventually PT definitions may change to explicit reference to type
specimens rather than species or larger clades.  That's way down the line,
if it happens at all.

8) These are just names, true.  There are more important biological issues
at stake that are less anal retentive and semantic.  But gosh darn it, we
had fun writing this paper!  Besides, clarity + stability of communication
are important goals in any taxonomic system, or in science in general for
that matter.  We hope that the paper will promote more clarity and
stability in theropod taxonomy.

Nuff said.  Happy Palm Sunday and stuff,

                        John R. Hutchinson
                 Department of Integrative Biology
                  3060 Valley Life Sciences Bldg.
                University of California - Berkeley
                     Berkeley, CA 94720 - 3140
                      Phone:  (510) 643-2109
                      Fax:    (510) 642-1822