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Date: Fri, 06 Feb 2004 12:13:52 -0500
From: "Moore, Gerry" <gerrymoore@bbg.org>
To: Kevin de Queiroz <Dequeiroz.Kevin@NMNH.SI.EDU>, phylocode@ouvaxa.cats.ohiou.edu
Subject: RE: RE: a comment on ancestor
I don't want to belabor this point because it is rather minor (as Phil
pointed out it is doubtful anyone is going to use the PhyloCode to name
non-monophyletic taxa), although it does have relevance to Igor's
earlier post. Under either the current wording or Kevin's re-wording,
Article 1.1 refers to the groups of organisms to be named as taxa, and
it further notes that "taxa may be clades or species". To me this
prevents one from naming taxa that are not clades (or species if and
when these are covered) under the PhyloCode. All of the Articles in the
PhyloCode that address names and definitions refer to names of clades.
The prohibition may be implicit but to me it is there nonetheless. =20
Gerry =20
-----Original Message-----
From: Kevin de Queiroz [mailto:Dequeiroz.Kevin@NMNH.SI.EDU]=20
Sent: Friday, February 06, 2004 11:19 AM
To: Moore, Gerry; phylocode@ouvaxa.cats.ohiou.edu
Subject: Re: RE: a comment on ancestor
I think Gerry has misinterpreted the rules that he cites as evidence
that the PhyloCode prohibits the naming of non-monophyletic taxa.
The full Article 1.1 is as follows: "The groups of organisms whose
names are governed by this code are called taxa (singular: taxon). Taxa
may be
clades or species, but only clade names are governed by this code." In
this context, it should be clear that the statement quoted by Gerry
("only clade names are governed by this code") is meant to clarify that
the present version of the PhyloCode governs the names of clades but not
those of species. It is not meant to to prohibit the naming of
non-monophyletic taxa. On the other hand, I can see how someone might
infer, given that "only clade names are governed by this code", that
names defined as referring to paraphyletic higher taxa are not governed
by the PhyloCode. To prevent this misinterpretation, the phrase in
question could be reworded "species names are not governed by this code"
(though I am not advocating this rewording).
Article 2.1 is simply a definition of the term "clade". It says nothing
to rule out other kinds of taxa.
Article 11.9 describes methods for restricting the application of names
through the use of qualifying clauses and the careful wording of
definitions (i.e., so that a name would not be used under certain
circumstances--for example, the name Pinnipedia could be defined so that
it would not be used in the context of phylogenies implying that the
aquatic adaptations of seals and sea lions had arisen convergently).
The methods in question do not prevent the naming of paraphyletic and
polyphyletic taxa; in fact, the definitions of the names of such taxa
require mechanisms very similar to the qualifying clauses mentioned in
this article. For example, the name Reptilia, if defined to approximate
its traditional paraphyletic composition, would be defined along the
following lines: the group composed of the most recent common ancestor
of Mammalia and Aves and all of its descendants except Mammalia and Aves
(I have used higher taxa rather than species as specifiers for the sake
of simplicity). Note that the first part of this definition ("the group
... descendants") is a standard node-based definition, but the second
part ("except Mammalia and Aves") could be considered a type of
qualifying clause (though it differs from the qualifying clauses
discribed in the PhyloCode in excluding certain descendant taxa from the
named group, making it paraphyletic, rather than restricting use of the
name to a subset of the possible phylogenies). =20
=20
Article 11.10 states that names remain eligible for use even if they are
worded so that they don't apply to any taxon in the context of certain
phylogenies (since they could still be used in the context of other
phylogenies). It refers specifically to clade names, but it does not
exclude the names of paraphyletic taxa.
In general, the references to clade names that Gerry interprets as
evidence that the PhyloCode prohibits the naming of paraphyletic taxa
simply reflect the fact the the PhyloCode is designed for naming clades.
The rules in question are not meant to prohibit the naming of
paraphyletic taxa; they simply emphasize the kind of taxa (clades) whose
names they are designed to govern.
Kevin
>>> "Moore, Gerry" <gerrymoore@bbg.org> - 2/6/04 8:43 AM >>>
I don't agree that the PhyloCode could be used to give explicit
definitions to names of non-monophyletic taxa. This assertion has also
found it way in print by Kevin and Phil (Taxon 50: 821-826. 2001):
"First it should be noted that although the PhyloCode is designed to
name clades, it does not expressly prohibit the naming of paraphyletic
groups."
The first article (1.1) in the PhyloCode "only clade names are governed
by this code." And the next article (2.1) defines clade as "an ancestor
and all of its descendents." Given this, any name given a definition
that identifies a non-monophyletic group would have no standing under
the PhyloCode. Arts. 11.9, 11.10 also make it clear that names that do
not identify a clade in the context of a given phylogeny are not to be
used.
The PhyloCode may not expressly prohibit the naming of non-monophyletic
taxa but it is pretty clear they are prohibited nonetheless. A code
that uses explicit definitions could be written so that it permits the
naming of non-monophyletic taxa but the PhyloCode is not written this
way.
Gerry Moore=20