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Date: Fri, 06 Feb 2004 11:19:26 -0500
From: Kevin de Queiroz <Dequeiroz.Kevin@NMNH.SI.EDU>
To: gerrymoore@bbg.org, 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).
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