Message 2000-10-0010: RE: RE: Nathan Wilson's question

Thu, 12 Oct 2000 15:39:58 -0400

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Date: Thu, 12 Oct 2000 15:39:58 -0400
From: Philip Cantino <>
Subject: RE: RE: Nathan Wilson's question

As soon as I read Kevin's recent message, I realized that I had
failed to send the following message, written yesterday, to the
listserv.  Instead, I accidentally sent it just to Gerry (who must
have wondered why I kept referring to him in the third person).

Well, better late than never.  I apologize for my error.



Gerry wrote (in a message to me, now forwarded to all):

>I took a look at this again last night and concluded
>that there really were two ways of looking at this. I hate to say this
>(since the PhyloCode warps away from it) but it boils down to how one
>"defines" Species 3.  If you regard Species 3 as the sum total of all it
>positions in the phylogeny then the approach I outlined in the attachment is
>logical.  However, if one is simply willing to regard species 3 as occurring
>at multiple nonnested clades (and not regard each position as a "part" of
>species 3) then the definition of Clade Z can be applied to the exclusion of
>some (in this case one) of the nonnested clades where Species 3 shows up.

Yes, that is it exactly.  As soon as I saw that Gerry had placed
species 3 in two different positions in his second cladogram, I
understood the difference in how we were viewing the situation.  It
had not occurred to me that part of species 3 would be placed in one
position and part in another, and this is why I couldn't understand
Gerry's argument that clade Z must include all of the non-nested
clades to which its specifier species belong.

In contrast, If I had drawn the cladograms, I would have shown
species 3 only once on the second cladogram, with lines connecting it
to both of its putative parent species (presumably species 9 in clade
B and species 2 in clade A).  This would reflect my view that once
the hybrid species is formed, the whole species is a member of both
clades A and B.  The LEAST INCLUSIVE clade containing species 3 and 4
would then include clade A but not clade B, thus the original content
of clade Z would not be changed as a result of the discovery that
species 3 is a hybrid.

I think that both Gerry's view and mine have merit.  His is correct
in that half of the genome of species 3 belongs to clade A and half
to clade B.  On the other hand, I don't think it makes nomenclatural
sense to divide a species up in this way.  The entity that is being
named is the whole species, not half of its genome.  This named
entity arose only once (assuming there was only one hybridization
event) and should therefore occur only once on the cladogram.

However, I do agree with Gerry that both interpretations are
possible, and therefore different people, given the same phylogeny,
may apply a definition in different ways.  This is potentially a
serious problem because it is contrary to principle 2 of the

I think the best solution is a modification of the one that Michel
Laurin proposed: If a specifier is found to be a hybrid, and one of
the parents of the specifier lies outside the defined clade under any
published phylogenetic hypothesis, the definition may be amended in
the usual fashion (see Note 13.1.2).  I think it is important to
include the qualifier "and one of the parents of the specifier lies
outside the defined clade under any published phylogenetic
hypothesis" in order to reduce the frequency of such emendations.
Many plant species are of hybrid origin, but generally the parents
are closely related.  If such a species is used as a specifier in the
definition of a large (i.e., upper level) clade, it will usually be
the case that both parents of the specifier are members of the
defined clade under all phylogenetic hypotheses.  We do not want to
suggest that people emend definitions in this situation.  The kind of
situation represented in Gerry's cladograms is likely to occur mainly
with lower-level clades composed of closely related species.

I also agree with Michel that the rule should include a note stating
that lateral gene transfer does not constitute hybridization.



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