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Date: Mon, 02 Oct 2000 10:21:06 -0400
From: "Moore, Gerry" <gerrymoore@bbg.org>
To: 'Nathan Wilson' <velosa@cinenet.net>
Cc: PhyloCode@ouvaxa.cats.ohiou.edu, "'cantino@ohio.edu'" <cantino@ohio.edu>
Subject: RE: Nathan Wilson's question
O.K. Nathan's position is now clear to me. We have different
interpretations on my original definition of the taxon name that represents
Clade Z. To some extent, our different intepretations stem from the
"Ancestors and Taxonomy" problem discussed by Lee (TREE 13:26. 1998).
Clearly, I think that specifiers that occur in more than one nonnested clade
and are used in phylogenetic defintions present possible problems. I take
one last stab at this issue after the summary below.
GM: To me whether or not it is one or two (or three etc.) of the specifiers
that happens to occupy nonnested clades is irrelevant. Are you saying that
in my example, Clade Z's circumscription would not have to be expanded to
include Clade B because only one of the specifiers (species 3) was shown to
occur in more than one nonnested clade? If so, I don't follow (more below).
NW: Close, but not quite. As long as there is all the clades that contain
both 3 & 4 are properly nested there is no problem. It is only when there
is a pair of non-nested clades that contain both 3 & 4 that you have a
problem. From your example, Clade Z is defined as the descendents of the
most recent common ancestor of species 3 and species 4. This says nothing
about ancestors of species 3 that are not descendents of that ancestor. As
long as none of these extra ancestors of species 3 are also ancestors of
species 4 that do not pass through the most recent common ancestor of 3 and
4, then the most recent common ancestor is still well defined. However, as
soon as 3 & 4 share more than one non-nested clade that don't also contain
all of the most recent ancestors of 3 & 4, the Clade(3+4)becomes undefined.
Actually my original definition (Clade Z: least inclusive clade containing
species 3 and species 4) does not say anything about ancestors. If I were
to apply Z to a clade, I would simply find (from the accepted phylogeny) the
least inclusive clade that includes species 3 and 4, regardless of any
interpretations of ancestry. To me, that clade must include clades A and B
since species 3 has been shown to belong to both clades (refer back to
original example). In my interpretation, excluding clade B from Z's
circumscription would be contrary to its definition (which says nothing
about ancestors).
Still, I now recognize how one might interpret this differently since
there is a less inclusive clade that does include species 3 and species 4
but does not include clade B. However, I would not apply Z to this clade
because it does not include "all" of species 3, since species 3 also occurs
in clade B.
This problem is significant because a primary goal of phylogenetic
nomenclature is that, given an accepted phylogeny, everyone will apply the
same name to a given clade. However, when specifiers are shown to occur in
multiple nonnested clades and there are different interpretations as to how
to apply the definitions that include such specifiers, this goal may not be
met. Thus, Michel Laurin's suggestion in an earlier post seems valid.
Cheers,
Gerry Moore
2 Oct. 2000