Message 2000-09-0008: RE: Nathan Wilson's question

Thu, 28 Sep 2000 15:13:09 -0700 (PDT)

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Date: Thu, 28 Sep 2000 15:13:09 -0700 (PDT)
From: Nathan Wilson <velosa@cinenet.net>
To: "Moore, Gerry" <gerrymoore@bbg.org>
Cc: PhyloCode@ouvaxa.cats.ohiou.edu, "'cantino@ohio.edu'" <cantino@ohio.edu>
Subject: RE: Nathan Wilson's question

On Thu, 28 Sep 2000, Moore, Gerry wrote:

> NW: Gerry Moore also brings up an interesting point about using members of
> non-nested clades as specifiers, but I think the example he gave doesn't
> quite make the point.  As Philip Cantino points out there is no problem
> under the current definitions if one of the two species belongs to two
> non-nested clades. 
>  
> Where did Phil say that?

In the email in which he first brought up non-nested clades.

> Under phylogenetic nomenclature a clade's circumscription must include
> all positions where the specifiers show up. 

It may be that this stated in the current draft of the PhyloCode.  I've
only read it couple of times and I wasn't looking for this specific
concept.  In any case, the issue is really whether non-nested clades break
the logical definition of clades.  Restricting our discussion to
node-based clades, there is nothing about the defintion from Note 9.4.1 of
the PhyloCode "the clade stemming from the most recent common ancestor of
A and B" that prevents A from belonging to two non-nested clades.  There
can still be a single most recent common ancestor between A and B.  It
simply means that any path from B to the clade containing both of A's
non-nested clades must pass through that most recent ancestor of A and B. 

The problem I was pointing out is that A and B might both belong to
non-nested clades and they might be the same non-nested clades.  At this
point there is no longer a single most recent common ancestor of A and B.
The simplest example is to imagine that there are two species, P1 and P2,
that manage cross in two different populations forming two new species, C1
and C2. In the current system the Clade (C1+C2) is not well defined since
you don't know if it is rooted at P1 or P2.  Claiming that it now becomes
equivalent to Clade (P1+P2) has the undesirable effect of pulling in all
the siblings of P1 and P2.  The small set C1, C2, P1, P2 is still an
interesting set to talk about even though it is distinct from
Clade(C1+C2+P1+P2).

> 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). 

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.

-Nathan



  

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