Message 2000-07-0010: Re: Stem-based taxon definitions

Mon, 31 Jul 2000 15:35:01 -0500 (CDT)

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Date: Mon, 31 Jul 2000 15:35:01 -0500 (CDT)
From: "Jonathan R. Wagner" <znc14@TTACS.TTU.EDU>
To: Kevin de Queiroz <Dequeiroz.Kevin@NMNH.SI.EDU>
Subject: Re: Stem-based taxon definitions

At 11:40 AM 7/31/00 -0400, Dr. de Queiroz wrote:
>This is irrelevant.  Every group is going to be paraphyletic or
>polyphyletic at some level,
        If you believe that para- and polyphyletic describe the inclusion or
exclusion of SPECIES, not of individuals, then this is not necessary. It is
very easy to conceive of an entirely monophyletic group of SPECIES, even if
this is a para- or polyphyletic group of ORGANISMS. Just as an organism can
be a paraphyletic assemblege of cells, so can a species be a paraphyletic
assembly of organisms. If I assert that a clade is a species and all of its
descendants, then that clade is purely monophyletic with respect to species,
since it contains an ancestral species and all of its descendant species.
        This is a consequence of species reality. I species are real
entities which produce new species, then we can talk about, and recognize,
para-, poly- and monophyletic groups of species. If species are real, then a
monophyletic group of species is as real as a monophyletic group of
organisms. Indeed, it is somewhat easier to concieve of since, for the most
part, species are not biparental.
        DNA does not reproduce cells, cells produce cells. Cells do not
produce organisms, organisms produce organisms. Organisms may found species,
and a single organism may perhaps be part of a species unto itself, but an
organism never IS a species, and it never SPAWNS a species. A clade, as a
real entity (rather than just a collective), is similarly begun by a species
(the ancestral species), but that species is never the clade and vice versa
(a consequence of this, however, is that there *can* be a monospecific
clade). Following this line of reasoning, clades are never polyphyletic or
paraphyletic... this is a tautological property of monophyletic groups. A
clade might be polyphyletic with respect to organisms, but again, not with
respect to species, just as a clan may be monophyletic with respect to
individuals, but paraphyletic with respect to cells.
        Am I just way off base here?

>and no one (except perhaps Baum and Shaw) seems
>to have a problem with the idea that species (and thus the clades derived
>from them) are paraphyletic or polyphyletic in terms of their component
>organisms, cells, or genes.
        I accept this as necessary and evident. Hoewever, this does NOT
require clades to be para or polyphyletic with respect to species.

>See the discussion of phyly in my 1999 paper
>(in Species: New Interdisciplinary Essays).
        I shall reread this as soon as I have time.

>Moreover, I didn't advocate
>changing the phrasing to "ancestral individual."  The solution is to leave
>the type of ancestor unspecified, thus allowing the ancestor to be part of a
>species (the part that's more closely related to A than to B; this is the
>relevance of the paper by de Queiroz and Donoghue, 1988).
        But then, what sort of common ancestor does a biparental species
have? it will have a different most recent common ancestor depending on
whether you follow the male or female line, won't it? I find it much easier
to deal with ancestral species than ancestors, even if it is just evading
the question.

>On the other hand, the problem you raised with the wording of stem-based
>definitions is based on a wording not used in the PhyloCode.  You stated the
        True enough.

>phrasing as "species A and all species sharing a more recent common
>ancestral species with A than with B."  This is not the wording used in the
>PhyloCode, which states the definition as follows:  "Y and all oganisms [not
>species] that share a more recent common ancestor [not ancestral species]
>with Y than with W."
        But a group of organisms is a clan or a clone, not a clade. Will we
be naming clans and clones under the phylocode?

>The wording
>actually used in the PhyloCode wouldn't result in a reference to a
>polyphyletic taxon.  

Take the same example, but pretend A-G are organisms.
>        A D'
>         D
>         D E
>          D  F'  
>           F F'
>           FF' B
>           F  GB
>            C G
>            CG
>            C

"individual A and all organisms that share a more recent common ancestor
with A than with B."
        Organism F' shares a MRC with A (i.e., F) than it does with B.
Organism F's most recent ancestor is C, which is also ancestral to B.
Therefore, it appears to me that the Phylocode wording does indeed result in
a polyphyletic group of organisms. Am I in error?

        You could, alternately, take an ultra-Hennigian approach, and
declare that the part of F after the spawning of F' (the part of my mom
which exists after 1973, in human terms) is separate, and consists of cells
closer to A than to B. This, to my mind, is analogous to cutting clades
across species lines. I favor clades which are monophyletic groups of (real)
species, not organisms. As such, they do not cut species lines.

     Jonathan R. Wagner, Dept. of Geosciences, TTU, Lubbock, TX 79409-1053
  "Why do I sense we've picked up another pathetic lifeform?" - Obi-Wan Kenobi


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