Message 2004-02-0021: Re: RE: a comment on ancestor

Mon, 09 Feb 2004 16:48:30 -0500

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Date: Mon, 09 Feb 2004 16:48:30 -0500
From: Kevin de Queiroz <Dequeiroz.Kevin@NMNH.SI.EDU>
Subject: Re: RE: a comment on ancestor

Igor Ya. Pavlinov wrote:

>And in some of the articles special
>consideration should be paid to not rare (rather, near to unversal)
>situations when a group is treated as holophyletic in one hypothesis and
>paraphyletic in another (Pinnipedia is good an example). All this is
>to make more clear what used to happen with the name in situation when
>name-bearing taxon losts its holophyletic status.

How a taxon name such as "Pinnipedia" is to be treated in the context of
different phylogeentic hypotheses should be clear from the way in which the
name is defined.  Thus, if Pinnipedia is defined simply as the least
inclusive clade contaning seals, sea lions, and walruses, this name will
always refer to a monophyletic (holophyletic) taxon, though it will include
only these three subgroups in the context of some phylogenetic hypotheses,
while it will include one or more fissipeds (animals without "flippers") in
the context of other hypotheses.  The name would never refer to a
paraphyletic or polyphyletic taxon.  In contrast, if a qualifying clause
similar to the one I described earlier (e.g., "provided that their aquatic
adaptations did not evolve convergently") were to be included, then the name
Pinnipedia would be used for the clade of seals, sea lions, and walruses in
the context of those phylogenetic hypotheses in which they formed a clade;
in the context of hypotheses in which these three taxa did not form a clade,
the name would not be used.  In order for the name to refer to a
monophyletic taxon in the context of some phylogenetic hypotheses and a
paraphyletic or polyphyletic taxon in the context of others, the name would
have to be defined along the following lines:  Pinnipedia = the taxon
composed of seals, sea lions, and walruses (and no other taxa) regardless of
their phylogenetic relationships.

>What seems to be also important, is treatements of procedures by which
>phylogenetic hypotheses are elaborated. For me, it is clear that trees
>obtained by middle-point rooting or UPGMA procedures are methodologically
>phenograms rather than cladograms. So, as a clade is thought to be
>recognized within a particular phylogenetic hypothesis only, then what
>criteria of validity of the hypothesis itself? Surely consideration of
>a topic within the Phylocode will cause many objections, but at least
>indication that not all trees are phylogenetic ones, although are called
>would be no less desirable than undication of criteria of publication

The method or methods used to infer phylogenetic relationships is a
taxonomic rather than a nomenclatural issue; therefore, it is outside of the
jurisdiction of the PhyloCode.  Consequently, systematists are free to use
whatever methods they like (even UPGMA!) to infer phylogenetic
relationships; however, some methods (such as UPGMA) will make it more
difficult for them to satisfy other requirements of phylogenetic nomenclatue
(such as providing a diagnosis), and their use may affect how widely the
conclusions are accepted by other researchers.  


Kevin de Queiroz
Division of Amphibians & Reptiles
Smithsonian Institution
P.O. Box 37012
NHB, Room W203, MRC 162
Washington, D.C. 20013-7012
Voice:  202-357-2212
FAX:  202-786-2979


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