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Date: Mon, 09 Feb 2004 16:48:30 -0500
From: Kevin de Queiroz <Dequeiroz.Kevin@NMNH.SI.EDU>
To: phylocode@ouvaxa.cats.ohiou.edu, igor_pavlinov@zmmu.msu.ru
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 as >paraphyletic in another (Pinnipedia is good an example). All this is needed >to make more clear what used to happen with the name in situation when the >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 validly >recognized within a particular phylogenetic hypothesis only, then what are >criteria of validity of the hypothesis itself? Surely consideration of such >a topic within the Phylocode will cause many objections, but at least some >indication that not all trees are phylogenetic ones, although are called so, >would be no less desirable than undication of criteria of publication >validity. 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 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 E-mail: dequeiroz.kevin@nmnh.si.edu