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Date: Mon, 19 Feb 2001 15:47:05 -0500
From: Kevin de Queiroz <Dequeiroz.Kevin@NMNH.SI.EDU>
To: PhyloCode@ouvaxa.cats.ohiou.edu
Subject: Re: RE: On the Other Phylogenetic Systematics, Nixon and Carpenter
I addition to the points raised by Harold Bryant, I thought I should = mention a couple of additional problems with Nixon and Carpenter's = paleoherb example. First, although under certain changes in the accepted = phylogenetic hypothesis, the composition of the taxon called "paleoherbs" = might change substantially in composition, it might be the case that these = changes are unimporrtant. The reason is that the name "paleoherbs" might = become synonymous with another taxon name, such as "angiosperms," in which = case the name "paleoherbs" might not continue to be used. Second, this is = somewhat of an unfair example in that the name "paleoherbs" is not really = governed by the traditional codes because it is an informal name not = associated with any particular rank. For this reason, it is not really = fair to use it as an example to contrast phylogenetic and traditional = systems of nomenclature, since it's use isn't governed by the traditional = system and thus is less constained than the use of names that are governed = by that system. =20 Kevin de Queiroz >>> "Bryant, Harold MACH" <HBryant@mach.gov.sk.ca> - 2/16/01 10:46 AM >>> As one of the "disciples" referred to in Nixon and Carpenter's paper, I thought I would comment on their paper, and especially their "paleoherb" example. It also provides a context for some comments on qualifying clauses. I had planned to comment on JW's earlier comments on the latter issue, but until today I hadn't found the time. N&C's paleoherb example certainly illustrates the potential for marked changes in the taxonomic content associated with a name given changes to phylogenetic hypotheses. This is not a new revelation; it has been = evident for some time (e.g., Schander and Thollesson [1995], Zool. Scripta 24:263-268) and was the stimulus for the development of various devices, including qualifying clauses, that can markedly increase the stability in the content of taxa with particular names with changes, or differences of opinion, regarding phylogenetic pattern. I find N&C's paper, and use of this example, misleading because they do not consider these options in the coining of a phylogenetic definition for this name, or in their discussion of the content issue. Also, they do not address the issue of whether it would have been appropriate to even define the name in the first place. = The PhyloCode (Rec. 9B) recommends extreme caution in defining names that = refer to poorly supported clades. If someone wanted to provide a phylogenetic definition for paleoherbs, the clade conceptualized by Donoghue and Doyle in their 1989 paper would be = best reflected in a definition that included a qualifying clause that identified= the phylogenetic situations in which the name would not apply to ANY = clade. Such a definition could be phrased in various ways but one form would be: "the least inclusive clade that contains species A and B (+ others as required), but does not include species C (+ others as required)." (the reference to the exclusion of C is the qualifying clause) Given this definition, the name would not apply to any clade on cladograms where C is included in the least inclusive ancestry circumscribed by A and B. I find this approach very appropriate. Most names are proposed within a = particular phylogenetic context (see Bryant 1997 Biol. J Linn. Soc. 62:495-503). On cladograms that lack that context (because of either changes in our understanding of phylogeny due to new information, or simply differences = of option in the choice of a reference phylogeny), I feel that best approach = is to simply not use that clade name in referring to that cladogram. = Certainly this approach avoids the marked changes in content evident in N&C's paleoherb example. N&C's discussion is also misleading in that they totally ignore the fact that with the current codes content associated with a taxonomic name can change or differ simply because of subjective differences of option regarding the boundaries between taxa, or the rank in the Linnean = hierarchy where they should be placed. This source of instability is eliminated = with PN, where changes in content are associated solely with changes or differences of option regarding phylogenetic pattern. I feel that the = jury is still out regarding the relative degree of stability in the content of named taxa due to differences in phylogenetic pattern (assuming that = devices such as qualifying clauses are used, and that care is exercised in the construction of phylogenetic definitions). When the additional sources of instability inherent to the traditional system are also taken into = account, I think there is a very good chance that the OVERALL level of stability = may even be higher with PN. (my discussion assumes that content stability is = a good thing - that is a point that could also be debated (my view: = sometimes yes, sometimes no) - however, there is no question that it is an important issue if for no other reason than this is the more frequent criticism of PN.) =20 Harold =20 ---------------------------------------------------------------------------= - ------------------------------------------------ Harold Bryant Royal Saskatchewan Museum 2340 Albert Street Regina, Saskatchewan S4P 3V7 Canada 306-787-2826 FAX 306-787-2645=20