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Date: Thu, 12 Oct 2000 18:43:15 -0400
From: Kevin de Queiroz <Dequeiroz.Kevin@NMNH.SI.EDU>
To: PhyloCode@ouvaxa.cats.ohiou.edu
Subject: Fwd: Re: RE: RE: Nathan Wilson's question
Phil Wrote: "I think that what Gerry had in mind (and he should correct me if I am = misinterpreting) is that some of the genome of species 3 is in clade A and = some in clade B. If so, the least inclusive clade that includes the full genome of species 3 is the larger one identified by Gerry, thus the application of the name for clade Z is ambiguous." To my way of thinking, that interpretation is incorrect. If we're = concerned with naming monophyletic groups of genes or genomes rather than = species, then the species in which the genes or genomes occur are = irrelevant. On the other hand, if we're concerned with naming monophyletic= groups of species (clades), then the fact that part of the genome of = species 3 comes from one source and another part from another means only = that certain clades are partially overlapping in terms of their species = composition. It doesn't create any ambiguity regarding the application of = the name. The only way to reach the conclusion that the name should be = applied to the larger clade in Gerry's example (and therefore that = application of the name is ambiguous) is to confuse levels by substituting = genomes for species in the definitions (which is effectively what has been = done in the diagrams that have species 3 in two places). Another way to = see the error is to consider the statement "some of the genome of species = 3 is in clade A and some in clade B". While true, what this statement = fails to acknowledge is that the part of the genome that is in clade A is = also in clade B, and the part of the genome that is in clade B is also in = clade A. The very notion of hybridization implies that that we can no = longer treat clades A and B as entirely separate (mutually exclusive) = entities. =20 Kevin=20 12 Oct 2000