As I said, I've been wondering about Article 1 and its similarity to the Glossary entry for "taxon". So I looked up what the rank-based codes have instead, and searched the PhyloCode for "tax". == The rank-based codes == Art. 1 of the ICZN http://www.nhm.ac.uk/hosted-sites/iczn/code/includes/page.jsp?article=1 is titled "Definition and scope" -- not of the ICZN, but of "zoological nomenclature": Art. 1.1 reads "Zoological nomenclature is the system of scientific names applied to taxonomic units (taxa; singular: taxon) of extant or extinct animals." Art. 1.1.1 explains what is meant by "animals". Art. 1.2 makes explicit what is included (e. g. fossils that don't contain any substance that belonged to the living animal), 1.3 makes explicit what is excluded, 1.4 asserts independence from the other rank-based codes. Art. 2 deals with taxa classified as animals at one time but not another, Art. 3 defines the starting point. Art. 1.1 of the ICBN (2006) http://ibot.sav.sk/icbn/frameset/0005Ch1Art001.htm reads: "Taxonomic groups of any rank will, in this _Code_, be referred to as taxa (singular: taxon)." Art. 1.2 and 1.3 introduce morphotaxa; Art. 2 and 3 introduce ranks. The ICNB, as of 1992, never explains "taxon". There isn't even a glossary! The term "taxa" appears for the first time in General Consideration 4 http://www.ncbi.nlm.nih.gov/books/n/icnb/A154/ -- it is evidently assumed that the code will be read by taxonomists, who already know what a taxon is. == Search results from the PhyloCode== Apart from Principle 5, for which see below, "taxon"/"taxa"/"subtaxa" occurs in four different ways: -- Where it could simply be omitted: 6.4, Art. 7.2, Example 1 of 11A (first occurrence), Glossary entry: phylogenetic definition. The first two cases have "name of a taxon"; in many other places, the PhyloCode just uses "name" instead. -- Where it could be replaced by "clade": Principles 1 through 4, Art. 6.5, 6.6, 9.10 (arguably), 10.1 (later "paraphyletic group" three times), 11.8 with both Notes, Example 1 of 11.9, 13.1, 13.3, 13.5, 14.1, Example 1 of Note 15.11.1, all Examples of 15.13, 21A, Glossary entries: accepted name, apomorphy-modified node-based definition, branch-modified node-based definition (first two occurrences). Many of these were probably written when we still expected to add rules for species names before implementation. -- Where it refers to taxa (potentially) recognized under rank-based codes: 9.8 (incl. Note 9.8.2 with Example), Example 2 of Note 9.8A.1, 10.1B (arguably), 10D, 10E (arguably), 10G (probably), Example 2 of 11.9, 11A (main text), Example 1 of 11A (second and third occurrence), 11C, 17.1, Notes 21.4A2 and -3, 21.4B with Examples 2 and 5, Example 3 of Note 21A.3, Glossary entries: categorical rank, definition, description, diagnosis, epithet, extant (arguably), homonym (arguably -- see 13.1), hybrid formula (arguably), phylogenetic system, rank, rank-based system, synonym (arguably -- see 14.1), taxon (first sentence), type. This usage is, importantly, _not_ covered by Art. 1 or by Phil's proposal for the Glossary entry of "taxon". -- Where it clearly refers specifically to clades and species: Glossary entries: apomorphy-based definition, branch-modified node-based definition (third occurrence), taxon (second sentence). In the Glossary entry for "branch-modified node-based definition", "taxa" could be replaced by "organisms". What, actually, is the status of the Glossary? Are its entries meant to have the force of Articles and apply exclusively to the PhyloCode, or are they meant to merely explain the terms used in nomenclature, as far as they happen to occur in the PhyloCode? Different entries seem to assume one or the other, sometimes apparently even both. == Suggestions == Abandon the implication that the PhyloCode is about the names of taxa. It is, for now at least, specifically about the names of clades. Therefore: -- Omit "taxon"/"taxa" where the term is unnecessary; replace it by "clade" or "organisms" where that is meant; keep it elsewhere. I'm not sure what to do with the Glossary entry for "apomorphy-based definition". -- Restrict the glossary entry for "taxon" to the following: "A grouping of organisms (e.g., a clade) that has been, or could be, given a name under a code of nomenclature. Taxa can be nested." This assumes that the Glossary is meant to explain the terms, not define them specifically for the PhyloCode. -- Delete Article 1. We might replace it with an article about scope and the starting point, but all that is already explained in the Preamble and the Principles. == What else I found during the search of the PhyloCode == -- The Example to Note 9.8.2 cites "Olmstead and Judd (20xx)". That should be rectified. -- Example 1 to Note 15.11.1 says that Angiospermae has synapomorphies. But Hennig was pickier than that. Being one clade, it has autapomorphies (auto- = self); only two or more taxa can share synapomorphies (syn- = together). -- Preamble item 1 should contain a reference to Art. 2, where "clade" is defined and explained. -- Perhaps "permits" should be replaced by "does not restrict" in Principle 6; that sounds less authoritarian. Also in Principle 6, "taxonomic opinion" should be shortened to "opinion" -- it is already explained immediately afterwards as "with regard to hypotheses about relationships"; to this explanation, we should probably add "or ranks" and reference Art. 3. -- Perhaps we should rewrite Principle 5. How about: "Phylogenetic context. This code assumes evolution (descent with heritable modification); it is concerned with the naming of clades and the application of clade names in the context of phylogenetic hypotheses." But, actually, this is all already implied in Preamble item 1, so maybe we should simply delete Principle 5.
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