<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear CPN members,<div><br></div><div>I want to assure you that I have not forgotten about our reconsideration of proposal 9 (see below). The issue that David M. raised is a serious one with no easy solution. Kevin and I have been actively working on it and hope before long to be able to send you a proposed revision of Note 11.1.1, which will at least reduce the frequency and gravity of the problem David has pointed out, though it will not eliminate it entirely. The problem illustrated by David's fish example is a consequence of our having broadened the PhyloCode's operational definition of the species category to accommodate those who do not accept the idea that a species is a population lineage segment. I am not suggesting that we revisit that decision, which I personally support, but if we retain a broad operational definition of "species" in the code, we may simply have to accept that differences in species concepts or hypotheses of species boundaries will result in occasional changes in the application of the names of low-level clades whose contents coincide with or overlap the membership of those species. As Kevin pointed out to me in our discussions of this problem over the past couple of weeks, variability in the application of clade names due to differing conceptualizations of the species used as specifiers is analogous to variability in the application of clade names due to differing phylogenetic hypotheses. In his view, and I agree, such variability results from legitimate scientific disagreements (whether about phylogenetic hypotheses or species boundaries), not from artificial considerations regarding taxonomic ranks. Tolerating these kinds of inconsistencies is just the price that we pay for trying to be inclusive with respect to the conceptualization of the species category.</div><div><br></div><div>I hope that we can send you a detailed proposed revision soon.</div><div><br></div><div>Phil</div><div><br></div><div><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">"Cantino, Philip" <<a href="mailto:cantino@ohio.edu">cantino@ohio.edu</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">November 8, 2012 3:37:17 PM EST<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Committee on Phylogenetic Nomenclature <<a href="mailto:cpn@listserv.ohio.edu">cpn@listserv.ohio.edu</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Re: [CPN] PLEASE VOTE on CBM-related proposals</b><br></span></div><br><div>I have not had time to think carefully about David's comments. At this point, proposals 1, 3, 4, 5, 6, 8, 9, and 10 have been approved by the majority of the CPN, and proposal 7 (deletion of Rec. 11.4B) was rejected in an earlier vote. However, we may want to reconsider proposal 9 in light of the issues David has raised. I will respond to David's comments in a few days after I have time to think about them more. <br><br>Item 2 (revision of Art. 21) and the glossary definition of "taxon" still remain to be considered after we revisit proposal 9, and Kevin and I have materials ready to send you on both of these remaining items. <br><br>Phil<br><br><br>On Nov 6, 2012, at 4:33 PM, David Marjanovic wrote:<br><br><blockquote type="cite">I am really sorry that I wasn't able to reply earlier. It turns out that <br></blockquote><blockquote type="cite">items 9 and 10 require more discussion than we've had over them -- and <br></blockquote><blockquote type="cite">now almost everybody has already voted. Here is my ballot:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">1) approve<br></blockquote><blockquote type="cite">3) approve<br></blockquote><blockquote type="cite">4) approve (I actually prefer "taxonomic rank" over "categorical rank" <br></blockquote><blockquote type="cite">because I think the former has a little less potential for confusion, <br></blockquote><blockquote type="cite">but that potential is low anyway)<br></blockquote><blockquote type="cite">5) approve<br></blockquote><blockquote type="cite">6) approve<br></blockquote><blockquote type="cite">8) approve (see 4; and I'm actually unhappy with "scientific name", <br></blockquote><blockquote type="cite">seeing as nomenclature isn't science, but I don't have a better idea!)<br></blockquote><blockquote type="cite">9) I disagree with the justification and, somewhat independently, with <br></blockquote><blockquote type="cite">the proposal. The apparent contradiction in the current wording of Note <br></blockquote><blockquote type="cite">11.1.1, pointed out in the justification, actually allows for naming <br></blockquote><blockquote type="cite">clades that overlap with species rather than containing them entirely. <br></blockquote><blockquote type="cite">Under at least some species concepts, this has no problem happening. The <br></blockquote><blockquote type="cite">potential example that comes to mind are the famous teleost fishes from <br></blockquote><blockquote type="cite">somewhere in Central America (I forgot all details) that have a <br></blockquote><blockquote type="cite">phylogenetic tree as follows, where each letter stands for the <br></blockquote><blockquote type="cite">population of one river (or river system or something):<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">--+--A<br></blockquote><blockquote type="cite"> `--+--B<br></blockquote><blockquote type="cite"> `--+--C<br></blockquote><blockquote type="cite"> `--+--D<br></blockquote><blockquote type="cite"> `--E<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">(In case your e-mail reader removes the leading spaces, this is a Hennig <br></blockquote><blockquote type="cite">comb.)<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Now, A and E can interbreed, making them the same species under one of <br></blockquote><blockquote type="cite">the Biological Species Concepts. B, C and D, however, cannot interbreed <br></blockquote><blockquote type="cite">either with each other or with A or E! Under the BSC in question, we are <br></blockquote><blockquote type="cite">thus dealing with a triply paraphyletic species.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Now suppose somebody wants to name the clade (CDE), and suppose it is <br></blockquote><blockquote type="cite">not known that A and E can interbreed, so that everybody agrees that E <br></blockquote><blockquote type="cite">is a distinct species. Further suppose that this species is used as a <br></blockquote><blockquote type="cite">specifier in the definition. What happens when it is discovered that A <br></blockquote><blockquote type="cite">and E can interbreed?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Under the current wording of Note 11.1.1, nothing happens; the type of E <br></blockquote><blockquote type="cite">remains the implicit specifier even if the name of A has priority over <br></blockquote><blockquote type="cite">that of E, so that the definition continues to apply to (CDE).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Under the proposed wording, A becomes part of the specifier. If the <br></blockquote><blockquote type="cite">definition is node-based or apomorphy-based, it suddenly applies to <br></blockquote><blockquote type="cite">(ABCDE) instead of (CDE). If it is branch-based with B or C as an <br></blockquote><blockquote type="cite">external specifier, it self-destructs -- it ceases to apply to any <br></blockquote><blockquote type="cite">clade, and the name is lost (for the time being).<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">...But all this is only true for people who happen to accept this <br></blockquote><blockquote type="cite">particular species concept. To people who use, say, any Phylogenetic <br></blockquote><blockquote type="cite">Species Concept, the whole synonymization of A and E never happened in <br></blockquote><blockquote type="cite">the first place. Consequently, _different people will use the same name <br></blockquote><blockquote type="cite">for different clades even though they agree on the phylogeny_. To <br></blockquote><blockquote type="cite">prevent _exactly this_ from ever happening is the first and foremost <br></blockquote><blockquote type="cite">purpose of the PhyloCode. We cannot make the application of definitions <br></blockquote><blockquote type="cite">dependent on species concepts. The only way I can see of preventing this <br></blockquote><blockquote type="cite">is to use only specimens as specifiers, explicitly or implicitly.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The use of implicit specifiers, and here we get back to the apparent <br></blockquote><blockquote type="cite">contradiction, looks silly at first (though see below!), but I think <br></blockquote><blockquote type="cite">it's the best option in some (OK, a few) cases -- those where the type <br></blockquote><blockquote type="cite">specimen isn't actually what people have in mind when they use the <br></blockquote><blockquote type="cite">species name that's attached to it, so that eventually the responsible <br></blockquote><blockquote type="cite">commission of the rank-based code in question steps in and declares a <br></blockquote><blockquote type="cite">neotype. The example that comes to mind is the dinosaur *Coelophysis <br></blockquote><blockquote type="cite">bauri*. The original type series (syntypes, IIRC), found and described <br></blockquote><blockquote type="cite">in the mid-late 19th century, are a few isolated incomplete bones; *C. <br></blockquote><blockquote type="cite">bauri* became extremely well known to scientists and the general public <br></blockquote><blockquote type="cite">when a large number of complete skeletons were found at another site and <br></blockquote><blockquote type="cite">stratigraphic level in the early-mid 20th century. Those skeletons, in <br></blockquote><blockquote type="cite">particular the famous plate with AMNH 7223 and 7224, is what people have <br></blockquote><blockquote type="cite">been de facto using as the type when comparing specimens from elsewhere <br></blockquote><blockquote type="cite">to *C. bauri*. A few years ago it turned out that the original types are <br></blockquote><blockquote type="cite">only diagnostic to Coelophysidae or Coelophysoidea or something. <br></blockquote><blockquote type="cite">Normally, *C. bauri* would have become a nomen dubium, and a new name <br></blockquote><blockquote type="cite">would have had to be created for the complete skeletons, massively <br></blockquote><blockquote type="cite">disrupting continuity of usage. Instead, following a petition, the ICZN <br></blockquote><blockquote type="cite">made AMNH 7224 the neotype, and everyone is happy. In such cases, the <br></blockquote><blockquote type="cite">implicit specifier designated by a species name should shift, too.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The same holds for species names that lack types at present: the <br></blockquote><blockquote type="cite">implicit specifiers that they designate should be whatever their <br></blockquote><blockquote type="cite">_future_ type specimens will be.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The justification continues: "Some PhyloCode users who believe the <br></blockquote><blockquote type="cite">species is nothing more than a Linnaean rank may not like this change, <br></blockquote><blockquote type="cite">but it shouldn't matter to them because they don't intend to use species <br></blockquote><blockquote type="cite">as specifiers anyway. They have the option of explicitly using type <br></blockquote><blockquote type="cite">specimens rather than species as specifiers, in which case the specimen <br></blockquote><blockquote type="cite">is truly the specifier (see proposed change #10 below)." But that's not <br></blockquote><blockquote type="cite">true. Whether species or specimens are the specifiers of a particular <br></blockquote><blockquote type="cite">definition would, under the proposed wording, depend on the definition, <br></blockquote><blockquote type="cite">not on the user! Under the current wording, all specifiers are <br></blockquote><blockquote type="cite">(implicitly or explicitly) specimens.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Implicit specifiers are not new to the PhyloCode. It expressedly allows <br></blockquote><blockquote type="cite">branch-modified and apomorphy-modified node-based definitions; their <br></blockquote><blockquote type="cite">specifiers are all members, known or unknown, of another clade that is <br></blockquote><blockquote type="cite">described by another definition.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">10) I would approve if "explicitly" were inserted near the beginning: <br></blockquote><blockquote type="cite">"When a type specimen is explicitly used as a specifier," that should be <br></blockquote><blockquote type="cite">taken as meaning that the authors really want that specimen to be a <br></blockquote><blockquote type="cite">specifier, future neotypes be damned. -- As explained above, I disagree <br></blockquote><blockquote type="cite">with the justification; but that's not actually relevant.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">If my line of argumentation is accepted, it might be a good idea to <br></blockquote><blockquote type="cite">write a Note about implicit vs. explicit specifiers to make sure authors <br></blockquote><blockquote type="cite">will understand that both options exist and that the choice is theirs.<br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">CPN mailing list<br></blockquote><blockquote type="cite"><a href="mailto:CPN@listserv.ohio.edu">CPN@listserv.ohio.edu</a><br></blockquote><blockquote type="cite"><a href="http://listserv.ohio.edu/mailman/listinfo/cpn">http://listserv.ohio.edu/mailman/listinfo/cpn</a><br></blockquote><br><br>_______________________________________________<br>CPN mailing list<br><a href="mailto:CPN@listserv.ohio.edu">CPN@listserv.ohio.edu</a><br><a href="http://listserv.ohio.edu/mailman/listinfo/cpn">http://listserv.ohio.edu/mailman/listinfo/cpn</a><br></div></blockquote></div><br></div></body></html>