<!doctype html public "-//W3C//DTD W3 HTML//EN"> <html><head><style type="text/css"></style><title>Re: [CPN] time to move towards a decision on the Cellinese</title></head><body> <div>Thanks for the prompt, Dave.</div> <div> </div> <div>I had not yet submitted any comments on the CMP proposal, but was one of the reviewers of the Systematic Biology manuscript. Since I signed my review and it is now in press, I don't think there is any reason to not simply share my review as a comment on this matter.  I realize the review of the ms. is not the same as a direct comment on the proposed change to the PhyloCode, but I think my impressions are implicit in the review itself. </div> <div> </div> <div>Dick</div> <div> </div> <div>Review of Cellinese, Baum, and Mishler:</div> <div>Contrary to rumors, the PhyloCode is alive and may actually be published this year.  Most of the bugs in naming clades have been worked out through a lot of give and take over the past couple of decades.  However, the remaining elephant in the room is species.  After much more discussion, the International Society of Phylogenetic Nomenclature (the group of systematists and paleontologists most interested in seeing a system of phylogenetic nomenclature) finally punted on the species problem, and the current draft of the PhyloCode explicitly leaves species to the traditional Codes.  This is not a happy arrangement for either the supporters of traditional nomenclature or phylogenetic nomenclature.  So, it is time that someone forces the issue into the light of day once again, before the PhyloCode goes to press.  The authors make their case here.  The source of the problem mostly devolves to the dual nature of "species" as a rank in Linnaean classification and as an evolutionary concept that exists as a lineage over time or as a functional ecological/evolutionary unit.  The problem is compounded by the conventional use of binomials, which imply ranks at two levels (genus and species).  The authors offer a solution: simply delete any mention of species in the PhyloCode.  The implications for this include that clades can be defined at whatever level in the phylogenetic hierarchy that evidence permits, which may, on occasion, be equivalent to species in traditional classifications, and that specifiers must be actual museum or herbarium specimens (or synapomorphies in the case of apomorphy-based names), but not species.  I think both of these suggestions are perfectly acceptable amendments to the PhyloCode (although the practicality of using specimens as specifiers for more inclusive clades becomes problematic, if standards require that authors have actually seen the specimens, as is commonly the case for species-level revisions under traditional codes in many journals today). I think it is important that this perspective be aired.  However, if there were an easy solution to this, it would have been agreed upon by now.  It is true that avoiding mention of 'species' in the Code would simplify things and provide for a stand-alone code of nomenclature.  It is also true that eliminating 'species' from the PhyloCode will still permit individual taxonomists to make use of the traditional codes to provide species descriptions, if they so desire, while permitting others to name taxa at any level they want to using PhyloCode, evidence permitting.  That being said, adopting this approach to the PhyloCode won't make it any easier to name taxa at the tips of branches.  It doesn't address the practicality of defining clades at the traditional species rank and that this will rarely be feasible due to issues having to do with sampling, incomplete coalescence of gene trees, and other complicating issues that make population-level phylogenetics very difficult.  It will likely always be easier to circumscribe a group of individuals by reference to a set of shared traits, by which they differ from other such groups, and a single specimen (type) that exhibit those traits.  At best, the result will be de facto the same as the present PhyloCode - people will still rely on traditional codes for naming species, while permitting the definition of clades at branch tips, where they may be equivalent to species under the traditional codes.  At worst, there will be a rash of terminal clades defined using specimens that are vouchers for various DNA sequences, but which cannot possibly represent all of the diversity found in the populations of what we now call species in nature, due to either inadequate sampling or molecular evolutionary issues such as differential lineage sorting among loci (or those branch tips simply going unnamed by those who refuse to use traditional codes and who can't justify defining clades at that level in the hierarchy).  Pick your poison.</div> <div> The homonym issue becomes more problematic with this proposal.  If common species epithets become widely converted to clade names, it will pose difficulties for bibliographic/informatic search functions.  Even if a registration number and authorities' names and year of publication are added to the name when published, the shorthand nomenclature used in publications is not going to include those unique attributes.  All of the actual changes suggested in the PhyloCode are simply rewordings or deletions based on eliminating references to species and leaving specimens only as specifiers.  The one exception, at least to my reading, was the recommended removal of Article 13.5.  I don't understand why the changes they recommend would eliminate the possibility (however remote it might be anyway) that the oldest name for a group might be a later homonym. The proposal here may be the best solution for those (including some among the authors) who promote abandoning "species" altogether as something unique either in taxonomic hierarchy or in evolutionary biology.  For those who aren't yet willing to abandon species (probably the large majority of systematists, and surely the large majority of biologists) this would, like the current version of the PhyloCode, still represent a stopgap measure that leaves species to the traditional codes and leaves the PhyloCode incomplete in this regard.  The proposed changes offer consistency and independence from the traditional codes in any formal way.  However, I'm not sure whether it would be more disruptive for a future code revision that finally comes to grip with the species problem, if it uses the current version of the code or the amended one proposed here as the starting point.  That is the question that those who will be responsible for final wording in the PhyloCode need to address. </div> <div> </div> <div> </div> <div> </div> <div>At 2:03 PM -0800 3/7/12, David Tank wrote:</div> <blockquote type="cite" cite>Dear CPN,</blockquote> <blockquote type="cite" cite> </blockquote> <blockquote type="cite" cite>There have been several weeks of silence on the discussion re: the Cellinese et al. species proposal, and I believe it is time to proceed to a vote.  Because this is a dense proposal with quite a few related topics and proposed changes to the code, as a committee we need to decide on a process for moving towards a decision.</blockquote> <blockquote type="cite" cite> </blockquote> <blockquote type="cite" cite>At this point I would like suggestions from you on how a vote should be structured.  Once we have a structure that we agree on, we can return a decision to the authors of the proposal.</blockquote> <blockquote type="cite" cite> </blockquote> <blockquote type="cite" cite>Thanks much.</blockquote> <blockquote type="cite" cite> </blockquote> <blockquote type="cite" cite>Dave</blockquote> <blockquote type="cite" cite> </blockquote> <blockquote type="cite" cite>PS - in case you have not been looking at Sys Biol advance access, the Cellinese et al. point of view is in press.  <a href="http://sysbio.oxfordjournals.org/content/early/recent" >http://sysbio.oxfordjournals.org/content/early/recent</a> </blockquote> <blockquote type="cite" cite>_________________________________ David C. Tank Assistant Professor & Director, Stillinger Herbarium University of Idaho 208.885.7033 <a href="mailto:dtank@uidaho.edu">dtank@uidaho.edu</a> http://www.phylodiversity.net/dtank/</blockquote> <blockquote type="cite" cite> </blockquote> <blockquote type="cite" cite>On Feb 6, 2012, at 2:55 PM, de Queiroz, Kevin wrote:</blockquote> <blockquote type="cite" cite> <blockquote type="cite" cite>Unfortunately, my comments apparently have not yet been distributed to the CPN (as a result of David M's move to Berlin), so I will send them to the CPN listserv after I send this message.  Before doing so, I would like to comment briefly Kevin Padian's message. Like those of Cellinese et al., Padian's arguments presuppose that the species category is nothing more than a rank.  This is evident in statements such as the following: "It is implicitly rank-based thinking to single out the species rank for special treatment, and this seems contradictory to the principles of the PhyloCode." "The question is to remove species as ranks with special privilege." Contrary to these statements and many in the proposal by Cellinese et al., the species category is no longer treated as just another taxonomic rank.  Instead, it is treated as different from the categories in the hierarchy of taxonomic ranks, with views ranging from a category with special properties to a category for an entirely different kind of entity.  This tradition traces at least back to Darwin and has become increasingly widely accepted over the years.  It underlies virtually all modern species definitions as well as a number of related ideas, including species individuality, species selection, and the distinction between macroevolution and microevolution.   This not to deny that the species category retains some elements of its former treatment as a taxonomic rank.   However, there is a HUGE difference between a retaining some historical baggage and truly being just another taxonomic rank.</blockquote> <blockquote type="cite" cite> Thus, I oppose the proposal of Cellinese et al. because their arguments are based on a false premise. Kevin de Queiroz On 2/5/12 5:46 PM, "Kevin Padian" <<a href="mailto:kpadian@Berkeley.EDU">kpadian@Berkeley.EDU</a>> wrote: Dear Colleagues, There has been no discussion of the Cellinese et al. proposal on the CPN listserv for some time.  Perhaps everyone has said his or her piece?  I am finding email an unsatisfactory way to resolve these problems, and I would ask again that people consider some kind of meeting at which this and other proposals can be raised and discussed.  Or, at least, let's set an "election day" on which to terminate comments and take votes.  (Please, not "Super Tuesday" ...) I would like to revive the discussion of the Cellinese et al. proposal. We have seen Phil and Michel propose modifications to the PhyloCode about the definition of species, but this does not address the proposal, which was to remove species as a special rank in PhyloCode.  This is what we should be voting on, I think, not merely how to reword some articles of the Code. There are other points of view in the systematic community, and in my view it would be good to consider them in order to make sure that there is a broad enfranchisement of positions.  Referring to Phil's first point about a broader glossary definition of species: for a lot of taxonomists, species don't need to be defined in the Phylocode by ANY definition.  We don't define genera, families, etc.  To do so, in the view of many, just clouds the issue.  If we remove any legal use of species names in the PhyloCode we can keep it purely focused on naming clades, and leave the species controversy aside.  The whole issue of species concepts is just a tar baby; it is far more productive for biologists to discuss how new lineages form in different groups of organisms, and then recognize subdivisions of lineages (including the arbitrary concept "species") as particular to those groups.  Taxonomy is, in a sense, bookkeeping; such accounting procedures can't adequately encompass the processes and patterns that describe the splitting of lineages. One of the most important points of the Cellinese et al. proposal is to remove the use of species names as specifiers.  They discuss reasons for this in their Systematic Biology paper, including the need for the Phylocode to be independent from the existing codes.  It would make sense if the PhyloCode could allow the mention of an existing species name as a specifier as a short cut for referring to its type specimen.  But the type specimen should be the legal specifier, not the name. In his discussion of Rec. 9c, Phil says:        "Often the entities that one needs to determine whether they belong to a particular clade are not specimens but, rather, species or clades.  I therefore suggest the following wording:        In order to facilitate the referral of less inclusive clades, as well as species and specimens that are not specifiers of the clade name, the protologue should include a description, diagnosis, or list of synapomorphies." But Cellinese et al. are saying precisely that traditional Linnaean taxa, including species, can never be precisely compared to clades named under the PhyloCode, given that they only have one specifier.  I don't think anyone on the CPN could disagree with this -- it is basically the main reason why we all want the Phylocode.  So species should be left out of this.  It could read:  "In order to facilitate the referral of less inclusive clades, as well as specimens that are not specifiers of the clade name, the protologue should include a description, diagnosis, or list of synapomorphies." Phil does not include genera or families as specifiers in his suggested wordings, only species.  It is implicitly rank-based thinking to single out the species rank for special treatment, and this seems contradictory to the principles of the PhyloCode. So, on balance, I think that the approaches that Phil and others have suggested to the proposal by Cellinese et al. do not address their central point, but rather shelve it and simply tinker with other wording.  I am</blockquote> <blockquote type="cite" cite>not in favor of the modifications that Phil and Michel suggest for this reason.  I don't know what a species is, any more than I know what an order is. The question is to remove species as ranks with special privilege.  Yes or no? -- Kevin Padian Department of Integrative Biology & Museum of Paleontology University of California, Berkeley CA 94720-3140 510-642-7434 <a href="http://www.ucmp.berkeley.edu/people/padian/home.php" >http://www.ucmp.berkeley.edu/people/padian/home.php</a> _______________________________________________ CPN mailing list CPN@listserv.ohio.edu http://listserv.ohio.edu/mailman/listinfo/cpn _______________________________________________ CPN mailing list CPN@listserv.ohio.edu http://listserv.ohio.edu/mailman/listinfo/cpn </blockquote> </blockquote> <blockquote type="cite" cite> </blockquote> <blockquote type="cite" cite> _______________________________________________ CPN mailing list CPN@listserv.ohio.edu http://listserv.ohio.edu/mailman/listinfo/cpn</blockquote> <div> </div> <div> </div> <x-sigsep><pre>-- </pre></x-sigsep> <div>Richard Olmstead Professor of Biology and Herbarium Curator, Burke Museum Department of Biology<x-tab>   </x-tab><x-tab>        </x-tab>For express mail services: Box 355325<x-tab>    </x-tab><x-tab>        </x-tab><x-tab>        </x-tab><x-tab>        </x-tab>Department of Biology University of Washington<x-tab>   </x-tab><x-tab>        </x-tab><x-tab>        </x-tab>Hitchcock Hall Rm 423 Seattle,  WA  98195-5325<x-tab>   </x-tab><x-tab>        </x-tab><x-tab>        </x-tab>University of Washington USA<x-tab>     </x-tab><x-tab>        </x-tab><x-tab>        </x-tab><x-tab>        </x-tab><x-tab>        </x-tab>Seattle, WA  98195 Office: 206-543-8850 lab:            206-543-6594 herbarium:      206-543-1682 FAX:            206-685-1728 email:          olmstead@u.washington.edu      http://www.biology.washington.edu/users/richard-olmstead</div> </body> </html>

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