By Dick Olmstead. -------- Original-Nachricht -------- Datum: Thu, 8 Mar 2012 13:30:49 -0800 Von: Richard Olmstead < olmstead at u.washington.edu > An: David Tank < dtank at uidaho.edu >, Committee on Phylogenetic Nomenclature < cpn at listserv.ohio.edu > Betreff: Re: [CPN] time to move towards a decision on the Cellinese et al. proposal Thanks for the prompt, Dave. 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. Dick =========================== Review of Cellinese, Baum, and Mishler: 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. 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. -------------- next part -------------- _______________________________________________ CPN mailing list CPN at listserv.ohio.edu http://listserv.ohio.edu/mailman/listinfo/cpn
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