[CPN] Comments part 5

[David Marjanovic]

By Dick Olmstead.

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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.
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