[CPN] time to move towards a decision on the Cellinese et al. proposal
Richard Olmstead
olmstead at u.washington.edu
Thu Mar 8 16:30:49 EST 2012
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.
At 2:03 PM -0800 3/7/12, David Tank wrote:
>Dear CPN,
>
>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.
>
>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.
>
>Thanks much.
>
>Dave
>
>PS - in case you have not been looking at Sys Biol advance access,
>the Cellinese et al. point of view is in press.
> <http://sysbio.oxfordjournals.org/content/early/recent>http://sysbio.oxfordjournals.org/content/early/recent
>
>_________________________________
>David C. Tank
>Assistant Professor & Director, Stillinger Herbarium
>University of Idaho
>208.885.7033
><mailto:dtank at uidaho.edu>dtank at uidaho.edu
>http://www.phylodiversity.net/dtank/
>
>On Feb 6, 2012, at 2:55 PM, de Queiroz, Kevin wrote:
>
>>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.
>>
>>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"
>><<mailto:kpadian at Berkeley.EDU>kpadian at Berkeley.EDU> 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
>>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
>><http://www.ucmp.berkeley.edu/people/padian/home.php>http://www.ucmp.berkeley.edu/people/padian/home.php
>>
>>
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>
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Richard Olmstead
Professor of Biology and Herbarium Curator, Burke Museum
Department of Biology For express mail services:
Box 355325 Department of Biology
University of Washington Hitchcock Hall Rm 423
Seattle, WA 98195-5325 University of Washington
USA Seattle, WA 98195
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email: olmstead at u.washington.edu
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