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--></style><title>Re: [CPN] time to move towards a decision on the
Cellinese</title></head><body>
<div>Thanks for the prompt, Dave.</div>
<div><br></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><br></div>
<div>Dick</div>
<div><br></div>
<div><font face="Times New Roman" color="#000000"><b>Review of
Cellinese, Baum, and Mishler</b>:</font></div>
<div><font face="Times New Roman" color="#000000">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. <br>
<br>
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. <br>
<br>
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).<br>
<br>
I think it is important that this perspective be aired. <br>
<br>
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. <br>
<br>
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.</font></div>
<div><font face="Times New Roman" color="#000000"><br>
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. <br>
<br>
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.<br>
<br>
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.</font><br>
<font face="Times New Roman" color="#000000"></font></div>
<div><br></div>
<div><br></div>
<div><br></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><br></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><br></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><br></blockquote>
<blockquote type="cite" cite>Thanks much.</blockquote>
<blockquote type="cite" cite><br></blockquote>
<blockquote type="cite" cite>Dave</blockquote>
<blockquote type="cite" cite><br></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><br>
</blockquote>
<blockquote type="cite" cite>_________________________________<br>
David C. Tank<br>
Assistant Professor & Director, Stillinger Herbarium<br>
University of Idaho<br>
208.885.7033<br>
<a href="mailto:dtank@uidaho.edu">dtank@uidaho.edu</a><br>
http://www.phylodiversity.net/dtank/</blockquote>
<blockquote type="cite" cite><br></blockquote>
<blockquote type="cite" cite>On Feb 6, 2012, at 2:55 PM, de Queiroz,
Kevin wrote:</blockquote>
<blockquote type="cite" cite><br>
<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.<br>
<br>
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:<br>
<br>
"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."<br>
"The question is to remove species as ranks with special
privilege."<br>
<br>
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><br>
Thus, I oppose the proposal of Cellinese et al. because their
arguments are based on a false premise.<br>
<br>
Kevin de Queiroz<br>
<br>
On 2/5/12 5:46 PM, "Kevin Padian" <<a
href="mailto:kpadian@Berkeley.EDU">kpadian@Berkeley.EDU</a>>
wrote:<br>
<br>
Dear Colleagues,<br>
<br>
There has been no discussion of the Cellinese et al. proposal on the
CPN<br>
listserv for some time. Perhaps everyone has said his or her
piece? I am<br>
finding email an unsatisfactory way to resolve these problems, and I
would<br>
ask again that people consider some kind of meeting at which this
and<br>
other proposals can be raised and discussed. Or, at least, let's
set an<br>
"election day" on which to terminate comments and take
votes. (Please,<br>
not "Super Tuesday" ...)<br>
<br>
I would like to revive the discussion of the Cellinese et al.
proposal.<br>
We have seen Phil and Michel propose modifications to the PhyloCode
about<br>
the definition of species, but this does not address the proposal,
which<br>
was to remove species as a special rank in PhyloCode. This is
what we<br>
should be voting on, I think, not merely how to reword some articles
of<br>
the Code.<br>
<br>
There are other points of view in the systematic community, and in my
view<br>
it would be good to consider them in order to make sure that there is
a<br>
broad enfranchisement of positions. Referring to Phil's first
point about<br>
a broader glossary definition of species: for a lot of
taxonomists,<br>
species don't need to be defined in the Phylocode by ANY definition.
We<br>
don't define genera, families, etc. To do so, in the view of
many, just<br>
clouds the issue. If we remove any legal use of species names in
the<br>
PhyloCode we can keep it purely focused on naming clades, and leave
the<br>
species controversy aside. The whole issue of species concepts
is just a<br>
tar baby; it is far more productive for biologists to discuss how
new<br>
lineages form in different groups of organisms, and then recognize<br>
subdivisions of lineages (including the arbitrary concept
"species") as<br>
particular to those groups. Taxonomy is, in a sense,
bookkeeping; such<br>
accounting procedures can't adequately encompass the processes and<br>
patterns that describe the splitting of lineages.<br>
<br>
One of the most important points of the Cellinese et al. proposal is
to<br>
remove the use of species names as specifiers. They discuss
reasons for<br>
this in their Systematic Biology paper, including the need for the<br>
Phylocode to be independent from the existing codes. It would
make sense<br>
if the PhyloCode could allow the mention of an existing species name
as a<br>
specifier as a short cut for referring to its type specimen. But
the type<br>
specimen should be the legal specifier, not the name.<br>
<br>
In his discussion of Rec. 9c, Phil says:<br>
"Often the entities
that one needs to determine whether they<br>
belong to a particular clade are not specimens but, rather,<br>
species or clades. I therefore suggest the following
wording:<br>
In order to facilitate the
referral of less inclusive clades, as<br>
well as species and specimens that are not specifiers of the clade<br>
name, the protologue should include a description, diagnosis, or<br>
list of synapomorphies."<br>
<br>
But Cellinese et al. are saying precisely that traditional Linnaean
taxa,<br>
including species, can never be precisely compared to clades named
under<br>
the PhyloCode, given that they only have one specifier. I don't
think<br>
anyone on the CPN could disagree with this -- it is basically the
main<br>
reason why we all want the Phylocode. So species should be left
out of<br>
this. It could read: "In order to facilitate the
referral of less<br>
inclusive clades, as well as specimens that are not specifiers of
the<br>
clade name, the protologue should include a description, diagnosis,
or<br>
list of synapomorphies."<br>
<br>
Phil does not include genera or families as specifiers in his
suggested<br>
wordings, only species. It is implicitly rank-based thinking to
single<br>
out the species rank for special treatment, and this seems
contradictory<br>
to the principles of the PhyloCode.<br>
<br>
So, on balance, I think that the approaches that Phil and others
have<br>
suggested to the proposal by Cellinese et al. do not address their
central<br>
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<br>
reason. I don't know what a species is, any more than I know
what an<br>
order is.<br>
<br>
The question is to remove species as ranks with special privilege.
Yes or<br>
no?<br>
<br>
<br>
<br>
<br>
--<br>
Kevin Padian<br>
Department of Integrative Biology &<br>
Museum of Paleontology<br>
University of California, Berkeley CA 94720-3140<br>
510-642-7434<br>
<a
href="http://www.ucmp.berkeley.edu/people/padian/home.php"
>http://www.ucmp.berkeley.edu/people/padian/home.php</a><br>
<br>
<br>
_______________________________________________<br>
CPN mailing list<br>
CPN@listserv.ohio.edu<br>
http://listserv.ohio.edu/mailman/listinfo/cpn<br>
<br>
<br>
_______________________________________________<br>
CPN mailing list<br>
CPN@listserv.ohio.edu<br>
http://listserv.ohio.edu/mailman/listinfo/cpn<br>
</blockquote>
</blockquote>
<blockquote type="cite" cite><br></blockquote>
<blockquote type="cite" cite><br>
_______________________________________________<br>
CPN mailing list<br>
CPN@listserv.ohio.edu<br>
http://listserv.ohio.edu/mailman/listinfo/cpn</blockquote>
<div><br></div>
<div><br></div>
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