[CPN] Fwd: PLEASE VOTE on CBM-related proposals

[Cantino, Philip]

Dear CPN members,

I want to assure you that I have not forgotten about our reconsideration of proposal 9 (see below).  The issue that David M. raised is a serious one with no easy solution.  Kevin and I have been actively working on it and hope before long to be able to send you a proposed revision of Note 11.1.1, which will at least reduce the frequency and gravity of the problem David has pointed out, though it will not eliminate it entirely.  The problem illustrated by David's fish example is a consequence of our having broadened the PhyloCode's operational definition of the species category to accommodate those who do not accept the idea that a species is a population lineage segment.  I am not suggesting that we revisit that decision, which I personally support, but if we retain a broad operational definition of "species" in the code, we may simply have to accept that differences in species concepts or hypotheses of species boundaries will result in occasional changes in the application of the names of low-level clades whose contents coincide with or overlap the membership of those species.  As Kevin pointed out to me in our discussions of this problem over the past couple of weeks, variability in the application of clade names due to differing conceptualizations of the species used as specifiers is analogous to variability in the application of clade names due to differing phylogenetic hypotheses.  In his view, and I agree, such variability results from legitimate scientific disagreements (whether about phylogenetic hypotheses or species boundaries), not from artificial considerations regarding taxonomic ranks.  Tolerating these kinds of inconsistencies is just the price that we pay for trying to be inclusive with respect to the conceptualization of the species category.

I hope that we can send you a detailed proposed revision soon.

Phil


Begin forwarded message:

From: "Cantino, Philip" <cantino at ohio.edu<mailto:cantino at ohio.edu>>
Date: November 8, 2012 3:37:17 PM EST
To: Committee on Phylogenetic Nomenclature <cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>>
Subject: Re: [CPN] PLEASE VOTE on CBM-related proposals

I have not had time to think carefully about David's comments.  At this point, proposals 1, 3, 4, 5, 6, 8, 9, and 10 have been approved by the majority of the CPN, and proposal 7 (deletion of Rec. 11.4B) was rejected in an earlier vote.  However, we may want to reconsider proposal 9 in light of the issues David has raised.  I will respond to David's comments in a few days after I have time to think about them more.

Item 2 (revision of Art. 21) and the glossary definition of "taxon" still remain to be considered after we revisit proposal 9, and Kevin and I have materials ready to send you on both of these remaining items.

Phil


On Nov 6, 2012, at 4:33 PM, David Marjanovic wrote:

I am really sorry that I wasn't able to reply earlier. It turns out that
items 9 and 10 require more discussion than we've had over them -- and
now almost everybody has already voted. Here is my ballot:

1) approve
3) approve
4) approve (I actually prefer "taxonomic rank" over "categorical rank"
because I think the former has a little less potential for confusion,
but that potential is low anyway)
5) approve
6) approve
8) approve (see 4; and I'm actually unhappy with "scientific name",
seeing as nomenclature isn't science, but I don't have a better idea!)
9) I disagree with the justification and, somewhat independently, with
the proposal. The apparent contradiction in the current wording of Note
11.1.1, pointed out in the justification, actually allows for naming
clades that overlap with species rather than containing them entirely.
Under at least some species concepts, this has no problem happening. The
potential example that comes to mind are the famous teleost fishes from
somewhere in Central America (I forgot all details) that have a
phylogenetic tree as follows, where each letter stands for the
population of one river (or river system or something):

--+--A
 `--+--B
    `--+--C
       `--+--D
          `--E

(In case your e-mail reader removes the leading spaces, this is a Hennig
comb.)

Now, A and E can interbreed, making them the same species under one of
the Biological Species Concepts. B, C and D, however, cannot interbreed
either with each other or with A or E! Under the BSC in question, we are
thus dealing with a triply paraphyletic species.

Now suppose somebody wants to name the clade (CDE), and suppose it is
not known that A and E can interbreed, so that everybody agrees that E
is a distinct species. Further suppose that this species is used as a
specifier in the definition. What happens when it is discovered that A
and E can interbreed?

Under the current wording of Note 11.1.1, nothing happens; the type of E
remains the implicit specifier even if the name of A has priority over
that of E, so that the definition continues to apply to (CDE).

Under the proposed wording, A becomes part of the specifier. If the
definition is node-based or apomorphy-based, it suddenly applies to
(ABCDE) instead of (CDE). If it is branch-based with B or C as an
external specifier, it self-destructs -- it ceases to apply to any
clade, and the name is lost (for the time being).

...But all this is only true for people who happen to accept this
particular species concept. To people who use, say, any Phylogenetic
Species Concept, the whole synonymization of A and E never happened in
the first place. Consequently, _different people will use the same name
for different clades even though they agree on the phylogeny_. To
prevent _exactly this_ from ever happening is the first and foremost
purpose of the PhyloCode. We cannot make the application of definitions
dependent on species concepts. The only way I can see of preventing this
is to use only specimens as specifiers, explicitly or implicitly.

The use of implicit specifiers, and here we get back to the apparent
contradiction, looks silly at first (though see below!), but I think
it's the best option in some (OK, a few) cases -- those where the type
specimen isn't actually what people have in mind when they use the
species name that's attached to it, so that eventually the responsible
commission of the rank-based code in question steps in and declares a
neotype. The example that comes to mind is the dinosaur *Coelophysis
bauri*. The original type series (syntypes, IIRC), found and described
in the mid-late 19th century, are a few isolated incomplete bones; *C.
bauri* became extremely well known to scientists and the general public
when a large number of complete skeletons were found at another site and
stratigraphic level in the early-mid 20th century. Those skeletons, in
particular the famous plate with AMNH 7223 and 7224, is what people have
been de facto using as the type when comparing specimens from elsewhere
to *C. bauri*. A few years ago it turned out that the original types are
only diagnostic to Coelophysidae or Coelophysoidea or something.
Normally, *C. bauri* would have become a nomen dubium, and a new name
would have had to be created for the complete skeletons, massively
disrupting continuity of usage. Instead, following a petition, the ICZN
made AMNH 7224 the neotype, and everyone is happy. In such cases, the
implicit specifier designated by a species name should shift, too.

The same holds for species names that lack types at present: the
implicit specifiers that they designate should be whatever their
_future_ type specimens will be.

The justification continues: "Some PhyloCode users who believe the
species is nothing more than a Linnaean rank may not like this change,
but it shouldn't matter to them because they don't intend to use species
as specifiers anyway.  They have the option of explicitly using type
specimens rather than species as specifiers, in which case the specimen
is truly the specifier (see proposed change #10 below)." But that's not
true. Whether species or specimens are the specifiers of a particular
definition would, under the proposed wording, depend on the definition,
not on the user! Under the current wording, all specifiers are
(implicitly or explicitly) specimens.

Implicit specifiers are not new to the PhyloCode. It expressedly allows
branch-modified and apomorphy-modified node-based definitions; their
specifiers are all members, known or unknown, of another clade that is
described by another definition.

10) I would approve if "explicitly" were inserted near the beginning:
"When a type specimen is explicitly used as a specifier," that should be
taken as meaning that the authors really want that specimen to be a
specifier, future neotypes be damned. -- As explained above, I disagree
with the justification; but that's not actually relevant.

If my line of argumentation is accepted, it might be a good idea to
write a Note about implicit vs. explicit specifiers to make sure authors
will understand that both options exist and that the choice is theirs.
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