[CPN] Window for comments on proposal

[David Marjanovic]

On 10.01.2012 19:27, David Tank wrote:

>  Hi all,
>
>  2 things.
>
>  First, yes, I think that we (CPN) should get this discussion going
>  now. If you haven't taken the time to read the proposal yet, now is
>  a good time - if you have, and would like to comment, great. A
>  couple folks have already - I've pasted that thread below.

Except for my first two comments, which weren't sent to the list, so I 
don't even know if everyone has seen them:

-------- Original Message --------
Subject:     Re: Proposal to amend the PhyloCode
Date:     Wed, 05 Oct 2011 23:23:57 +0200
From:     David Marjanovic <david.marjanovic at gmx.at>
To:     Nico Cellinese <ncellinese at flmnh.ufl.edu>
CC:     Brian Andres <brian.andres at yale.edu>, feander at siu.edu, Philip 
Cantino <cantino at ohio.edu>, Kevin de Queiroz <dequeirozk at si.edu>, 
Jacques Gauthier <jacques.gauthier at yale.edu>, 
walter.joyce at uni-tuebingen.de, Michael Keesey <keesey at gmail.com>, Michel 
Laurin <michel.laurin at upmc.fr>, Richard Olmstead 
<olmstead at u.washington.edu>, Kevin Padian <kpadian at berkeley.edu>, David 
Tank <dtank at uidaho.edu>, Brent Mishler <BMishler at calmail.berkeley.edu>, 
"David A. Baum" <dbaum at wisc.edu>, torsten.eriksson at nrm.se

I am not sure if we are supposed to open the discussion or wait for the
publication -- the manuscript is, after all, already in review. However,
if the former is the case...

Preamble, item 1: I agree with the proposal.

Art. 1.1:
Current: "The groups of organisms whose names are governed by this code
are called taxa (singular: taxon). Taxa may be clades or species, but
only clade names are governed by this code."
Proposal: "The groups of organisms whose names are governed by this code
are called taxa (singular: taxon). Only clade names are governed by this
code."
Why mention taxa at all, when all taxa governed by the PhyloCode are
clades? I would like to suggest the following: "This code governs the
names of clades of organisms." We could then merge this article with
Art. 2.1 if we think a one-sentence article is too short. :-)

Art. 2.1: I agree with the proposal, though I like Keesey's "ancestral
set" even better.

Art. 2.2, Note 3.1.1: I agree with the proposal.

Art. 9.4 and 11, and Note 13.2.2: I disagree with the proposal. This is
because some well-known extant species that were named long ago, like
*Crocodylus niloticus*, do not have a type specimen at all, and they
will only be given one if doubts about their monophyly will ever come
up. I don't see why such species should be disallowed as specifiers. I
also like the current situation in which a specifier can change when the
type specimen of the species that is actually meant changes (because a
lectotype is selected from a series of syntypes, or because a neotype is
designated -- disclaimer: I have not tried to find out if the ICBN uses
these terms in the same ways as the ICZN, if at all). If PhyloCode users
had to select a specimen that belongs to such a species as a specifier,
this would, in practice, probably amount to de facto selecting a type
specimen under the rank-based code in question; I don't think that's a
good thing.

Art. 9.5: I agree with the proposal.

Art. 9.7: Unnamed subclades will likely be indicated, in many cases, by
lists of included species, so I don't think the proposal would change much.

Rec. 9c: I agree with the proposal, though "organisms" would be better
than "specimens" (a museum specimen can consist of several organisms).

Art. 10.5: I agree with the proposal.

Art. 10.9: This is a tricky one.
1) Specific epithets are (usually) not unique, so converting one
*vulgaris* or *mongoliensis* will prevent all others from being
converted in that shape.
2) Converting an epithet will, in practice, lead to defining the species
with that name even for users of the rank-based codes. And that amounts
to imposing one species concept on everyone. I do not like that at all.
3) I admit that I have dinosaur privilege. Among Mesozoic and older
vertebrates, the number of genera with more than one species is
negligible, so that most LITUs already have a uninominal which already
looks like a clade name and is already unique (except for intercode
homonyms like the archosaur and flowering plant *Galtonia*). This is
because most species concepts are not even applicable, so that species
are only named at all because the ICZN requires it and because it allows
authors to honor more colleagues than otherwise. I understand this is
very different from the situation most neontologists find themselves in.

Art. 13, general proposal: I disagree. This proposal would require
biologists to learn not just the names of the taxa they work on, but
also the authors and year of each of these names. On average, that's
perhaps a fivefold increase of effort (many taxon names have more than
one author, I know some with 13 and 19). Further, it will increase
vanity among authors of clade names; clades should be named to make
talking about them easier, not to make oneself immortal.

Art. 13.1, 13.3 and 13.5, and Note 13.2.3: These proposals almost define
homonyms out of existence and therefore, again, require that biologists
learn all relevant authors and years. I do not like that prospect at all
-- and I am rather unusually good at remembering numbers!

Art. 21: I agree with the idea of removing the implication that there is
such a thing as a species name under the PhyloCode (which is clearest in
Art. 21.5 and 21.2). However, Art. 21 contains more than that; therefore
I do not agree with the proposal to abolish it in its entirety.
1) At a minimum, the current Art. 21.4 with Rec. 21.4A and B (and all
their notes and examples) should be kept, because they recommend how to
go about naming species without having to take actions incompatible with
the PhyloCode and without causing confusion when two systems of
nomenclature are used in the same publication.
2) Rec. 21.4C is a different matter; it recommends Kevin de Queiroz's
species concept. I think it should be replaced by a Recommendation which
urges authors of species names to state which species concept they have
in mind and to provide evidence that their new species is in fact a new
species under that concept -- this touches on the PhyloCode because some
species concepts (like the one by Baum 2009) require species to be clades.
3) Completely independently of the proposal, Art. 21.3 should not be an
Article. It consists of a note (the statement that, because of Art. 3.1,
the PhyloCode does not govern names at subspecific and lower ranks) and
a recommendation ("their use to refer to [...] is discouraged"). If
kept, they should be made a Note and a Recommendation.
4) Art. 21.5 and Rec. 21A are pretty much identical. If kept, they
should be merged into a Recommendation.

Thus, I would like to submit my own proposal for amending Art. 21 in the
next e-mail (this one is long enough).

-------- Original Message --------
Subject:     Proposal to amend Article 21
Date:     Thu, 06 Oct 2011 01:54:05 +0200
From:     David Marjanovic <david.marjanovic at gmx.at>
To:     Nico Cellinese <ncellinese at flmnh.ufl.edu>
CC:     feander at siu.edu, Philip Cantino <cantino at ohio.edu>, Kevin de 
Queiroz <dequeirozk at si.edu>, Jacques Gauthier 
<jacques.gauthier at yale.edu>, walter.joyce at uni-tuebingen.de, Michael 
Keesey <keesey at gmail.com>, Michel Laurin <michel.laurin at upmc.fr>, 
Richard Olmstead <olmstead at u.washington.edu>, Kevin Padian 
<kpadian at berkeley.edu>, David Tank <dtank at uidaho.edu>, Brent Mishler 
<BMishler at calmail.berkeley.edu>, "David A. Baum" <dbaum at wisc.edu>, 
torsten.eriksson at nrm.se

The entire text of what the amended Art. 21 would look like follows:

==============================

21.1. This code does not govern the establishment or precedence of
species, subspecies or variety[*] names. To be considered available
(ICZN) or validly published (ICBN, ICNB), a (new or replacement) name
for a species, subspecies or variety must satisfy the provisions of the
appropriate rank-based code (e.g., ICNB, ICBN, ICZN). This article
contains recommendations on how to avoid confusion when performing
nomenclatural acts concerning species, subspecies or varieties in
publications that use clade names in ways that conform to this code.

[* Question: is this an exhaustive list? The ICZN and the ICNB recognize
only the rank of subspecies below that of species; varieties, used in
botany, are explicitly forbidden in zoology and bacteriology.]

[current Note 21.1.1 deleted]

Note 21.1.1. In any particular classification, a species, subspecies or
variety may be identical in content to a clade, and a clade may be
assigned the rank of species. In such cases, intercode synonymy may
occur between this code and a rank-based one, because names governed by
this code have a different form from species, subspecies or variety
names governed by the ICNB, ICBN or ICZN. However, such redundancy is
likely to be limited: assigning a rank to a clade name governed by this
code is not a nomenclatural act, and the rank-based codes do not
recognize the adoption of any species concept as a nomenclatural act --
under most species concepts, species need not be clades. This situation
is similar to monospecific genera under the rank-based codes (cases
where a genus and its type species are identical in content in a
particular classification).

[current Art. 21.2 and 21.3 deleted]

Rec. 21A [currently Art. 21.4 and Rec. 21.4B]. To satisfy the
requirements of the rank-based codes, a name implicitly or explicitly
associated with the rank of genus must be used when establishing a new
or replacement name for a species, subspecies or variety. For names
governed by the ICZN, this practice must be followed throughout the
publication that establishes the name (ICZN article 11.4
http://www.nhm.ac.uk/hosted-sites/iczn/code/includes/page.jsp?article=11&nfv=#4 

). When choosing a generic name, authors should consider the
nomenclatural consequences under both the appropriate rank-based code
and this code. In general, a generic name[*] that is also an established
clade name (Example 1), or is simultaneously being established as a
clade name (Examples 2, 3), should be selected if possible. Otherwise,
an existing generic name[*] may be used, even if the monophyly of the
taxon associated with it is unknown or doubtful (Examples 3, 4). If the
species to be named cannot be assigned to any taxon with which a generic
name[*] has been associated under the appropriate rank-based code, the
only option is to publish a new name to serve as a generic name under
that code (Examples 4, 5, 6). This name may be simultaneously
established as a clade name under this code (Example 5).

[* Rec. 21.4B currently says "a generic name (ICNB, ICBN) or genus-group
name (ICZN)". This is wrong. Under the ICZN, the name of a species must
contain the name of a genus; it is not allowed to use the name of a
subgenus instead -- a subgeneric name may only be used in addition. Of
course, it is allowed to promote a subgenus to genus rank, but this is a
nomenclatural act separate from the naming of a new species.]

[No changes to the Examples, except that Example 4 contains an instance
of *Hypotheticus* that is not italicized.]

Rec. 21B [currently Rec. 21.4A and Rec. 21.5A]. When establishing a new
or replacement name for a species, subspecies or variety under the
appropriate rank-based code, some mechanism should be used to indicate
whether the generic name is an established clade name under this code.
If symbols are used, their meaning should be made clear.

[No changes to the Examples, except to replace "prenomen" with "generic
name" throughout.]

Rec. 21C [replaces current Rec. 21.4C]. When establishing a new species
name under the appropriate rank-based code, the protologue should state
which species concept the authors have in mind, and it should include a
description of the evidence indicating that the new species fulfills
that concept, even though the rank-based codes have no such requirements
or recommendations.

[current Art. 21.5 and Rec. 21A deleted]