[CPN] Fwd: proposed revisions of Note 9.3.1: call for a vote

Wed May 1 17:54:28 EDT 2013

I’d like to elaborate on Phil’s explanation for the deletion of three categories of clades from Art. 2.2.  As explained in the article (in press) that I sent to the CPN, the categories “node-based clade” and “branch-based clade” are incorrect in the context of a system that recognizes both relationship trees (in which nodes represent taxa [“species”] and branches represent ancestor-descendant relationships) and lineage trees (in which branches represent taxa [“species”]).  The reason is that in the context of a relationship tree, ALL clades are node-based.  Similarly, in the context of a lineage tree with the added stipulation that the ancestors specified by phylogenetic definitions are entire species rather than parts thereof (obviously not the previous interpretation of the PhyloCode but one that is accepted by various other authors cited in my article), ALL clades are branch-based.  In this context, it makes no sense to use the terms “node-based” and “branch-based” to distinguish between different categories of clades.  Phil and I considered the possibility of substituting “minimum clade” and “maximum clade” for “node-based clade” and “branch-based clade” but decided against it for the following reason:  Minimum and maximum clades are not really distinct types of clades (this has been the point of several critics of the distinction between node-based and branch-based definitions who adopt the interpretation that the ancestors of clades are entire species rather than parts thereof); they are simply clades whose names are definited using minimum clade and maximum clade definitions. Thus, it seems more appropriate to reserve the minimum/maximum clade terminology for definitions and not use them for clades. (Similarly, a clade itself is not really based on an apomorphy [it’s based on common descent in the sense of deriving its existence from that process], though the definition of a clade name may be so based.)

Nonetheless, I agree that the current wording of the article could give the (incorrect) impression that only crown and total clades are recognized under the PhyloCode.  Michel did not like Phil’s proposed solution of adding a clarifying note, so I will suggest an alternative solution that modifies the current wording of the first part of the article rather than adding a note.  I suggest something along the following lines (this is just a draft to get the idea across; if approved by the CPN, Phil and I would have to work on the exact wording):

2.2.  Some clades are represented by extant organisms and others only by extinct ones.  Two subcategories of clades that have some extant representatives are associated with specific naming conventions and are therefore defined here. 
     [Then give the definitions of "crown clade" and "total clade".]

Kevin

________________________________________
From: cpn-bounces at listserv.ohio.edu [cpn-bounces at listserv.ohio.edu] on behalf of Michel Laurin [michel.laurin at upmc.fr]
Sent: Wednesday, May 01, 2013 1:19 PM
To: cpn at listserv.ohio.edu
Subject: Re: [CPN] Fwd:  proposed revisions of Note 9.3.1: call for a vote

Dear Phil (and others),

On 01/05/13 15:00, Cantino, Philip wrote:
Dear Michel (and other CPN members),

In rewording Art. 2.2, we did not intend to imply that crown and total clades are the only types of clades recognized by the code.  We proposed deleting the other three types of clades from the list because they are really kinds of definitions and names rather than categories of clades (see our comments in brackets immediately before Art 2 in the proposal).  However, I can see how people would interpret our wording to mean that these are the only kinds of clades recognized by the code.  I suggest that we address this problem by adding a new Note 2.2.1, worded something like this:  "Art. 2.2 is not intended to imply that crown clades and total clades are the only clades whose names are governed by this code.  Minimum clade definitions, maximum clade definitions, and apomorphy-based definitions can be used to define the names of clades that are neither crown nor total."
    I don't see the advantage of this change. If simplification is what is aimed at, the fact that we would need to add explanations would negate the effect of deleting three kinds of definitions. And even that explanation is only half-convincing. Paleontologists might think that we are accommodating their needs as an after-thought, and might wrongly think that their clade name/definitions combinations are somehow not important in PN, as implemented in the ICPN. Besides, the spirit of this change seems to run counter with the move towards a more general formulation (maximal and minimal clades, and earlier, branch-based rather than stem-based). There has been relatively little use of the ICPN so far (by comparison with the number of systematics papers), so do we even have a big enough sample to tell that most clades named and defined under the ICPN in the next 10 years are likely to be crown-based or total clades? And do we have the stats about what has been done so far? I don't. Personally, I would be cautious to put anything in the code that might discourage some potential users. It is hard enough to get our colleagues to use the ICPN as it is.

Regarding the wording of apomorphy-based clades and apomorphy-modified crown clade definitions, are the wordings you highlighted the only ones you are concerned about?
    No, I did not really highlight anything. I just inserted a note in the paragraph.
If so, I don't understand why you don't have the same concerns about the other wordings that use "exhibited" rather than synapomorphic.
    I do have concerns about all proposed formulations of apomorphy-based definitions in the proposed amendment. I would suggest this:

" An apomorphy-based definition may take the form "the clade originating in the ancestor in which apomorphy M, synapomorphic with A, originated. " or " the clade for which M, synapomorphic with A, is an apomorphy " or " the clade characterized by apomorphy M synapomorphic with A " (modified parts in bold text).
As a basis for discussion, it would be helpful if you would send the listserv the exact wording you would like for each formulation of these two kinds of definitions (at least those formulations that you would like to change).
    See above.

Best wishes,
Phil

    Best wishes,

    Michel
Begin forwarded message:

From: Michel Laurin <michel.laurin at upmc.fr<mailto:michel.laurin at upmc.fr>>
Subject: Re: [CPN] proposed revisions of Note 9.3.1: call for a vote
Date: May 1, 2013 3:05:43 AM EDT
To: "cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>" <cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>>

Dear colleagues,

    I am sorry that I did not have time to look at this text earlier. I have problems with the formulation for apomorphy-based clades, in which "synapomorphic with" was omitted of some kinds of allowed definitions. This is a mistake in my opinion because it leaves ambiguity; often, convergent apomorphies are indistinguishable from synapomorphic ones. So "synapomorphic" MUST be present in such kinds of definitions.

    The removal of minimal and maximal clades defined based on extinct taxa is a big mistake, in my opinion. These are the kinds of clades that paleontologists deal with most of the time, and they may conclude (with some justification) that this clade is not for them.

    Thust, for now, I vote against this amendment, although I am in favor of the rest of it. But I would like to see these issues fixed before I approve the changes.

    See the attached text for annotations showing where exactly the problems are.

    Best wishes,

    Michel

On 01/05/13 00:54, Cantino, Philip wrote:
Dear CPN members,

There has been little discussion of the proposed revisions to Note 9.3.1, so I'm calling a vote on it.  The version I am asking you to vote on is the one I sent yesterday, which incorporates responses to the two points David M. raised.  It is attached again to this message.  A simple Yes (to approve) or No (to reject) is all that is needed.  Please send your vote to the listserv, not to me personally.

Please try to vote by the end of the day this Friday, but if that schedule is too tight for some of you, let me know and I'll extend it a few days.

Thank you.

Regards,
Phil

Begin forwarded message:

From: "Cantino, Philip" <cantino at ohio.edu<mailto:cantino at ohio.edu>>
Subject: Re: [CPN] proposed revisions of Note 9.3.1
Date: April 29, 2013 1:00:59 PM EDT
To: Committee on Phylogenetic Nomenclature <cpn at listserv.ohio.edu<mailto:cpn at listserv.ohio.edu>>

Dear CPN members,

Kevin and I discussed the specific suggestions made by David (copied below).

1) Rather than replacing "synapomorphy" with "autapomorphy" in the wording of apomorphy-based definition, as David proposed, we think that it should be replaced with "apomorphy", and that the same change be made in the wording of the apomorphy-modified crown clade definition.  Although David is right that an apomorphy of a clade is an autapomorphy when viewed in relation to other clades (the outgroups), it is a synapomorphy of the members of the clade being named, which is why we used the term synapomorphy.  However, given that it can be viewed either way, the term "apomorphy" is clearer.

2) We agree with David's suggestion that "and" be changed to "or" in the definition of a total clade in Art. 2.2.

I am attaching a new version of the proposed changes that incorporates these new modifications.

David, thank you for your careful reading of the proposal.

Does anyone else have any comments?  Tomorrow is the day I said I would call for a vote if there was no active discussion.

Phil

On Apr 25, 2013, at 5:35 PM, David Marjanovic wrote:
> ==================
>
> Concrete points about the current proposal:
>
> I am particularly happy about the replacement of "most/least inclusive" by "largest/smallest". The former are unambigous, but sound abstract enough that -- for a long time -- they managed to confuse me anyway.
>
> In the proposal to change the definition of "apomorphy-based clade", replace "synapomorphy" by "autapomorphy" (twice). Hennig liked inventing terminology, and he wanted to express every possible concept in a single word made from Greek components; therefore _one_ clade has autapomorphies (auto- = "self") while _two_ sister-groups (or more in case of a hard polytomy) have synapomorphies (syn- = "together"); the synapomorphies of two sister-groups are automatically autapomorphies of the smallest clade they form together, which makes the terms redundant in many cases, but still, there they are, and one clade can't have _syn_apomorphies together with just itself. -- The use of "apomorphy" in that section is correct; that term just means "derived character state" without saying derived relative to what.
>
> By using "and" in strategic places, the proposal to change the last point of Article 2.2 implies that total clades must contain entire species (even if they contain other organisms in addition). In turn, this implies that there cannot be clades within a species. This is correct under Hennig's species concept, but not under whatever concepts the ancestor worshippers think they use. Simply use "or" like in the proposal to change the preceding point (the one about crown clades).
>

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--
Michel Laurin
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Muséum National d’Histoire Naturelle
Batiment de Géologie
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--
Michel Laurin
UMR 7207
Muséum National d’Histoire Naturelle
Batiment de Géologie
Case postale 48
43 rue Buffon
F-75231 Paris cedex 05
FRANCE
http://www2.mnhn.fr/hdt203/info/laurin.php