[CPN] Proposed additions to the PhyloCode (Art. 9)
Max Langer
mclanger at ffclrp.usp.br
Mon Jun 25 14:29:33 EDT 2018
Well, that point at least is clearer to me now.
I thought that "but not Ursus ..." counted as much as a qualifying clause
as "provided that it does not include Ursus ...".
But as the former is not considered a qualifying clause, my case
that "external
specifiers will appear in minimal clade definitions only as qualifying
clauses" does not stand.
Thanks for clarifying,
max
2018-06-25 15:08 GMT-03:00 de Queiroz, Kevin <deQueirozK at si.edu>:
> Dear Michel et al.
>
>
>
> I’m not in favor of the change suggested by Michel because I don’t think
> it is appropriate to say “especially” here. The situation is that external
> specifiers can be used (with the “or” operator) either with or without
> qualifying clauses to make names inapplicable in the context of particular
> phylogenies. To continue with my previous example, both of the following
> definitions would function similarly, making the name Pinnipedia
> inapplicable in the context of phylogenies in which either bears,
> procyonids, or mustelids (or some combination of those taxa) are descended
> from the MRCA of seals, sea lions, and walruses:
>
>
>
> 1) With qualifying clause: Pinnipedia := the smallest clade containing
> Otaria byronia de Blainville 1820, Odobenus rosmarus Linnaeus 1758, and
> Phoca vitulina Linnaeus 1758, provided that it does not include Ursus
> arctos Linnaeus 1758 or Procyon lotor (Linnaeus 1758) or Mustela erminea
> Linnaeus 1758.
>
>
>
> 2) Without qualifying clause: Pinnipedia := the smallest clade containing
> Otaria byronia de Blainville 1820, Odobenus rosmarus Linnaeus 1758, and
> Phoca vitulina Linnaeus 1758 but not Ursus arctos Linnaeus 1758 or Procyon
> lotor (Linnaeus 1758) or Mustela erminea Linnaeus 1758.
>
>
>
> Kevin
>
>
>
> *From: *Michel LAURIN <michel.laurin at mnhn.fr>
> *Date: *Saturday, June 23, 2018 at 6:23 PM
> *To: *Kevin de Queiroz <deQueirozK at si.edu>
> *Cc: *Committee on Phylogenetic Nomenclature <cpn at listserv.ohio.edu>, Max
> Langer <mclanger at ffclrp.usp.br>
> *Subject: *Re: [CPN] Proposed additions to the PhyloCode (Art. 9)
>
>
>
> Dear Kevin,
>
> With this added information, I find the text much clearer. I would only
> suggest a one-word change in this part:
>
>
>
> Original wording:
>
>
> "For example, it would be
> appropriate to use “or” when using a minimum-clade definition with multiple
> external specifiers, *including* those used in qualifying clauses, to
> render the defined
> name inapplicable in the context of phylogenetic hypotheses in which any
> one (or
> more) of the external specifiers is more closely related to some of the
> internal
> specifiers than those internal specifiers are to other internal specifiers
> (see Art.
> 11.12, Example 1)."
>
> Suggested modification:
>
>
>
> "For example, it would be
> appropriate to use “or” when using a minimum-clade definition with multiple
> external specifiers, *especially* those used in qualifying clauses, to
> render the defined
> name inapplicable in the context of phylogenetic hypotheses in which any
> one (or
> more) of the external specifiers is more closely related to some of the
> internal
> specifiers than those internal specifiers are to other internal specifiers
> (see Art.
> 11.12, Example 1)."
>
>
>
> This is because it seems that this applies mostly in the context of
> qualifying clauses. Or would this also work in other portion of definitions?
>
>
>
> Best wishes,
>
>
>
> Michel
>
>
> ------------------------------
>
> *De: *"Kevin de Queiroz" <deQueirozK at si.edu>
> *À: *"michel laurin" <michel.laurin at mnhn.fr>, "Committee on Phylogenetic
> Nomenclature" <cpn at listserv.ohio.edu>
> *Cc: *"Max Langer" <mclanger at ffclrp.usp.br>
> *Envoyé: *Vendredi 22 Juin 2018 21:04:15
> *Objet: *Re: [CPN] Proposed additions to the PhyloCode (Art. 9)
>
>
>
> Dear Michel,
>
> Right; the most recent version of the PhyloCode (version 5) is not up on
> the website, though it is available from Phil on request. I'm pasting Art.
> 11.12, Example 1 below.
>
> 11.12. In order to prevent use of a name under certain hypotheses of
> relationships, clade composition, or both, phylogenetic definitions may
> include qualifying clauses specifying conditions under which the name
> cannot be applied to any clade (see Examples 1 and 2).
>
> Note 11.12.1. The following conventions are adopted for abbreviated
> qualifying clauses such as those in Examples 1 and 2: | = on the condition
> that; ~ = it does not; () = contain; ∨
> = or; anc = the ancestor in which the clade originated. See Note 9.4.1
> for the other abbreviations used in these examples.
>
> Example 1. The name Pinnipedia is traditionally applied to a group
> composed of sea lions (Otariidae), walruses (Odobenidae), and seals
> (Phocidae). However, under some phylogenetic hypotheses, the sister group
> of one or more of these taxa is a group of terrestrial carnivorans (e.g.,
> Ursidae, Procyonidae, Mustelidae). If the name Pinnipedia were to be
> defined as “the clade originating with the most recent common ancestor of
> Otaria byronia de Blainville 1820, Odobenus rosmarus Linnaeus 1758, and
> Phoca vitulina Linnaeus 1758, provided that it does not include Ursus
> arctos Linnaeus 1758 or Procyon lotor (Linnaeus 1758) or Mustela erminea
> Linnaeus 1758”, then the name would not be applicable to any clade in the
> context of phylogenetic hypotheses in which the most recent common ancestor
> of Otaria byronia, Odobenus rosmarus, and Phoca vitulina was also inferred
> to be an ancestor of Ursus arctos or Procyon lotor or Mustela erminea. The
> phrase “provided that it does not include Ursus arctos Linnaeus 1758
> (Ursidae) or Procyon lotor (Linnaeus 1758) (Procyonidae) or Mustela erminea
> Linnaeus 1758 (Mustelidae)” is a qualifying clause. This definition may be
> abbreviated min Ñ (Otaria byronia de Blainville 1820 & Odobenus rosmarus
> Linnaeus 1758 & Phoca vitulina Linnaeus 1758) | ~ (Ursus arctos Linnaeus
> 1758 ∨ Procyon lotor (Linnaeus 1758) ∨ Mustela erminea Linnaeus 1758)
> (see Note 11.12.1).
>
>
> Kevin
>
> P.S. I'm not sure if the "or" symbols will come through. I had to
> reinsert them after pasting.
>
> On 6/21/18, 6:05 PM, "Michel LAURIN" <michel.laurin at mnhn.fr> wrote:
>
> Dear Kevin,
>
> That is much clearer, but some of this info needs to go into the text,
> unless it already is. A problem is that the current version ends with "see
> Art. 11.12, Example 1)", but I found no such article in the latest posted
> version of the PhyloCode, and so, I did not find the example either.
>
> Best wishes,
>
> Michel
>
> ----- Mail original -----
> De: "Kevin de Queiroz" <deQueirozK at si.edu>
> À: "michel laurin" <michel.laurin at mnhn.fr>, "Committee on
> Phylogenetic Nomenclature" <cpn at listserv.ohio.edu>
> Cc: "Max Langer" <mclanger at ffclrp.usp.br>
> Envoyé: Jeudi 21 Juin 2018 23:12:13
> Objet: Re: [CPN] Proposed additions to the PhyloCode (Art. 9)
>
> Dear Michel,
>
> The problem is that if "and" is used in this context (qualifying
> clause), the definition will not function as intended. For example, if one
> wants the name Pinnipedia to be inapplicable in the context of phylogenies
> in which either ursids or mustelids or both taxa are descended from the
> MRCA of seals, sea lions, and walruses, one must use "or" rather than "and"
> (Pinnipedia := the smallest crown clade containing seals, sea lions, and
> walruses, provided that it does not include ursids or mustelids). If "or"
> is used, then the name Pinnipedia will not be applicable if either ursids,
> or mustelids, or both taxa are descended from the MRCA of seals, sea lions,
> and walruses. If "and" is used instead, then the name will only be
> inapplicable if BOTH ursids AND mustelids are descended from the MRCA of
> seals, sea lions, and walruses. That is, the definition could result in
> ursids being included in Pinnipedia, or mustelids being included in
> Pinnipedia, contrary to the intent of the author. See the distinction
> between logical disjunction ("or" operator) and logical conjunction ("and"
> operator).
>
> Best,
> Kevin
>
> On 6/21/18, 3:20 PM, "CPN on behalf of Michel LAURIN" <
> cpn-bounces at listserv.ohio.edu on behalf of michel.laurin at mnhn.fr> wrote:
>
> Dear all,
>
> I generally agree with the changes, but I find this part
> problematic:
>
> "For example, it would be
> appropriate to use “or” when using a minimum-clade definition with
> multiple
> external specifiers, including those used in qualifying clauses,
> to render the defined
> name inapplicable in the context of phylogenetic hypotheses in
> which any one (or
> more) of the external specifiers is more closely related to some
> of the internal
> specifiers than those internal specifiers are to other internal
> specifiers (see Art.
> 11.12, Example 1)."
>
> I do not find obvious that using "or" in this context should be
> interpreted in this way. I think that if we keep this text, more
> explanation, not in a note, is in order. I interpret the "or" as leading to
> ambiguity in interpretation and I would simply discourage (perhaps forbid)
> it.
>
> Best wishes,
>
> Michel
>
> ----- Mail original -----
> De: "Philip Cantino" <cantino at ohio.edu>
> À: "Committee on Phylogenetic Nomenclature" <cpn at listserv.ohio.edu
> >
> Cc: "Max Langer" <mclanger at ffclrp.usp.br>
> Envoyé: Lundi 18 Juin 2018 17:58:27
> Objet: [CPN] Proposed additions to the PhyloCode (Art. 9)
>
> Dear CPN members,
>
> Kevin and I are proposing the attached additions to Article 9 to
> clarify points of confusion that we became aware of in the process of
> editing Phylonyms contributions. These are probably the last changes in
> the code that we will propose before the manuscript is finalized.
>
> If you have comments or questions, please send them to the
> listserv by June 30. If there is no ongoing discussion at that point, I
> will call for a vote. Please do not vote yet, in case there is discussion
> before June 30.
>
> Best regards,
> Phil
>
>
> _______________________________________________
> CPN mailing list
> CPN at listserv.ohio.edu
> http://listserv.ohio.edu/mailman/listinfo/cpn
> --
> Michel Laurin
> CR2P, UMR 7207
> Muséum National d'Histoire Naturelle
> Bâtiment de Géologie
> Case postale 48
> 43 rue Buffon
> F-75231 Paris cedex 05
> FRANCE
> http://www2.mnhn.fr/hdt203/info/laurin.php
> E-mail: michel.laurin at mnhn.fr
> --
> Michel Laurin
> CR2P, UMR 7207
> Muséum National d'Histoire Naturelle
> Bâtiment de Géologie
> Case postale 48
> 43 rue Buffon
> F-75231 Paris cedex 05
> FRANCE
> http://www2.mnhn.fr/hdt203/info/laurin.php
> E-mail: michel.laurin at mnhn.fr
>
>
>
> --
>
> Michel Laurin
> CR2P, UMR 7207
> Muséum National d'Histoire Naturelle
> Bâtiment de Géologie
> Case postale 48
> 43 rue Buffon
> F-75231 Paris cedex 05
> FRANCE
> http://www2.mnhn.fr/hdt203/info/laurin.php
> E-mail: michel.laurin at mnhn.fr
>
> _______________________________________________
> CPN mailing list
> CPN at listserv.ohio.edu
> http://listserv.ohio.edu/mailman/listinfo/cpn
>
>
--
Max Cardoso Langer Ph.D. (Bristol, UK)
Departamento de Biologia
Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto
Universidade de Sao Paulo (USP)
Av. Bandeirantes 3900
14040-901 Ribeirao Preto, SP, BRAZIL
Phone: +55 16 3315 3844
FAX: +55 16 3315 4886
http://sites.ffclrp.usp.br/paleo/
*A semântica é o último refúgio dos canalhas.*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.ohio.edu/pipermail/cpn/attachments/20180625/ae53fe13/attachment-0001.html>
More information about the CPN
mailing list