[CPN] Proposed additions to the PhyloCode (Art. 9)
Max Langer mclanger at ffclrp.usp.brMon Jun 25 14:29:33 EDT 2018
- Previous message: [CPN] Proposed additions to the PhyloCode (Art. 9)
- Next message: [CPN] Proposed additions to the PhyloCode (Art. 9)
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
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 >
- Previous message: [CPN] Proposed additions to the PhyloCode (Art. 9)
- Next message: [CPN] Proposed additions to the PhyloCode (Art. 9)
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
More information about the CPN mailing list