[CPN] Proposed additions to the PhyloCode (Art. 9)
de Queiroz, Kevin
deQueirozK at si.edu
Mon Jun 25 15:11:39 EDT 2018
Dear Michel et al.,
To my way of thinking, the qualifying clause is indeed clearer in suggesting that the name would not apply to any clade in such a case, and I prefer it for that reason. However, the other case is analogous to other types of definitions that lack explicit qualifying clauses but in which the name will not apply to any clade in the context of certain phylogenies because there is no clade that fits the definition, so I think we want to allow it as well.
Here’s the original example that got us thinking about such things:
Halecostomi := the smallest crown clade containing Amia (bowfins) and Perca (teleosts) but not Lepisosteus (gars).
This definition does not have a qualifying clause, but it will not apply to any clade in the context of phylogenies in which gars are more closely related to either bowfins or teleosts than either of those taxa are to each other (because there will be no clade that contains both Amia and Perca but not Lepisosteus).
Kevin
From: Michel LAURIN <michel.laurin at mnhn.fr>
Date: Monday, June 25, 2018 at 2:20 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 et al,
My point is that it is not really clear, in your second example (below), that the definition would not apply here; it is clear only in the first case. But I made my point, no need to insist. If everybody else thinks that it is clear, I don't mind if this stays as it is.
Best wishes,
Michel
________________________________
De: "Kevin de Queiroz" <deQueirozK at si.edu>
À: "michel laurin" <michel.laurin at mnhn.fr>
Cc: "Committee on Phylogenetic Nomenclature" <cpn at listserv.ohio.edu>, "Max Langer" <mclanger at ffclrp.usp.br>
Envoyé: Lundi 25 Juin 2018 20:08:54
Objet: Re: [CPN] Proposed additions to the PhyloCode (Art. 9)
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 • (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
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Michel Laurin
CR2P, UMR 7207
Muséum National d'Histoire Naturelle
Bâtiment de Géologie
Case postale 48
43 rue Buffon
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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
--
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
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