[Previous by date - RE: Ichthyornis paper]
[Next by date - Re: Panstems]
[Previous by subject - Re: RE: crown clade convention]
[Next by subject - Re: REPOST: Crowns, Panstems, and their Correspondence to ea=]
Date: Thu, 09 Sep 2004 15:40:25 -0400
From: [unknown]
To: phylocode@ouvaxa.cats.ohiou.edu
Subject: Re: REPOST: Crowns, Panstems, and their Correspondence to ea=
>My responses to TMK=3D92s comments are enclosed in these symbols.< I notice that a number of the abstracts follow de Queiroz and Gauthie= r =3D 2002 in creating panstem/crown pairs, in each case with the name of t= he =3D panstem formed by adding the prefix "Pan-" to the name of the crown c= lade. =3D I've commented on this and discussed it on another forum, and thought= I'd =3D summarize some thoughts here. CORRESPONDENCE =3D20 It is, of course, interesting to note that crowns and panstems have a= 1:1 =3D correspondence with each other, and it does seem that this would warr= ant =3D at least a recommendation with regards to the definition and/or nomen= clatur=3D e of these clades, possibly having them always be named in pairs. I'm= =3D curious; does anyone think a rule would be warranted? >We took a straw vote on this (i.e., universal use of the Pan- prefix= for =3D panstems) at the Paris meeting. Only a few people, including myself,= were =3D in favor of such a rule, though many supported a recommendation. Nam= ing =3D the clades in pairs is a related, but different, issue (see below).< There is one instance where the correspondence is not really 1:1, at = least =3D for practical purposes, and that is, of course, if the extant outgrou= p to =3D a crown clade is also the immediate ancestor. In this case the panste= m and =3D the crown clade become heterodefinitional synonyms. Does anyone think= that =3D this means certain crown clades should not have panstems named for th= em? I =3D personally think that it's fine for the two clades to be heterodefini= tional=3D synonyms, as our understanding may shift. (Of course, in every insta= nce, =3D the crown clade should be senior to the panstem.) >I would also treat these names as heterodefinitional (subjective) = =3D synonyms, given that we never actually know that the two names refer = to =3D the same clade.< "EXTANT" This has been discussed before, and is mentioned in Note 9.4.1, which= =3D states that the author should clarify their exact meaning for the wor= d =3D "extant". It seems to me it may be preferrable for the code to define= a =3D consistent meaning. The most stable and easily applicable definition = I can =3D think of is "living and published at the time of the definition's = =3D publication", but I'd certainly like to see others' suggestions. Shou= ld =3D "...and published..." be included? It would help maintain the stabili= ty of =3D previously established crown and panstem clades. >The approach we have taken is not to have a rule specifying the mean= ing =3D of =3D93extant=3D94 but to have a rule stating that a specified meani= ng (the =3D same one that TMK suggested) is to be adopted if the original author = did =3D not specify the meaning. This gives the authors of definitions more = =3D freedom but also prevents ambiguity. Here is the rule: 9.5. If the author of a crown clade definition (Note 9.4.1) did not = =3D specify the meaning of "extant" or "crown clade" or an analogous term= used =3D in the definition (e.g., "living", "Recent"), then subsequent authors= are =3D to interpret that definition as referring to organisms or species tha= t =3D were extant on its publication date (Art. 5).< DEFINITIONS I notice two schools of thought in the abstracts for the upcoming mee= ting =3D as to definitions for crown and panstem clades. In Sereno's definitio= ns, =3D there really are no panstems, only stem-based clades that happen to h= ave =3D extant specifiers. The crown clades, then, are defined in terms of th= e =3D stem-based clades: Stem =3D3D Clade(A <-- B) (A and B are extant) Crown =3D3D Clade(extant Stem) However, in other abstracts, such as the one for Gauthier et al.'s pa= per =3D on major amniote clades, it goes the other way: the panstem is based = on =3D the crown. Crown =3D3D Clade(A + B) (A and B are extant) Panstem =3D3D Clade(Crown <-- extant non-Crown) In the former, the stem-based clade is the more stable one, while, in= the =3D latter, the node-based (crown) clade is more stable. It seems preferr= able =3D to me that the crown be the more stable one, but I'd be very interest= ed to =3D hear other opinions. I would allow one exception, and that is Wagner's brilliant definitio= ns =3D for _Panbiota_ and _Biota_ which, while not exactly following the = =3D stem-modified crown approach (it would be impossible to do so, as the= re is =3D no outgroup), are in the same spirit, with the crown clade being modi= fied =3D by a more inclusive clade. >I found this comment very interesting, as I hadn=3D92t noticed this = =3D difference until TMK pointed it out. I=3D92m not sure what he means = when he =3D says that one definition is more stable than another in this context.= =3D What is clear to me is that the stem concept is primary in the first = =3D approach in that the crown concept is based on it, while in the secon= d =3D approach the crown concept is primary with the (pan) stem concept bei= ng =3D based on it. Although I=3D92ve always thought of things the second w= ay (up =3D until now), the reason was that I had never considered the alternativ= e. =3D Now that the alternative has been pointed out, I like it just as well= . In =3D other words, even though I might be expected to favor the primacy of = =3D crowns, I don=3D92t. Both approaches seem equally reasonable. My in= terpreta=3D tion: perhaps this is a reason for naming the clades bounded by exta= nt =3D organisms in pairs (see TMK=3D92s first comment, above), as I have my= self =3D suggested (though not clearly distinguishing this issue from the rela= ted =3D one about how the names are to be formed). That is, perhaps we shoul= d =3D have a rule stating that establishing a name for one clade of this ty= pe =3D (crown or total) automatically establishes a name for the other membe= r of =3D the pair. Of course, this only works if the names are tied to one = =3D another, as in the Pan- convention. Notice, however, that it does no= t =3D require the Pan- convention (and here I=3D92m generalizing this conve= ntion =3D to include other prefixes than Pan- that could be used for total/stem= =3D clades). That is, we could have a convention that bases the name on = the =3D crown on that of the stem rather than vice versa. For example, rathe= r =3D than using Mammalia for the crown and PanMammalia for the stem, we co= uld =3D use something like AcroMammalia from the crown and Mammalia for the s= tem. =3D My preference, for reasons outlined in several papers, is the former = =3D (i.e., Mammalia and PanMammalia). However, this does not mean that I= =3D prefer the primacy of crowns when it comes to definitions (as opposed= to =3D names). That is, even if I were to use Mammalia for the crown and = =3D PanMammalia for the stem, I could still define the names as follows: PanMammalia =3D3D Clade (Mammalia [Homo sapiens and Ornithorhynchus = =3D anatinus] not Reptilia [Testudo graeca and Lacerta agilis]) Mammalia =3D3D Clade (extant PanMammalia). =3D20 Of course, this approach pretty much forces one to name the clades in= =3D pairs, since one wouldn=3D92t know what name to use for the stem unti= l one =3D had decided on a name for the crown, but as I said above, perhaps nam= ing =3D these clades in pairs is a good idea.< NOMENCLATURE While it seems like a good idea to delineate the correspondence betwe= en =3D crown and panstem clades, I see some issues ahead with using the "Pan= -" =3D prefix. (And I thought mandated affixes were something PhyloCode was = =3D trying to get away from....) >The PhyloCode is not necessarily trying to get away from standard = =3D affixes=3D97only from tying particular affixes to particular ranks.< A number of currently named taxa actually do start with "Pan-", and a= re =3D not panstem clades. Is someone who is not familiar with carnivoran = =3D taxonomy to see the clade _Panthera_ and assume it is the panstem of = =3D "Thera"? (When, in actuality, by the philosophy being followed, it wo= uld =3D be a crown clade, and "Panpanthera" the panstem!) >To solve this problem, people have suggested conventions involving = =3D hyphens and/or double capitalization. Thus, Panthera would not be a = =3D panstem name, but PanThera (or Pan-Thera) as well as PanPanthera (or = =3D Pan-Panthera) would.< Among dinosaurs, there is a _Panoplosaurus_ which is certainly not a = =3D panstem clade containing _Oplosaurus_ (which is an actual unrelated = =3D dinosaur genus). >See previous comment.< Then there are some existing "Pan-" taxa which have actually been nam= ed =3D after other taxa, such as _Panarthropoda_ and _Pancrustacea_. These w= ere =3D not named as the panstem clades for _Arthropoda_ and _Crustacea_, = =3D respectively, but for more inclusive groups. >As far as I can tell, the original authors of the name Pan-Crustacea= =3D (Walossek and M*ller, 1990) did use that name for the total clade/pan= stem =3D of Crustacea. You=3D92re right about Panarthropoda (Nielsen, 1995).= That =3D name would have to be redefined so that it applied to the total clade= of =3D Arthropoda (remember, the PhyloCode is not retroactive). To achieve = a =3D unified system, some names, such as this one, would have to be define= d =3D differently than originally used. The only way around this problem w= ould =3D be to use affixes that had never been used before=3D97ever, but this = =3D strategy isn=3D92t ideal either.< Closer to home, if we were to have panstem clades separating our spec= ies =3D =66rom its closest living relatives, it seems they would be "Panhomo"= and =3D "Panpan" (_Pan_ being the crown clade of chimps, not the panstem clad= e for =3D ""). "Panhomo" is rather confusing, as it looks like a combination of= =3D _Pan_ and _Homo_. >This seems like a minor drawback.< (On another topic, while it may seem like there can be no crown clade= =3D called _Homo_, as there is only one extant species, I submit that the= re is =3D one: "the clade stemming from _Homo sapiens_". Of course, this would = =3D necessitate removing _neanderthalensis, _erectus_, etc. from _Homo_, = which =3D would be highly disruptive, to say the least....) >I (and several others=3D97Wagner, Wolsan) have independently noticed= that =3D this kind of definition is possible. I call it ancestor-based.< Another point to make about the proposed naming convention for crown/= panste=3D m pairs is that, while it may be obvious that _Panmammalia_ is the pa= nstem =3D of _Mammalia_ (even if, for example, _Panderichthys_ is not the panst= em of =3D "Derichthys"....), it's not obvious that _Mammalia_ is a crown clade = =66rom =3D its name alone. If there is a mandated prefix for panstems, why not o= ne =3D for crowns as well? (I'm not saying I would like one, just why one an= d not =3D the other?) >A standard crown prefix is certainly possible. As I argued in my ta= lk at =3D the Paris meeting, the disadvantage is that it creates discontinuity = by =3D replacing existing names with new ones. Of course, the same could be= =3D argued for the stem clades, but if we want a relationship between the= =3D names of the members of a crown-stem pair, at least one of the names = has =3D to change. I suppose the difference here has to do with what one = =3D considers the primary reason for the Pan- convention. In my view, th= e =3D primary reason is not to identify a name as the name of a member of t= he =3D class of total clades generally but to identify it as the name of the= =3D total clade corresponding to a particular crown. To identify the nam= es =3D associated with the members of the classes of crown and total clades,= I =3D prefer to use symbols (inverted triangle and inverted triangle with a= =3D basal leg, respectively).< One solution might actually be found in the traditional system, where= taxa =3D may optionally be written with a title, e.g. Kingdom Animalia, Class = =3D Reptilia, Order Primates, etc. Why not have a similar option for Phyl= oCode =3D taxa, so that the names themselves can be free to be formed in any ma= nner? =3D Crown Clade _Amniota_, Panstem Clade _Synapsida_, Stem Clade _Saurisc= hia_, =3D etc. (I find it often handy to use just "Clade" as a title when contr= asting=3D with traditional taxa, e.g., Clade _Reptilia_ vs. Class Reptilia.) >Yes, some people are already explicitly stating the type of clade. = In =3D addition, there=3D92s no reason why both conventions can=3D92t be use= d =3D simultaneously (e.g., Crown Clade Mammalia, Stem Clade PanMammalia).< Of course, this has the disadvantage of not nomenclaturally linking = =3D panstems with their crowns. (Although it might be useful in any event= .) =3D Another thought would be to allow punctuation just in this case, name= ly, a =3D hyphen: _Pan-Mammalia_, _Pan-Amniota_, _Pan-Vertebrata_, etc. Then it= =3D would be clear that _Panoplosaurus_ is not a panstem clade, while = =3D _Pan-Sauria_ is. >Exactly; see my earlier comment.< Kevin 9 Sep 2004 Kevin de Queiroz Division of Amphibians & Reptiles Smithsonian Institution P.O. Box 37012 NHB, Room W203, MRC 162 Washington, D.C. 20013-7012 Voice: 202.633.0727 FAX: 202.357.3043 E-mail: dequeirk@si.edu