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Date: Tue, 19 Oct 2004 23:23:16 +0200
From: [unknown]
To: PML <phylocode@ouvaxa.cats.ohiou.edu>
Subject: Re: crown clade convention (long)
I apologize if this post seems somewhat confused. This cheap flatscre= en has turned yellow, and that somehow makes it hard to concentrate. I also apologize for its length; I hope that this way I'll need only two e-m= ails to comment this entire thread. ----- Original Message ----- =46rom: "Kevin de Queiroz" <Dequeiroz.Kevin@NMNH.SI.EDU> Sent: Tuesday, October 19, 2004 7:39 PM >> Jason Anderson asked: ?why are we persisting on keeping Tetrapoda att= ached to the crown, and use Holotetrapoda for the apomorphy-based definitio= n, when using Tetrapoda and Neotetrapoda (or whatever) is logically just as consistent, but additionally, will maintain consistency with the lite= rature, and moreover might help to bring more workers onside?? The short answer to this question is that neontologists have persiste= ntly ignored names coined specifically for the crown, preferring to use th= e well-known names in an imprecise manner. If neontologists actually u= sed Neotetrapoda for the crown, it would make a lot of sense to use Tetra= poda for an apomorphy clade and Neotetrapoda for the crown, as Jason argue= s. The problem is that they don?t. Although the name Neotetrapoda was propo= sed some time ago, it is almost never used by neontologists, who continue= to use Tetrapoda when making statements that properly apply to the crown (?tetrapods express gene y?). Note that the problem here is not only= the imprecise use of the name Tetrapoda but also the fact that Neotetrapo= da, the name that was coined specifically for the crown clade, is not used in precisely those situations in which it would be most appropriate to u= se that name. << Well... - Neotetrapoda is not widely known. I am certain that by far most of = those neontologists simply don't know it exists. - Tetrapoda has occasionally had a rank (superclass), while Neotetrap= oda has never had one, as far as I know or can imagine. When Neotetrapoda was coined, almost everyone was still concerned with ranks, and preferred= names that had ranks over such that lacked them. This practice still has ef= fects; even proponents of phylogenetic nomenclature often prefer using widel= y used names over using less widely known but more precise names when they j= ust sketch the outlines of a tree in their texts. - Neotetrapoda was coined at a time when very, very little was known = about tetrapod phylogeny. There was no perceived difference between the traditional group and the crown-group -- except for *Ichthyostega* (f= ew people knew the two or three others), about which neontologists simpl= y didn't care. I don't quite understand why we should canonize forever the casual ap= proach used by many neontologists. The PhyloCode presupposes evolution, afte= r all. To talk about evolution while ignoring fossils is not a good idea. Neontologists are stuck on the 3-dimensional surface of 4-dimensional biology. They usually don't even _need_ the precision that paleontolo= gists need when talking about a phylogenetic tree. >> In addition, using the best known name for the crown creates a situat= ion in which the best known name is tied to the clade for which the maximum = number of justifiable inferences can be made about the presence of character= s in its extinct members (if all living members of the crown exhibit a par= ticular character?such as expression of gene y?it is justifiable to infer tha= t the extinct members did too, but the same does not hold for extinct taxa = outside of the crown). Given this situation, it makes more sense to apply Te= trapoda to the crown and coin a new name for the apomorphy clade. << This is a good argument, but perhaps not as good as it first seems. T= he real problem, what's really going on here is, I think, the tendency to gen= eralize =66rom a small subset to an entire clade _with a well-known name_. Th= ere are incidents when features found in living birds, or only in _some_ of t= hose, have been generalized to all of Dinosauria! Perhaps -- I'm just guess= ing here -- the pompous introduction of specific new names for certain (!= ) crown-groups would make the abovementioned neontologists more aware o= f the need to be precise -- in those rather few cases where it is a need in= the first place. Besides, I think that statements about the expression of a gene are u= sually not going to lead to a noticeable misrepresentation of the larger-than-crown-croup with the name in question. >> Furthermore, using a name that refers to the same apomorphy for the apomorphy clade, such as Tetrapodomorpha or Holotetrapoda, goes a lon= g way towards alleviating the problem of breaking the mental association be= tween the Greek word roots tetra + poda and the clade to which paleontologi= sts have traditionally been applying them. << (Less important... Tetrapodomorpha is preoccupied by the panstem, the sistergroup of Dipnomorpha which includes the lungfish. Both names ar= e widely used. Like Tetrapoda, Dipnoi has been used for something large= r than the crown-group since the 19th century... oops... fossil lungfish wer= e known before living ones were recognized... so perhaps this isn't a good ex= ample.) >> Nevertheless, there are a couple of reasons why it makes more sense t= o ask paleontologists to give up their long-established and logically consi= stent uses of names rather than to try to get neontologists to use those na= mes correctly. The first is that neontologists have proven resistant to = using new and unfamiliar names for the crowns, while (in contrast) paleonto= logists have demonstrated that they are more open to changing their use of wi= dely known names. << I wouldn't say so. Lacertilia vs Sauria seems to be a case of widespr= ead change in the neontological community, like Carinatae vs Neognathae, = the abandonment of Pisces, Anamnia and now even Agnatha, or the surprisin= gly widespread use of Archosauria (which, outside of phylogenetic nomencl= ature, includes only the crocodiles among the living, so it is redundant for neontologists; in PN it also includes the birds). >> One indication of this openness is the fact that many of the advocate= s of the crown convention are paleontologists (e.g., Jacques Gauthier, Tim= Rowe, Michel Laurin). << This could bear a certain risk that phylogenetic nomenclature is bein= g adapted to what neontologists are _perceived_ to be doing, not what t= hey really _are_ doing... I fear. I'm concerned because very few neontolo= gists have weighed into this debate -- not just on this list or in Paris, b= ut also (to my limited knowledge) in the literature. It's certainly not good = if my fears are true and WE (paleontologists) are talking about THEM. >> Additional evidence comes from the case of the name Mammalia, which w= as among the first for which the crown convention was advocated. What i= s significant here is that even paleontologists who initially resisted = the crown convention for Mammalia are now coming to accept it. Perhaps w= hat all these people are realizing is that there are significant benefits to changing their use of the name to achieve consistency with its use in= the neontological literature. << I would say that there is rather little neontological literature that= deals with crown-group Mammalia as a whole. The monotremes are much too oft= en either ignored or regarded as curiosities; this has far-reaching consequences because far fewer internodes separate them from the trad= itional beginnings of Mammalia than from the last common ancestor of marsupia= ls and placentals. It's sort of the opposite of the situation with the birds= . :-) >> The second reason is that there are simply far more neontologists tha= n paleontologists. In other words, far fewer people have to change the= way that they currently do things if we adopt the convention of tying the= widely known names to the crowns than if we use less well known names for th= e crowns. << The other way around neontologists wouldn't so much have to _change_ = their usages as to make them more precise. Do they mean "Tetrapoda" when th= ey write it? Do they mean "living land vertebrates"? Do they mean anythi= ng in between? I think in many cases they haven't thought about this themse= lves. But in many other cases they have -- and write phrases like "must hav= e been present in the common ancestor of living tetrapods", note "living". > >>> Jason Anderson <janderson@westernu.edu> 10/18/04 21:43 PM >>> > > Larry Whitmer has written an > entire monograph on a cladistically-based method for inferring "sof= t tissue" > data using fossils, and I am very sensitive to the extent we can in= fer the > presence of structures not directly preserved. Its my training. Witmer's "extant phylogenetic bracketing" has become so popular that = there now are, um, popular summaries of how it works. An example is the sec= tion "Parsimony and anatomy" on this little webpage: http://www.dinosauria.com/jdp/misc/parsimony.htm. > [...] changing the meaning of this name is abrogating our responsib= ility to > educate nonsystematists of the importance of careful rigor in use o= f > technical names, and is allowing the ignorance of some workers to d= rive our > decisions in name conversion, rather than honestly evaluating how p= eople > working with these technical names use them currently. And I think = that is a > distinction that should be considered. Unfortunately a survey of the neontological literature for such names= and their usages would have about the size of a master's thesis... > I can imagine it is easier to think of taxa as > relatively fixed if my primary concern were those species alive > today--because what we see is what we get. However, speaking for my= self, I > think of taxa as unknowable in any precise way (a probability cloud= would be > an apt analogy), because there is always another fossil to be found= that > might possibly completely alter my understanding of relationships. = I prefer > stem-based taxa as a result, which can always be subdivided later, = when more > plesiomorphic forms, perhaps less morphologically distinct from a > "well-known" but descendant group, are found. I have a new apprecia= tion for > node-based taxa after the Paris meeting (but still think there is t= oo much > "top-down" thinking). In paleontology, I find node-based taxa useful to join two stem-based= taxa together in a node-stem triplet, but also because the more stable of = them have comparatively fixed diagnoses. They are also useful for denoting= the start of "adaptive radiations" (which usually means the start of a no= de-stem triplet). > Yes, to those who would characterize me as being concerned about my "special > taxa", you bet I am fond of this name, and all of the names of the = groups I > work with. All specialists are, more or less; its our life's work. = And yes, > I care less about the names used for other clades I do not work wit= h. Its > easy for me to make pronouncements about my preference for, say, Ma= mmalia to > be a crown-based clade. I have nothing invested in it emotionally. = So, > shouldn't the specialists make these decisions, since they are stuc= k with > the result? I think this is a very good reason for why even well-known names shou= ld be defined by those who actually work on them, their close relatives and= their delineations, rather than by an overarching convention. > Might the feeling that one is being told which name should be > used for the group one works on by a small, self-appointed group no= t > engender resentment among some systematists who might otherwise be = onside? Thank you for reminding me of this. We -- all supporters of phylogene= tic nomenclature together -- are still a pretty small group, and we are e= ntirely self-appointed! We better make very careful decisions, or many of the systematists "out there" will never consider taking PN seriously. > Does an apomorphy-based definition > this really create more confusion and "fuzzy tree thinking" among w= orkers? In the particular case of Tetrapoda, there are two potential problems= with an apomorphy-based decision. The one is practical: several taxa betwe= en the finned *Panderichthys* and the limbed *Acanthostega* are known from incomplete remains that don't tell us if digits were present, so we c= ould not decide whether they are tetrapods. The other is theoretical, and = applies to all apomorphy-based definitions -- while currently it looks like d= igits are generated by a switch in the expression pattern of one gene (so d= igits are either clearly present or clearly not), we could be wrong, and we= could one day find a species in which the presence of digits is individual variation. My opinion is that Tetrapoda is one of the very few cases = where, for the time being, an apomorphy-based definition is the best solutio= n; should it become impracticable, or should the fossil record around it= s base improve drastically (I hear it has begun to do so), the Commission co= uld change this into a node-based definition. > You may feel safe from future > messages of this length, because I have a ton and a half of deadlin= es > looming and cannot take this chunk of time again until January. Erm... Obviously I'm not trying to blame you... it's just... I fear... if ev= eryone has so little time, either I will totally dominate the discussion her= e, or we will be surprised in early 200n of how many problems we have simpl= y never thought, or of course both. All three outlooks are rather frightening= . Perhaps it's just the yellow screen that makes me so pessimistic... :-)