Message 2004-10-0186: Re: crown clade convention (long)

Tue, 19 Oct 2004 23:23:16 +0200

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Date: Tue, 19 Oct 2004 23:23:16 +0200
From: [unknown]
To: PML <>
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=
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=
and moreover might help to bring more workers onside??

The short answer to this question is that neontologists have persiste=
ignored names coined specifically for the crown, preferring to use th=
well-known names in an imprecise manner.  If neontologists actually u=
Neotetrapoda for the crown, it would make a lot of sense to use Tetra=
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=
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=
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


- Neotetrapoda is not widely known. I am certain that by far most of =
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=
that had ranks over such that lacked them. This practice still has ef=
even proponents of phylogenetic nomenclature often prefer using widel=
y used
names over using less widely known but more precise names when they j=
sketch the outlines of a tree in their texts.
- Neotetrapoda was coined at a time when very, very little was known =
tetrapod phylogeny. There was no perceived difference between the
traditional group and the crown-group -- except for *Ichthyostega* (f=
people knew the two or three others), about which neontologists simpl=
didn't care.

I don't quite understand why we should canonize forever the casual ap=
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=
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 =
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=
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 =
of the crown).  Given this situation, it makes more sense to apply Te=
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=
=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=
have been generalized to all of Dinosauria! Perhaps -- I'm just guess=
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=
first place.

Besides, I think that statements about the expression of a gene are u=
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=
the Greek word roots tetra + poda and the clade to which paleontologi=
have traditionally been applying them.

(Less important... Tetrapodomorpha is preoccupied by the panstem, the
sistergroup of Dipnomorpha which includes the lungfish. Both names ar=
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=

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=
uses of names rather than to try to get neontologists to use those na=
correctly.  The first is that neontologists have proven resistant to =
new and unfamiliar names for the crowns, while (in contrast) paleonto=
have demonstrated that they are more open to changing their use of wi=
known names.

I wouldn't say so. Lacertilia vs Sauria seems to be a case of widespr=
change in the neontological community, like Carinatae vs Neognathae, =
abandonment of Pisces, Anamnia and now even Agnatha, or the surprisin=
widespread use of Archosauria (which, outside of phylogenetic nomencl=
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=
Michel Laurin).

This could bear a certain risk that phylogenetic nomenclature is bein=
adapted to what neontologists are _perceived_ to be doing, not what t=
really _are_ doing... I fear. I'm concerned because very few neontolo=
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=
among the first for which the crown convention was advocated.  What i=
significant here is that even paleontologists who initially resisted =
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=
neontological literature.

I would say that there is rather little neontological literature that=
with crown-group Mammalia as a whole. The monotremes are much too oft=
either ignored or regarded as curiosities; this has far-reaching
consequences because far fewer internodes separate them from the trad=
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=
paleontologists.  In other words, far fewer people have to change the=
that they currently do things if we adopt the convention of tying the=
known names to the crowns than if we use less well known names for th=

The other way around neontologists wouldn't so much have to _change_ =
usages as to make them more precise. Do they mean "Tetrapoda" when th=
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=
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 <> 10/18/04 21:43 PM >>>
> Larry Whitmer has written an
> entire monograph on a cladistically-based method for inferring "sof=
> 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 =
now are, um, popular summaries of how it works. An example is the sec=
"Parsimony and anatomy" on this little webpage:

> [...] changing the meaning of this name is abrogating our responsib=
> educate nonsystematists of the importance of careful rigor in use o=
> technical names, and is allowing the ignorance of some workers to d=
> decisions in name conversion, rather than honestly evaluating how p=
> working with these technical names use them currently. And I think =
that is
> distinction that should be considered.

Unfortunately a survey of the neontological literature for such names=
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=
> an apt analogy), because there is always another fossil to be found=
> might possibly completely alter my understanding of relationships. =
> stem-based taxa as a result, which can always be subdivided later, =
> plesiomorphic forms, perhaps less morphologically distinct from a
> "well-known" but descendant group, are found. I have a new apprecia=
> 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=
together in a node-stem triplet, but also because the more stable of =
have comparatively fixed diagnoses. They are also useful for denoting=
start of "adaptive radiations" (which usually means the start of a no=

> Yes, to those who would characterize me as being concerned about my
> taxa", you bet I am fond of this name, and all of the names of the =
> work with. All specialists are, more or less; its our life's work. =
> 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=
> be a crown-based clade. I have nothing invested in it emotionally. =
> 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=
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=
> engender resentment among some systematists who might otherwise be =

Thank you for reminding me of this. We -- all supporters of phylogene=
nomenclature together -- are still a pretty small group, and we are e=
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=

In the particular case of Tetrapoda, there are two potential problems=
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=
not decide whether they are tetrapods. The other is theoretical, and =
to all apomorphy-based definitions -- while currently it looks like d=
are generated by a switch in the expression pattern of one gene (so d=
are either clearly present or clearly not), we could be wrong, and we=
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 =
for the time being, an apomorphy-based definition is the best solutio=
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=
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=
> looming and cannot take this chunk of time again until January.

Obviously I'm not trying to blame you... it's just... I fear... if ev=
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...



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