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Re: TETRAPODS, PHYLOGENETIC TAXONOMY, AND CLEAR DEFINITIONS



>
>How is a taxon defined?  A crown-based taxon is defined as "the last common
>ancestor of X and Y, and all descendants of that ancestor."  A node-based
>taxon is
>defined as "X and everything closer to X than to Y."


Actually, you've just defined a stem-based group.  Node-based and
crown-based groups are essentially the same thing, although crown groups
are typically delimited by living end members.


 In either case, you have the
>_definition_ of the taxon, and as a separate matter you have the
>_diagnosis_ of
>the taxon, or how you tell if organism A belongs to this taxon or not.  The
>diagnosis has a list of features which are considered autapomorphies for the
>taxon, and if A is

This really was no different in the Linnean system.  We can consider a
taxon to have several properties:  name definition, diagnosis, group
membership, timing of origin.  The Linnean system effectively tried to
maximize the stability of the diagnosis, but diagnoses were still labile:
were we to diagnose Dinosauria on the basis of a perforate acetabulum and
inturned femoral head, and then discover some new fossil with one but not
the other, the diagnosis would still require modification.

No one is claiming that phylogenetic taxon names will have stable group
memberships or diagnoses.  The attempt is to maximize the meaning of the
name, which from a biological perspective is important.

An example of what I mean by maximizing name stability and why you should
care (and I apologize for not using a dinosaurian example):  Crocodylus.
These are the "true crocodiles," occurring throughout the tropics.  These
are the largest living reptiles.  They eat people.  They swim the oceans.
Really cool beasts.

If you look at any published compendium of croc fossil diversity, you'll
find Crocodylus from the Cretaceous, Paleocene, and Eocene.  But molecular
data - primarily protein distances at first, and now mitochondrial
sequences - were strongly pointing to a divergence among living species
within the past 3 to 6 million years.  Were the fossils misidentified?
Were molecular rates within Crocodylus amazingly slow?  Ten years of debate
raged.

The problem, though, is that no two people were using the name "Crocodylus"
in the same way.  The molecular people were using the *crown-group*
Crocodylus, but paleontologists were using Crocodylus as some sort of
form-taxon - if it's not a gator or gharial, it's gotta be Crocodylus.  The
oldest fossil crown-group Crocodylus are about 5 million years old. This
debate should never have occurred, and resulted from a lack of stability in
the meaning of a name.

We expect lability in the diagnoses and group memberships.  This is true no
matter what system you use. For more on this, I recommend the following,
which take somewhat different stands:

Bryant, H.N.  1994.  Comments on the phylogenetic definition of taxon names
and conventions regarding the naming of crown clades.  Systematic Biology,
43:124-130.

(Bryant had another paper in Biological and/or Zoological Journal of the
Linnean Society on this recently, but I can't find my copy right now.  Let
me know if anyone wants the details.)

Cantino, P.D., R.G. Olmstead, and S. Wagstaff.  1996.  A comparison of
phylogenetic nomenclature with the current system:  a botanical case study.
Systematic Biology, 313-331.


>
>Now, what do you do if you get an organism that has every feature on your
>list,
>but for some reason you can't tell if it's actually within the defined clade?
>That is, for a crown group, you can't tell if it actually is a descendant
>of the
>LCA; or for a node group, you can't tell if it's actually closer to X or to Y.

Depends on where it falls out in a phylogenetic analysis.  In the situation
you describe, I would expect it to fall out as part of an unresolved
polytomy at the base of the group.  The safest option is to list it as a
member of the next most inclusive group, with a note that it may belong to
something more specific.  A fragmentary basal theropod might be Theropoda,
cf. Ceratosauria or cf. Herrerasauridae.



>
>
>> So what?  If everyone agrees on what the name refers to, then there is no
>> reason for it to mean anything.  Sometimes they are cute, sometimes they are
>> neat (as in the case of Einiosaurus' etymology) but no where does it say, no
>> where has it ever said, and no where has anyone ever suggested that the
>>named
>> NEED to mean something useful.
>
>I'm a computer programmer by trade.  That's how I work; that's how I
>think.  In
>computer code, names carry information, and naming conventions are at
>least the
>second most important thing about program design.

Taxon names are not like computer code.  They are more like personal names.
Philosophically, a taxon is an individual.  This is why it is inappropriate
to refer to The Dinosauria - it should be Dinosauria, just as it's Jon
Woolf, not The Jon Woolf.

The properties of an individual are expected to change over time.  I would
predict that the characteristics currently distinguishing you from all
other humans have not remained stable throughout your lifetime.




 It's a cardinal rule for me:
>Don't Screw Around With Names.  Ever.  If a programmer doesn't use naming
>conventions, it instantly tags them as a sloppy thinker and almost certainly
>error-prone in other ways too.  And it makes the program a whole lot harder to
>follow.

Again, I don't think computer code is a valid model for taxonomy.  The
goals and underlying philosophies are very different.





>
>So, when names in other fields follow rules, I find them a whole lot easier to
>understand.  And when names don't follow rules, I get annoyed.  Life is
>difficult
>enough already -- why make it even more difficult?

As it happens, some of us who take phylogenetic taxonomy seriously -
including the Cantino paper listed above - agree with you and object when
common names are redefined in such a way that literature ties are lost.
This is why I would rather not have seen Reptilia defined as it currently
is.  But priority is still priority, and under no current system is
"appropriateness" a valid basis for ditching a name.



Names don't _need_ to mean
>anything useful, but if they _do_ mean something useful, then you've just
>substantially cut the time and space required to communicate information.
>"Tetrapoda" is a good name for the group made of all four-legged
>vertebrates and
>their descendants, because it presupposes very little. If you just know
>the Greek
>translation of the word, you understand basically what the group is.  But
>"Tetrapoda" is a very poor name, IMO, for "the last common ancestor of Man and
>Bullfrog, and all descendants of that ancestor," because it presupposes
>much more
>on the part of the reader.  You have to know what animals are and aren't
>descendants of that LCA before you know what the group includes.  Does the
>crown-group Tetrapoda include _Seymouria_? Anthracosaurs?  Microsaurs?
>_Diadectes_?  _Edaphosaurus_?  All of those have four legs, a
>differentiated head
>and neck, and a number of other traits that mark them as land-capable.  Is
>that
>enough to call them a tetrapod?  Should it be enough?  What traits separate
>members of this crown group from nonmembers?  Is there any way to tell that
>_Hylonomus_ is a descendant of that LCA, but _Seymouria_ isn't?  I don't
>know.  Do
>you?

The way to tell is to follow the literature.  The assumption we make when
we define taxa phylogenetically is that readers will also be following the
phylogenetic conclusions, which are far more important than the names
anyway.



>
>Or try an example from dinosaurs, since this is the Dinosaur List.
>Somewhere not
>long ago I read an analysis of early dinosaurs that said that since the
>identifying autapomorphies for theropods were already present in
>_Eoraptor_ and
>_Herrerasaurus_, and that therefore the sauropodomorphs and ornithischians
>must
>have originated earlier than that.  But if I recall right, _Eoraptor_
>itself is
>barely a dinosaur, let alone a theropod.  It meets the diagnosis of a
>dinosaur,
>but only by the skin of its teeth.  If it's the first _diagnosable_
>dinosaur, how
>do you tell that, say, _Plateosaurus_ is not a descendant of _Eoraptor_?

By conducting a phylogenetic analysis and discovering (a) autapomorphies in
Eoraptor that would disqualify it as the immediate common ancestor of
Plateosaurus or (b) recovering a tree that removes Plateosaurus by several
nodes  from Eoraptor.





>
>Do you see what I'm getting at?  In at least some circumstances, saying
>that "X is
>not a member of group Y" requires you to prove a negative.


Not exactly.  It requires you to support a positive - that Y is a member of
a group with Z.

Moreover, I don't think scientists try to prove anything, ever.  Rather, we
try to falsify.  The hypothesis that Eoraptor is the immediate ancestor of
Plateosaurus can be falsified by discovering a phylogenetic pattern that
refutes it.

[shortened]

>No, but there is apparently something that you aren't getting.
>_Morganucodon_ is
>a small, somewhat shrewlike fossil from the Early Jurassic.  It has
>differentiated
>teeth, semi-erect posture, a dentary-squamosal jaw joint, evidence of
>endothermy,
>a bunch of unusual specializations about the ear and braincase -- in
>short, it has
>every feature I've ever seen or heard used to diagnose mammalness in fossils.
>None of the authorities I've read can point to any trait or suite of
>traits that
>distinguish crown-group mammals from morganucodonts.  Most are pretty
>unequivocal
>in calling _Morganucodon_ a mammal, even though it clearly dates from
>before the
>probable LCA of monotremes and therians.  So, how can you possibly tell
>that it
>_isn't_ a descendant of that LCA and therefore a member of Mammalia?


Have a look at Rowe (1988, Jour. Vert. Paleo.) or the papers (esp. that by
Rowe) in the Mammal Phylogeny volumes for the details.

[shortened]
>
>This is an interesting statement, for a couple of reasons.  First, what
>makes you
>think cladistic analyses are any more objective than the old Linnaean methods?

I'm not sure "objective" is the right word here.  But, phylogenetic methods
do have two big, big plusses:

1.  When presented properly (and I know they're not always so presented),
they're explicit.  They come with a matrix.  You don't like my codings?
Here's the data - have at it.  Redo it, rerun it yourself.  And to the
criticism that no one really goes through those big matrices - I know of
two people doing just that with mine, and I've done it with the matrices of
several others, both on theropods and crocs.

2.  The methods are repeatable.  Someone can go back through the literature
or, better yet, go back to the specimens, cross-check my codings, plug the
matrix back in, and see if the same tree(s) come up.

No one is denying that cladistic analyses are purely objective.  As long as
they're conducted by bipedal primates, it won't happen, especially with
morphological data.  But they are much more explicit and repeatable.



chris


-=--=--=--=--=--=--=--=--=--=
Christopher Brochu

Postdoctoral Research Scientist
Department of Geology
Field Museum of Natural History
Lake Shore Drive at Roosevelt Road
Chicago, IL  60605  USA

phone:  312-922-9410, ext. 469
fax:  312-922-9566

cbrochu@fmppr.fmnh.org