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favorite dino & cladistics questions (very long)



I've compiled my reply to several different threads into one message.  The
question of interest to most people comes first, the longer one which will
interest fewer second, the reallllyyyyyy long one which will interest the
fewest last.

As to the question of my favorite dinosaur: to nobody's suprise, it is
_Tyrannosaurus rex_.  We share the same first two initials, and before I was
convinced it wasn't possible, I wanted to be a _Tyrannosaurus_ when I grew
up.  Finding out that that wasn't an option, I decided to be a paleontologist...

Most of the points I would have brought up on the current cladistics threads
have already been posted (by Brochu, Wagner, and others).  Here are a few
additional thoughts:

Joseph Daniel wrote:
>One question that I have had with cladistics for a long time was the
>time factor.  As an example, the ceratosaurs at least used to be
>considered "basal" or "primitive" theropods, right?  Yet they didn't
>appear until tens of millions of years after the earlier more derived
>theropods, a huge expanse of time in which a great deal of evolution
>could and probably did occur. 

Okay, a few things to clear up:
A) Ceratosaurs have not (or at least should not have) been considered
"primitive" theropods (where "primitive" means "retains the ancestral
condition"). It is true that they retained a few features lost in some or
all other major theropod groups (such as a four-fingered manus: oh, wait,
that actually ISN'T a tetanurine, nor even an avetheropod, synapomophy...
Heh, heh, heh, heh... ;-), but Ceratosauria is diagnosed by no less than
nineteen derived character states not found in other theropod groups.  In
some ways, even Coelophysis or Ceratosaurus are more advanced (i.e., contain
more specializations from the ancestral condition) than basal tetanurines
such as Eustreptospondylus or Piatnitzkysaurus.

B) The oldest ceratosaurs are essentially contemporaneous with the oldest
known dinosaurs.  Recalibration of the Triassic timescale and new
stratigraphic work in the American southwest have revealed that the lower
parts of the Chinle Formation (or Group, depending on the nomenclature you
use) are at least as old as the Ischigualasto Fm.  This puts coelophysoid
ceratosaurs as contemporaries of _Herrerasaurus_, _Eoraptor_, and
_Pisanosaurus_.

C) The chances of any individual, or even individual taxon, becoming buried
(and a potential fossil) is very rare, as indicated by field and
experimental taphonomy.  Multiply that by that the probability that
particual column of sediment becomes lithified, the probability that that
section is not subsequently metamorphosed or melted, the probability that
particular section is later exposed in the latter decades of human history,
and the probability that someone happens by that section to see the fossil
and recover it (and the futher probability of that someone brining the
fossil to scientific attention).  This is the reason the fossil record is as
spotty as it is.  We know only a tiny fraction of the life forms that
existed in the past: Leithia, muse of paleontology, is very stingy in her
rewards.

Jonathan Woolf, replying to J. Wagner, wrote

>> We need to have clear definitions so that we won't have the ambiguity
that can
>> be involved.  How tetrapodish do you have to be to be a tetrapod?
>
>Good question.

Exactly, especially given the recent discovery of the Pennsylvania fingered
fish and the recognition of the fishiness of Acanthostega, Ichthyostega,
etc.  A nice gradation there.

>Do you have a good answer?  I don't.  That's my main objection to
>what some people have done with phylogenetics -- it doesn't make any sense
to me.

The last phrase is reasonable.

>Or rather, it doesn't make any sense that people cling so rigidly to it
when it's
>so easy to envision a situation where the rules break down.

This sentence, however...
Phylogenetic taxonomy was developed PRECISELY because of the ambiguity of
diagnosis-based definitions.  To use a dinosaurian example, a sacrum with
three or more vertebrae, a perforate acetabulum, and upright hindlimbs were
all once part of the diagnosis of Dinosauria.  That was fine, because all
dinosaurs had them, and none of their known close relatives did (or, if they
did, they were structurally different).

Then along comes _Lago/Marasuchus_, _Pseudolagosuchus_, _Eoraptor_, and
_Herrerasaurus_.  None of these have all of those features, but each has at
least one.  This provides us with a quandry of what to do with the name
"Dinosauria".  Among the possibilities:
a) Abandon it.
b) Arbitrarily choose a SINGLE particular diagnostic character.
c) Arbitrarily choose a particular inferred ancestor.

"a" is just ignoring the situation: there should still be a label to use,
and so it just breaks down to "b" or "c". "b" has been proposed, and needs
to be based on a single character (because multiple-character definitions
are what produced the problem in the first place).  However, single
characters could potentially be converegent, and evolution has a habit of
making some nice intermediate forms.  For example:

If "feathers" become the defining (as well as a diagnostic) character for
Aves, what does that do for _Sinosauropteryx_.  Its structures are not true
feathers, but they aren't scales.  Is it a part bird?
If "four limbs with digits" becomes the defining character for Tetrapoda,
what does that do for _Eusthenopteron_, or the new Penn. fish (whose name
I've forgotten: sorry Ted!), or _Acanthostega)?  How "limby" does a lobe
have to before it is considered a limb?

Option "b" was NOT ignored because it wasn't considered: it most assuredly
was!  Indeed, it survived long enough (in a modified version) to be called
the "apomorphy-based phylogenetic definition" of de Queiroz & Gauthier.
However, it has proven unworkable precisely for the reasons above (problems
of convergence, problems of recognition of intermediate forms of the
character state). Some of us tried to employ this type of definition, but it
has not been successful (e.g., p. 1108 of Journal of Paleo. 68 (1994)
defines "Arctometatarsalia" as "the first theropod to develop the
arctometatarsalian pes and all of its descendants".  There were problems
with such a definition, as noted in Holtz (1996)).

So, the proposed option "c": ancestor based definitions.  Recognizing that
diagnoses will come and go, and that particular compositions of clades will
vary from study to study, de Queiroz & Gauthier proposed a system by which
names could be applied with a minimum of working parts.  It is an elegant
(in the engineering sense) solution to a sticky problem: definitions based
on the relationship of two (and only two) taxa.  Naturally the choice of the
taxa used and the name applied are arbitrary (and this has resulted in the
majority of debate here!), but starting from the assumption that all
terrestrial organisms are a clade, these definitions will always describe
some clade.  It might not be an important clade (to you or to me, although
to a specialist in that taxon it might be...), it might be a previously
named clade (aka a synonym), but it will describe a clade.

>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.

Operationally, a form which has every single feature in the list IS going to
be recovered as a member of that clade in that analysis.

Please, people, remember: except for the two defining taxa, the membership
of a particular organism in a particular clade is an analytical result.
Like all analytical results, this membership is falsifiable with further
discovery.

For example, the ONLY definite members of Maniraptoriformes Holtz 1996 are
_Ornithomimus_ and Neornithes.  Whether Tyrannosauridae, Troodontidae,
Dromaeosauridae, Coelophysidae, or Amiidae belong to this node-defined taxon
or not is the product of an analysis, and future studies may demonstrate
that any given form once considered maniraptoriform isn't.  (And those new
studies THEMSELVES are potentially falsifiable, and so on, and so on.  This
is a process called "Science").

So, in the examples you give, those taxa which demonstrate the particular
suites of characters for those clades would be discovered as members of
those clades.  However, additional study may reveal new characters, or
require the reanalysis of old characters, or reveal new taxa with novel
combinations of characters.  Additional analysese using this new data may
reveal the initial conclusions were wrong.  Thems the breaks.

The following statement I find quite amusing, actually:

>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?  

Funny, that's what Phylogenetic Taxonomy is trying to do: make the names
follow rules.  However, the rules employed are the definition (the important
part, as evolutionary biologists), not the etymology (not important, except
to a philologist).

>Is there any way to tell that
>_Hylonomus_ is a descendant of that LCA [of Bullfrog and Man - TRH], but
_Seymouria_ >isn't?  I don't know.  Do you?

Ummm, yes.  It's called "phylogenetic analysis" aka "cladistics" aka
"Hennigian systematics".  It involves a search for the "best fit" tree out
of multitudes of possible trees based on the distribution of derived
character states.  If, in such a tree, _Seymouria_ falls within the most
restrictive clade containing frogs and humans, it is considered a member of
Tetrapoda in that analysis.  If not, it isn't.

As to what those particular characters are, and their distribution, see the
work of Laurin and Reisz, who've looked at seymouriamorphs in greater detail
than anyone else, past or present.  It is their work which produced the
(surprising to me) result that these taxa lie outside the frog-man clade.
The Tree of Life web page on Seymouriamorpha has more details on this than
most people could possibly want.

Could they be wrong?  Damn straight!  How could we show that?  Gather new
evidence, run new analyses.

Now, something near and dear to my heart:
>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_?

You are conflating several differnt things here:
A) Sereno & Novas, and others, in a series of papers have presented their
data to support the hypothesis that _E_ & _H_ share a more recent common
ancestor with birds than with ornithischians and sauropodomorphs, and are
thus true theropods.  I and Padian (and a few others) have challenged some
of the character evidence, and suggested in our own analyses that _E_ & _H_
do not have such a position.  We have an agreed upon system of names and
definitions: what differs is the results of our analyses.
Since my & Padian's paper is not yet in print, nor is Sereno et al.'s
monograph on the osteology of _Eoraptor_, this answer is far from settled.
However, this has nothing to do with the definitions used: it has to do with
the particular observations and interpretations of character evidence by
different scientists.
        So, I might agree with you that _E_ "meets the diagnosis of a
dinosaur, but only by the skin of its teeth."  However, Sereno & Novas &
cetera would disagree, and say that there is additional evidence to show
that it is clearly a saurischian, and a theropod.

B) As mentioned above, it is NOT the first _diagnosable_ dinosaur: it occurs
on exactly the same horizon as _Herrerasaurus_ and _Pisanosaurus_.
Furthermore, this horizon is not older than dinosaur bearing units in other
parts of the world.  _Eoraptor_ may indeed be the most *primitive* dinosaur,
but appears too late in time to be ancestral to _Plateosaurus_: the
existence of ornithischians, sauropodomorphs, and coelophysoids at the same
time indicates that the Dinosauria had already diverged into several
different lines by the time _Eoraptor_ lived.  Morphologically may give us
the best current glimpse of what the ancestral dinosaur looked like, but it
is too late in the fossil record to BE the direct ancestor of _Plateosaurus_.

>What I object to is the elevation of PS from
>a tool to an end-in-itself.  I get the distinct feeling that too many
people are
>building too many cladograms and classifications based on a desire to get
>everything into a slot, not a desire to better understand the evolution and
>relationships of these animals.

You may indeed have this feeling, but it is entirely wrong from my personal
experience.  However, the method of phylogenetic systematistics has been
developed to move the study of evolutionary relationships from art to
analysis; phylogenetic taxonomy is simply a tool to put labels onto those
trees, by means of a system or rules.

I don't know anyone who works on systematics who isn't interested in the
evolution and relationships of the taxa they work on.  It is not as if
people are forcing us to do this...

>Does it actually mean anything significant that
>_T. rex_ is closer to _Ornithomimus_ than either is to _Velociraptor_?

To you: absolutely jack.  To me: a disseration.  Also, some of us happen to
be interested in the history of theropods other than birds, and recognizing
phylogenetic relationships can help us determine (for example) the likely
anatomical conditions of the ancestral tyrannosaur.  You might predict a
different ancestor for a grouping (_T_ + _O_) + _V_ than in (_T_ + _V_) +
_O_.  In the former example, arctometatarsality was developed in the
tyrannosaur line prior the two-fingered manus, but in the latter it is
ambiguous.  This will mean different potential life styles for the ancestral
tyrant dinosaur.

>Because as far as I know, you can't tell just by looking at the fossil that
>_Morganucodon_ falls outside the crown group Mammalia.

You can't, maybe I can't, but to a paleomammologist, there are a LOT of
anatomical details which show that _Morganucodon_ lies outside Theria +
Monotremata (as accepted by the majority of paleomammologists for quite
sometime). If either of us goes to the detailed literature on the subject,
though, there would hopefully be illustrations of the appropriate
characters. This isn't a statement that the character evidence isn't there:
it is a statement that you and I are not specialists in the field of
paleomammology.  I'm comfortable with that fact: are you?

I'm not a sphenodontid worker, either, so *I* can't tell right off the bat
that _Sapheosaurus_ is more closely related to _Sphenodon_ than to
_Cleveosaurus_.  However, if I am interested in it, I can consult Reynoso &
Clark's paper in the latest JVP, go through their analysis, and see their
justification.  If I am skeptical about these results, I can do some of my
own research and observations, run a new study, and compare the results.


Thomas R. Holtz, Jr.
Vertebrate Paleontologist     Webpage: http://www.geol.umd.edu
Dept. of Geology              Email:th81@umail.umd.edu
University of Maryland        Phone:301-405-4084
College Park, MD  20742       Fax:  301-314-9661