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Re: Phylogenies, science, tea-time and more...

Unfortunately (IMNSHO), the name Carnosauria was _immediately_ reintroduced
to designate the sistergroup of Coelurosauria (...a name that should have
been dropped as well...). So, while *Tyrannosaurus* and *Megalosaurus* are
no longer carnosaurs, *Allosaurus*, *Carcharodontosaurus*, *Sinraptor* and
*Monolophosaurus* are still carnosaurs.

Yep, that's one thing I know! :-) Anyway I don't think it's a bad thing that
old names are redefined under cladistic rules (you seem to disapprove the
continued usage of the term Carnosauria), and kept in usage, although I admit
respect for historical usage might lead to two quite different directions:
save the name whatever it comes to mean or nuke it whenever it doesn't
correspond to its original meaning... Well, if we must rename every clade
every time the phylogeny shifts around, we really are in trouble. But that's
not really what I was talking about.

I object to the use of "Carnosauria" because that name comes with a concept (big theropod... pictures like Burian's semi-sprawling *Tarbosaurus*). At least it's anchored to *Allosaurus* :-)

Ja! But the problem is that in a large part of current dino research anatomy
is no more than a tool for building some matrix, that, stuffed into some
computer program, will release the new version of a phylogeny, just to be
destroyed two months later. I'm not saying cladistics are coming from nowhere and
pointless, just that they seem to be a little bit too overriding these days.

There are two reasons. Firstly, the number of characters used per study currently grows faster than linearly. Some people add tens of characters to their matrices and publish the updates on average once per year. The other is the addition of taxa -- by discovery. *Eotyrannus*, *Dilong* and perhaps *Tanycolagreus* and the redescribed *Coelurus* can tell us more about the phylogenetic position of Tyrannosauroidea than we could have found out earlier.

And I do think (but I have no experience, so this could be complete nonsense)
that a deep knowledge of anatomy should be something a human brain can cope
with well enough to identify phylogenetic relationships, first at species
level, and then higher up.

A deep knowledge of anatomy can contribute a lot to finding previously overlooked characters and to coding them correctly (like, coding non-independent characters as one character rather than 2 or 10, recognizing them as size- and/or ontogeny-related...). And it should. :-)

After all, most of the important dinosaur clades were
identified  well before cladistics, on a morphological basis.

Their interrelationships, however, weren't. Remember when some people thought Dinosauria was triphyletic simply because nobody had tried to show otherwise?

Now I know interrelationships among these groups are quite tricky to figure
out, but I'm not convinced that a whole bunch of, say, maniraptor
phylogenetic analyses are better than one thorough anatomical, computerless comparative
study of basal members of the various maniraptoran clades.

What would that comparative study do in terms of phylogenetics? Would it be computerless cladistics? Or would it produce a scenario-based phylogeny, the scenario being based on "cladistics with 3 characters"?

That's largely
what cladistic analyses want to be, but frankly, saying that A is more closely
related to B than to C because it shares 5 apomorphies with the former and 3
with the latter doesn't look like a reliable method to me.

It may not be reliable*, but it's scientific. I mean, the alternative would in effect be to say that A is more closely related to C _because_ these two only shares 3 apomorphies! See above.

I like reweighting, though. But then, it is _dishonest_ to _only_ publish reweighted trees, as the "Basal Ornithopoda" chapter of D2 does.

* This is something we can try to _quantify_. Some people prefer to draw stippled lines -- I prefer to read "bootstrap value = 79 %". Yet another big advantage of cladistics. (It is, however, possible to produce clades that are both wrong and strongly supported...)

It works very fine
for massive phylogenetic evidence, like "tyrannosaurs are coelurosaurs", but
when we get to more subtle aspects or fragmentary specimens, constant and
massive changes in the results of analyses show that they're not that useful.

Not yet. :-) More characters, more taxa. More, more, more.

If your tree is so unstable, you clearly have far too few characters*, and
probably too few taxa as well.

* Get a look at the "Basal Tetanurae" chapter in The Dinosauria II. The
analysis in there has 638 characters. It will teach you what I mean by "too
few characters".

Not "my" tree. I don't have any.

Just generally speaking. They like to do that in English.

I'm just
seeing that most new papers imply some new tree, and that there's no real
reason to, at first glance, believe someone in particular is right. A 600-more
characters analysis means that the researcher(s) (I'm still waiting for my
copy of the book, should arrive in a week or two...) behind have real in-depth
knowledge of the anatomy of the beasts they're talking about, which is usually
not the case, just because that research has not been done for most new or
little-known species.

I think if you try to check the states of 638 characters in 75 taxa, you learn all that anatomy by doing it, if you didn't learn it before... It is common, BTW, to use unpublished data (from personal observations of specimens) in large cladistic analyses. At least of theropods.

Then, in any  cladistic tree, if some topology is weakly
supported, then it cannot really be  trusted. If it is strongly supported,
then the cladistic method probably wasn't  necessary to find it out.

Every once in a while a very strongly supported clade emerges, and people think "why didn't I think of that earlier". Take the molecular analyses that again and again and again make whales and hippos sistergroups. Morphologists used to think it must be wrong. But early this year and late last year morphological analyses found the same. The mystery of artiodactyl phylogeny is no longer the position of the whales but that of the ruminants!

A really meaningful phylogenetic analysis, just like a really  thorough
anatomical study (when dealing with a reasonably large group or
 reasonably well preserved bunch of
specimens), used to imply a monograph, or at  least a long paper.


[...] if some new species is described from just one incomplete
specimen, then a discussion on its phylogenetic position, based
on careful  examination of what is known
(I mean, an actual TEXT about that), should work  just as well,
or better, than a computer calculation.

I think this depends on how detailed the computerized analysis is. If it's as detailed as the text, it should be at least as reliable.

but  doesn't it come also from inadequate study of those
reasonably well  preserved specimens we have at hand?

Of course. My bird matrix
is an extreme case  of this. [...]

Seems like we're quite much agreeing in fact...

Yes. (Most of those birds are exceptionally poorly described, however, so that case is really extreme.)

You can indeed quantify many morphological traits, but 1) I'm not sure
quantification is the best way to approach morphology (that is, to do it well,
you have to know all those other variables you've just cited, and to explain
how you use them),

I think it just needs to be done carefully and explicitely. If time permits (and as computers keep getting faster, it normally does), simply repeat the analysis with different coding assumptions. Has been done in the literature.

The thing I can't grasp about parsimony is why one femur
character and another cranial one should have more weight
than one single  vertebral one, for example.

The reason is simple. There is no objective method of determining the true weight of a character. So we must resort to parsimony.

Model-based approaches that take branch length into account, however, are coming. There is one paper that uses Bayesian methods for morphology (...but doesn't explain how, at least not yet).

I feel cladistics are sometimes a bit like asking  "are American
democrats or republicans?", and answering that according to the  last
elections it's most parsimonious to conclude they're republicans. I know
that this is a very rough caricature, but anybody working in cladistics is
confronted to just that kind of problem.
By the way, what are "Bayesian  methods"?

They try to resolve precisely this problem! :-) It would help if I had actually understood them... anyway... this approach has been used in many recent molecular analyses. You start with... I don't know how you start. I only remember the two most important features: The results come with "posterior probabilities", a support value similar to bootstrap & jackknife, except more reliable, because it's based on a kind of statistics called MCMC (Markov chain Monte Carlo); and you can apply complex weighting schemes (GTR...) by not giving everything the same "prior probability". The main advantage is that it produces probabilites rather than yes-or-no answers.

And, more generally, is it really more  interesting
to know  where Torvosaurus fit on the cladistic  tree than to
know what it looked like and  how it  lived?

This is a false dichotomy! If we don't know its place in the tree of life,
we _cannot_ find out certain aspects of what it looked like and how it
lived. "Nothing in evolution makes sense without a good phylogeny."

Is it not supposed to be the other way round? How can we figure out where it
fits on the tree if we don't previously know what IT is, independantly of

That's true, but...

As far as I know, knowing that
tyrannosaurs are closer to birds than to allosaurs did not improve in any way
our understanding of how tyrannosaurs lived.

It has. To start with, phylogenetic bracketing teaches us that the default assumption should be that *Tyrannosaurus rex* had feathers, while the evidence is at best equivocal for *Allosaurus*. Then we can go on about... perhaps its respiratory system, which may well have been more birdlike than that of *Allosaurus*, which in turn could imply different metabolic rates, different running speeds, whatever. Even how we interpret the biomechanics of its legs, hips and tail is influenced by our knowledge on its phylogenetic position. And so on. Hey, its brain!

Really. "Nothing makes sense in evolution, except in the light of a good phylogeny". I'll try to look up the exact wording and the authors. :-)

The best thing about cladistics is that it has introduced tree-thinking.

Right. But it also tended to nuke down grade thinking, which was also very
informative, not from a phylogenetic point of view, but from a conceptual one.

Actually grade-thinking is a part of tree-thinking. The difference is that each grade contains different taxa for different characters -- this "detail" tended to be overlooked.

Herbivory is not a phylogenetic group, but it's a hell of an useful notion
if you study an ecosystem...

Herbivory is an autapomorphy of many clades. :-)