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Re: Phylogenies, science, tea-time and more...
Unfortunately (IMNSHO), the name Carnosauria was _immediately_
to designate the sistergroup of Coelurosauria (...a name that should have
been dropped as well...). So, while *Tyrannosaurus* and *Megalosaurus*
no longer carnosaurs, *Allosaurus*, *Carcharodontosaurus*, *Sinraptor*
*Monolophosaurus* are still carnosaurs.
Yep, that's one thing I know! :-) Anyway I don't think it's a bad thing
old names are redefined under cladistic rules (you seem to disapprove the
continued usage of the term Carnosauria), and kept in usage, although I
respect for historical usage might lead to two quite different
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
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
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
pointless, just that they seem to be a little bit too overriding these
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
And I do think (but I have no experience, so this could be complete
that a deep knowledge of anatomy should be something a human brain can
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
Now I know interrelationships among these groups are quite tricky to
out, but I'm not convinced that a whole bunch of, say, maniraptor
phylogenetic analyses are better than one thorough anatomical,
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"?
what cladistic analyses want to be, but frankly, saying that A is more
related to B than to C because it shares 5 apomorphies with the former
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",
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
Not yet. :-) More characters, more taxa. More, more, more.
If your tree is so unstable, you clearly have far too few characters*,
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
Not "my" tree. I don't have any.
Just generally speaking. They like to do that in English.
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
characters analysis means that the researcher(s) (I'm still waiting for
copy of the book, should arrive in a week or two...) behind have real
knowledge of the anatomy of the beasts they're talking about, which is
not the case, just because that research has not been done for most new
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
you have to know all those other variables you've just cited, and to
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
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
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
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
informative, not from a phylogenetic point of view, but from a conceptual
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
if you study an ecosystem...
Herbivory is an autapomorphy of many clades. :-)