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Re: Phylogenies, science, tea-time and more...
Enough for an introduction. I was reading the discussion following Nick's
intervention in favor of getting rid of silly postcranial characters and
fragmentary taxa in theropod phylogenetic analysis, and was suddenly
cought by the
need of telling what I think about all this.
I hate to spoil all the fun... but apparently someone needs to kill the joke
by explaining it: Nick is parodizing the way ornithischian phylogenetics is
almost always done. By applying it to theropods, he demonstrates what
nonsense results when one only puts a few skulls into one's matrix. He is
crying desperately for someone to do a serious phylogenetic analysis of
Ornithischia. (Probably he'll end up doing it himself, alone.)
It certainly was a good thing to
nuke the old crumbling linnean tree and get rid of "thecodonts" and
"carnosaurs", which were mostly synonyms of ignorance.
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.
I know this also depends on money, research credits, and anyway
everydoby wants to be as modern and up to date as possible... But I dare
this is NOT science. For me, dinosaur paleontology is mostly anatomy,
stratigraphy, paleobiology and paleoecology. The first two items are the
dry and hard
data on which the other two more attractive ones are based.
But where does phylogenetic systematics fit in there?
It is based on anatomy, it is partly based on paleobiology, and paleobiology
including -ecology are partially based on it.
But after this is done, I can't see the sheer utility of those numerous
You add some abscure species known from two
teeth and one caudal vertebra and the tree gets completely changed... Get
of some characters you don't like and Corythosaurus might appear as a
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
I think Nick is right at pointing that part of the rampant phylogenetic
instability comes from including too fragmentary taxa,
Ironically, missing data are usually much more harmless than one might
think. There are theoretical studies on this to supplement my personal
experience (and doubtless the much richer one of others).
but doesn't it come also from inadequate study of those
reasonably well preserved specimens we have at hand?
Of course. My bird matrix
http://www.unet.univie.ac.at/~a0000265/cladogram.htm is an extreme case of
this. I haven't seen any of the specimens I've coded there, I have relied
completely on the literature which is often very superficial. By examining
the specimens -- or reading good monographs on them, which don't exist -- I
could perhaps cut the number of question marks in half. (That's the most
important reason why I don't consider it publishable -- even though I fear
it is better than any published analysis of Mesozoic birds, for example in
the sheer number of taxa that aren't included anywhere else).
As a student in social sciences, I have got quite a good knowledge of the
good and bad points of quantitative and qualitative methods. Cladistics
quantitative method, everyting being based on the NUMBER of shared
and the like. When reading sociology works, I tend to strongly dislike
studies based on pure statistics, while I believe interviews of "real"
often thrilling. Is it that silly to say that we could somewhat turn back
actually thoroughly interviewing fossils instead of comfortably use some
unreliable statistical method?
I don't think this metaphor works. In sociology you have to cope with plenty
of phenomena that are not quantifiable to start with. In morphology, those
are rare... and actually just causes of ignorance. An example is the
question whether a particular character should be ordered, and if so, in
which way, or even which characters to include in the analysis at all.
Learning more about the ontogeny, inheritability, variability etc. of the
character in question (and on its dependence on other characters!) can force
us to exclude several possibilities, ideally all except one. (Unfortunately,
papers on phylogenetic analyses rarely explain the choices that were made in
BTW, I wouldn't call parsimony statistics... maximum likelihood and
especially Bayesian methods do use statistics... and as long as we aren't
talking about molecular data of taxa with long branches, I wouldn't call any
of them "unreliable"!
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."
The best thing about cladistics is that it has introduced tree-thinking.