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Re: Benton 1985, etc.
Okay, David, sure more taxa is better than fewer taxa. That goes
Still, if all you want to do is find out if pteros are closer to one
taxon or another, you can find out with a dozen of each. Or five if
you want to get down and dirty.
This is wrong, and I'm speaking from experience. Using just 7 "microsaurs"
and 6 dissorophoid temnospondyls plus an outgroup or two to find out the
position of Lissamphibia in the tree will not get you a robust or defensible
result (even when the albanerpetontids are included, *Eocaecilia* is coded
after its 2007 redescription, and *Rubricacaecilia* is considered). This
does not change even if you add the only well-known lysorophian
(*Brachydectes*). For example, plenty of character states come out as
autapomorphies of the ingroup, even though e. g. other temnospondyls that
are not in the matrix retain the plesiomorphy. To find out the position of
Lissamphibia, or arguably even its monophyly, you must, I repeat, must make
a full-grown analysis of all limbed tetrapods. Any less than that doesn't
work. (I even have unpublished reasons to think that the latest such
analysis, with 102 taxa and 341 characters, still didn't resolve the
question, though that may have more to do with the way of coding than the
size of the matrix.)
For an outgroup, be safe. Try Ichthyostega.
Most certainly not. *I.* is so far away that you are inviting long-branch
attraction. Plus, it has its own bizarre autapomorphies (like that middle
ear phenomenon) which would increase that long-branch attraction even
further. Also, using a single outgroup is a bad idea: several are necessary
to determine the character state distribution at the base of the ingroup.
People who only use *Allosaurus* or *Allosaurus* and *Sinraptor* as
outgroups for a coelurosaur analysis don't even find tyrannosauroid
monophyly (see the *Mahakala* paper vs Rauhut 2002) because *Tyrannosaurus*
is much more similar to the carnosaurs than *Dilong* is. The only suitable
outgroup (if finding out the position of the pterosaurs is the only goal) is
a lot of stem-diapsids (plus perhaps a few other sauropsids as well) because
you must make an analysis of the entire diapsid crown.
I've also checked matrices for miscodings: Irmis et al. 2007 and Hill
2005. It's daunting, but it can be done. You asked about time put in?
10 years with time out for meals, sleeping, etc. It's fun, so the
work goes fast.
10 years just for your amniote analysis, and not counting your day job?
re: pteros next to the Archosauromorpha. Well, lots of interest there.
Benton 1985 nests pterosaurs between Lepidosauria and Trilophosaurus +
Rhynchosaurs + Prolacertiformes + Archosauriformes. With Trilophosaurus
and Rhynchosaurs actually closer to Lepidosauriformes (they are
Rhynchocephalians with unfused ankles) than Archosauriformes, that's a
very good nesting.
Also, why do you get *T.* and the rhynchosaurs as rhynchocephalians? Surely
you know that the "beaks" of rhynchocephalians and rhynchosaurs are not
primary homologues (the latter, like that of *T.*, being real beaks,
consisting of the pmx with presumably a horny covering, the former being
acrodont fused teeth)?
The only other nesting that is not
reflected in the comprehensive cladogram
(which is, again, not a cladogram, because it's not the outcome of a
is Prolacerta with Macrocnemus. In the absence of other taxa, evidently
convergence won out here.
See? Throwing too few taxa at a complicated problem with lots of convergence
does not work.
In 23 years since Benton 1985, no one has published a matrix that
includes any lepidosauriformes with pterosaurs. If you can find one,
please send it to me. That's a powerful a priori paradigm at work.
That's true. I'll probably be the first to do it.
You wrote: "No, I can't imagine that finger IV grew secondarily, so
it cannot have done that"? I'm not saying you're wrong; I'm saying
that if you're right, you're right for the wrong reasons.
Parsimony is the reason I use.
Then you don't need to mention a single character. Parsimony works across
the whole matrix. It is what tells us that toe V did indeed grow in
You wrote: *_WRONG_*. Benton had Younginiformes (as a whole!!!) and
"Lepidosauriformes" derived from a common ancestor, and he had that
common ancestor and Archosauromorpha derived from another common
ancestor. This common ancestor is *_NOT_* "Youngina and kin". Why do you
keep making such confusions? An ancestor on a cladogram is a node, not a
It's shorthand, David. Youngina and kin means Younginiforms + more
That's an outright misleading shorthand. Please abandon it.
You wrote: Why can't it happen that, at least with our imperfect
knowledge of the imperfect fossil record, two large groups can be
sister-groups of each other?
That's a world view that is the current paradigm.
And that makes it wrong? :-)
That world view
permits pterosaurs, ichthyosaurs and diadectids, among others, to
remain mysterious and poorly connected from other amniotes.
Yeah, and? What makes you think we must already have found all of their side
Besides, it's not true. Ichthyosaurs and thalattosaurs, for example, are
quite similar, and diadectids and *Tseajaia* don't differ in much more than
their teeth while being very similar to *Limnoscelis* and a bit less similar
to Amniota as a whole.
This results from using suprageneric taxa and just a few dozen taxa at
most (i.e. your suprageneric "two large groups").
It is not at all necessary that those large groups in the example be OTUs.
A comprehensive cladogram, on the other hand, using species and a few
hundred taxa demonstrates that such enigmas do indeed have close generic
sister taxa somewhere on the tree. And you'll be able to chart and see
the spectral blend of morphologies across the tree.
This is only a good argument if that blend is the most parsimonious tree.
Try not to hang your hopes on just one character. I'll just hazard a
guess, but I'll bet this unpublished pterosaur has a prepubis, an
elongated pedal digit V, hyper-elongated manual digit IV, multiple cusp
teeth, chevrons parallel to the centra, an elongated coracoid, a sternal
complex (interclavicle + clavicle + sternum), a non terminal naris, an
antorbital fenestra without a fossa and other characters no
To be fair, ao fenestrae without fossae are seen just outside the archosaur
crown-group, two nodes away from Dinosauromorpha, or three if the pterosaurs
re: Huehuecuetzpalli: you wrote: What is so pterosaurian about it? Well,
its actually closer to Cosesaurus, which leads to pteros, but here goes:
1. non terminal naris
2. ascending process of premaxilla extends beyond naris
3. low distinct coronoid process (a bump)
4. posteriorly sharp quadratojugal making poor contact with quadrate
It doesn't have a quadratojugal at all.
5. short descending process of squamosal
6. clavicles, interclavicle
7. posterior lean to quadrate
All of this, the lack of a qj included, is normal for squamates. What do you
mean by "clavicles, interclavicle" -- surely not their presence, which is a
8. eight cervicals (pre-scapula verts)
Please, please, please get another definition. This one depends on the size
and the life position of the scapula -- the former is variable and the
latter not trivial to reconstruct as well as very unstable post mortem. I
recommend the transition between cervical ribs (short) and dorsal ribs
9. low scapula
You mean "poorly ossified scapula". Squamate scapulae -- in fact tetrapod
scapulae in general -- ossify from the glenoid upward, and *H.* is a baby.
You must code all immature specimens as unknown for this character.
10. poorly ossified carpals (phylogenetic, not ontogenetic character --
this is how the centralia migrate to become preaxial carpals and
Dude, this is an ontogenetic character. Denying it doesn't make it
otherwise. Don't act as if you knew nothing about tetrapod ontogeny in
general and squamate ontogeny in particular. You are making yourself
This doesn't mean that there's zero phylogenetic signal in this character.
The signal lies in the "point" in ontogeny at which the carpals ossify. In
many aquatic tetrapods they never ossify, so you can clearly use "carpals
ossified IN ADULTS: no (0), poorly (1), fully (2)" as a character (if you
quantify it). But simply saying that this ossification is "not ontogenetic"
is nothing short of ridiculous. Never mind the, as far as I can see,
complete lack of aquatic features in *H.*, and the obvious fact that it's a
baby (all epiphyses are still separate, as mentioned, even those of the
11. manual digit IV is the longest
12. metacarpals III and IV subequal
13. manual digit V reduced but retaining three phalanges
14. fibula less than half diameter of tibia
15. unfused tarsals
16. metatarsals III and IV subequal and longer than I and II
17. pedal digit IV the longest
18. Metatarsal V short and torsioned
19. Pedal 5.1 elongated.
Sounds all normal for squamates or even larger groups -- 18 for example is a
famous autapomorphy of the diapsid crown-group, and 11 and 17 are the normal
state of affairs for the whole clade of pentadactyl vertebrates (plus
probably *Tulerpeton*). In other words, you are citing plesiomorphies as if
they were apomorphies. You're even aware of that: you say "retaining" in 13.
What does 15 mean? Unfused astragalocalcaneum? I bet *H.* doesn't have that,
because the astragalocalcaneum fuses in squamates before it even
chondrifies. I'll check.
20. Tail chevrons are preserved parallel to centra. Was this their
orientation in life?
I'll try to find out.
21. Posterior tail attenuated.
Can you quantify this?
22. and it's the right size
It isn't any size. It's a baby.
Besides, when you sent me your matrix 2 1/2 years ago, size was a binary
character: bigger or smaller than a house cat. This is not how to deal with
a continuous character. Why not make a lot more states out of it? (This
would allow you to give *H.* a minimum size: however large the adult may
have been, it can't have been smaller than the preserved specimen, so the
proper coding would be partial uncertainty rather than just a question
mark.) And how did you determine the limit between the states? Surely you
didn't just pick it arbitrarily, but did some kind of math?
Having size as a character in the matrix is also dangerous because it's
difficult to exclude that you have any size-related characters in the