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Re: Hone and Benton 2007 (their second paper)

----- Original Message ----- From: "David Peters" <davidrpeters@earthlink.net>
Sent: Thursday, May 17, 2007 2:39 PM

Prior offers to Dr. Hone to review the
manuscript were ignored or refused.

The author suggests referees, and the editor chooses them, using the suggestions as a base but not as an exhaustive list of possibilities. Sure you've experienced how peer-review works?

p. 1, col. 2. Recently I found out that I made a mistake when I
included Protorosaurus and Prolacerta with the clade that includes
Macrocnemus, Tanystropheus and their relatives (which Dilkes 1998
called the Tanystropheidae, I think). While Protorosaurus and
Prolacerta are sister taxa, I would use protorosaurs for the clade of
just those two, plus Boreopricea, and the term Prolacertiformes for
the clade that includes those three, plus the Archosauriformes which
arise out of them. I note you defined your clades by a priori
inclusion of certain generic taxa without performing an overall study
to see if this was so. Nor did you refer to any such study or not did
you test prior studies. So you're already out on a limb that you
cannot defend except with 'the tradition of the literature'.

I agree that a great big analysis of archosauromorph phylogeny is sorely needed. Unfortunately, the simiosaurs may or may not be crown-group diapsids, so any such analysis would have to encompass the whole of Diapsida, and because the turtles could be diapsids or not, it would have to be inflated into a full-scale amniote analysis. I hope to do such an analysis as part of my thesis, but, erm, I won't regard it as scooping if someone else does it at the same time :-}

Your comment: "pterosaurs appear suddenly...in full possession of all
their highly derived characters" ignores my 2000 paper that showed
that except for the wings, Cosesaurus, Longisquama and Sharovipteryx
had many characters previously known only in pterosaurs  (see below)
-- even with the many errors I've discovered subsequently that only
add to that number of shared characters.

If this is convergent (and/or based on misinterpretations), then pterosaurs do indeed appear "suddenly [...] in full possession of all their highly derived characters". I'm not expressing an opinion here (having neither studied the matter in detail nor read Atanassov's thesis), just mentioning that Hone & Benton are not necessarily wrong.

p. 3 col. 1. You're right. I did not perform Bootstrap anaylyses. I
used Hueristic Analysis. I was just introduced to PAUP during this
study and I had no mentors guiding me through the process.

And you know, this shows. Bootstrap and heuristic search (not "analysis"!) are not alternatives. A heuristic search is what you have to do to find the most parsimonious trees when you have too many taxa for an exhaustive or a branch-and-bound search. Bootstrapping is what you do _after_ you have found the most parsimonious trees to test how robust they are; it has been explained a couple of times on this list, so please search the archives.

The outgroup taxa were usually the ones to the left on the charts, the
basal taxa. You'll note that I used the data of others and I made
that clear. Their outgroup was my outgroup.

Cladistic analysis starts from the assumption that the ingroup is monophyletic with respect to the outgroup. If it isn't, the resulting tree will be grossly distorted.

Yes, I included and excluded characters often without explanation.
The paper as it stands was already so large that I had to pony-up
$1000 to cover the cost of printing the extra pages.

Wow. Was there no possibility of having online appendices or of making two papers out of it? We (me & thesis supervisor) used both possibilities when our manuscript was returned by Systematic Biology after peer-review with "it's good, we'll take it if you shorten it -- perhaps take the part on the confidence interval on the first appearance of Lissamphibia in the fossil record out and publish it elsewhere".

In paragraph # one you say: "in summary" when logic would suggest
that the summary paragraph should appear at the end -- after you've
made your arguments. Up to this point, you haven't made any arguments
or shown specific problems.

Nobody expects a scientific article to be written in real time. First you do the work, then you write the paper, and you don't write it in the order in which it will be printed (e. g. the abstract is usually written last, for good reasons).

Eudimorphodon was capable of digitigrade bipedal progression. You
evidently missed my paper in Ichnos 2000.
Peters D., 2000, Description and interpretation of interphalangeal
lines in tetrapods. Ichnos 7, 11–41 which covers all your issues with
bipedality and trackways.

Well, unless you found trackways _of *Eudimorphodon*_, interphalangeal lines won't help you finding out whether the beast was capable of sustaining digitigrade bipedal locomotion for any serious amount of time. I can walk and run digitigradely; I just can't sustain it for more than a few minutes because it hurts. For that matter, I can walk a few steps in an _unguligrade_ stance, before I have to stop because it hurts. Hey, I can gallop*, both with plantigrade and with digitigrade hands -- but my wrists are so unstable that I usually have to stop after 10 m or so with a wrist that is rather useless for the next minute. My point is that all my interphalangeal lines are compatible with me being digitigrade (be that bipedally or quadrupedally), but it still doesn't make sense to call me digitigrade (or quadrupedal).

* Not sure if I ever get all fours off the ground at the same time, but at least the movements fit.

They're you'll find that all but one set of current trackways are all
made by beachcombing pterosaurs gathering or feeding quadrupedally.

If by "beachcombing" you mean "walking in a rather straight line at an impressive speed"... I've seen such a trackway in Crayssac, and you know of it, too. I've also seen the trackway of the landing pterosaur in Crayssac. After IIRC one bipedal step, it's quadrupedal.

You may not be familiar with the 'Sauria aberrante' track reported in
1964 from South America. It's a digitigrade, bipedal anurognathid.

Maybe. :-)

My cladistic analyses did not follow normal practice because they
were initial attempts without a manual. The paper was peer-reviewd
and found to be acceptable.

There are peer-reviewers who don't know either how cladistic analysis works, and then of course few peer-reviewers will read a data matrix in the first place, for obvious reasons. I'm just saying...

Polytomies I would blame on the original authors and my

I'd blame it on a lack of data.

Eudimorphodon ranzii is a poor choice as a basal pterosaur?????

Do you mean as an outgroup in a cladistic analysis of Pterosauria?

1. Any time someone has nothing good to say about another scientist's
paper, I  suspect bias or animosity toward it.

<calm voice, as in Mr. Spock: "Fascinating."> Frankly, I find this opinion outrageous. Isn't it obvious that you have it backwards? When someone has nothing _bad_ to say about a scientist's paper, they are most likely not a scientist. Scientists _expect_ each other to do _great_ work; that's the basic assumption and doesn't need to be mentioned. Haven't you seen what book reviews in scientific journals look like? "Marvelous book, sorely awaited for years. -- However, [3 pages of mistakes of all sizes from middle to tiny, exponential distribution towards tiny]. -- This masterpiece will be an invaluable resource that everyone interested in anything will need to have on their bookshelf."

key point:  2. You  clobbered my methods -- but you failed to
mention and argue against some of the key synapomorphies of the
Fenestrasauria : the  unique elongated fifth toe, the anterior
extension of the ilium,  the loss of the thyroid fenestra, all the
factors that went into the attenuated tail, the  combination of the
sternal complex, the retention of the elongated fourth finger, the
uropatagium, the unique design to the antorbital fenestra,  the
elongated naris, the spike-like quadratojugal, the multi-cusped
teeth , etc.   --- none of which are found in archosauriformes, let
alone relevant archosaurs, let alone dinos + Scleromochlus.

If more apomorphies than the above support a Pterosauromorpha-Dinosauromorpha sister-group relationship, the above list must be attributed to convergence.

3. You also failed to provide a better match from among all known
taxa for pterosaurs than I provided in 2000.

In their analysis, there is a better match: Dinosauromorpha.