Re: Hone and Benton 2007 (their second paper)

[David Marjanovic <david.marjanovic@gmx.at>]

----- 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
> inexeperience.

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.