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David Hone on archosauromorph phylogeny
Another one posted on David's behalf.
Part 2, for the second paper.
Mickey Mortimer and a few others commented about the content of this
paper. To cut an excessively long story as short as possible, this
paper is part of one enormous chapter of my PhD thesis dealing with
pterosaurian 'origins' and reviewing various methods and anaylses etc.
of various clades (supertrees, pterosaurs, matrix coding,
prolacertiforms etc.). Anyway, as a paper the chapter was rejected for
basically being more like a monograph than a paper, and so the easiest
thing to do was to split out the methodology sections and much of the
discussion. This left what ultimately became the current paper separate
as it dealt with methodological issues surrounding the hypothesised
pterosaurs / basal archosaur* relationships (*a catch all term as the
specifics of Peters' and Bennett's relationships are rather different).
Well, needless to say the main paper with all the various analyses and
datasets and the bulk of the discussion has been held up in endless
reviews while the (now) published part sailed through. Thus the whole
thing looks rather incomplete as basically the first 4/5ths of the
paper are more or less missing, hence the lack of in-depth analyses of
the hypotheses. Not expecting this to happen, I had kept this paper
short and as more of a review than anything else expecting it to be
backed by the rest of the companion piece. So basically watch this
space for more (in about another 2 years at this rate, sorry!).
I appreciate that this is (in some respects) a huge cop-out to much of
what has been discussed about the paper, but the data and analyses do
exist, and I do expect them to be published eventually (reviews have
Well, thats enough of that for those with only a passing interest.
However, David Peters also sent me (and CC'd to the DML) a colossal
e-mail about the paper (probably longer than the damn paper itself) and
while I simply will not rebuff the whole thing a line at a time, there
are a couple of key points that I think do need to be addressed.
If I may say so, I think the intent of the paper has been over-analysed
or missed by David Peters (admittedly without the knowledge of my
larger unpublished analysis) and so I have been taken to task on
missing themes that were deliberately lacking. Answers are interspersed
with some of DP's comments.
> Unwin, Bennett, and two others not known to me refereed the
This is a mistake - Unwin and Bennett were not referees. They saw and
commented on the manuscript independently of the review process. Dave
Unwin saw it as he was my external examiner to my PhD defence. Chris
Bennett had been of help discussing various aspect of pterosaur
evolution and so he was credited in the acknowledgements. Both he and
David Peters only received copies after publication and I think this is
the first Chris has seen of it for several years.
The referees who formally gave a 'yay' or 'nay' on the manuscript and
its contents were anonymous.
Mark Wilkinson & Olaf Bininda-Emonds were not referees (see below).
> Your comment: "pterosaurs appear suddenly...in full possession of all
> their highly derived characters" ignores my 2000 paper that showed
> except for the wings, Cosesaurus, Longisquama and Sharovipteryx had
> characters previously known only in pterosaurs (see below) -- even
> the many errors I've discovered subsequently that only add to that
> of shared characters.
No, it means I don't agree with your assertions in the 2000 paper about
the relationships of those taxa to the pterosaurs, thus my statement is
valid for my interpretations. Nor have I seen anything published since
that makes me think otherwise. I will leave this (and many other
potential comments) here. I disagree strongly with many of David
Peters' observations, interpretations, methodologies and conclusions
and I stand by my work. Quibbling over them will not convince either
> You're right about Bennett's 'exclusion of hind-limb characters'
> If anything he should have added characters -- or more importantly,
Well, I think there is a great limit to the taxa and characters that
can be added (research in progress). Chris' analysis overall is superb
(something which goes unsaid in the paper), and his descriptions of
both the characters and their coding is superb. Phylogeneticsis take
note, this is how cladistics papers should be done! I guess Chris gets
damned with faint praise that I really could only find one error in his
1996 paper, and that is one that he does (sort of ) concede within the
paper itself that he may have overreached with his 'legless' analysis.
> In paragraph # one you say: "in summary" when logic would suggest
> 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. In other words, and to use your words: you have
> summaries and included arguments without explanation. And you've
> tipped your hand as to the outcome, which appears to be biased.
Yes, but I am writing the paper in hindsight!!! I didn't write the
introduction, then do the analysis, then write the discussion. I did
the analysis then wrote the whole paper. That paragraph is there to
help the reader follow the paper. These comments suggest bias on my
part. There was none.
> Results from what supermatrix? This is the first mention. And where
> is it?
Whoops. That is my error. That is part of the (unpublished analyses)
and so of course should get no mention here as it is no longer
included. I may well submit and erratum update on this.
> Oh, man. look at that list of referees, starting with Dave Unwin and
> Bennett, the two people in the world who have demonstrated in print
> they despise my work.
They are not referees. See above.
> I don't know the other two. For anyone ' in the
> know,' this confirms the bias. I'm sure they were delighted to see
> reach print.
They had nothing to do with it, and do not think that they did. Olaf
and Mark had viewed that paper at a much earlier stage when it was
attached to the larger analysis. Both are experts in cladistic analyses
and cladistic methodologies. I studied under Mark Wilkinson as an
undergraduate student. There were two anonymous referees and the editor
(Andrew Smith - also a phylogeneticist) who reviewed the paper and had
final say in what was in and out.
> > key point: 2. You clobbered my methods -- but you failed to
> and argue against some of the key synapomorphies of the
> Fenestrasauria :
Yes as with different methods the phylogenies are completely different
and thus those synapomorphies disappear (though i have not checked
specifics) are so are no longer relevant.
> 3. You also failed to provide a better match from among all known
> taxa for
> pterosaurs than I provided in 2000. Cladistics only provides a best
> Your job was to provide a better one than I did. Your job was to
> show how
> each of the characters described above had a better phylogenetic
> match in
> Archosauria, which you champion in your Conclusion. You had a chance
> you blew it.
Nope. My job was to provide a review and I did. My analyses are my
chance to provide an alternative, though of course in this paper I
conclude that (by default admittedly) 'ornithodirans' provide the best
source of pterosaur ancestors. Not every paper has to say something new
or original. Science does move forward, but everything has to be
reviewed, recycled and reanalysed. The same will happen to my papers
and eventually everyone will be happy. I am just saying that right now,
based on the evidence presented so far, arguing that pterosaurs are
strongly linked to basal archosaurs / prolacertiforms etc. is not
> Don't follow tradition. That's religion.
I didn't, please do not suggest that I did. I evaluated the evidence
and found the methods and conclusions wanting, since it was
unchallenged in the literature, I challenged it.
> Even if you make mistakes during testing, like I did, at least you'll
> the satisfaction of having tried.
I have tried (see above - again a cop-out as no-one can see it but
those who have been involved in its writing and review, but that will
have to do for now). Its all in the mix in review with more to follow
and more still in my PhD, its just not in the paper.
Sorry for the extreme length of all of this, but I felt much of that
needed to be said as it had come out on the DML. There are numerous
other points I can elaborate on, but frankly, the basics are in the
paper and in my opinion (rather obviously, but also by definition that
of the referees and editors) I did what I set out to do properly, and
Now, lets get back to dinosaurs.
Dr David W.E. Hone
Bayerische Staatssammlung für Paläontologie und Geologie
Tel: +49 / (0)89 / 2180 6613
Fax: +49 / (0)89 / 2180 6601