David Hone on archosauromorph phylogeny

[Mike Taylor <mike@indexdata.com>]

Another one posted on David's behalf.

--

Dear DML-ers,

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 
been positive).

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larger unpublished analysis) and so I have been taken to task on 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 
> manuscript.
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  
> 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.
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 
party.

> You're right about Bennett's 'exclusion of hind-limb characters'  
> problem.
> If anything he should have added characters -- or more  importantly, 
> taxa.
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  
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. In other words, and to use your words:  you have 
> made
> summaries and included arguments without explanation.  And you've 
> already
> 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  
> Chris
> Bennett, the two people in the world who have demonstrated in  print 
> how
> 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 
> this
> 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  
> mention
> 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 
> match.
> 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 
> and
> 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 
valid.

> 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  
> have
> 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 
fairly.

Now, lets get back to dinosaurs.

Dave

_______________________________________________
Dr David W.E. Hone
Bayerische Staatssammlung für Paläontologie und Geologie
Richard-Wagner-Straße 10
D-80333 München
Germany

Tel: +49 / (0)89 / 2180 6613
Fax: +49 / (0)89 / 2180 6601

www.askabiologist.org.uk