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Re: Pneumaticity in Triassic pterosaurs

--- On Sat, 5/16/09, David Marjanovic <david.marjanovic@gmx.at> wrote:

> From: David Marjanovic <david.marjanovic@gmx.at>
> Subject: Re: Pneumaticity in Triassic pterosaurs
> To: davidpeters@att.net, "DML" <dinosaur@usc.edu>
> Date: Saturday, May 16, 2009, 1:45 PM
> ----- Original Message ----- From: "David Peters"
> <davidpeters@att.net>
> Sent: Saturday, May 16, 2009 3:54 PM
> > [1] There is no monophyletic Diapsida containing
> Archos and Lepidos. [2] Did I not send you my tree? [3] Your
> tree problem may be due to the assumption of monophyly in
> Diapsids.
> (1) You mean the upper temporal fenestra evolved twice? 


> Yes, four years ago, along with the character list and a
> weird list that was meant to indicate where state 1 of which
> character occurs. It led to a long discussion. I remember
> some highlights. -- Not that long ago, you submitted that
> thing for publication (after having accepted my
> nomenclatural advice, but apparently not any other). I know
> that because my thesis supervisor is Michel Laurin, who was
> one of the referees. The manuscript got rejected (without
> any influence from me) because... well, as it came out last
> year, you didn't even know how to make a data matrix for
> phylogenetic, as opposed to phenetic, analysis, and that
> showed. Bigtime. 

First of all, if Dr. Laurin was a referee, then you just blew his anonymity. I 
hope that's okay with your mentor.

Second, specifically, how, in your view, does a phylogenetic data matrix differ 
from a phenetic one when dealing with fossil organisms? Are not both concerned 
with morphology, characters and ratios?  

Third, if a given matrix and its scores deliver a single MPT in which all 
sister taxa are similar in size, shape, niche and chronology, isn't that a good 

(3) Sorry for the misunderstanding. _I_
> don't have such a problem yet, because I'm still
> stuck in the early stages of _making_ the matrix (tetrapod
> phylogeny, the side project now included in the thesis, is
> very time-consuming, too); I was summarizing the literature
> of the last 10 to 15 years. My analysis won't make any
> assumption on the topology within Amniota, because I'm
> trying to find out where the turtles sit, basically whether
> they are diapsids. That wouldn't possible if I built
> that kind of assumption into the analysis. (I'll use
> various seymouriamorphs and lepospondyls as the outgroups,
> so that I can test whether the diadectomorphs are theropsids
> -- a hypothesis defended by Berman and various coauthors
> throughout the 1990s, but then dropped when much larger
> analysis found the diadectomorphs outside.)
> > Good luck on your thesis.
> Thanks!
> > I can show you the path of most parsimony if
> you're interested.
> Erm, PAUP* will do that... :-)

By that I meant, if you are accidentally excluding any pertinent taxa, you 
should be told.

And then on to the M. Habib replies:

> Probably the idea is that if taxa are too distant
> phenetically -- that is, by a subjective, intuitive estimate
> of phenetic distance, not even by any attempt at
> quantification --, they can't be sister-groups. 

No, simply that a larger test found better sister taxa here excluded.

>This overlooks a few things:
> - That they are found as sister-groups means they share
> derived character states with each other and not their next
> closest relatives;

Sometimes very few, so few that the inclusion of another taxon or two can 
unseat the relationship. Witness: pterosaurs and Scleromochlus.

> - It is a feature, not a bug, that phylogenetics cares only
> about synapomorphies and ignores symplesiomorphies --
> resemblance consists of both;

Okay. Still, for good results, the overall gamut needs to be tested and 
affirmed before subsets of that gamut are tested.

> - Evolution happens -- some taxa run off very far, if
> that's where natural selection drags them;

True, but the larger test indicates better sister taxa than the inclusion set 
of the Prolacerta paper, and most others, allows.

> - For the probably twentieth time, the vertebrate fossil
> record -- let alone our knowledge of it!!! -- simply
> isn't complete enough that we could expect to do what
> the Unnameable Ones ask us to do (to present them a complete
> series of transitional fossils documenting each and every
> speciation-or-whatever between two arbitrary endpoints). 

Respectfully, that's an opinion, David. If I can do it, you can too. Also, when 
you say 'complete series' I hope you don't mean every mother's son. What I'm 
saying is you'll be able to line them up like the famous Australopithecus to 
Homo sapiens march. Or as I did from bacteria to humans in "From the Beginning" 
(1991)now available only from Amazon. The whole idea is just to get a picture 
of what really happened. 

> fact, that's not limited to vertebrates. It does not
> even hold for ammonites and conodonts; that's why
> stratophenetics (using total resemblance and stratigraphy to
> construct a tree and then interpret that tree as a
> phylogenetic one) does not work.

Okay. If you're referring to my submission, the stratigraphy was added after 
the phylogenetics, just to see where things fell. And if THAT'S the source of 
the phenetic confusion, hopefully this chronology of events will settle the 

Best, as always,