[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Subject Index][Author Index]

Re: Brusatte et al. 2008 question



David,

I'll try to answer this the best I can.  Maybe someone who is more familiar
with supertrees can do better.

First off...the "new phylogeny" he mentions is a phylogenetic analysis
paper that is either in review or in press.  Now this "in press" analysis
is the same that forms the basis for the analysis in the Science paper.
However, numerous separate in-group analyses were run for the Aetosauria,
Phytosauridae, etc... and then the results of these were incorporated into
the base study forming a "supertree".  Thus all four hundred something
characters were not entered into a single matrix and run.  This is also why
you don't get the same tree when you run the matrix given, you need to
incorporate all of the in-group trees as well.

We will have to wait until the main analysis is published before we can
critically examine their phylogenetic hypothesis.

Bill


************************************************************************
Bill Parker
Vertebrate Paleontologist
Division of Resource Management
Petrified Forest National Park
P.O. Box 2217
1 Park Road
Petrified Forest, AZ 86028
(928) 524-6228 x262


|---------+---------------------------->
|         |           David Peters     |
|         |           <davidpeters@att.|
|         |           net>             |
|         |           Sent by:         |
|         |           owner-DINOSAUR@us|
|         |           c.edu            |
|         |                            |
|         |                            |
|         |           09/23/2008 09:18 |
|         |           AM EST           |
|         |           Please respond to|
|         |           davidpeters      |
|---------+---------------------------->
  
>------------------------------------------------------------------------------------------------------------------------------|
  |                                                                             
                                                 |
  |       To:       DML list <dinosaur@usc.edu>                                 
                                                 |
  |       cc:       (bcc: William Parker/PEFO/NPS)                              
                                                 |
  |       Subject:  Brusatte et al. 2008 question                               
                                                 |
  
>------------------------------------------------------------------------------------------------------------------------------|




I'm trying to understand the difference between a cladistic character
list and a database the tries to quantify overall similarity.

I've been in contact with Steve Brusatte and he was kind enough to
send me the datamatrix for Brusatte et al. 2008, with the cautionary
footnote "our dataset is NOT a cladistic dataset.  It should not be
used to derive a tree." Having never heard of a database that did not
result in a phylogenetic cladogram, I ask anyone who may know, wha't
the difference?. Steve stopped communicating when I asked that
question.  He may be too busy.

The Brusatte et al. 2008 database does not result in the same tree as
was published. Far from it. And Steve considered that far from
unexpected. With regard to the mismatching of the database and
"cladogram," Steve said, "The confusion stems from the fact that we
refer to a "new phylogeny," but this new phylogeny is only shown in
our paper, and the proper character list will appear elsewhere.

Is that weird?

Quantifying overall similarity sounds like parsimony. But evidently
there's a subtle difference. The subtlety is escaping me. Help!


...........................

And with regard to David M's earlier comment to my earlier note:

    DP:  3. Scleromochlus, with its teenie-tiny hands and spike like
digit V
     is the sister taxon to pterosaurs. Sister taxa just outside of this
     clade don't have a long manual digit IV or a long pedal digit V
     either. In fact, those are hard to find anywhere here
[Proterosuchus
     is not included]. Was there a miracle in the appearance of wings
and
     toes? Maybe Hone and Benton can help here.


DM: No miracle here. *Scleromochlus* underwent reductions, and the
pterosaurs underwent expansions instead. The MRCA of *S.* +
Pterosauria did _not_ look like *Scleromochlus*.

As mentioned above, no mentioned outgroups (MRCAs) have a long manual
digit IV either, but reduced or vestigial. Same with pedal digit V.
Besides, better sister taxa are known with all the necessary
characters. I guess they mated outside their clade to get the miracle
baby with long finger four and a new toe five. So no good MRCA
candidate for many branches back. That's a red flag IMHO

And with regard to Scleromochlus, all you have to do is reconstruct
the poorly preserved quadrate leaning forward, rather than the
assumptive back lean and it becomes a flat-headed bipedal croc-omorph
with a particular affinity to another flathead, Gracilisuchus. Doing
that also reduces that hyper-elongated retroarticular process
proposed by Benton 1999.

David Peters
davidpeters@att.net