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Re: Herbivory widespread in Coelurosauria

Nearly all of Mickey's comments (err *cough* criticisms) are addressed
in the extensive supplementary materials accompanying our PNAS paper
including the Yanornis/Confuciusornis EEH issue, the situation
regarding non-independence of characters states, and coding of taxa as
state absence rather than N/A.

The character data-set in our study is built for the statistical
packages used and are *not* intended to be or used as phylogenetic
characters, therefore different parameters apply.

After 6 months of data crunching involving several thousand
iterations, and multiple perturbations of the data including
variations in tree topology, character states, and even missing data
sensitivity tests (which also demonstrate that our signal is robust
even if one were to disagree on a percentage of morphological codes)
we, unlike Mickey, are confident in our statistics.

Happy holidays to all,

On Tue, Dec 21, 2010 at 12:41 AM, Mickey Mortimer
<mickey_mortimer111@msn.com> wrote:
> An interesting study, but I note in figure 2 Yanornis is shown as having 
> extrinsic evidence of herbivory while Confuciusornis is left with an 
> ambiguous entry.  Yet both taxa are known from specimens preserving fish 
> remains, as the supplementary information table S1 correctly indicates.  By 
> their rules in table S1, Confuciusornis should be marked as having character 
> 8 (evidence of carnivory: present only) since it has character 7 (vertebrate 
> gut content: present only), which would then make it marked as lacking 
> character 9 (extrinsic evidence of herbivory).  Similarly, Yanornis should be 
> marked as having character 8, which would force 9 to be polymorphic since it 
> also preserves direct evidence of herbivory.
> There's also more of our friend the incompletely coded matrix.  Looking at 
> Confuciusornis and Yanornis for instance since we're already dealing with 
> them, neither is coded as lacking a U-shaped symphysis.  Yanornis isn't coded 
> for its unserrated premaxillary teeth, densely packed teeth or short ischium. 
>  Strangely, neither characters 1 nor 3 are coded for any taxon in the matrix.
> Also, Confuciusornis is miscoded as having a decurved anterodorsal dentary 
> margin, lacking a ventrally displaced mandibular glenoid and having an 
> ischium over 66% of pubic length.  It's also coded as lacking an inset 
> dentary tooth row, conical anterior dentary and+or premaxillary teeth, 
> elongate premaxillary teeth, unserrated premaxillary teeth, lanceolate cheek 
> teeth, recurved teeth, ziphodonty, heterodont dentition, procumbant 
> premaxillary teeth or having replacement waves between teeth, but all of 
> these should be inapplicable since it lacks teeth.  Yanornis is miscoded as 
> lacking tooth recurvature.
> This is out of 31 characters, mind you.  So that's 21 wrong codings out of 
> 62.  Note too there are unecessary characters such as "dentary exhibits tooth 
> loss", when the list already contains "rostral dentary exhibits tooth loss" 
> and "caudal dentary exhibits tooth loss."  Also "rostral teeth (premaxillary 
> or dentary) conical to subconical" when it contains "premaxillary teeth 
> conical or subconical (e.g., “incisiform”)" and "rostralmost dentary teeth 
> conical: absent (0), present (1)."
> So while I don't doubt the general observation that maniraptoriforms were 
> more herbivorous than most other theropods, I'm skeptical of the character 
> distributions and statistics.
> Mickey Mortimer
> ----------------------------------------
>> Date: Mon, 20 Dec 2010 20:59:27 -0700
>> From: xrciseguy@q.com
>> To: dinosaur@usc.edu
>> Subject: Herbivory widespread in Coelurosauria
>> A free .pdf is available at the link:
>> http://www.pnas.org/content/early/2010/12/10/1011924108.abstract
>> Guy Leahy

Lindsay E. Zanno, PhD
Department of Geology
The Field Museum
1400 S. Lake Shore Dr.
Chicago, IL 60605-2496
Ph. (312) 665-7665