RE: Herbivory widespread in Coelurosauria

[Mickey Mortimer <mickey_mortimer111@msn.com>]

Thanks for the reply, Lindsay.

Regarding the Yanornis/Confuciusornis issue, your supplementary information 
does contain the following.  "The ornithurine avian Yanornis martini exhibits 
evidence of seasonal dietary switching including plant and fish materials among 
preserved gut contents (22, 24), and is therefore coded EEH present.  
Accordingly, the presence of fish remains in the gullet of a specimen of the 
avian Confuciusornis sanctus (IVPP V 13313) (25) is not considered evidence 
against possible herbivory and the taxon is coded as EEH unknown."  I 
understand the choice to code Yanornis as having EEH even with the conflicting 
data, but I don't see the justification for Confuciusornis.  You might as well 
say that the presence of a lepidosaur in Oviraptor isn't evidence against 
possible herbivory (which is also true) and code it as EEH unknown.  I don't 
doubt that Confuciusornis was partially herbivorous- its beak seems better 
adapted to eating plants than fish, but I don't think the fact another included 
bird that ate fish also ate plants has any bearing on Confuciusornis' diet.

Regarding non-independent characters, you do discuss them and the fact they 
weren't taken to account for statistical correlations, which is good.  But you 
state in the paper "Here we find quantitative evidence for herbivory in 44 
coelurosaurian species across six major theropod subclades (29 with seven or 
more confirmed CHTs—the minimum number present in all terminal taxa exhibiting 
positive EEH evidence; Fig. 2 and Table S3)."  Yet there are taxa like 
Protopteryx which only have seven or more correlated herbivorous traits because 
they're coded multiple times for the same thing (conical premaxillary teeth and 
posterior dentary toothless in this case), while another taxon might actually 
have seven or more independent traits.  So those cases don't really seem 
comparable to me.  That was my concern there.

Also, as I noted on my website after I sent the email, the bald eagle has at 
least eight of the traits- decurved anterior dentary, creating anterior gap 
between jaws; ventrally concave dentary; dentary exhibits tooth loss; 
premaxilla edentulous; mandibular symphysis fused; ischium over 66% of pubic 
length; opisthopubic pelvis; more than ten cervical vertebrae.  You do state 
"Although several features (e.g., rostrodorsal trending mandibular symphysis 
and dentary convexity) achieve a widespread distribution in modern birds (49), 
their presence in O. hoazin demonstrates that these traits are consistent with 
a plant-based diet in theropod dinosaurs."  I suppose they're consistant with 
herbivory, but their correlation with herbivory is more doubtful since even a 
hypercarnivore doesn't lose them.  I would be interested in seeing a 
statistical study of living birds with known diets that indicates dentary 
curvature, cervical number, ischial length, etc. is actually correlated with 
herbivory.

You do state "Pairwise comparisons cannot process missing data; therefore, 
nonapplicable characters are considered absent (state 0)" in the materials and 
methods section, but you couldn't have run pairwise comparisons between all 
taxa for all characters because almost every taxon does have some missing data 
in the matrix, often when the elements in question are unpreserved.  So you 
presumably didn't do a pairwise comparison between Pelecanimimus and 
Anserimimus with regard to dental serration, for instance.  I'm no statistitian 
so I might be misunderstanding things, but I would think that means you could 
have also not done a comparison between Pelecanimimus and Struthiomimus since 
the latter actually has an unknown state too.

Even ignoring the inapplicability issue, that's still 9 miscodings out of 62 
(15%) for Cofucisusornis and Yanornis.  As I said, I don't doubt the general 
conclusion that most maniraptoriforms were more herbivorous than most other 
theropods, it's just the details I have issue with.

Mickey Mortimer

----------------------------------------
> Date: Wed, 22 Dec 2010 05:49:52 -0600
> From: lzanno@fieldmuseum.org
> To: dinosaur@usc.edu
> Subject: Re: Herbivory widespread in Coelurosauria
>
> D-List,
> 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,
> Lindsay
>
> On Tue, Dec 21, 2010 at 12:41 AM, Mickey Mortimer
>  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
> lzanno@fieldmuseum.org