RE: Dakotadon (Early Cretaceous ornithopod) redescribed

["Thomas R. Holtz, Jr." <tholtz@umd.edu>]

> -----Original Message-----
> From: owner-DINOSAUR@usc.edu [mailto:owner-DINOSAUR@usc.edu] On Behalf Of 
> Mickey Mortimer
> Sent: Tuesday, September 22, 2015 9:34 PM
> To: dinosaur@usc.edu
> Subject: RE: Dakotadon (Early Cretaceous ornithopod) redescribed
> 
> Unfortunately, the phylogenetic analysis is fatally flawed so that its 
> results cannot be trusted.  As I wrote in my Feedback on
PeerJ...
> 
>  The authors state "we did not proceed to calculate a maximum agreement 
> subtree from that set of MPTs because we have
> philosophical objections to the methodology behind that practice (i.e., 
> removing OTUs from the final tree topology to seemingly
> improve resolution even though  character data from the full set of included 
> OTUs influenced the final results)."  Yet that
practice is
> near-universal for a reason- it allows you to use the most information to 
> determine the topology.  Taxa with unique combinations
of
> characters can have major and unpredictable results on a tree, even if they 
> themselves have an unresolved position.
>  Then by a posteriori removing the less resolved taxa from the trees, you get 
> to see what resolution exists while still utilizing
their
> information.  Remember, resolution is only important for displaying and 
> understanding trees.  A resolved tree is not more accurate
or
> desirable than a less resolved tree, and if it's resolved by excluding data a 
> priori, is objectively worse.
>
Yes. I noticed that, too. And it makes me sad.

People have to get over several things:

1) Consensus trees (of any sort) are NOT results. They are summary of results. 
Your results are the individual MPTs, which the
consensus tree tries to summarize (maximizing information depending on the 
type: strict, semistrict, Adams, etc., etc.)

2) You are actually allowed to show more than one tree in a paper (especially 
when it isn't printed on paper, so you aren't being
charged page charges!!) Show the strict consensus with its massive polytomy, 
and then show trees with individual rogue taxa deleted.
The topologies that remain ARE your result; they were in every single equally 
most parsimonious tree!!

3) And if you want, rerun the trees after removing the taxa with no new 
contributions to the data, if any. This protocol has existed
for (wow, has it really been?) 20 years now: 
http://sysbio.oxfordjournals.org/content/44/4/501.short


Thomas R. Holtz, Jr.
Email: tholtz@umd.edu         Phone: 301-405-4084
Senior Lecturer, Vertebrate Paleontology
Office: Geology 4106, 8000 Regents Dr., College Park MD 20742
Dept. of Geology, University of Maryland
http://www.geol.umd.edu/~tholtz/
Phone: 301-405-6965
Fax: 301-314-9661              

Faculty Director, Science & Global Change Program, College Park Scholars
Office: Centreville 1216, 4243 Valley Dr., College Park MD 20742
http://www.geol.umd.edu/sgc
Fax: 301-314-9843

Mailing Address:        Thomas R. Holtz, Jr.
                        Department of Geology
                        Building 237, Room 1117
                        8000 Regents Drive
                        University of Maryland
                        College Park, MD 20742-4211 USA