RE: At long last! Turner, Makovicky & Norell on dromaeosaurids

[Jaime Headden <qi_leong@hotmail.com>]

Well, we can start with ....

1.
*Falcarius utahensis* -- which was both cited and the analysis of Zanno et al. 
which was produced in respect to it also cited -- was not included.


"The inclusion of Falcarius in the present dataset could result in this 
character optimizing at a different position on the tree or it may be that some 
version of a partially fused ‘‘semilunate’’ carpal complex is characteristic of 
a more inclusive coelurosaur clade." - Turner et al. 2012:pg.103.

"We can include it, but didn't."

2.
NGMC 91 ("Dave") is subsumed into *Sinornithosaurus millennii*, along with 
*haoiana* (and on a related note, *gui* is subsumed into *zhaoianus* -- 
variation between specimens is presumed to be individual). The authors make 
some bones about disregarding the utility of juvenile animals in the dataset:

"As we have discussed earlier, we view it as problematic to include 
*Epidendrosaurus* in a phylogenetic analysis because of the extremely poor 
level of preservation, which results in much missing data, and the likely 
juvenile status of the holotype specimen. Our exploratory analysis reinforces 
this latter point. All three recovered synapomorphies are subject to 
ontogenetic changes and the observed morphology and proportions of the holotype 
of *Epidendrosaurus* may very well be different from its adult phenotype. We 
advise exclusion of *Epidendrosaurus* from primary phylogenetic analyses of 
paravians until more information is known about its adult morphology and a 
significant number of more cells in the data matrix can be populated." - Turner 
et al. 2012:pg.132.

Despite this, *Juravenator starki* and MPC-D 100/44 (as "IGM 100/44") are 
included, but also juvenile and may, in fact, be perinates, while *Mei long* 
doesn't fare much older on the basis of neurocentral fusion and a lack of 
concensus on how to assess "age-related" features irrespective of a 
phylogenetic consideration (that is, outside of concerns for which group 
certain features are "diagnostic" for). Turner et al. further note that while 
*Bambiraptor feinbergi* (incorrectly written as "feinbergorum") has been 
referred to as a juvenile, and possibly of *Saurornitholestes langstoni*, 
cortical remodelling has occurred in the fibula. This is done as a "personal 
obs." remark, which reveals another problem (one which Mike Taylor made issue 
with here: 
http://svpow.com/2012/02/06/blog-citations-are-better-than-pers-comms/):

3.
The reference to an "in press" paper occurs twice, both for the same paper.
The reference to an "in review" paper occurs twice, again both for the same 
paper, different from the review one.
"personal observation", "pers. obs." or "personal obs." occurred three times.
"personal communication", "pers. comm." or "personal comm." occurred five times.

That is, there were twelve separate instances where, instead of directly 
referring to the subject where the empirical statement they allude to can be 
verified, they are not there to be checked. Moreover, if it is relevant, even 
on a personal level, they could have been included in the analysis. There is no 
reason a monograph being updated from a thesis prepared years before should not 
have the opportunity to include these things, such as a small figure and 
discussion including points on how the fibula includes remodelling, and how 
this indicates skeletal maturity.

4.
As mentioned, "Microraptorinae" is included, and like Longrich & Currie, which 
I mentioned in connection to my last post and my blog post, the authors 
attribute the name to Senter et al., 2004, who explicitly coined 
"Microraptoria" instead, and with specific reference to the absence of a 
rank-affiliated nomenclature. "Eudromaeosauria," explicitly named as such by 
Longrich and Currie in that very paper, does not receive the same treatment, 
which is only a matter of how the authors _did not check the paper_. It gets 
worse:

"*Jinfengopteryginae*, new clade name
...
We name this new clade of troodontids for two reasons. First, the clade 
represents a distinct group that is the sister taxon to nearly all other 
troodontids, therefore having a specific name for this group serves a practical 
purpose in discussions of troodontid relationships and evolution. Second, the 
clade possesses strong character support (six unambiguous synapomorphies) and 
high jackknife support, rendering it relatively stable. A stem-based clade name 
was chosen in order to provide a taxonomic framework for additional troodontid 
taxa that may be found or are undescribed and prove to be close relatives to 
this basal troodontid clade." - Turner et al. 2012:pg.107.

It's fine to name the taxon, if you need to. But it seems to read that "-inae" 
is a useful form to name stem-based clades; but also that "stem-based" is a 
reference to the definition: the form of the clade NAME should have nothing to 
do with the formulation of the name. This is a holdover from the rule or 
convention of using "type species" to name ranks, but also a small group of 
PhyloCoders who argue that the NAME form should follow the TYPE of clade 
definition it is being applied to, so that stems, nodes, crowns, etc. would all 
have little labels or formulation. -inae here is a stem, as it "subdivides" an 
-idae name. However, this is also itself a holdover from Linnaean Systematics, 
a convention I wish would die an ignominious death (yes, I'm biased on this 
perspective). Not only does this refer to Linnaean Systematics, it refers to 
the unbending problem that created "Microraptorinae" in the first place, and 
forces systematists to "rename" clades among the -ini-to-oidea spectrum of 
"family-rank" nomenclature. This is messy record-keeping, and it is unnecessary 
as, without this convention, the names NEVER have to be changed, recognized, 
printed, etc. One name, one meaning, one use.

Turner et al. further state:
"The clade names applied in the present study (fig. 6) were selected to 
maximize and facilitate tree discussions and conform most closely to 
contemporary use among basal coelurosaur and avialan workers. However, in no 
way are they rank based in a classical sense." - Turner et al. 2012:pg.15.

It should be noted that it is in "coelurosaur and avialan workers" that the 
drift away from "contemporary" use of rank-like nomenclature has occurred most 
sharply in vertebrate paleontology. It is rather some schools that adhere to 
the conventions of the past, but these are generally not the schools that 
dominate in the American East Coast. This should be no defense of the use of 
"-inae," "-idae," or the attempts of some workers to eschew references to ranks 
altogether. Their form belies their origin, and however comforting it is to 
continue using them it is unwise to continue the trend when you argue against 
it in practice.

5.
The scapula of MCF PVPH 78, holotype of *Unenlagia comahuensis* is depicted in 
"lateral view", to show off the "laterally" face glenoid. The scapula of UA 
8656, holotype of *Rahonavis ostromi* is _also_ shown in "lateral view," but it 
is shown directly 90° around the long axis of the scapula, so instead, what you 
see is the "dorsal" perspective of the first scapula. The scapula glenoid of 
the second scapula is NOT apparent in lateral view, yet we understand the 
humerus _must_ be capable of dorsal abduction/elevation. Get your perspectives 
and measurements straight! (Err, this is not pointed at anyone in particular; 
this is pointed at ALL OF YOU. 
http://qilong.wordpress.com/2011/07/16/diet-in-oviraptorosaurs-vii-measuring-the-mandible-part-1-alignment/)

6.
"Two birds *Jeholornis prima* (Zhou and Zhang, 2002a) and *Shenzhouraptor 
sinensis* (Ji et al., 2002a) occur in the Early Cretaceous Jiufotang Formation. 
Described just a few months apart, these two taxa exhibit near identical 
morphology and have been considered synonymous (Zhou and Zhang, 2006b) and 
potentially synonymous (Chiappe and Dyke, 2006). We agree with the 
interpretation of these authors and consider *Shenzhouraptor sinensis* a junior 
synonym of *Jeholornis prima*. *Jeholornis prima* was scored based on firsthand 
examination of IVPP V13274, IVPP V13353 and the published descriptions of Zhou 
and Zhang (2002a, 2003a) and Ji et al. (2002a)." - Turner et al. 2012:pg.89.

This issue floats around a bit, and even Wikipedia jumps in on it, where 
*Jeholornis prima* is considered to be the correct name for both taxa, when 
synonyms. In specific, Zhou & Zhang, 2006, refer to the unbounded date in Ji et 
al. (2002), where only the month/year is given, and the issue was a monthly 
publication, which indicates the date is July, 2002; _Nature_, in which Zhou 
and Zhang published their taxon, was explicitly published on 25 July, 2002. 
They were also not named "months apart," though a digital version of Zhou & 
Zhang (2002) was online ahead of print in June. Zhou & Zhnag (2006) argued that 
when disputes like this occur, the ICZN follows the "weekly" publication, but 
this is only partly true. I've not read the paper for some years and no longer 
have a copy, but checking with the ICZN offers other possible considerations.

"Article 21. Date of publication.
...
21.3. Date incompletely specified. If the day of publication is not specified 
in a work, the earliest day on which the work is demonstrated to be in 
existence as a published work is to be adopted as the date of publication, but 
in the absence of such evidence the date to be adopted is 21.3.1. the last day 
of the month, when month and year, but not day, are specified or demonstrated, 
or 21.3.2. the last day of the year when only the year is specified or 
demonstrated."

This would mean that Ji et al., 2002 is "effectively" published on 31 July, 
2002, six days after *Jeholornis prima* and as a subjective synonym is 
objectively junior. However, further reading reveals a wrinkle:

"21.7. Date not specified. If the date of publication is not specified in a 
work, the earliest day on which the work, or a part of it, is demonstrated to 
be in existence as a published work is to be adopted as the date of publication 
of the work or of that part. In the absence of evidence as to day, the 
provisions of Article 21.3 apply."

No date was forthcoming. The wrinkle comes when you consider that, if there was 
an explicit reference to date of publication or a demonstration of 
availability, then _that_ date takes precedence over the ambiguity of the print 
form. This date comes via George Olshevsky, who reported 
(http://dml.cmnh.org/2002Nov/msg00292.html):

"But there is proper evidence, in the form of press releases and Chinese news 
articles dated July 23, 2002 (China Daily), that Shenzhouraptor appeared in 
print at least two days before Jeholornis."

That date can be linked directly 
(http://www.chinadaily.com.cn/en/doc/2002-07/23/content_129001.htm) which is 
odd, considering even Wikipedia references this, but ignores the wrinkle. Thus, 
it can be argued (as Mickey does here: 
http://home.comcast.net/~eoraptor/Avialae.htm#Shenzhouraptorsinensis) that 
*Shenzhouraptor sinensis* is the valid name, and the senior subjective synonym.

The ICZN also suggests: "Recommendation 21F. Correction of date. If an author 
of a new scientific name or other nomenclatural act is aware that the date 
specified in the work containing it is incorrect or incomplete, he or she 
should publish a correction in some suitable manner."

7.
Oh, you thought I was done?

*Citipati osmolskae* apparently isn't an oviraptorid, or *Chirostenotes 
pergracilis* is one. Either way, both species cluster to the exclusion of other 
taxa in the oviraptorid section of Turner et al.'s analysis, and through 
virtually all permutations. This is supported by 8 putative synapomorphies, but 
the inclusions are not exactly exclusive of other taxa: Char. 25, Secondary 
palate: long, extensive palatal shelves on maxilla; 35, Shape of the 
quadratojugal: without horizontal process posterior to ascending process 
(forming a reversed-L shape); 40, Prefrontal: greatly reduced in size 
[Ordered]; 41, Frontals: narrow anteriorly as a wedge between nasals; 91, In 
cross-section, premaxillary tooth crowns: suboval to subcircular; 101, Cervical 
and anterior trunk vertebrae: opisthocoelous [Ordered]; 197, Ascending process 
of astragalus: separated by transverse groove or fossa across base; 233, 
Obturator process [of ischium]: triangular with caudal end confulent with shaft.

Several of these characters have a broader distribution, but also occur in the 
"outgroup" oviraptorosaurs (e.g., *Caudipteryz zoui*, *Khaan mckennai*, etc.) 
and thus should have no real bearing on the cohesion of the taxa in question; 
this includes the opisthocoely of the vertebrae, form of the ischial obturator 
process, a "secondary palate", the form of the groove at the ascending process. 
Some are obviously not present or perceptible: both species either do not 
preserve or do not possess a wedge-like anterior form of the frontals that 
divide the posterior nasal margin, or a distinct prefrontal bone (i.e., it is 
more than merely "greatly reduced," it simply doesn't exist as in animals in 
which is it distinct from the frontal or lachrymal, the latter to which it may 
be fused. And finally, neither species (no matter which specimen you use) has 
"premaxillary teeth," so their form cannot be assessed. That leaves absence of 
the "posterior" horizontal process of the quadratojugal, which is true for 
virtually all oviraptorosaurs.

Turner et al. conflate *Protarchaeopteryx robusta* into *Incisivosaurus 
gauthieri*; it is not simply a matter of treating them as a single collective 
of species, but as a single species, but with the _wrong_ species as the label 
for both -- *Protarchaeopteryx robusta* was named in 1997; *Incisivosaurus 
gauthieri* in 2002. There is some undemonstrated form of conflation of 
specimens for the sake of expedience, as this also occurs with *Chirostenotes 
pergracilis*, which is in this paper a conflation of various possible but 
undemonstrable synonymous taxa; moreover, it obscures the actual diversity of 
the forms remarked when they actually do differ. *Chirostenotes pergracilis* is 
coded for extensive cranial material, so it is presumed the skull is coded not 
just from ROM 43250 but also from CM 78000 and 78001, the "Triebold" or "Hell 
Creek oviraptorosaur" (see here for discussion: 
http://qilong.wordpress.com/2012/01/22/the-hell-creek-oviraptorosaur-should-or-shouldnt-it-be-chirostenotes-pergracilis/,
 but especially here: 
http://qilong.wordpress.com/2011/01/28/splitting-chirostenotes/). Appendix 1 
includes a list of "first hand revised" specimens for the taxa discussed in the 
paper, but specimens that are clearly being mentioned and coded are not 
included, either by inclusion from the references or specific specimens 
mentioned. This seems an oversight.

Anyways: Rather than use "generalized form" for OTUs, the specific label is 
applied but the general complex of specimens is used, but not even referenced. 
This may allow the convention of cohesion of the characters and limited need to 
play with taxa after the trees are created, but it is not the only way.

Cheers,

Jaime A. Headden
The Bite Stuff (site v2)
http://qilong.wordpress.com/

"Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)

"Ever since man first left his cave and met a stranger with a different 
language and a new way of looking at things, the human race has had a dream: to 
kill him, so we don't have to learn his language or his new way of looking at 
things." --- Zapp Brannigan (Beast With a Billion Backs)


----------------------------------------
Date: Thu, 23 Aug 2012 02:14:08 +0000
From: jaseb@amnh.org
To: david.marjanovic@gmx.at; "dinosaur@usc.edu"@listproc.usc.edu
Subject: RE: At long last! Turner, Makovicky & Norell on dromaeosaurids

I have not had time to read this tantalizing new work, but it is loaded with 
new photographs of the source fossils and tons of analysis, twists and turns. 
Surely everyone on this list will have this resource close at hand for many 
years to come.

Note that it has all kinds of information for those of us who study bird 
origins. It finds no support for the phylogeny of Xu et al., 2011; it moves 
Xiaotingia into the Troodontidae, and moves Archaeopteryx back into Avialae. 
Furthermore it recovers Epidendrosaurus as a basal avialan (the MOST basal one, 
before Archaeopteryx), and places Epidexipteryx as just outside the split 
between Avialae and deinonychosaurs, possibly giving us a glimpse or a model 
for what the ancestral paravian looked like.

It also recovers the most basal dromaeosaur as Mahakala, a short - armed form. 
In this study, when we look at the most basal paravians and their closest 
sister groups, we see many forms that do not look extremely flighty 

(Epidexipteryx, Incisivosaurus, Mahakala). This may renew the possibility that 
the ancestral paravian did NOT glide or fly, nor even necessarily have long 
wings. Only an ancestral state analysis can assess this question empirically.

I look forward to a fruitful DML discussion on this pivotal piece.