Wednesday, August 29, 2012

Having your ideas published without attribution, and having your names with priority ignored

Gao et al. (2012) provide an excellent description of DNHM-D3078, a new Sapeornis specimen.  While the illustrations and photos are of high quality and I agree with their main conclusion all "sapeornithids" are synonymous, I'm calling the authors out on two issues.

First, I agree Sapeornis angustis, Didactylornis and Shenshiornis are synonymous with Sapeornis chaoyangensis because it's MY idea.  Gao et al. took it without acknowledgement. 

Compare my blog post from August 2010 to their discussion of Shenshiornis-
"Likewise, the differences between Shenshiornis primita and S. chaoyangensis proposed by Hu et al. (2010) are either mistaken or questionable in light of the holotype’s preservation (LPM B00018). We do not observe the proposed differences in the length of either the prenarial portion of the premaxilla or the maxillary process of the premaxilla (compare with Zhou and Zhang, 2003:fig. 3), the morphology of the teeth (Fig. 3), the number of sacral vertebrae (compare with Zhou and Zhang, 2003:fig. 4), or the length of metatarsals I and V (approximately 25% the length of the metatarsus; contra Hu et al., 2010); in all these respects, the morphology of these characters is the same as in specimens assigned to S. chaoyangensis. Additionally, the degree of tapering of the anterior margin of the ilium of the holotype of S. primita does not differ significantly from that of specimens of S. chaoyangensis. This margin is not preserved in the holotype of S. chaoyangensis and was incorrectly reconstructed as broad and rounded by Zhou and Zhang (2002, 2003). Our examination of other specimens of S. chaoyangensis (e.g., DNHMD1197, DNHM-D2523) indicates that the anterior margin of the ilium of this taxon is thinner and more tapering than that figured by Zhou and Zhang (2002, 2003) and, presumably, the reference used for comparisons by Hu et al. (2010). Furthermore, the caudal series of the holotype of S. primita is so poorly preserved that the alleged presence of 10 free caudal vertebrae cannot be verified. Morphologically, the holotype of S. primita cannot be discriminated from the holotype (or referred specimens) of S. chaoyangensis; the only significant difference between these two specimens is that the former is approximately 28% smaller than the latter."

Or my entry discussing Sapeornis angustiis posted on October 2009 to their discussion of that species-
"Sapeornis angustis was identified as a species different from the larger S. chaoyangensis on the basis of having fewer sacral vertebrae (six instead of the seven described for S. chaoyangensis) and rather subtle quantitative differences (i.e., narrower humeral deltopectoral crest, narrower furcular rami, shorter hypocledium, longer metacarpal I, and shorter pubic symphysis). Nonetheless, considering that the holotype of S. angustis (IVPP V13396) is likely a subadult (as noted by Provini et al., 2009), these differences can be explained as ontogenetic or intraspecific variability. We also interpret other differences to be the result of preservational biases or errors in measurements. For example, the deltopectoral crest of the holotype of S. angustis is comparable to that of the similarly sized DNHM-D3078 in being narrower than that of larger specimens of S. chaoyangensis, and in having a less abrupt distal angle. Such a difference is likely ontogenetic, because juvenile birds tend to have less developed humeral deltopectoral crests (L.M.C., pers. observ.). The proposed narrowness of the furcula is also questionable, because in the holotype of S. angustis this bone is poorly preserved and partially obscured by the right coracoid; therefore, this apparent
difference cannot be ascertained with confidence. In addition, Provini et al. (2009) correctly noted that some sacral vertebrae might be overlapped by the ilium and ischia; therefore, the smaller number of synsacral vertebrae may well be preservational. Perhaps the most striking difference noted by Provini et al. (2009) is the presence of a proportionally longer metacarpal I in S. angustis. However, our observations of the manus of IVPP V13396 indicate that the measurements provided by Provini et al. (2009) are incorrect. Based on our measurements (Table 2), the length of metacarpal I in S. angustis is 25% that of metacarpal II, exactly the same ratio as in the holotype of S. chaoyangensis."

At the same time, I wrote on Didactylornis.  Compare with their discussion-
"The differences used to distinguish Didactylornis jii from S. chaoyangensis are not much clearer. This species was diagnosed as having only two manual digits (i.e., a completely reduced digit III), an elongated first phalanx of manual digit I, and four, instead of five, phalanges in pedal digit IV (Yuan, 2008). However, the manus and pes of the holotype (CDPC-02-08-001) are poorly preserved (Yuan, 2008) and it is reasonable to assume that these apparent differences are taphonomic, particularly when considering the minute size of the digit III of sapeornithids, and the fact that the proximal phalanges of the digit IV of the holotype appear partially overlapped with the distal end of the metatarsals and other pedal digits. In fact, if one were to argue that the first phalanx of manual digit I is as long as claimed by Yuan (2008), this bone would leave no space for metacarpal I (see Yuan, 2008:fig. 1); thus, such argument would lead to the rather startling conclusion that CDPC-02-08-001 retains a digit I when its metacarpal has been completely reduced."

Incidentally, Li et al. (2010) also proposed Didactylornis was a probable synonym, but merely stated "these apparent differences may easily result from poor preservation or damage" without going into detail.  This was received in May 2010, seven months after my posting, but at least it wasn't a major conclusion of the paper or argued with the same points.  Note Gao et al. don't cite Li et al. either (and that the Zhang in each paper are different, so no authors were shared).

Now, I'm aware my writing was not published in a journal, so someone could reply that I have no claim to the idea, since blogs and websites are not "official" literature.  Thus Gao, Chiappe, Chinsamy et al. were free to use my idea without attribution.  But is that really the standard we want in our field?  If a hypothesis and its support are not written in paper peer-reviewed journals, it's up for grabs for anyone else who wants to put it in the latter venue?  Here's an idea- what if workers have the professional courtesy to ask the originator of an idea to be a coauthor?  Or link to their website.  Chiappe used a "pers. obs." in this paper after all, which is even less verifiable.  Or a worse but still more ethical idea- just list the person in the acknowledgements for coming up with that idea.  Speaking of the acknowledgements, I suppose no one in peer review noticed this?  Am I to believe none of the eleven workers responsible for this paper's publication were aware of my writings?  My post is the third result on Google for "Sapeornis Shenshiornis" and the second for "Sapeornis Didactylornis", after all.  My website and the DML aren't exactly obscure among Mesozoic dinosaur workers.

The second issue I have with Gao et al. is even worse in a way, since here they are ignoring published literature.  You know what a discussion of "sapeornithid" taxonomy should include?  Omnivoropteryx.  Can you guess what genus wasn't even mentioned in this paper?  Omnivoropteryx.  Gao et al. use Sapeornithidae when Omnivoropterygidae was named four years earlier.  What ever happened to the ICZN and priority?  Are Gao et al. really immature enough to be spiteful against Czerkas for his terrible ideas and in house journal/book?  We know Chiappe and such are aware of Omnivoropteryx.  The funny thing is that the latter genus actually helps the synonymy arguments since it shows the same proportional trends.  I'll note that the authors of other omnivoropterygids are also guilty of ignoring Omnivoropteryx, and that Provini et al.'s (2009) silence is particularly troubling, as Omnivoropteryx's holotype shares all the supposedly diagnostic characters of S. angustis where they can be observed (small size, short forelimb, low deltopectoral crest with unprojected distal edge, short pubis).  If any of you reviewers ever see sapeornithid or Sapeornithidae in a paper, make sure to do the right thing.

References- Czerkas and Ji, 2002. A preliminary report on an omnivorous volant bird from Northeast China. Feathered Dinosaurs and the Origin of Flight. The Dinosaur Museum Journal. 1, 127-135.

Provini, Zhou and Zhang, 2009. A new species of the basal bird Sapeornis from the Early Cretaceous of Liaoning, China. Vertebrata PalAsiatica. 47(3), 194-207.

Li, Sullivan, Zhou and Zhang, 2010. Basal birds from China: A brief review. Chinese Birds. 1(2), 83-96.

Gao, Chiappe, Zhang, Pomeroy, Shen, Chinsamy and Walsh, 2012. A subadult specimen of the Early Cretaceous bird Sapeornis chaoyangensis and a taxonomic reassessment of sapeornithids. Journal of Vertebrate Paleontology. 32(5), 1103-1112.

Friday, August 24, 2012

Turner et al. 2012- great review, sloppy analysis

Back in October 2011, Turner et al. redescribed Mahakala and included a phylogenetic analysis which basically combined the TWG matrix with Clarke's bird matrix.  This analysis of 102 taxa and 472 characters was not backed up with a matrix or character list in the paper.  However, Turner et al. did state "The character list, data matrix, and supplemental analysis data are available at and at"  Following links from the first page leads to , which didn't and still doesn't have the dataset.  The second page doesn't seem to have links to any datasets.  Emailing Turner resulted in no reply.  I'm very grateful for Norell's help and hospitality during my AMNH visits, but it's concerning to have not only an unavailable dataset, but also false statements in a paper about a dataset's availibility.

Regardless, Turner et al. (2011) stated their dataset was "developed by Turner et al. (in press).", a paper on dromaeosaurid systematics and paravian phylogeny, and theropod workers have been waiting ever since.  Eleven months later, the paper has been published, and this post will contain my thoughts on it.  Having a matrix of 111 taxa and 474 characters, it's actually different than the Mahakala analysis, meaning the latter has STILL not been published.

First of all, it's useful to know the paper is an updated version of parts of Turner's 2008 thesis.  Besides this, the thesis contains the Mahakala redescription noted above, a redescription of Jinfengopteryx's skull, and a description of "Ichabodcraniosaurus" IGM 100/980 (though Turner doesn't name it).  Unfortunately, the thesis has several major issues and these were not altered for the published version.

But before my usual scathing critique, let's look at the good.  The paper provides updated diagnoses for many dromaeosaurids (notable exceptions are Pamparaptor, Itemirus, Luanchuanraptor, Ornithodesmus and Dromaeosauroides among taxa generally thought to belong to the family).  Even better, there are numerous useful photos, including Adasaurus(!!!!) and new material of Utahraptor.  Though why they felt the need to waste 4 of 7 Utahraptor photos on the previously well described and illustrated premaxilla is a mystery.  Now that Adasaurus holotype photos have finally been published, I'm free to distribute mine, so those will be strewn throughout this review.  One juicy fact is "The only description of [Achillobator] is nefarious in that it was published without the knowledge of any of the junior authors based on a preliminary draft left in Mongolia in 1997."  Like Senter (2011), Turner et al. synonymize Tsaagan and Linheraptor, though they do this properly by evaluating the latter's supposed diagnosis.  Overall, this section is excellent.

Skull of Adasaurus mongoliensis IGM 100/20 in posterolateral view.

The phylogenetic analysis is where things start to fall apart.  The good news is it's better than most TWG analyses in ordering most of the characters that need it and having explicit state definitions for the 0 state.  Also, he's improved on the Turner et al. (2007) analysis that added Daspletosaurus in that he now codes its postcranium.  Another good thing is that the crown birds seem genuinely coded and not just assumed to be the same in regard to states usually diagnosing deeper branches.  In general, combining Clarke's bird matrix into the TWG matrix is a great way to quickly and easily give a better look at Mesozoic paravian phylogeny.  But here, it seems to have been done hastily and inconsistently. 

Take the taxon sampling for instance.  Numerous taxa are excluded supposedly because they could not be examined firsthand (Borogovia, Urbacodon, Tochisaurus, Geminiraptor, Sinusonasus, Gansus, Ambiortus, Archaeorhynchus).  Yet other taxa are admitted to be coded based only on literature (Xiaotingia, Xixiasaurus, Liaoningornis, Pengornis, Cathayornis, Concornis, Songlingornis, Baptornis, Hesperornis, Iaceornis, Ichthyornis; 35 included taxa if you trust Appendix 1).  Yet surely a basalmost "euornithine" like Archaeorhynchus is more important to include than a fragmentary possible crown bird like Iaceornis.  Similarly, if the goal is to test paravian relationships, why add taxa like Albertosaurus, Proceratosaurus and Albinykus, but not Yandangornis, Zhongjianornis, Protarchaeopteryx or Falcarius?  The latter is explained in Turner's thesis, where he says since Zanno is examining therizinosaurs, he didn't want to scoop her, but Zanno's papers are all out now and Falcarius was already coded for TWG matrices like Li et al. (2009). 

I mentioned Appendix 1 earlier, which is a list of which references and specimen numbers the authors used and examined firsthand.  But it's clearly wrong.  Daspletosaurus is coded completely, but the two provided references don't allow coding for most of it.  Harpymimus and Garudimimus both have Kobayashi and Barsbold (2005a, b) listed, but those were not used for most of the characters since the TWG codings were taken directly from Norell et al. (2001).  Many taxa have listings which are contradicted in the main text.  I note "Neuquenraptor sp." (near certainly Pamparaptor) is listed here too and was included in the thesis analysis, but not the published analysis.  Oops.  More distressing is that Citipati osmolskae is said to be based on IGM 100/978 and 100/979, but actually the TWG portion of its codings are directly from the IGM 100/42 OTU of Norell et al. (2001).  So that OTU is actually a chimaera.

Cervical vertebrae of Adasaurus mongoliensis IGM 100/20 in right lateral view.

But what about the coding?  First, it's obvious the TWG part of the matrix was just copied from all of the earlier iterations going back to Norell et al. (2001) for most taxa.  So Harpymimus is still woefully incompletely scored despite being well described for seven years now, and Tsaagan is still only coded for the holotype despite Turner synonymizing it with the very complete Linheraptor in this very paper.  Sadly, this paper is the first real TWG example of my favorite pet peeve.  See if you can tell what I mean based on Turner's codings for Tarbosaurus-


Now you don't even have to know what the characters are to see the problem.  Tarbosaurus is known from well described basically complete specimens, so nearly all of those question marks shouldn't be there.  Baptornis is uncoded for almost every non-Clarke-based character.  Patagopteryx is uncoded for many as well.  For the Clarke-based characters, Troodon, Jinfengopteryx, most of Saurornitholestes, the front half of his jinfengopterygine troodontids and the back half of Alxasaurus and Graciliraptor are uncoded.

Turner didn't recover Songlingornithidae, which seems odd since Clarke did.  Wanna know why?  He didn't notice Clarke et al. (2006) accidentally switched a few pectoral characters in their matrix, then partially recoded them himself.  It's just sloppy.

Dorsal vertebrae, sacrum, pelvis and femur of Adasaurus mongoliensis IGM 100/20.

When it comes to understanding Clarke's bird characters and applying them to non-birds, Turner makes some mistakes.  He codes all long-tailed theropods polymorphic for caudal transverse process length (some avians have very short processes on their free caudals, but instead of just comparing long-tailed theropod proximal caudals, I guess Turner coded all their free caudals, which of course start out with long processes that decrease to nothing distally).  Turner "rewords" the alvarezsaurid TWG character of a transversely convex distal ulna (visible in front/back view) with the ornithothoracine Clarke character of a posteriorly convex distal ulna (visible in side view), so that alvarezsaurids and ornithothoracines are both coded as having the same character.  Another example is how he codes the obturator tuber of birds as an obturator process, when birds lack an obturator process (see Hutchinson, 2001 for details).  But then he codes birds as lacking the obturator tuber, leaving it only known in some dromaeosaurids, when actually those dromaeosaurids share the obturator tuber with birds.

Turner's conclusions also seem inappropriate.  Try this one on for size- "On the other hand, only 1 additional step is required to place Troodontidae as the sister taxon to Avialae (fig. 73).  These only slightly less parsimonious topologies could be interpreted as an indication of weakness in deinonychosaurian monophyly. We are inclined to interpret (and think it is more readily borne out by the data) that this is instead a reflection of the overall morphological similarity of the basal members of each paravian clade (e.g., compare Mahakala to IGM 100/1126 or Archaeopteryx)."  But but... the refutation is too obvious to even state.  Interestingly, the quote is straight from his thesis (replacing I with we), so apparently adding Xiaotingia, Anchiornis and other taxa didn't change this number.  As those two genera are the basalmost troodontids in his topology and are very bird-like, it would be quite the coincidence for them to not affect this test, so I wonder if Turner truly did re-run the constraint analysis after the changes were made to his thesis' analysis.

Lower leg and pes of Adasaurus mongoliensis IGM 100/20.  Note the small pedal ungual II is incorrect (Kubota, pers. comm. to Senter, 2012).

Or "Constraining Rahonavis ostromi as a basal avialan requires seven additional steps beyond the most parsimonious topology, and constraining Rahonavis to a more derived placement within Avialae requires 11 additional steps (fig. 79). Taken together with the strong morphological support for the Unenlagiinae clade and strongly unparsimonious nature of an ‘‘avialan’’ Rahonavis, it has emerged that there is no reason to
consider Rahonavis as a problematic taxon."  So six steps is supposedly unambiguous enough to be non-controversial, but he finds Dilong to be closer to birds than tyrannosaurids and it takes twelve more steps to constrain as a tyrannosauroid (as stated in the thesis).  By that logic non-tyrannosauroid Dilong must be incredibly secure.  Ugh.

So my basic message is, the review section is excellent with tons of useful new information, but the phylogenetic analysis is more flawed than most TWG efforts.

References- Turner, 2008. Phylogenetic relationships of paravian Theropods. PhD Thesis. Columbia University. 666 pp.

Turner, Pol and Norell, 2011. Anatomy of Mahakala omnogovae (Theropoda: Dromaeosauridae), Togrogiin Shiree, Mongolia. American Museum Novitates. 3722, 1-66.

Turner, Makovicky and Norell, 2012. A review of dromaeosaurid systematics and paravian phylogeny. Bulletin of the American Museum of Natural History. 371, 1-206.

Thursday, August 23, 2012

Adasaurus' skull!

So Turner et al. (2012) has been published and FINALLY we can see Adasaurus a mere 29 years after it was described.  Was that so hard?  Here's a high resolution photo I haven't been allowed to share, but now that the same view has been published (figure 10A) I can't see the harm.

Skull of Adasaurus mongoliensis holotype IGM 100/20.
Look forward to a detailed review of Turner et al.'s paper tonight.

Reference- Turner, Makovicky and Norell, 2012. A review of dromaeosaurid systematics and paravian phylogeny. Bulletin of the American Museum of Natural History. 371, 1-206.

Thursday, August 16, 2012

When new data appears in creationism papers

Well that title ought to get the views.  You may recall a while back when I complained about Senter not stating his Tsaagan OTU included Linheraptor or his Parvicursor OTU included the Tugrik parvicursorine.  Well, I have to apologize for that because it turns out, Senter did state these things explicitly, but in a paper I didn't know about until this week.  While I'm ultimately responsible for my mistake, since Senter did reference his earlier paper in his Yurgovuchia one, let's look at the form of that reference-

"For this analysis we used the phylogenetic data matrix of a recent study [36], with the following improvements."

I had assumed reference 36 was his 2010 creation paper or maybe the Geminiraptor update, but no, it's a 2011 creation paper.  You know what would have made it obvious?  If PLoS ONE used normal author+date citations instead of numbers.  This part is not a criticism of Senter at all, but instead of PLoS ONE.  While I strongly support that journal and will no doubt submit there myself in the future, the citation system has got to go.

Another aspect of this situation is somewhat Senter's fault, which is that a paper designed to combat a creationist claim is the source of a major overhaul of an important dinosaur matrix.  In fact, it's worse than that.  Senter already included new information in his original 2010 anti-creation paper, yet this one is a response to Young Earth Creationist Todd Wood's critiques of the earlier paper, and completely overhauls the matrix.  I'm all for scientists engaging with creationists, but it's an odd venue to debut important scientific information.  The DML had never even noticed the paper, so I had to learn of it through a Tetrapod Zoology comment.  Again, I would have learned about the paper if I would have looked up reference 36 in the Yurgovuchia paper, so it is ultimately my fault.  But don't you think "Using creation science to demonstrate evolution 2: morphological continuity within Dinosauria" is an odd paper to propose the synonymy of two dromaeosaurids, or to add 38 new characters to your analysis and renumber every character?

Readers' thoughts?