Basal Archosauromorpha paper – Ezcurra 2016

Another paper repeating the ‘sins’ of the past,
based on an incomplete taxon inclusion list (that also includes taxa that should not be included). And a huge amount of otherwise excellent work! It proves once again that first hand access to specimens and an overly large character list will not bring full resolution to a small taxon list cobbled together by tradition, rather than testing.

I envy, am proud of and have to feel sorry for 
Martin Ezcurra (2016). He went around the world gathering data, obviously took a huge amount of time studying the specimens and writing this paper, but he’s stuck with that less than adequate traditional taxon list rather than the testing offered by the wide gamut taxon list (large reptile tree) in ReptileEvolution.com. He’s using 96 taxa (vs. 674 at ReptileEvolution.com). He’s using 600 characters. That should be more than enough, and it is more than enough (less than half that number will do), but more taxa is really what Ezcurra needs.

Just a few notes
Ezcurra wrote: “Jesairosaurus lehmani was described in detail by Jalil (1997). Despite its short neck, this species has been considered since its original description as a member of “Prolacertiformes.” Nevertheless, the phylogenetic position of this species has not been further tested in more recent quantitative analyses.” Yes it has, Here Jesairosaurus nests with drepanosaurs at the base of the Lepidosauriformes, not with Macrocnemus, as shown by Ezcurra (Fig. 1). Drepanosaurs were excluded by Ezcurra.

Figure 1. Ezcurra 2016 tree of basal archosauromorphs. He has basically repeated the mistakes of Nesbitt 2011 here.

Figure 1. Ezcurra 2016 tree of basal archosauromorphs. He has basically repeated the mistakes of Nesbitt 2011 here. Colors denote taxa that lie outside the gamut of the Archosauriformes + Protorosauria under study here.

Ezcurra is still including the thalattosaur, Vancleavea which nests with Doswellia in the Ezcurra tree. It just doesn’t belong in a study on archosauriforms.

He still holds to the tradition of a monophyletic Diapsida proven invalid here.

Ezcurra is still including pterosaurs in an archosauriform study
Proterochampsia (now including Vancleavea) is still recovered by Ezcurra as the proximal outgroup. Phytosauria and Lagerpeton are sister taxa. How is this possible? What characters do they share? They certainly don’t look alike. He notes Peters (2000) then writes, “The phylogenetic analysis conducted here [Ezcurra 2016] constitutes the best data matrix compiled so far to test the position of pterosaurs within Archosauromorpha because of the broad sample of Permo-Triassic species, including the undoubted pterosaur Dimorphodon macronyx.”  Martin, but you’re not looking, really looking at your results. Your proximal outgroup should look kind of like a pterosaur. Right?

Ezcurra notes that 33 extra steps
are needed to place Dimorphodon with Tanystropheidae and 19 synapomorphies support the Ornithodira. That might be true in his study. Hard to imagine how that is possible though. I will try to plow through his 600 characters to figure it out.  Convergence is rampant in the Reptilia. More synapomorphies support pterosaurs outside the Ornithodira when pertinent taxa are not excluded (see below).

Ezcurra writes, “Future analyses focused on testing the higher-level phylogenetic relationships of pterosaurs should also incorporate a broader sample of early pterosaurs and some enigmatic diapsids that were found as more closely related to pterosaurs than to other archosauromorphs by Peters (2000) and are not included in the current taxonomic sample (i.e., Langobardisaurus pandolfi, Cosesaurus aviceps, Sharovipteryx mirabilis and Longisquama insignis). However, it seems extremely unlikely that the addition of these enigmatic diapsids, which are unambiguously considered to not be members of Archosauriformes (e.g., Peters, 2000Senter, 2004), will affect the higher-level phylogenetic position of pterosaurs.”

In Science, the word ‘seems” and “extremely unlikely” need to be tested, especially when Langobardisaurus, for instance, shares so many traits with Tanystropheus and Macrocnemus. And especially when they have been tested sixteen years ago (Peters 2000). The word “enigmatic” is inappropriate here, unless Ezcurra just preferred to avoid them and stay with the traditional nod and move on.

Many good color photos of specimens here.
Precise descriptions. Like Nesbitt (2011) he’s just not playing with a full deck — of taxa.

Ezcurra’s tree
had 1.8 million+ possible MPTs. The large reptile tree was fully resolved with a single tree and high Bootstrap values. His analysis 3 recovered 40 MPTs by dropping largely incomplete taxa. That’s often a good idea. No reconstructions were offered, except for some skulls. No gradual accumulations of derived traits for odd partners like pterosaurs, Vancleavea, Doswellia, etc. Many purported sisters do not look alike.

Still not sure how
these trees don’t nest Tropidosuchus and Lagerpeton together. They are virtually identical.

Figure 2. Ezcurra tree with Bremer supports AFTER pruning incomplete taxa.

Figure 2. Ezcurra tree with Bremer supports AFTER pruning incomplete taxa. Many oddly paired sisters still show up here.

Ezcurra comments on Choristodera
“The problematic phylogenetic position of choristoderans may be a result of an unsampled early evolutionary history. The phylogenetic position of choristoderans is also ambiguously resolved in this analysis, but is constrained to the base of either Lepidosauromorpha or Archosauromorpha.” Actually the early history is sampled (here), just not included in this analysis.

Ezcurra has to be feeling pretty confident.
He writes, “Much of the general topology of the phylogenetic trees recovered in this analysis agrees with that found by several previous workers (e.g., Sereno, 1991Dilkes, 1998Gottmann-Quesada & Sander, 2009Ezcurra, Lecuona & Martinelli, 2010Nesbitt, 2011Ezcurra, Scheyer & Butler, 2014).”

I’d feel more confident
if all sister taxa looked alike and a gradual accumulation of traits could be traced for every taxon. Ezcurra needs more taxa to weed out the problems here. This study carries with it the sins of past studies.

PS
I was unable to open the Ezcurra data files on either Mesquite or MacClade.

References
Ezcurra MD 016.The phylogenetic relationships of basal archosauromorphs, with an emphasis on the systematics of proterosuchian archosauriformsPeerJ 4:e1778https://doi.org/10.7717/peerj.1778
Nesbitt SJ 2011. The early evolution of archosaurs: relationships and the origin of major clades. Bulletin of the American Museum of Natural History 352:1–292 DOI 10.1206/352.1.
Peters D 2000. A reexamination of four prolacertiforms with implications for pterosaur phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106:293-336

Excuses for not posting last week…

  1. I finally wrote another paper and submitted it. That took all week.
  2. There wasn’t much other paleo news to get excited about (unless I missed something?).

Now that I’m back to looking at other things,
all I see is a pachypleurosaur with small hands and feet of uncertain affinities, Dawazisaurus (Cheng, Wu, Sato and Shan 2016). I note the authors did not test it against Hanosaurus and Dianmeisaurus, where it nested in the large reptile tree.

I’m pleased and surprised to see that readership does not flag
on quiet weeks. And for some reason Sunday was a big day. Thank you all for your continued interest.

References
Cheng Y-N, Wu X-C, Sato T, Shan H-Y 2016. Dawazisaurus brevis, a new eosauropterygian from the Middle Triassic of Yunnan, China. Acta Geologica Sinica (English) 90:401-424.

 

Turtles: Still not diapsids

Updated 02-25-2016 with a new pareiasaur skulls in dorsal view image (figure 2) based on updated data on Bunostegos 02-24-16.

This just in from today’s Dinosaur Mailing List.

Schoch and Sues
previously published on turtle origins and Pappochelys here, from which figure 1 was lifted.

Highlights from Schoch and Sues 2016:
New fossils from Germany reveal that turtles had ancestors with a diapsid skull.

That would be Pappochelys, which nests as a basal sauropterygian (an archosauromorph diapsid), far from turtles, and Odontochelys, a basal soft-shell turtle, not a basal turtle, despite the reappearance of teeth.

The turtle plastron formed in part from thickened gastralia.
Actual turtle sisters, like Scutosaurus and the pareiasaurs, did not have gastralia, so the plastron is not formed of gastralia.

The closed anapsid skull of turtles evolved late in the stem group.
Not so according to a larger gamut study, the large reptile tree. No turtle ancestors among the Pareiasauria had diapsid skull openings. And the LRT tests 658 taxa from a wide gamut of reptiles, so there is ample opportunity for all taxa to nest where they find it most parsimonious to nest.

There may also be confusion regarding the presence of a supratemporal in turtles (it is big bone, the remains of the former horn, but it is traditionally and widely misidentified, even today). There is also confusion regarding diapsids, which are diphyletic with lizards not related to archosaurs except through basalmost Viséan amniotes.

The traditional parareptile hypothesis of turtle origin is rejected. 
The Parareptilia is far from monophyletic so it should be rejected as a clade. Unfortunately, the authors are not considering the horned turtle Meiolania as the basalmost turtle and toothy horny Elginia as its proximal sister. Those two nest at the origin of turtles.

From the Shoch and Sues 2016 abstract
“The origin of turtles has been a persistent unresolved problem involving unsettled questions in embryology, morphology, and paleontology. New fossil taxa from the early Late Triassic of China (Odontochelys) and the Late Middle Triassic of Germany (Pappochelys) now add to the understanding of (i) the evolutionary origin of the
turtle shell, (ii) the ancestral structural pattern of the turtle skull, and (iii) the phylogenetic position of Testudines. As has long been postulated on the basis of molecular data, turtles evolved from diapsid reptiles and are more closely related to extant diapsids than
to parareptiles, which had been suggested as stem group by some paleontologists. The turtle cranium with its secondarily closed temporal region represents a derived rather than a primitive condition and the plastron partially evolved through the fusion of gastralia.”

Unfortunately
More parsimonious sisters appear among derived pareiasaurs. Pappochelys nests with basal placodonts, which independently developed turtle-like shells twice while a related taxon, Sinosaurophargis developed a third convergent shell. Schoch and Sues used too few taxa, too few pertinent taxa, and too many suprageneric taxa in an attempt at covering a wide gamut of reptiles. The large reptile tree (LRT) uses enough taxa, enough pertinent taxa and no suprageneric taxa to find the origin of every reptile on the inclusion list (658 at last count).

Figure 1. Schoch and Sues cladogram (black) with branches not recovered by the LRT (red) and LRT relationships (colored arrows). As you can see, using suprageneric taxa really does put one in a hopeful cloud, but species and specimen-based taxa will see you to your goals.

Figure 1. Schoch and Sues cladogram (black) with branches not recovered by the LRT (red) and LRT relationships (colored arrows). As you can see, using suprageneric taxa really does put one in a hopeful cloud, but species and specimen-based taxa will see you to your goals.

You can see a YouTube video
on the origin of turtles here, which was blogged earlier here.

Figure 3. Dorsal views of bolosaur, diadectid, pareiasaur, turtle and lanthanosuchian skulls. The disappearance of the turtle orbit in lateral view occurs only in hard shell turtles.

Figure 2. Dorsal views of bolosaur, diadectid, pareiasaur, turtle and lanthanosuchian skulls. The disappearance of the turtle orbit in lateral view occurs only in hard shell turtles. 

References
Schoch RR and Sues H-D 2016. The diapsid origin of turtles. Zoology (advance online publication) doi:10.1016/j.zool.2016.01.004
http: // www.sciencedirect.com/science/article/pii/S0944200616300046?np=y

Buitreraptor: not a dromaeosaur, not a sister to Rahonavis

A long-snouted theropod
Buitreraptor gonzalezorum (Makovicky, Apesteguía & Agnolin, 2005, Fig. 1) was recovered as “a near-complete, small dromaeosaurid that is both the most complete and the earliest member of the Maniraptora from South America, and which provides new evidence for a unique Gondwanan lineage of Dromaeosauridae with an origin predating the separation between northern and southern landmasses.”

The authors nested
Buitreraptor between Rahonavis and Austroraptor + Unenlagia distinct from troodontids and traditional dromaeosaurs like Velociraptor

Unfortunately 
the large reptile tree  nests Buitreraptor with the troodontid/pre-birds Aurornis and Anchiornis, two taxa published long after the publication of Buiteraptor. Wikipedia does not make this correction. I was unable to find any prior work linking these taxa.

Figure 1. Buitreraptor skull with bones and missing bones colorized.

Figure 1. Buitreraptor skull with bones and missing bones colorized. That naris is enormous! And fragile! The maxillary fenestra, anterior to the antorbital fenestra, is quite large, lightening the long skull.

By comparison
Aurornis (Fig. 2) also has a large naris and maxillary fenestra, but not nearly as large. Aurornis is Late Jurassic. Buitreraptor is Cenomanian (earliest Late Cretaceous). So that evolutionary chronology makes sense.

Figure 2. Aurornis in several views alongside Archaeoperyx to scale.

Figure 2. Aurornis in several views alongside Archaeoperyx to scale.

Stem like coracoid
Unlike Aurornis, Buitreraptor had an elongated and waisted coracoid, so it is likely that Buitreraptor developped the habit of flapping by convergence with birds, parabirds and pseudo birds.

Rahonavis 
still nests with basal therizinosaurs.

References
Makovicky, PJ, Apesteguía S, Agnolín FL. 2005. The earliest dromaeosaurid theropod from South America. Nature 437: 1007–1011. Bibcode:2005Natur.437.1007Mdoi:10.1038/nature03996PMID 16222297.

 

Xiongguanlong: not a tyrannosauroid

I hate to keep doing this…
I know it pisses off theropod-o-philes.

A few years ago
Li, et al. 2010 described a new theropod dinosaur, Xiongguanlong, as “a longirostrine tyrannosauroid from the Early Cretaceous of China” which they nested between Eotyrannus + Dilong and Tyrannosaurus + other Late Cretaceous tyrannosaurs.

Figure 1. Xiongguanlong does not nest with tyrannosaurs, but with other long rostrum theropods, including Denocheirus and Sinocalliopteryx.

Figure 1. Xiongguanlong does not nest with tyrannosaurs, but with other long rostrum theropods, including Denocheirus and Sinocalliopteryx.

Unfortunately,
the large reptile tree nests Xiongguanlong along with other longistrine theropods, like Deinocheirus (Fig. 2), Sinocalliopteryx and the spinosaurs. I have not yet encountered any valid longirostrine tyrannosauroids. Dilong and Guanlong also nest close to these long-rostrum theropods. They were removed from the tyrannosauroids earlier here and here. Eotyrannus was likewise removed from the tyranosauroids here, and nested with Tanycologreus close to the base of the dromaeosaur/troodontid + bird split.

Figure 2. Deinocheirus skull. This long rostrum theropod nests close to Xiangguanlong and shares many traits with it.

Figure 2. Deinocheirus skull. This long rostrum theropod nests close to Xiongguanlong and shares many traits with it.

I keep hoping one of these taxa
are going to shift the tree topology back toward the traditional thinking, but each new taxon just drops into place, adding their leaf to the tree.

Figure 3. Theropod cladogram with the addition of Xiongguanlong nesting with Deinocheirus and Sinocalliopteryx.

Figure 3. Theropod cladogram with the addition of Xiongguanlong nesting with Deinocheirus and Sinocalliopteryx, not tyrannosaurs.

Li et al. report
“Xiongguanlong marks the earliest phylogenetic and temporal appearance of several tyrannosaurid hallmarks such as a sharp parietal sagittal crest, a quadratojugal with a dramatically flaring dorsal process and a flexed caudal edge, premaxillary teeth bearing a median lingual ridge, and a flaring axial neural spine surmounted by distinct processes at its corners.”

“Remarkably, Xiongguanlong has dorsally smooth nasals. Unlike the conical tooth crowns of taxa such as Tyrannosaurus, Xiongguanlong has mediolaterally compressed tooth crowns. The cervical vertebrae display only a single pair of pneumatic foramina, and the dorsal centra are not pneumatic in contrast to Albertosaurus and more derived tyrannosaurids. Xiongguanlong is remarkable in having a shallow and narrow snout forming more than two thirds of skull length…most tyrannosaur ids have short deep snouts mechanically optimized for powerful biting.”

No blame here. 
Li et al could have extended their comparative search to Sinocalliopteryx, which was published in 2007, but the skull of Deinocheirus was not published until 2014, so they are not to blame for missing such possibilities. These things happen.

References
Li D, Norell MA, Gao K-Q, Smith ND and Makovicky PJ 2010. A longirostrine tyrannosauroid from the Early Cretaceous of China. Proceedings of the Royal Society B 277:183-190.

Deinocheirus: not an ornithomimosaur

Following a long list of blog posts
that reported an inability here (Fig. 3), in the large reptile tree, to nest various theropods in their traditional nodes, today Deinocheirus (Fig. 1) nests not with ornithomimosaurs, like Struthiomimus, but at the base of the spinosaur clade. Here Deinocheirus nests between Sinocalliopteryx and Dilong + Guanlong, none of which have elongate dorsal spines and all of which have long teeth.

Figure 1. The skull of Deinocheirus. Note the new interpretation of the anteriorly flaring nasals. Note how the mandible does not completely close cranially when the anterior tips touch. I wonder if this was a sieving organ lined with baleen-like structures. That hypothesis goes with the very deep mandible and the equal lengths of both upper and lower jaws.

Figure 1. The skull of Deinocheirus. Note the new interpretation of the anteriorly flaring nasals. Note how the mandible does not completely close cranially when the anterior tips touch. I wonder if this was a sieving organ lined with baleen-like structures. That hypothesis goes with the very deep mandible and the equal lengths of both upper and lower jaws.

Previous studies
assumed that Deinocheirus was an ornithomimosaur, because it had very similar manus and forelimb proportions. When the skull was discovered, it was likewise toothless. The large reptile tree finds that those traits were convergent with ornithomimosaurs.

Figure 2. Deinocheirus specimens and a composite illustration.

Figure 2. Deinocheirus specimens and a composite illustration.

Deinocheirus mirificus (Osmólska & Roniewicz, 1970, Latest Cretaceous, 70 mya 11m) was originally and later considered a giant and basal ornithomimosaur. The large reptile tree (see below) nests Deinocheirus between Guanlong and Sinocalliopteryx in the spinosaur clade.

Figure 4. Sinocalliopteryx currently nests as a provisional sister to Deinocheirus, awaiting the discovery of transitional sister taxa.

Figure 4. Sinocalliopteryx currently nests as a provisional sister to Deinocheirus, awaiting the discovery of transitional sister taxa.

Like ornithomimosaurs, Deinocheirus was toothless and had long slender arms with a metacarpus of subequal metacarpals. Like spinosaurs, Deinocheirus had long dorsal neural spines. Like SinocalliopteryxDeinocheirus had an elongate rostrum, a tall orbit and nasals that flared laterally at the nares.

Figure 2. Here, in this subset of the large reptile tree, Ornitholestes nests at the base of the Microraptor clade, close to the base of the Tyrannosaurus clade.

Figure 2. Here, in this subset of the large reptile tree, Ornitholestes nests at the base of the Microraptor clade, close to the base of the Tyrannosaurus clade.

I’m sure theropod workers
can’t be happy that the detailed nestings of their cladograms are not verified here. Tradition may have misguided them, perhaps in this case. Using the matrices of prior workers without testing them for typos and scoring errors may be another problem.

Pure speculatiion
I wonder if the very elongate teeth of Sinocalliiopteryx somehow evolved into water straining structures in Deinocheirus. Only a transitional taxon with more, longer, thinner teeth or similar structures are ever found. It will also likely have a deeper mandible. Both taxa may have fed in water. A third taxon, Spinosaurus, is also considered a piscivore.

References
Ibrahim N et al. 2014. Semiaquatic adaptations in a giant predatory dinosaur. Science 345 (6204): 1613–6.
Ji S, Ji Q, Lu J and Yuan C 2007. A new giant compsognathid dinosaur with long filamentous integuments from Lower Cretaceous of Northeastern China. Acta Geologica Sinica, 81(1): 8-15.
Lee YN, Barsbold R, Currie PJ, Kobayashi Y, Lee HJ, Godefroit P, Escuillié F and Chinzorig T 2014. Resolving the long-standing enigmas of a giant ornithomimosaur Deinocheirus mirificus. Nature 515 (7526): 257–260.
Osmólska H and Roniewicz E 1970. Deinocheiridae, a new family of theropod dinosaurs. Palaeontologica Polonica. 21:5-19.
Sereno PC, et al. 1998. A long-snouted predatory dinosaur from Africa and the evolution of spinosaurids. Science 282 (5392): 1298–1302.

wiki/Sinocalliopteryx
wiki/Suchomimus
wiki/Deinocheirus

 

 

A cladogram issue illustrated

This post is dedicated to
reader Neil B. who suggested I review the reference below (Bapst 2013). It is a paper on the limits of resolution using theoretical cladograms. Frankly, it is over my head. Apologies, Neil. I stand by my large reptile tree cladogram as an reflection of actual evolutionary events. The tree is a practical application, not a theoretical one. However, let me offer some theory below (It probably duplicates something that has been published before that I am unaware of. If so, don’t turn me in!)

Some workers,
perhaps most current workers, follow the paradigm that you need at least 3x as many characters in order to attempt to resolve a list of taxa in phylogenetic analyses. In counterpoint, the large reptile tree currently employs only 228 characters versus a current total of 640 taxa with full resolution.

So what’s going on? 
‘In practice’ does not seem to be following ‘in theory.’ Of course, all the theoretical problems go away when you employ subsets of the large reptile tree, using only 12 to 50 taxa instead of the whole list. These subsets also employ 228 characters (most of them, I hope, parsimony informative), and that raises the ratio of those analyses above 3x. But that’s not even necessary.

Here’s a simplified solution that seems to help explain this issue.
You might think 1 character dichotomy should split 2 taxa, and it does. But one character dichotomy also lumps two taxa on each sides of that split. Ratio: 1 character/4 taxa.

Figure 1. Characters vs. taxa in analyses. Note one character lumps and splits 4 taxa. Two characters lumps and splits 8 taxa. Three characters lumps and splits 12 taxa given the present list of traits.

Figure 1. Characters vs. taxa in analyses. Note one character lumps and splits 4 taxa. Two characters lumps and splits 8 taxa. Three characters lumps and splits 12 taxa given the present list of traits.

I’ve only extended this example
to three character dichotomies splitting and lumping 12 taxa with complete resolution using a 1:4 character:taxon ratio.

Now imagine
having a trait trichotomy (like fins, feet AND flippers) or four trait options (add limbless to this list) and you can see the possibilities for nesting more taxa with complete resolution increase greatly with relatively few characters. Of course, we’ll never completely fill in the large grids. It gets complicated fast with missing taxa and incomplete taxa and evolution going the way it wants to go without regard for the order of the matrix.

This then
is how the large reptile tree is able to keep adding taxa without adding characters. I don’t think I’ve even come close to hitting the limit for taxa yet. The 3x rule does not appear to hold true here. Rather the maximum number of taxa looks to be several multiples of the number of characters in theory, a smaller number in practice.

If one can define a new species
by a set of traits that no other species has, one should be able to split that taxon apart from all other taxa in phylogenetic analysis. Right? That’s all we’re trying to do here. So far, the large reptile tree is succeeding — and it does better (more robust bootstrap scores) as mistakes are corrected. If anyone has an old matrix, they should ask for for the latest update here.

References
Bapst DW 2013. When Can Clades Be Potentially Resolved with Morphology?
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062312