Sometimes it takes the paleo crowd an ‘epoch’ to accept new data

A few short bios here demonstrate 
that paleontology often takes a lonnnggg time to accept data, break with paradigm and adopt new hypotheses. Judge for yourself whether this is due to data, peer pressure, public opinion, inertia, fear, pride, being too busy or what have you.

Thomas Henry Huxley
In the 1860s TH Huxley proposed a relationship between birds and dinosaurs. According to Wikipedia: “Huxley had little formal schooling and was virtually self-taught. He became perhaps the finest comparative anatomist of the latter 19th century. After comparing Archaeopteryx with Compsognathus, he concluded that birds evolved from small carnivorous dinosaurs, a theory widely accepted today.” But not back then.

“Darwin’s ideas and Huxley’s controversies gave rise to many cartoons and satires (cartoon attacks continue in the present day). It was the debate about man’s place in nature that roused such widespread comment: cartoons are so numerous as to be almost impossible to count.”

“Although Huxley was opposed by the very influential Owen, his conclusions were accepted by many biologists, including Baron Franz Nopcsa (that’s good to know!), while others, notably Harry Seeley, argued that the similarities were due to convergent evolution. After the work of Heilmann, the absence of clavicles in dinosaurs became the orthodox view despite the discovery of clavicles in the primitive theropod Segisaurus in 1936. The next report of clavicles in a dinosaur was in a Russian article in 1983.” Even so, that paradigm was not broken for another 17 years. See below.

John Ostrom
According to Wikipedia, “Ostron, revolutionized modern understanding of dinosaurs in the 1960s. His 1964 discovery of Deinonychus is considered one of the most important fossil finds in history. The first of Ostrom’s broad-based reviews of the osteology and phylogeny of the primitive bird Archaeopteryx appeared in 1976.” That’s his legacy. However, his life, as he lived it, was apparently something different and something we can all empathize with.

According to the Hartford Courant (2000), “In 1973, Ostrom broke from the scientific mainstream by reviving a Victorian-era hypothesis (see above) that his colleagues considered far-fetched: Birds, he said, evolved from dinosaurs. And he spent the rest of his career trying to prove it.” With the announcement of the first dinosaurs with feathers from China, Ostrom (then age 73) was in no mood to celebrate. He is quoted as saying, ““I’ve been saying the same damn thing since 1973, `I said, `Look at Archaeopteryx!'” Ostrom was the first scientist to collect physical evidence for the theory. Ostrom provoked a debate that raged for decades. “At first they said, `Oh John, you’re crazy,”’ Ostrom said in 1999.

Robert Bakker
Wikipedia reports, “One alternate hypothesis challenging Seeley’s classification (the dichotomy of Saurischia/Ornithisichia) was proposed by Robert T. Bakker in his 1986 book The Dinosaur Heresies. Bakker’s classification separated the theropods into their own group and placed the two groups of herbivorous dinosaurs (the sauropodomorphs and ornithischians) together in a separate group he named the Phytodinosauria (“plant dinosaurs”). The Phytodinosauria hypothesis was based partly on the supposed link between ornithischians and prosauropods, and the idea that the former had evolved directly from the later, possibly by way of an enigmatic family that seemed to possess characters of both groups, the segnosaurs. However, it was later found that segnosaurs were actually an unusual type of herbivorous theropod saurischian closely related to birds, and the Phytodinosauria hypothesis fell out of favor.” Yes, the segnosaurs are indeed derived theropods, but the Phytodinosauria is recovered in the large reptile tree. Click here for a supporting opinion (not supported by a cladogram).

There are several hundred daily readers of this blog
Many read it because they hate it. Others because they find something interesting enough here to keep coming back. Still others drop in to see what’s up only when something big or controversial comes around.

Only every so often
does the world of paleontology comes around to agree with conclusions first found here. The ‘Eoraptor as a phytodinosaur’ hypothesis comes to mind as an example.

On the other hand,
I’ve noticed if I have anything to do with a hypothesis (pterosaur origins, reptile origins, dinosaur origins, etc.), others completely avoid the taxa, avoid the hypothesis and to top it off, Hone and Benton (2009) went so far as to attribute my published work to another worker after earlier (Hone and Benton 2007) making the correct attribution. It can be crazy out there. Not sure why…

Perhaps there is a reason for this conservatism
As readers have seen here on many, many occasions, a long list of paleontologists have come up with incorrect hypotheses, especially in the realm of systematics. As has been demonstrated, much of this is due to relying on old matrices, inappropriate taxon exclusion and inclusion, problems minimized with a large gamut study like the large reptile tree. But that is something that most paleontologists are currently loathe to accept or even test. Then again…

Conspicuous by its absence, Cartorhynchus was excluded from Ji et al. 2016.
Earlier we looked at a new ichthyosaur cladogram by Ji et al. 2016. Yesterday it crossed my mind that the cladogram did not include the Early Triassic Cartorhynchus, which Motani et al. 2014 considered a strange “basal ichthyosauriform.” Earlier here and here we nested Cartorhynchus as a basal sauropterygian/ pachypleurosaur. Montani, Ji and Rieppel were coauthors on both studies. So that team was aware of Cartorhynchus and two years had passed since publication. So, what happened? I can only wonder if the large reptile tree had some influence.

References
Ji C, Jiang D-Y, Motani R, Rieppel O, Hao W-C and Sun Z-Y 2016. Phylogeny of the Ichthyopterygia incorporating recent discoveries from South China. Journal of Vertebrate Paleontology 36(1):e1025956. doi: http://dx.doi.org/10.1080/02724634.2015.1025956
Motani R, Jiang D-Y, Chen G-B, Tintori A, Rieppel O, Ji C and Huang D 2014. A basal ichthyosauriform with a short snout from the Lower Triassic of China. Nature doi:10.1038/nature13866

wiki/Cartorhynchus

 

Cladogram quirk and basalmost Euarchosauriformes

Updated July 31, 2020
with so many additional taxa, the LRT is no longer completely resolved. Many headless taxa nest with skull only taxa, which leads to loss of resolution. The LRT is built taxon upon taxon, day by day. Updated data on Browniella and Euparkeria are provided along with an updated subset of the LRT. The new data moved Browniella closer to Osmolskina.

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I’ve claimed on several occasions 
that my cladogram was fully resolved and all of its subsets were also fully resolved. While that is typically true, everyone prefers a cladogram with more strength, where the taxa are lumped and separated by at least three points in Bootstrap Analysis. When that happens the Bootstrap tree will also be completely resolved (= all scores 50-100).

I found a quirk
And as I write this I am going to figure out why this happened and wonder if it can be repaired. Typically a bad score or several bad scores are responsible for any lack of resolution. Not sure if that’s the case this time.

Follow me
as I describe the setup and the problem. I’m looking to apply Bootstrap scores to members of the basal Archosauriformes with the addition of Teyujagua, a proterosuchid we looked at earlier.

1. A heuristic search algorithm using PAUP of the entire cladogram: fully resolved. 
2. The same deleting all anamniotes and lepidosaurormorpha — the new Archosauromorpha (Eldeceeon and all derived taxa) remains: fully resolved.
3. The same deleting all basal archosauromorphs and synapsids: the protodiapsida (Myceteosaurus and all derived taxa) remains: fully resolved.
4. The same deleting all basal protodiapsids and basal diapsids: the new younginiforms  (Spinoaequalis and all derived taxa) remains: fully resolved.
5. The same deleting all aquatic younginiforms: the terrestrial younginiforms: Spinoaequalis + the SAM K7710 specimen(s) of Youngina and all derived taxa) remains: fully resolved.
6. Now, working backwards: The same deleting all dinosaurs: 6 trees retained. Loss of resolution in the Protodinosauria. Several incomplete taxa based on drawings there. We’ll reexamine that clade in a later post.
7. The same adding Herrerasaurus: fully resolved. A more complete data specimen solves the problem in #6.
8. The same deleting all archosaurs: fully resolved.
9. The same deleting the protoarchosaurs (the Gracilisuchus clade): fully resolved.
10. The same deleting all the poposaurs: fully resolved.
11. The same deleting all the Arizonasaurus/Ticinosuchus/Aetosaurus clade: fully resolved. 
12. The same deleting all remaining Rauisuchia (Vjushkovia through Postosuchus): fully resolved.
13. The same deleting all erythrosuchidae and ornithosuchidae: 2 trees retained. Loss of resolution at the Euparkeria node.
14. The same adding Garjainia: fully resolved. 
15. The same deleting all Choristodera: fully resolved.
16. The same deleting all Chanaresuchidae and Parasuchia: fully resolved.
17. At this point with a single tree scoring 447, I attempted a Bootstrap analysis. Basically all that is left here are the basal terrestrial younginiforms including several Youngina and Youngoides specimens, protorosaurs and basal archosauriforms up to and including all tested proterosuchids + Euparkeria, Osmolskina and Garjainia. Here  the small Proterosuchus skull (BPI/1/4016) and Elaphrosaurus rubidgei (RC59) are apparently mucking up the works, even though they do not nest together otherwise.
18. The same adding Diandongosuchus, a basal parasuchian: fully resolved.
19. At this point with a single tree scoring 488, warrants another Bootstrap analysis. Again Elaphrosuchus scores insufficiently distinct from several other included taxa to lack a score of 50+ across four other clades. And a very low score of 51 separates Elaphrosuchus from the BPI/1/4016 specimen of Proterosuchus. Both are skull only taxa and both have a certain amount of damage.
20. The same deleting the new taxon, Teyujagua: Bootstrap scores all above 50. So that addition caused problems.

Are there scoring errors here? 
Or do these taxa converge? Or do two sisters lack any data points in common? Let’s find out by taking a closer look at the offending parties.

[About a day or two elapses at this point in the narrative]

Scoring errors
There were many errors around these nodes, hopefully all are now repaired. I reexamined several drawings, photos and tracings. Unfortunately fossil bones don’t come with overlying colors, so they have to be interpreted.

I also added a taxon
(Figs, 1, 2). It turned out to be a key transitional taxon. Score corrections and the new taxon boosted 5/6 of the Bootstrap scores.

Figure 1. The SAM 4967a specimen attributed to Euparkeria. Images from Sookias et al. 2020 with colors and reconstruction added here.

Adding the ‘other Euparkeria‘: SAM PK K6047A
While reexamining the images of the Euparkeria holotype in Ewer 1967, I compared the rostrum that has a naris (SAM PK K6047A) with the classic holotype (SAM PK K 5867) that lacks a naris (Fig. 1). The fossils did not match. The dimensions were off (orbit vs antorbital fenestra, etc.) and the teeth were different in length. Ewer provides two images of the 6047 specimen, lacking data for the middle rostrum between the pix. The tracing (Fig. 1) recovers a basal euarchosauriform with a longer rostrum and narrower orbit, more like that of its phylogenetic predecessor, the BPI/1/4016 specimen of Proterosuchus (Fig. 3). This taxon ties Euparkeria more closely (more gradual transition in traits) to Proterosuchus (Figs. 2, 3).

There is also a SAM PK K6047B specimen
and it has been named Browniella africana by Broom (1913) I have not seen it. I do not know if it resembles or was found with the 6047A specimen. Most workers consider this taxon a junior synonym of Euparkeria.

Sookias and Butler 2013
reviewed the Euparkeriidae, but did not mention the 6047A or B specimens, except, perhaps as two of the eleven specimens that comprise their hypodigm. They defined the clade in this fashion: “Euparkeriidae Huene 1920. Stem-based definition –the most inclusive clade containing Euparkeria capensis Broom 1913a but not Crocodylus niloticus Laurenti 1768 or Passer domesticus Linnaeus 1758. (new).” I have not tested all the taxa listed by Sookias and Butler, but their definition seems to be overly broad.

Figure 1. Subset of the LRT focusing on Archosauriformes. Clade colors match figure 2 overlay.

What do we learn here?

1. Incomplete taxa can cause loss of resolution, as everyone knows. The addition of a more complete cousin can provide the remedy.
2. Scoring errors also lead to loss of resolution.
3. There is only one tree, the tree of Nature, that we are trying to model here. So there IS a correct solution to this problem.
4. Adding taxa almost always provides traits that make phylogenetic transitions more gradual. The only exceptions are terminal taxa, those that lack descendants.
5. Known proterosuchids still do not represent ontogenetic (maturation) stages. They are phylogenetically distinct taxa that lead to more derived clades (Figs. 2,3).
6. There is still no evidence for the sisterhood of Euparkeria with the verified sisters Turfanosuchus and Gracilisuchus  (Sookias and Butler 2013, Butler et al. 2014).
7. Phylogenetic miniaturization preceded and was part of the basal archosauriform radiation.
8. It is important for professionals not to assume that different specimens represent a single species. Minor differences might turn out to be key traits as demonstrated here.

Figure 3. Click to enlarge. Updated image of various proterosuchids and their kin. When you see them all together it is easier to appreciated the similarities and slight differences that are gradual accumulations of derived taxa. In the white zone are specimens considered proterosuchids.

Finally: the value of a large gamut cladogram
becomes more valuable with every added taxon. More gradual transitions become apparent and bias is further minimized.

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References
Broom R 1913. On the South-African Pseudosuchian Euparkeria and Allied Genera. Proceedings of the Zoological Society of London 83: 619–633.
Butler RJ, Sullivan C, Ezcurra MD, Liu J, Lecuona A and Sookias RB (2014). New clade of enigmatic early archosaurs yields insights into early pseudosuchian phylogeny and the biogeography of the archosaur radiation. BMC Evolutionary Biology 14:1-16.
Ewer RF 1965. The Anatomy of the Thecodont Reptile Euparkeria capensis Broom Philosophical Transactions of the Royal Society London B 248 379-435.
doi: 10.1098/rstb.1965.0003
Sookias RB and Butler RJ 2013. Euparkeriidae. Geological Society, London, Special Publications published online January 24, 2013 as doi: 10.1144/SP379.6

 

 

 

Is this the missing skull of the basal bird, Archaeornithura?

Updated March 16, 2016 with new images. The beak, if present, is ephemeral, questionable. Only two scores changed.

The spectacular plate and counter plate
of the basal ornithouromorph bird, Archaeornithura (Figs. 1-3, Early Cretaceous, Wang et al. 2015) appear to present every aspect of this specimen in full detail, but only the back of the skull (the occipital plate) appears to be readily preserved on the split surfaces.

Figure 2. That little patch by the shoulder could be the beak, eye and cranium of Archaeornithura.

Where is the rest of the skull? 
It might be here (Fig. 2). At least part of it, the beak tip, scleral ring and cranial bones (frontal and parietal) give the impression of being there. I can’t be sure working from photos alone, but when you put the parts on a reconstruction of the rest of the body (Fig. 3), the parts fit both morphologically and phylogenetically.

Figure 3. Reconstruction of the basal ornithuromorph bird, Archaeornithura with skull added. Feathers and ribs omitted. The length of the tail is hard to determine.

Despite the rather short arms, 
the long wing feathers (Fig. 1) made the wings large enough for flapping flight. The robust and long coracoids attest to the ability to flap with great vigor. The sternum is not flat, but more deeply keeled than in more primitive birds. The large pelvis anchors strong leg muscles. The fragile pubes framed larger air sacs. Despite robust sacral vertebrae that broadened the hips, the tail was reduced and without a robust parson’s nose-type pygostyle, which developed by convergence in other birds clades and in more derived ornithuromorphs. The perching toe was not so well developed and all pedal unguals were rather small, similar to those of wading pterosaurs like Ctenochasma.

Hedging paragraph:
I don’t think there is no way to tell how long the beak of Archaeornithura was given the present data. Currently I have the beak tip not very separated from the occiput giving it a rather short skull. Alternatively the length of the skull might be measured from the in situ beak tip to the in situ occiput. Then this bird would have had a longer rostrum, more like that of its beach combing analog among pterosaurs, Ctenochasma. Perhaps other specimens will help fill in the data gap here.

References
Wang M et al. (7 other authors) 2015. The oldest record of ornithuromorpha from the early cretaceous of China. 6:6987 DOI: 10.1038/ncomms7987

wiiki/Archaeornithura

 

The Origin of Dinosaurs x2 (2010) revisited

Several years ago
the top vertebrate paleontologists in the world (Brusatte et al. 2010) reported on the origin of dinosaurs. Coincidentally Langer et al. (2010) wrote a similar report.  It is now 6 years later. Let’s see how well those report have held up as they compare to the current data (2016) in the large reptile tree.

Figure 2. The origin of dinosaurs to scale. Gray arrows show the direction of evolution. This image includes Decuriasuchus, Turfanosuchus, Gracilisuchus, Lewisuchus, Pseudhesperosuchus, Trialestes, Herrerasaurus, Tawa and Eoraptor.

From the Brusatte et al. introduction
“During the past 25 years, numerous new fossils, reinterpretations of long-forgotten specimens, and numerical analyses have significantly revised our understanding of this major macroevolutionary event, which is one of the most profound and important evolutionary radiations in the history of life.”

What has stood the test of time:

1. Dinosaurs are archosaurs: birds+crocs and last common ancestor
2. Archosaurs are diapsid reptiles = Eudibamis, Petrolacosaurus and all their descendants.
3. Dinosaurs are: “Triceratops horridus, Passer domesticus, and all descendants of their most recent common ancestor.” Or alternatively: ““the least inclusive clade containing Megalosaurus and Iguanodon.” Thus dinosaurs are monophyletic.
4. The suite of traits common to dinosaurs include: 1) upright and fully erect posture [shared with basal crocs and dinosauromorphs]; 2) an enlarged deltopectoral crest on the humerus [shared with Trialestes]; 3) a “specialized” hand; 4) a perforated acetabulum (hip socket) [which may close]; 5) a well-developed fourth trochanter on the femur; 6) a lesser trochanter on the femur; 7) and a simple hinge ankle joint with proximal tarsals fixed immovably to the tibia and fibula [shared with basal crocs and dinosauromorphs].
5. Dinosaurs likely originated during the Middle Triassic. They are diverse at the earliest Late Triassic.
6. Herrerasaurus and Eoraptor are some of the most complete specimens of any early dinosaur.
7. Langer: Herrerasaurs are basal to the Ornithischia-Saurischia dichotomy, but the actual dichotomy is Theropoda/Phytodinosauria
8. Langer: The oldest dinosaurs include Herrerasaurus, Eoraptor, Staurikosaurus, Saturnalia and Panphagia all from the Carnian (early Late Triassic). These are also among the most primitive dinosaurs. Missing from this list is Barberenasuchus, also Carnian, not commonly considered a dinosaur, but nests as a sister to Eodromaeus.

What has not stood the test of time:

1. Archosaurs (crocs + dinos alone) no longer include pterosaurs
2. Diapsids no longer include lizards, snakes, rhynchocephalians (including rhynchosaurs and trilophosaurs) and pterosaurs. Those have a diapsid skull by convergence.
3. Arizonasaurus is no longer an archosaur since crocs and birds had a more recent common ancestor, a sister to Gracilisuchus.
4. The clades Crurotarsi (= Pseudosuchia) and Avemetatarsalia (= Ornithodira, Ornithosuchia) are now junior synonyms for older nomenclature based on their inclusion sets (Archosauriformes and Reptilia respectively).
5. Pterosaurs no longer nest with archosaurs, but with lepidosaurs, in a new clade known as the Tritosauria nesting between basal rhynchocephalians and basal protosquamates.
6. Lagerpeton is not a dinosauromorph, but a sister to Tropidosuchus.
7. Marausuchus is does not nest outside the Dinosauria, but as a basal theropod.
8. Sacisaurus, Silesaurus and Asilisaurus are not the immediate sisters of dinosaurs. Rather they now nest with poposaurs, the proximal outgroup to the Archosauria (crocs + dinos only).
9. Overlooked by Brusatte et al., Lewisuchus, Zupaysaurus, Pseudhesperosuchus, Trialestes, and their kin are the now the immediate sisters of dinosaur, the true dinosauromorphs.
10. Some manner of feathers now diagnose the Dinosauria, which primitively had naked (not scaly) skin, like a plucked chicken.
11. Herrerasaurus and Eoraptor are no longer incerta sedis but the most basal dinosaur and one of the basal phytodinosaurs respectively.
12. Zupaysaurus no longer nests as a theropod, but a dinosauromorph
13. Berberosaurus no longer nests as a theropod, but as the basalmost phytodinosaur
14. Ornithischia no longer branch off first from Saurischia, but are derived from basal phytodinosaurs. Sauropodomorpha are sisters to basal Ornithisichia with Daemonosaurus and Chilesaurus at the base.
15. Langer: Eusaurischia (Sauropodomorpha + Theropoda) is a junior synonym for Dinosauria
16. Langer: Silsauridae (all taxa closer to Silesaurus than to Marasuchus + Heterodontosaurus) is a junior synonym for Poposauria, if kept monophyletic.
17. Langer: the basal-most dinosaurs were not probably omnivorous,
18. Langer: herrerasaurs were not theropods
19. Langer: there is no Onithischia-Saurischia dichotomy. Saurischia is a junior synonym  for Dinosauria.
20. Langer: Agnophitys is a dinosaur sister to Marasuchus.
21. Langer: Putative dinosaur Saltopus is a basal archosaur close to Gracilisuchus.

Figure 1. Click to enlarge. Subset of the large reptile tree focusing on the Archosauria (crocs + dinos). Sharp-eyed observers will find minor changes here.

Staurikosaurus
Langer et al. (2010) mentioned Staurikosaurus (Colbert 1970) as the first consensual early dinosaur to be collected. Here it nests as a basal theropod, basal to a clade of theropods that is often overlooked that includes Marasuchus, Procompsognathus and Segisaurus. Yes, Staurikosaurus has but two sacral vertebrae. So do other clade members.

Guaibasaurus
Langer et al. (2010) also mentioned Guaibasaurus (Bonaparte et al., 1999) who reported, “The mesotarsal condition and the outline of the distal section of tibia indicate the saurischian nature of this new form, but the almost unreduced medial wall of the acetabular portion of ilium shows an unrecorded primitive condition within the cited group. Several features suggesting affinities with both the Prosauropoda and Theropoda, imply that Guaibasaurus candelariensis may belong to the ancestral group for both of them.” The large reptile tree nests Guaibasaurus as a basal theropod and as the sister to Marasuchus + Procompsognathus, not far from Staurikosaurus. 

The Novas (1992) dinosaur definition
According to Langer et al., Novas (1992b) provided the first phylogenetic definition of Dinosauria as ‘‘the common ancestor of Herrerasauridae and Saurischia + Ornithischia, and all of its descendants’’. The addition of herrerasaurs does not change the current tree (Fig. 1). Padian & May (1993) explicitly restricted the use of Dinosauria to the clade composed of Saurischia and Ornithischia, exclusive of ‘‘Herrerasaurus and its allies’’. But Novas has priority. Moreover, the last common ancestor of Saurischia and Ornithischia is currently a herrerasaur. The diagnosis of the Dinosauria has seen some changes over the years. Many are traits that are not covered by the large reptile tree. Please check out the references below for lists and histories of those lists.

What does the large reptile tree diagnose dinosaurs?
The following suite of traits are found in basal dinosaurs and not their proximal outgroups, Trialestes, the Pseudhesperosuchus clade. However many of these traits are found elsewhere on the tree. And many traits are lost in more derived dinos.

1. Naris opening lateral
2. Parietal skull table weakly constructed
3. Mandible tip straight (neither upturned nor down)
4. Interclavicle poorly ossified or absent
5. Coracoid shape disc-like, even if fused (elongate or strap shape in outgroup)
6. Radiale and ulnare not elongated (as in outgroup)
7. Manus with long penultimate phalanxes and raptorial claws
8. Femoral head interned and sub rectangular (reversed in the Marasuchus clade).
9. Longest metatarsal: 3
10. Proximal metatarsals: 1 and 5 reduced

Bipedality
has long been touted as a key dinosaurian trait, but dinosaurs evolved from basal bipedal crocodylomorphs, like Gracilisuchus and Scleromochlus. Interesting that Scleromochlus has been often associated with unrelated pterosaurs. Pterosaur removal sets things a little straighter in the retelling of the dinosaur ancestry story. Scleromochlus has not often been touted as a dinosaur ancestor, but by virtue of its false association with pterosaurs in various cladograms, it has always been there.

The long coracoids and proximal carpals of basal bipedal crocs
have set them apart from consideration as possible dino ancestors. But if you just let the software do its job, then you’ll recover nestings that indicate the elongate coracoids and proximal carpals became reduced to shorter, more primitive conditions in basal dinos.

Traits found in dinosaurs exclusive of Herrerasaurus:

1. Feathers (not on the matrix, but worth mentioning)
2. Skull shorter than cervicals
3. Cranium convex
4. Naris opening
5. Maxilla ventral margin straight
6. Jugal qj process straight
7. Quadrate curls posterodorsally
8. Jaw joint aligned with ventral maxilla
9. Canine maxillary teeth not present
10. Nine or more cervical vertebrae
11. Some caudal vertebrae 3x longer than tall
12. Tibia not shorter than femur
13. Metatarsus not shorter than half the tibia
14. Phalanges on metatarsal 5: 0 (reversed in higher clades)

Then if wanted to
you could simply list all the traits of Herrerasaurus, the basalmost dinosaur, knowing full well that Herrerasaurus itself is derived from the first, as yet undiscovered, dinosaurs.

References
Bonaparte JF, Ferigolo J and Ribeiro M 1999. A new early Late Triassic saurischian dinosaur from Rio Grande do Sol state, Brazil” (PDF). Proceedings of the Second Gondwanan Dinosaur Symposium, National Science Museum Monographs 15: 89–109.
Brusatte SL, Nesbitt SJ, Irmis RB, Butler RG, Benton MJ and Norell MA 2010. The origin and early radiation of dinosaurs. Earth-Science Reviews 101 (2010) 68–100.
Colbert EH 1970. A Saurischian dinosaur from the Triassic of Brazil. American Museum Novitates 2405; 1-39
Langer MC. Ezcurra MD, BittencourtJS, Novas FE 2010. The origin and early evolution of dinosaurs. Biological Review 85, 55–110.

Teyujagua: Not “transitional between archosauriforms and more primitive reptiles”

A new paper by Pinheiro et al. 2016
reports that the small skull (UNIPAMPA 653) of a new genus, Teyujagua paradoxa (Figs. 1, 2), is “transitional in morphology between archosauriforms and more primitive reptiles. This skull reveals for the first time the mosaic assembly of key features of the archosauriform skull, including the antorbital and mandibular fenestrae, serrated teeth, and closed lower temporal bar. Phylogenetic analysis recovers Teyujagua as the sister taxon to Archosauriformes…”

Well, that might be true if
you restrict the taxon list to the few (44) taxa employed by Pinheiro et al.

But when you expand the taxon list
to the size of the large reptile tree (660+ taxa) where we already have a long list of Youngina, Youngoides (Fig. 1) and Youngopsis sisters to Archosauriformes, then Teyujagua nests as a phylogenetically miniaturized sister to the NMQR 1484/C specimen attributed to Chasmatosaurus alexandri (Fig. 1). Like another phylogenetically miniaturized descendant of chasmatosaurs, Elachistosuchus huenei MB.R. 4520 and BPI 2871 (Figs. 3, 4), Teyujagua also turned its once large antorbital fenestra into a vestige (Figs. 1, 2).

Figure 1. Teyujagua compared to sister taxa, including Youngoides, Proterosuchus and Chasmatosaurus. Teyujagua is a phylogenetic miniature in which the antorbital fenestra became a vestige. Note the posterior jugal, which may or may not have supported a now missing quadratojugal anterior process.

I can see why the authors got so excited about their discovery.
The Teyjjagua skull looks like a little Chasmatosaurus skull without the antorbital fenestra. That’s because it IS one. In their own words, “This skull represents a previously unknown species that is the sister taxon to Archosauriformes and which fills a major morphological gap in understanding of early archosauriform evolution.”

Unfortunately, the authors were dealing with an antiquated cladogram
in which Youngina is basal to lizards and archosaurs… among many, many other atrocities.  They report, “Our novel cladistic analysis recovered two most parsimonious trees with 872 steps. The strict consensus of these topologies positions Teyujagua as the sister taxon of Archosauriformes, a position previously occupied by the Lower Triassic Prolacerta.”

So this is where it really pays off
to use several specimens from the Youngina grade and several specimens from the Proterosuchus grade along with 660+ opportunity taxa to nest with.

Figure 2. The rostrum of Teyujagua with the vestigial antoribital fenestra circled here. You can see how the maxilla grew over the opening. Once again, this is data that should have been announced from firsthand observation by PhD level paleontologists, not from a casual observer of photographic data.

Diagnosis (from the paper)
“Archosauromorph with the following unique character combination: confluent, dorsally positioned external nares; maxilla participating in orbital margin; antorbital fenestra absent; trapezoidal infra temporal fenestra with incomplete lower temporal bar; teeth serrated on distal margins; surangular bearing a lateral shelf; external mandibular fenestrae present and positioned beneath the orbits when the lower jaw is in occlusion (autapomorphic for Teyujagua).”

Comments on the diagnosis
The NMQR 1484/C specimen of Chasmatosaurus (Fig. 1) is pretty well preserved except for the premaxilla/narial region. Given the morphology of the Teyujagua rostrum, the NMQR specimen likely shares the trait of a dorsal naris, perhaps with a slender ascending process of the premaxila, which might be lost in both specimens. The maxilla actually does not appear to reach the orbit. The antorbital fenestra remains present as a closed over vestige. The lower temporal bar might be incomplete, but just as likely the anterior process of the quadratojugal might be taphonomically missing, as in the NMQR specimen (Fig. 1). Other proterosuchids have similar tooth serrations. The mandibular fenestra is further forward, but the posterior mandible is also deeper. The specimen is indeed distinct enough to merit a unique generic name, as is the case with several of the Chasmatosaurus/Proterosuchus specimens, which do NOT represent a growth series.

Phylogenetic miniaturization
has reduced the antorbital fenestra in BPI 2871 and Elachistosuchu, which nest at the base of the Choristodera. Both nest as descendants of larger Chasmatosaurus specimens in the large reptile tree.

Figure 3. Elachistosuchus (Janensch 1949, Sobral et al. 2015) is a sister to BPI 2871, a basal choristodere.

Not mentioned by the authors
The miniaturized skull of Teyujagua has fewer teeth than in sister or ancestors, but matching the condition in Euparkeria (Fig. 1), a related taxon only one node away at the base of a sister clade.

Figure 4. Rostral area of BPI 2871, formerly considered a younginid and here nesting at the base of the Choristodera as a descendant of Chasmatosaurus.

If you don’t remember
this earlier post (2011), Youngoides (UC1528, Fig. 5) had the genesis of an antorbital fenestra. It is the current proximal sister to the Archosauriformes in the large reptile tree.

Figure 5. GIF movie tracing the antorbital fenestra with fossa and surround bones of the FMNH UC 1528 specimen of Youngoides romeri. This is one of the earliest and most primitive appearances of the archosauriform antorbital fenestra, previously overlooked.

In summary, the authors report
“Teyujagua presents an unexpected combination of basal archosauromorph and typical archosauriform features. For example, Teyujagua resembles basal archosauromorphs in lacking an antorbital fenestra and retaining open lower temporal bars1. However, Teyujagua possesses external mandibular fenestrae and serrated teeth, features previously considered unique to Archosauriformes.”

Unfortunately, the authors appear to forget
that the antorbital fenestra can phylogenetically disappear and Chasmatosaurus demonstrates that the quadratojugal can wither phylogenetically or taphonomically disappear. It is a fragile bone.

References
Pinheiro FL, França MAG, Lacerda MB, Butler RJ and Schultz CL 2016. An exceptional fossil skull from South America and the origins of the archosauriform radiation. Nature Scientific Reports 6:22817 DOI: 10.1038/srep22817.

Finding the foot of Yi qi

The fossil scanoriopterygid bird,
Yi qi (Xu et al. 2015) is infamous for purporting to have a long extra bone (the so-called ‘styliform element’) somehow anchored to the wrist (see below) that many experts, including Dr. Kevin Padian (2015, see below), regarded as acting like a bat finger to stretch and support a bat-like wing membrane (not feathers). No sister taxa, all of them scansoriopterygid birds, have even a hint of such a bone. Here at pterosaurheresies alone that bone was determined to be a displaced radius on one wing and a displaced ulna on the other. Without these displaced bones, the forearms do not have their radius or ulna counterpart, which is standard equipment in all tetrapods with limbs. Not sure why this went unnoticed by the experts.

On a side note,
the foot was not reconstructed because the bones were very faint and intermixed with tail bones (Fig. 1). Dr. Padian reported that nothing below the waist was known. That is incorrect. He must have been shown only one plate or counter plate.

With the recent reconstruction of a sister taxon,
Omnivoropteryx, which has an odd (autapomorphic) long pedal digit 4, a second attempt was made to trace and reconstruct the foot of Yi qi (Fig. 1). If the tracing is correct, then the reconstruction of the Yi pes greatly resembles that of it sister, Omnivoropteryx, as one would expect. However, digits 3 and 4 are similar in length. In some other scansoriopterygids, digit 4 is shorter to much shorter.

This tracing
is just about at the limit of DGS capabilities without a higher resolution dataset. Fortunately a sister taxon provides a blueprint to model this foot against. And yes, the caudal vertebrae are confusing as they mix in with the pedal elements. And yes, some of the bones are only represented by faint impressions distally and proximally with the rest filled in using a-z bracketing.

Figure 1. The foot (pes) of the scansoriopterygid bird, Yi qi, both in situ and reconstructed. The amber bones are causals.

Back to the ‘styliform element’
Dr. Padian (2015) reports, “Their (Xu et. al) find opens two cans of worms: about interpreting unique structures in fossils and about what it means to fly. The styliform element, which may be a hypertrophied wrist bone or a neomorphic calcified structure, is longer than any of the animal’s fingers and is curved at both ends. It is probably not a true finger. How the structure is attached to the wrist is not clear, because its proximal end seems quite  squared off; this means that we also do not know if or how it could move.  What could this element be except a support for some kind of aerofoil? The authors infer this on the basis of its position and the presence of membranous tissue in the wrist area.”

Note that 
Dr. Padian does not consider the possibility that the ‘styliform element’ is either a displaced radius or ulna, despite matching lengths and morphologies. This lack of recognition is rare, but not unknown. For instance, in 2000 I did not recognize the stem of the displaced prepubis in Cosesaurus.

Fliapping
Padian also notes: “Furthermore, in flapping animals the outboard skeletal elements (wrist, hand and so on) are primarily responsible for thrust, the essential component of powered flight, but these are not particularly long in Yi qi. So, at present we can shelve the possibility that this dinosaur flapped.” This appears to be an oversight statement. Not only does Yi qi have an elongate hand, the point is: it doesn’t matter how large or feathered a forelimb is. Even flightless birds, including most baby birds, flap. However tetrapods that flap for locomotion all have locked down and elongate coracoids. Perhaps Padian meant ‘flying.” If so, he is likely correct. Scansoripterygids have been discovered with tail feathers, but not bird-like wing feathers. This may have been the first clade of flightless birds. As we learned yesterday, the dromaeosaurid, Balaur was not a basal flightless bird. If you want to see what basal flightless birds actually look like, check out the scansoriopterygids.

References
Padian K. 2015. Paleontology: Dinosaur up in the air. Nature (2015) doi:10.1038/nature14392
Xu X, Zheng X-T, Sullivan C, Wang X-L, Xing l, Wang Y, Zhang X-M, O’Connor JK, Zhang F-C and Pan Y-H 2015. A bizarre Jurassic maniraptoran theropod with preserved evidence of membranous wings.Nature (advance online publication)
doi:10.1038/nature14423

Sapeornis vs. Balaur

Sapeornis (Fig. 1) was a basal bird that retained teeth, but had a short tail with a pygostyle and had large wings. It was certainly flapping and flying. Earlier we nested Sapeornis between Archaeopteryx and all higher birds, including all extant birds.

Yesterday the reported link between Sapeornis and Omnivoropteryx was snipped. The latter is a scansoropterygid bird. Workers, it appears, occasionally like to compare Sapeornis to novel fossils, even when comparisons are not warranted.

When the ‘bizarre’ dromaeosaur with double killer claws
Balaur (Csiki et al. 2010), was reexamined by Cau, Brougham and Naish 2015, one of their results nested Balaur with Sapeornis (Figs. 1, 2).

Figure 1. Balaur compared to various dromaeosaurids and to Sapeornis, both to scale and enlarged for detail. Cau, Brougham and Naish wondered if Balaur was the first neoflightless bird. A casual glance finds many similarities, but analysis sets the record straight.

Thus, Cau, Brougham and Naish 2015,
and later Naish’s own blog post, wondered if Balaur was the first flightless bird. They nested it after Archaeopteryx (Fig. 2). By contrast, in the large reptile tree, Balaur nests where both Csiki et al. (2010) and Brusatte et al. (2013) nested it: with dromaeosaurs. On a reduced list of traits (Balaur lacks a skull) shifting Balaur over to Sapeornis adds 12 steps, which is not a large number considering the number of intervening taxa (12 nodes).

Figure 2 The Cau et al tree based on the Brusatte et al. tree. Note the nesting of Balaur among long-tailed post-Archaeopteryx birds, but a sister to Sapeornis, which has a pygostyle. Click to enlarge.

Naish notes (pro-dromaeosaurid):

1. This dromaeosaurid interpretation of Balaur looks reasonable on the basis of the animal’s size and foot anatomy, and Balaur is certainly dromaeosaurid-like in a general sense.

Naish notes (pro-avian):

1. “Balaur is anatomically weird when interpreted as a dromaeosaurid,
2. Balaur is likely not a dromaeosaurid, but a secondarily flightless bird.
3. It has a reduced third finger (lacking a claw),
4. extensive fusion between the hand and wrist bones,
5. a strangely broad, extensively fused pelvis with pubic bones that bow outwards for most of their length and are strongly swept back,
6. fusion between the tibia and fibula,
7. fusion between the tibia and ankle bones,
8. an especially stocky, heavily built, partially fused-up foot
9. and a long hallux (first toe) with an especially big claw.
10. “All of the features I just mentioned – yes, all of them – are present in Avialae,”
11. In addition, the manual unguals of Balaur are not as strongly curved as those of most dromaeosaurids
12. the flexor tubercles (the bony lumps on the undersides of the unguals that anchor ligaments used in ungual flexion) are comparatively weakly developed, thus Balaur was in possession of a non-raptorial hand
13. Godefroit et al. (2013), in their description of the Jurassic avialan Aurornis, published a phylogeny where Balaur is an avialan, closer to Pygostylia (the short-tailed bird clade) than is Archaeopteryx.
14. And Foth et al. (2014), in their study of a new Archaeopteryx specimen, also found Balaur to be a member of Avialae, again closer to crown-birds than Archaeopteryx.”

The large reptile tree notes

1.  if Balaur is avian purported avian sister taxa are all a magnitude smaller
2. and developing larger wings, not smaller ones.
3. the pes of Balaur is robust, not bird-like in general proportions or morphology.
4. the non-raptorial manus and larger gut of Balaur (based on the wider pubis) suggests herbivory or omnivory. That alone would make it bizarre among dromaeosaurs, but not so bizarre among theropods.
5. Balaur fuses the scapulocoracoid. Sapeornis does not.
6. Balaur has a four-part sternum, like other dromaeosaurids. Sapeornis lacks a sternum, but sister taxa have a single sternum.
7. Balaur has a large olecranon process. Sapeornis does not.
8. Balaur has a subequal manus and pes. Sapeornis has a larger manus.
9. Balaur has a smaller humerus than tibia. Sapeornis has a larger humerus.
10. Balaur aligns mc2-3 with m1.1. Sapeornis aligns mc2-3 beyond m1.1
11. Balaur mc2 is the longest. Sapeornis mc2=mc3.
12. Balaur metatarsus is shorter than half the tibia. Sapeornis, not shorter
13. Balaur aligns mt2-3 with mt1. Sapeornis aligns p1.1 IF rotated anteriorly, but it is rotated posteriorly.
14. Balaur has one phalanx on mt5. Sapeornis has three.
15. Balaur is larger than 60 cm long. Sapeornis is not.

Plus

1. Balaur fuses distal tarsals to metatarsals. So does Velociraptor. Not Sapeornis.
2. Balaur retains standard anterior caudal vertebrae. Sapeornis compresses them as part of a pygostyle morphology.
3. Balaur does not have a bird-like expanded deltopectoral crest. Sapeornis does.
4. Balaur does not retain any traits which would indicate that its ancestors were small, perching, flapping birds like Archaeopteryx and Sapeornis.

Sure, Balaur is a bizarre dromaeosaur. 
It might even be an herbivore. But those traits listed by Naish must be considered convergent with one bird or another, because they are not all found in one tested bird (like Sapeornis). The large reptile tree does not nest Balaur outside of the dromaeosaurs with present data. Birds have bowed pubes because they have enlarged air sacs. Ultimately bird pubes separate distally to accommodate even larger air sacs. That’s not the case with bulky Balaur. As a scientist, Naish should have thought about that and the following dromaeosaur synapomorphies shared with Balaur before suggesting that Balaur was a sister to the bird Sapeornis.

Unlike birds, Balaur has

1. a four-part sternum, like other dromaeosaurs.
2. a killer claw,  like other dromaeosaurs.
3. an anteriorly-directed pedal digit 1, like other dromaeosaurs.
4. is goose sized, like other dromaeoaurs.
5. robust pedal bones, like other dromaeosaurs.
6. smaller fore limbs than hind limbs, like other dromaeosaurs.
7. deep, robust dorsal vertebrae, like other dromaeosaurs.

Naish should have listened to himself 
when he wrote, “Balaur is certainly dromaeosaurid-like in a general sense.” 

Naish saw the specimens first hand.
I did not. Naish did not create his phylogenetic matrix first hand. I did. Naish did not include various specimens of Archaeopteryx as ITU (individual taxonomic units). I did. Naish did not put reconstructions of the two taxa, Balaur and Sapeornis, next to one another and next to competing candidates for a final check. I did. It’s good practice.

When someone is trying to prove a point,
whether valid or not, they generally don’t weigh all aspects evenly. They try to prove their point. We’ve seen Naish do this before with tragic consequences to his own reputation. I don’t think Naish and his team weighed all aspects of Balaur evenly. If Balaur really did nest between Archaeopteryx (but which one?) and Sapeornis, then it really should have looked like one or the other or an amalgam of both. Instead, it’s just one more example of an ‘strange bedfellow’ that actually nests elsewhere when tested on the large reptile tree.

Comments made above
should have been made by the manuscript referees. Some are listed in the acknowledgements to the paper. Critical thinking seems to be fading in paleontology. That’s why this blog exists.

One should never trust anyone’s interpretations,
observations or cladistic analyses, especially if things don’t look right. Instead, one should repeat the observation, experiment or analysis for oneself. That’s what I do here. As you already know, if something doesn’t look right, it probably isn’t. We’ve seen paleo-oddities paraded before that are not so odd after all when properly nested.

References
Brusatte, et al. 2013. The osteology of Balaur bondoc, an island-dwelling dromaeosaurid (Dinosauria: Theropod) from the Late Cretaceous of Romania. Bulletin of the American Museum of Natural History, 374:1-100.
Cau​ A, Brougham​ T and Naish​ D. 2015. The Phylogenetic Affinities of the Bizarre Late Cretaceous Romanian Theropod Balaur bondoc (Dinosauria, Maniraptora): Dromaeosaurid or Flightless Bird? PeerJ. 3: E1032. DOI: dx.doi.org/10.7717/peerj.1032
Csiki Z, Vremir M, Brusatte SL, Norell MA 2010. An aberrant island-dwelling theropod dinosaur from the Late Cretaceous of Romania. Proceedings of the National Academy of Sciences of the United States of America 107 (35): 15357–15361.
Foth C, Tischlinger H and Rauhut, OWM 2014. New specimen of Archaeopteryx provides insights into the evolution of pennaceous feathers. Nature 511, 79-82.
Godefroit P, Cau A., Dong-Yu H., Escuillié F, Wenhao W and Dyke G 2013. A Jurassic avialan dinosaur from China resolves the early phylogenetic history of birds. Nature 498, 359-362.
Lee MSY, Cau A, Naish D, Dyke GJ. 2014. Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds. Science 345(6196):562–566 DOI 10.1126/science.1252243.

YouTube video by Wiz Science.

Omnivoropteryx reconstructed and nested

A recent addition
Omnivoropteryx sinousaorum (Czerkas & Ji 2002, Fig. 1) now nests in the large reptile tree as a sister to Epidexipteryx (Fig. 4), a derived scansoropterygid bird.

Figure 1. Omnivoropteryx reconstructed from X-ray photographs (Figs. 2, 3) Some workers think this bird looks like an oviraptorid. I think it looks like an anurognathid.

From the Wikipedia article
“Omnivoropteryx (meaning “omnivorous wing”) is a genus of primitive flying bird from the early Cretaceous Upper Jiufotang Formation of China.

Figure 2. The Omnivoropteryx skull X-ray with DGS color tracings. These were used to reconstruct the skull in lateral view.

“The authors
who described Omnivoropteryx, Stephen Czerkas and Qiang Ji, stated that their specimen closely resembles Sapeornis (Fig. 5), but the pubis was longer and, since no skull was known for Sapeornis, they did not consider the two names synonyms. The later discovery of Sapeornis skulls shows that they were indeed similar to Omnivoropteryx. This may make Omnivoropteryx a junior synonym of Sapeornis, and the name may be abandoned.”

Now that you can see
the two taxa together, do you agree that they are conspecific? BTW, they nest in separate clades in the large reptile tree.

Figure 3. Omnivoropteryx shares the plate with parts of another bird. (identified as Microraptor by a reader)

Omnivoropteryx was preserved
with parts of another bird (Fig. The only data I have found comes from an X-ray.

Figure 4. Epidexipteryx, another scansoriopterygid with a bird-like pelvis. The toes are not known.

Epidexipteryx (Fig. 4) is a sister
to Omnivoropteryx. Both share a long third finger. Omnivoropteryx also has a long fourth toe. Unfortunately sister taxa do not preserve the toes. This clade produced some anurognathid mimics.

Figure 5. Sapeornis does not nest as a sister to Omnivoropteryx.

Sapeornis
is basal to living birds. The scansoriopterygid clade, of course, became extinct.

References
Czerkas SA and Ji Q 2002. A preliminary report on an omnivorous volant bird from northeast China.” In: Czerkas, SJ (editor): Feathered Dinosaurs and the origin of flight. The Dinosaur Museum Journal 1:127-135.

wiki/Omnivoropteryx

Soft tissue in Cretaceous dino bone. Still controversial.

The T-rex collagen (Schweitzer et al. 2016) controversy is back, this time on PlosOne.

From the abstract
“Recovery of still-soft tissue structures, including blood vessels and osteocytes, from dinosaur bone after demineralization was reported in 2005 and in subsequent publications. Despite multiple lines of evidence supporting an endogenous source, it was proposed that these structures arose from contamination from biofilm-forming organisms. To test the hypothesis that soft tissue structures result from microbial invasion of the fossil bone, we used two different biofilm-forming microorganisms to inoculate modern bone fragments from which organic components had been removed. We show fundamental morphological, chemical and textural differences between the resultant biofilm structures and those derived from dinosaur bone. The data do not support the hypothesis that biofilm-forming microorganisms are the source of these structures.”

From the comments
Tom Kaye writes: “We are delighted to see that seven years after publication, our biofilm hypothesis still has enough merit to generate a manuscript to test it experimentally. Our comments below.

1. The two week growth period was arbitrary.
2. No details of the nutrient supply over time.
3. Biofilms mineralize as is well known by plaque on teeth. Ultra-pure water means no minerals to modify the biofilm.
4. Iron is the basis for Dr. Schweitzer?s claims of extraordinary preservation. No iron is available in this experiment, but the resulting biofilms are compared to dinosaur ?vessels? with iron. 
5. The experiment DID produce tubular branching structures fully consistent with the claims of Kaye et al 2008.

The design of the experiment with limited inputs insured only limited outcomes which were then compared to a natural process that included factors outside the range of the experiment. Mineralized or iron reinforced biofilms could never be expected in the results of this experiment by design. 

We look forward to further experiments that mimic the natural process of biofilm formation.” 

Schweitzer’s Reply to the Kaye Comments:
“Kaye’s original comments, and our responses below each .

1. The two week growth period was arbitrary.
Mr Kay misunderstand the point of the current paper. Our intent in undertaking the current project was to test the hypothesis that biofilm would 1. invade fossil bone under naturally occurring conditions that might reasonably exist in dinosaur bone; and 2. take on the shape and character of vessels (uniform wall diameter, coherency and retention of branching patterns, and retention of an open lumen). We also tested the hypothesis that specific antibodies can differentiate source and composition of materials retained in fossils. We did accomplish these goals with a growth period of 2 weeks (also see below). There is much in the literature about optimal phases of microbial growth, and there is precedent for this growth period in the literature, cited below. Additionally, much is already known about the conditions of growing biofilm; that was not the point of this manuscript. Conditions used in labs to generate optimal biofilm growth (ie, continual flow of water, additional nutrients, agitation, etc as employed by Kaye et al 2008) would not occur in dinosaur bone exposed in the Montana badlands. That was what we tried to imitate.
Note also that Tom does not address our chemical/molecular data at any point in these comments, only our approach for growing biofilm. We were able to show biofilm growth in bone under highly regulated conditions, which was our goal, thus how we might have done it differently is irrelevant to our central hypothesis (see below). Furthermore, duration of growth period, once the biofilm invaded bone, was not pertinent to our central questions. It could grow forever and not produce the vertebrate proteins recognized by our antibodies. Chemically, the biofilm hypothesis is not supported. Neither is it supported morphologically.

2. No details of the nutrient supply over time.  
See below, and our inoculation details in the methods provided in the paper.

3. Biofilms mineralize as is well known by plaque on teeth. Ultra-pure water means no minerals to modify the biofilm.  
There are adequate minerals present in the bone “framework” in which we conducted our experiments, and microbes are perfectly capable of mobilizing these as a mineral source. Yes, biofilms do mineralize, and in that capacity no doubt play a role in preserving some “soft” materials in the rock record through consolidation. Biofilm can overgrow flat materials, like skin or feathers, in a thin layer which, when mineralized, will preserve aspects of the underlying structure (but obviously not the chemistry of the original material unless it is also preserved)… But NO data, including that presented by Kaye et al. 2008, support the hypothesis that mineralized biofilm will result in solid-walled three-dimensional structures with a lumen. Additionally, we have shown here that when minerals are REMOVED, any shape that was initially present is immediately lost. Thus, mineralized biofilm is not supported as a source for our solid walled, easily manipulated, lumen-possessing structures consistent with vertebrate vessels.

4. Iron is the basis for Dr. Schweitzer?s claims of extraordinary preservation. No iron is available in this experiment, but the resulting biofilms are compared to dinosaur ?vessels? with iron. 
Iron is quite obviously not the only means of preservation, just one we have tested and demonstrated experimentally. We proposed that iron-generated reactive oxygen species were responsible for chemical crosslinking that acted as a fixative to stabilize the vessels before decay. The biofilms used in our experiment were chemically fixed, thus an adequate model with which to compare “iron-fixed” dinosaur vessels.

5. The experiment DID produce tubular branching structures fully consistent with the claims of Kaye et al 2008.
Absolutely *NOT*. A ‘tubular structure’ by definition contains a lumen. We never observed a lumen in these biofilm structures (as we stated in the text); thus they were NOT tubular structures. The vessels, consistent with all vertebrate blood vessels, always demonstrate a lumen, in all analyses, from SEM to TEM sections and in sectioning for LM/fluorescence. Furthermore, as we state in the paper, once the bone was removed through demineralization the biofilms were disrupted with the slightest agitation and did not hold any shape even when fixed—that is why sections of these materials differ so completely from dinosaur vessels also figured. The vessels were physically removed from the chelating buffers used to demineralize the bone, washed multiple times, collected into embedding bullets, and sectioned, and still retained both structure and lumen. This was impossible to accomplish with the biofilm, even when fixed.

6. The design of the experiment with limited inputs insured only limited outcomes which were then compared to a natural process that included factors outside the range of the experiment. Mineralized or iron reinforced biofilms could never be expected in the results of this experiment by design. 
This is simply not true. In Kaye’s original paper, he grew biofilms on a flat surface under conditions of controlled recirculated water flow and nutrients added, which are not “natural” conditions occurring inside a fossil bone, buried in or exposed on the surface of sediments; thus his original paper also included factors “outside the range” of natural processes. As stated above, minerals can be (and often are) mobilized from bone itself and most certainly would have been required deep in dinosaur cortical bone in the arid, isolated badlands of Montana, where access to minerals and nutrients were limited primarily to the dinosaur bone itself and access to water was limited and sporadic. The process of microbial mobilization of bone mineral and organic matrix leaves characteristic alterations in bone microstructure, which were not observed in our specimens. For the experiments in the current paper, our goal was to attempt to mimic what might occur in nature, under natural conditions, in dinosaur cortical bone. To preserve any fossil material requires that the materials are stabilized before they can decay. Thus, the initial stages of the decay/stabilization process is capable of being approximated in the lab in relatively short time spans. Our previous experiments showed that without some kind of fixative, blood vessels isolated from bone degrade almost to completion in less than a week. Because stabilization must occur, or at least begin, within this range, a two week growth period overlapped this value. Kaye’s own contention (2008) is that structures he observed in isolated pieces of ‘float’ bone fragments, mostly from turtle plastron/carapace, resulted from modern biofilm invasions. Thus, our experiment tested these conditions rigorously.

Furthermore, conventional wisdom states that fossil bone does not retain original organics. Precisely because of this conventional and widely held belief, we designed our experiment to account for this presumed lack of organics, and this step of removing organics from bone was vital to our initial hypothesis. Although we have shown using multiple methods in multiple fossils that organics most likely persist in bone, we tested, again, this starting and widely held assumption. On the other hand, it is well known that microbes will grow almost anywhere there is organic material available to them, so to work with untreated bone still retaining organics would provide no new information. Thus, our experimental design required removing the organics from bone, to better approximate what is believed by many to best represent the composition of fossil material. This step was important to testing our hypothesis, which we state clearly in the paper. When Kaye argues that “No details were provided as to nutrient level or other parameters of the biofilm”, our response is that these details were not pertinent to our central hypothesis. We simply show that when additional nutrients are supplied, biofilm *will* grow in “naked” bone. There is precedent for this, cited in Neu et al 2003, where it is stated “a study is described in which a river inoculum was used as a sole source of nutrients (and inoculated only once, similar to our study) and the after 4 weeks the biofilm plateaued and no longer grew”. Based on these findings, then, we chose to halt the experiment half way, when we could observe biofilm growth but before sloughing of cells occurred, thus optimizing molecular response if it were present, as well as optimizing the chance of recovering coherent intact biofilm.” 

7. We look forward to further experiments that mimic the natural process of biofilm formation. 
We are satisfied that we have ruled out biofilm as a source of our vessels with abundant and varied data and will not pursue this. We will continue to base our future research on the well-supported hypothesis that these structures are endogenous. Multiple lines of evidence support this hypothesis, including recovery of sequences of multiple vertebrate proteins commonly associated with blood vessels and other bone organic components, but which are not generated by or associated with biofilm-producing organisms, the presence of which cannot therefore be explained by a biofilm origin. The data we present here, rigorously testing this alternative hypothesis, further eliminate the possibility that these arise from biofilm. Biofilms do not contain vertebrate proteins. Biofilms do not cross react with antibodies to vertebrate proteins. Dinosaur blood vessels do not respond to antibodies against bacterial proteins. Biofilms are morphologically distinct from blood vessels, are not cylindrical, and do not contain a lumen. There is no evidence to support a biofilm origin for the vessel structures recovered from these and other dinosaur materials.”

Once again,
I can’t weigh in on this argument. Both sides are steadfast. Only one can be correct. I know how both of them feel. A lot of work on both sides has come to loggerheads. Full disclosure: I have seen and tugged on the rubbery biofilms in the Tom Kaye lab.

References
Kaye TG, Gaugler G, Sawlowicz Z. Stepanova A. 2008. Dinosaurian soft tissues interpreted as bacterial biofilms. PLoS One. 2008;3(7):e2808. doi: 10.1371/journal.pone.0002808. pmid:18665236
Schweitzer MH, Moyer AE and Zheng W-X 2016. Testing the Hypothesis of Biofilm as a Source for Soft Tissue and Cell-Like Structures Preserved in Dinosaur Bone. DOI: 10.1371/journal.pone.0150238

M. Schweitzer on 60 minutes here

Kaye pictures here:
http://scienceblogs.com/grrlscientist/2008/07/30/a-closer-look-at-dinosaur-soft/

Pterosaur and bat wing origins

It has been a long time
since some aspect of pterosaur biology was covered here, what with theropods, turtles and lizards stealing the spotlight lately. It is also remarkable that the origin of bats continues to be the hottest topic (by far) at the PterosaurHeresies day-after-day. Let’s take a look at both today and see what we can learn.

Figure 1. Bat embryo wing shape compared to Pterodactylus. Note the ability to fold (relax) the wings until they virtually disappear in both cases. Also note the origin of bat wings paralleling those of pterosaur wings in that during embryology the bat wing also has a narrow chord. Distinct from pterosaur wings the bat wing more deeply develops long after birth. Last minute note: bat hind limbs sprawl, unlike most mammals, but like Pterodactylus hind limbs (but not Dimorphodon and kin, they had erect hind limbs). 

Bat wings
According to the evidence shown above in the embryo bat, the fingers and the wing membrane do not achieve adult proportions until long after birth. Babies cling to their mothers. The wing membrane of the embryo converges with that of pterosaur in having a very shallow at the elbow wing chord, but it diverges during ontogeny because it deepens with maturation. The Myotis embryo lacks uropatagia. That, too, develops later in the process (see above) and reaches its fullest extent long after birth. Adult image here.

A casual look around the Internet 
shows that the deep chord wing membrane model of pterosaurs promoted by Hone, Elgin, Bennett and Witton have been widely adopted. And that’s akin to hogwash and alchemy, not Science. In Science you don’t make up excuses (like membrane shrinking) to match preconceptions. You observe reality. Facts are facts. No one has yet produced a pterosaur specimen with a deep chord wing membrane. By contrast, all available examples (like Figs. 2, 4) demonstrate the opposite.

Figure 2. Here is the Vienna specimen of Pterodactylus in situ and with matrix removed. Now compare this figure with figure 3, which shows the wings and uropatagia unfolding. There is no way to turn this into a deep chord wing membrane. And it decouples the forelimbs from the hind limbs. Why don’t other pterosaur workers accept this. Because they are too deeply married to the false paradigm.

Now
let’s unfold those Pterodactylus wings (Fig. 3)

Figure 3. The Vienna Pterodactylus. Click to animate. Wing membranes in situ (when folded) then animated to extend them. There is no shrinkage here or in ANY pterosaur wing membrane. There is only an “explanation” to avoid dealing with the hard evidence here and elsewhere that the pterosaur wing was stretched between the elbow and wing tip. Any other explanation is alchemy and hogwash.

You may remember that the deep chord/single uropatagium theory
goes back to Sharov (1971) who vaguely traced wing membranes as they appeared on Sordes without regard for taphonomy. Click here for more details on Sordes.

Fig. 4. The Sordes uropatagium is actually displaced wing material carried between the ankles by the displaced radius and ulna.

And the origin of the pterosaur wing
of course, goes back to the nonviolent Cosesaurus, which had trailing fibers from the forelimb first noticed by Ellenberger 1993 and Peters 2009 and also here and here.

References
Ellenberger P 1993. Cosesaurus aviceps . Vertébré aviforme du Trias Moyen de Catalogne. Étude descriptive et comparative. Mémoire Avec le concours de l’École Pratique des Hautes Etudes. Laboratorie de Paléontologie des Vertébrés. Univ. Sci. Tech. Languedoc, Montpellier (France). Pp. 1-664.
Peters D 2009. A reinterpretation of pteroid articulation in pterosaurs. Journal of Vertebrate Paleontology 29: 1327-1330
Sharov AG 1971. New flying reptiles from the Mesozoic of Kazakhstan and Kirghizia. – Transactions of the Paleontological Institute, Akademia Nauk, USSR, Moscow, 130: 104–113 [in Russian].