Notes on lizard hands and feet with comparisons to the bird finger issue

Chalcides ocellatus is a basal extant skink. It has a basic (plesiomorphic) hand and foot, each with five digits and very few derived traits (Fig. 1, like the fusion of m4.3 + m4.4 and the fusion of mc1 + c1).

By contrast, another species, C. chalcides, the Italian three-toed skink, has but three toes on both the manus and the pes, which are, at best, tiny vestiges on tiny vestigial limbs.

Figure 1. The manus and pes of Chalcides ocellatus from Young et al. 2009, cleared and stained to show the bones in natural articulation.

Figure 1. The manus and pes of Chalcides ocellatus from Young et al. 2009, cleared and stained to show the bones in natural articulation at left. Ghosted with PILs added at right. Click to enlarge.

From the Young et al. (2009) abstract:
“Digit identity in the avian wing is a classical example of conflicting anatomical and embryological evidence regarding digit homology. In recent years, gene expression as well as experimental evidence was published that supports the hypothesis that this discrepancy arose from a digit identity shift in the evolution of the bird wing. A similar but less well-known controversy has been ongoing since the late 19th century regarding the identity of the digits of the three-toed Italian skink, Chalcides chalcides.The data confirm that the adult and the embryological evidence for digit identity are in conflict, and the expression of Hoxd11 suggests that digits 1, 2, and 3 develop in positions 2, 3, and 4. We conclude that in C. chalcides, and likely in its close relatives, a digit identity frame shift has occurred, similar to the one in avian evolution.” 

The three-toed skink (Chalcides chalcides, Fig. 2) is more derived than the five-toed skink. Digits 4 and 5 are outwardly absent from both the manus and pes. But note the buried vestige of digit 4 in both the manus and pes. The phase shift described by Young et al. happens during embryology (not shown here). In the adult basic homologies are maintained. The medial digit is #1.

Figure 2. Manus and pes of 3-toed Chalcides chalices. Note the broad base of mc1, similar to that in the figure 1.

Figure 2. Manus and pes of 3-toed Chalcides chalices. Note the broad base of mc1, similar to that in the figure 1. A vestige of digit 4 is present in both the manus and pes.

Here’s a possible explanation for apparent “Phase Shift” during embryogenesis.
Looking at the entire family tree of amniotes and tetrapods, it appears that this so-called “phase shift” may have its roots in basal tetrapods which had more than 5 fingers and toes (Fig. 3) and our genes remember that part of our ancestry. Remember there are gills in tetrapod embryos, too~! And gills goes back in further in our genetic ancestry.

As in Acanthostega,
that little bud developing medially on the embryo bird manus (Fig. 3) is probably not digit 1. Rather, it appears to be homologous to digit “pre-1” on Acanthostega (Fig. 3), making a brief appearance during embryo development before disappearing as embryo growth continues. I don’t think the proper term for this is “phase shift”. Rather it is an ephemeral and short-lived appearance of digit pre-1 that probably occurs in most tetrapods.

Figure 3. Is this the source of the phase shift? At left, an embryo bird wing. Center an right, manus and pes of Acanthostega, a stem tetrapod with more than five digits. Orange dots identify homologies with five digit tetrapods.

Figure 3. Is this the source of the phase shift? At left, an embryo bird wing. Center an right, manus and pes of Acanthostega, a stem tetrapod with more than five digits. Orange dots identify homologies with five digit tetrapods. Click to enlarge.

Has this been considered before in academic publications? If so, it’s a convergent hypothesis.

References
Young RL, Caputo V, Giovannotti M, Kohlsdorf T, Vargas AO, May GE ,a and Wagner GP 2009. Evolution of digit identity in the three-toed Italian skink Chalcides chalcides: a new case of digit identity frame shift. Evolution and Development 11:6, 647–658.

Sirenoscincus mobydick: the only terrestrial tetrapod with ‘flippers’

Sakata and Hikida 2003
introduced us to a new and extant fossorial (burrowing) lizard (Sirenoscincus yamagishii. Fig.1). The authors described having “an elongated body and eyes covered by scales, lacking external ear openings and pigmentation through- out the body, resembles Cryptoscincus and Voeltzkowia. However it differs from these or any other scincid genera known to the present in having small but distinct forelimbs, each with four stout claws, and complete lack of hind limbs.”

Figure 1. Sirenoscincus-yamagishii, a new skink with forelimbs and no hind limbs. Note the four fingers.

Figure 1. Sirenoscincus-yamagishii, a new skink with forelimbs and no hind limbs. Note the four fingers.

Sirenoscincus is a very tiny lizard
with 53 presacral vertebrae and a tail longer than the snout vent length. The snout is pointed and the lower jaw is countersunk, like a shark’s mouth. The forelimbs are tiny with indistinct fingers and four stout claws. An outgroup taxon, Gymnophthalmus, also has tiny fingers and the medial one is a vestige.

Then a second Sirenoscincus species was discovered
S. mobydick (Miralles et al. 2012, Fig. 2; see online interview here). “The specicific epithet refers to Moby Dick, the famous albino sperm whale imagined by Herman Melville (1851), with whom the new species shares several uncommon characteristics, such as the lack of hind limbs, the presence of fipper-like forelimbs, highly reduced eyes, and the complete absence of pigmentation.”

Figure 3. Sirenoscincus mobydick.

Figure 2. Sirenoscincus mobydick.

S. mobydick has only five scleral ring bones, the lowest of any lizard. The authors reinterpreted several scale patterns on the holotype species. So, mistakes do happen, even at a professional level. Those mistakes get corrected and no one gets upset (hopefully unlike the blogosphere!).

Figure 2. Sireonscincus mobydick, named for its flippers, unique for any terrestrial tetrapod.

Figure 3. Sireonscincus mobydick, named for its flippers, unique for any terrestrial tetrapod. Colors added.

Fossorial skinks are often described by their scale patterns.
Unfortunately that doesn’t work with prehistoric skeletons, so I was only able to add only the bone traits of Sirenoscincus mobydick to the large reptile tree (subset shown in Fig. 7). The skeletal traits nested S. mobydick between two skinks Gymnophthalmus and Sineoamphisbaena, another taxon with forelimbs only (granted, the posterior half is not known). Like Sineoamphisbaena, Sirenoscincus prefrontals contact the postfrontals, unlike those of most lizards. In derived taxa the quadrate leans almost horizontally. That’s not the case with Sirenoscincus, which has a vertical but bent quadrate.

Figure 4. Sirenoscincus mobydick pectoral and pelvic girdles. Colors added.

Figure 4. Sirenoscincus mobydick pectoral and pelvic girdles. Colors (other then the original red) are added here.

Miralles et al. (2012) reported,  “Due to the absence of molecular data the phylogenetic position of the genus Sirenoscincus is still an enigma, even if we can reasonably claim it belongs to the Malagasy scincine clade.” In the last few days author, A. Miralles reported via email that molecular data have recently nested S. mobydick with skinks. 

Figure x. Chalcides guentheri and C. occellatus, two skinks were morphology quite similar to that of Sirenoscincus.

Figure 5. Chalcides guentheri and C. occellatus, two skinks with morphologies quite similar to that of Sirenoscincus. C. oscellatus has longer legs. Note the wrapping of the maxilla over the premaxilla which is continued in Sirenoscincus mobydick which has a smaller orbit. Also note the prefrontal and postfrontal are closer to contact in C. ocellatus.

An outgroup taxon is Chalcides (Fig. 5) where you’ll note the same long overlap of the maxilla over the premaxilla. A sister, Sineoamphisbaena also has an underslung mandible, but much more robust forelimbs (only the humerus is known). Could this be a redevelopment? Or has the cladogram missed something, needing more taxa perhaps, to fill this gap? No doubt new taxa will fill these various morphological gaps.

Figure 6. Sineoamphisbaena is a sister to Sirenoscincus in which the prefrontal contacts the postfrontal.

Figure 6. Sineoamphisbaena is a sister to Sirenoscincus in which the prefrontal contacts the postfrontal. The lower jaw is countersunk and the upper teeth don’t point down, they point in (medially).

New data has revised the relationship of skinks to reptiles in the large reptile tree (Fig. 7). Some to most of the confusion (here or earlier) likely results from the massive convergence in burrowing lizards. And some portion is also due to having good data (old line drawings) replaced by better data (rotating online images), often thanks to the good scientists over at Digimorph.org.

Figure 7. Here's where Sirenoscincus nests in the lizard family tree.

Figure 7. Here’s where Sirenoscincus nests in the lizard family tree.

References
Miralles A et al. 2012. Variations on a bauplan: description of a new Malagasy “mermaid skink” with flipper-like forelimbs only (Scincidae, Sirenoscincus Sakata & Hikida, 2003). Zoosystema 34(4):701-719.
Sakata S and Hikida T 2003. A fossorial lizard with forelimbs only: description of a new genus and species of Malagasy skink (Reptilia: Squamata: Scincidae). Current Herpetology 22:9-15.

A little Triassic Ichthyosaur: Phalarodon

Figure 1. Phalarodon, a little mid Triassic ichthyosaur. Note the deep depression in the dorsal skull.

Figure 1. Phalarodon, a little mid Triassic ichthyosaur. Note the deep depression in the dorsal skull. Bones in situ and restored here to in vivo positions and skull bones colorized. Note the actual size is not much larger than shown here. 

From the Liu et al. 2013 abstract:
Phalarodon atavus from the Germanic Muschelkalk Basin was previously represented only by cranial elements.Here we report a nearly complete and articulated specimen of P. atavus from the Middle Triassic Luoping Biota, Yunnan, South China. This is the first specimen of P. atavus from outside the Germanic Basin. This discovery demonstrates a peri-Tethyan distribution of P. atavus. The new specimen is also the first one preserving the postcranial anatomy of this species, providing the opportunity to evaluate its sustained swimming ability. Inferences made on its functional morphology suggest that this species was probably adapted for active foraging. Tooth crown morphology suggests that P. atavus may have preferred externally soft prey.”

The mixosaurian body plan is recognized as an evolutionary intermediate between the basal stem plan represented by Early Triassic forms and the parvipelvian plan of largely post-Triassic ichthyosaurs. Size-independent criteria indicate this specimen (LPV 30872) is a subadult. It is a tiny ichthyosaur, not much larger than the image shown above.

Sinosaurosphargis is from the same equatorial deposits. The Germanic deposits were also equatorial at the other end of the Tethys Ocean bounded on all sides by continents and peninsulas.

Giant Cymbospondylus (Fig. 2) also nests with Mixosaurus and Phalarodon. Note the share trait of side-by-side dips in the cranium with the upper temporal fenestra as “drains” in these basins, areas that probably housed jaw muscles.

Figure 1. Cymbospondylus overall in situ.

Figure 2. Cymbospondylus overall in situ.

References
Liu J et al 2013. The first specimen of the Middle Triassic Phalarodon atavus (Ichthyosauria: Mixosauridae) from South China, showing postcranial anatomy and per–Tethyan distribution. Palaeontology  56:849-866.

New reconstruction of Mycterosaurus, a basalmost protodiapsid

Earlier here and here we looked at Mycterosaurus (Fig. 1). This cat-sized taxon nests as a basalmost protodiapsid (along with Archaeovenator), not far from the basalmost synapsids, Aerosaurus, Varanops etc. and their last common ancestor, Protorothyris, a basal taxon which does not have a lateral temporal fenestra. Other basal protodiapsids include Milleropsis and Erpetonyx and these ultimately give rise to diapsids like Spinoaequalis and Petrolacosaurus in the large reptile tree. This new reconstruction (Fig. 1) is based on more precise data from Berman and Reisz (1982) than originally available from Williston (1915).

Figure 1.Mycterosaurus. Click to enlarge. This is a sister to the basalmost protodiapsid, and thus an ancestor of birds and crocs.

Figure 1.Mycterosaurus. Click to enlarge. This is a sister to the basalmost protodiapsid, and thus an ancestor of birds and crocs. There is an interesting shift in the dorsal vertebral neural spines that is not present in related taxa.

This subset of the large reptile tree (Fig. 2) shows relationships at the base of two large clades of reptiles, Synapsida and Diapsida (sans lepidosauriformes, which have convergenently developed a similar temporal morphology).

Figure 2. A subset of the large reptile tree showing the relationships of protosynapsids, synapsids, protodiapsids and diapsids. Traditionally nested with synapsids as varanopids, the protodiapsids have rarely, if ever, been tested with diapsids.

Figure 2. A subset of the large reptile tree showing the relationships of protosynapsids, synapsids, protodiapsids and diapsids. Traditionally nested with synapsids as varanopids, the protodiapsids have rarely, if ever, been tested with diapsids.

Mycterosaurus longiceps (Middle Permian, Williston 1915, Berman and Reisz 1982) nested with Heleosaurus as a basal protodiapsid. Botha-Brink and Modesto (2009) also correctly nested it with Mesenosaurus and Heleosaurus but considered those taxa varanopid synapsids unrelated to diapsids. 

The tip of the snout is unknown in Mycterosaurus, but probably straight as in sister Heleosaurus. Berman and Reisz 1982 considered the AMNH 7002 specimen (above) another Mycterosaurus, but it has recurved canines more like those of Mesenosaurus, the maxilla is lower and the jugal had a different shape.

No DNA studies link mammals (synapsids) to birds and crocs (diapsids) yet embryological studies show that both develop of jugal with a quadratojugal process, something lizard and turtle embryos do not produce. I continue to be perplexed about DNA vs. morph studies. But I also continue to urge cladogram builders to include key taxa, like Mycterosaurus in studies on basal diapsids and vice versa.

References
Berman DS and Reisz RR 1982. Restudy of Mycterosaurus longiceps (Reptilia, Pelycosauria) from the Lower Permian of Texas. Annals of Carnegie Museum 51, 423–453.
Botha-Brink J and Modesto SP 2009. Anatomy and Relationships of the Middle Permian Varanopid Heleosaurus scholtzi Based on a Social Aggregation from the Karoo Basin of South Africa. Journal of Vertebrate Paleontology 29(2):389-400.
Broom R 1907. On some new fossil reptiles from the Karroo beds of Victoria West, South Africa. Transactions of the South African Philosophical Society 18:31–42.
Willistion SW 1915. A New Genus and Species of American Theromorpha: Mycterosaurus longiceps. The Journal of Geology 23(6):554-559.
wiki/Mycterosaurus

TIme to Flip Plataleorhynchus (a spoonbill pterosaur)

Howse and Milner (1995)
described a spoonbill rostrum lacking teeth in place. They correctly compared it to the much smaller pterosaur Gnathosaurus and called their English find Plataleorhynchus stretophorodon (Fig. 1, BMNH R 11957). As you can see, it was much bigger.

Figure 1. Plataleorhynchus stretophorodon as originally interpreted (at far left) as newly interpreted (near left) with comparisons to Gnathoosaurus (right). Note the exposure is in dorsal view, not palatal view, and the premaxilla includes only 4 teeth, as in other pterosaurs.

Figure 1. Plataleorhynchus stretophorodon as originally interpreted (at far left) as newly interpreted (near left) with comparisons to Gnathoosaurus (right). Note the exposure is in dorsal view, not palatal view, and the premaxilla includes only 4 teeth, as in other pterosaurs. Yes, the premaxilla ‘pops up’ three times from beneath the maxilla and nasals in Gnathosaurus. Click to enlarge.

Unfortunately
Howse and Milner did not realize they were looking at the rostrum in dorsal aspect. And for that reason, perhaps,  they did not correctly figure the lateral extent of the premaxilla (Fig.1). No pterosaur has more than four teeth erupting from the premaxilla and Plataleorhynchus was no exception. So the premaxilla had a very short anterior exposure, rather than encompassing the entire spoonbill, as Howse and Milner interpreted the fossil from firsthand observation.

Howse and Milner did correctly note differences in the rostral shape and relative tooth size between Plataleorhynchus and Gnathosaurus, and also correctly noted that no other known pterosaur was closer. So, by this evidence, some mistakes don’t matter in the end.

Like Gnathosaurus and other ctenochasmatids,
Plataleorhynchus had dorsally expanded maxillae that contacted one another over the premaxilla aft of the spoonbill. Due to their orientation mistake, Howse and Milner identified the second dorsal appearance of the premaxilla as the palatine.

Howse and Milner thought the palate had a horny pad based on the rugosity that was exposed. That rugosity, (here considered dorsal) is also present in Gnathosaurus, but not as prominent. The reason or origin for the rugosity on the dorsal tip of Plataleorhynchus is difficult to explain, but may be related to the further extent of the maxillae and perhaps some sort of small horny crest.

Also note
the palatal extent of the premaxilla is much smaller in the comparable Gnathosaurus than envisioned for Plataleorhynchus by Howse and Milner. In Gnathosaurus I’m not sure how the teeth were not shaken loose. The roots appear to be exposed on the palate (Fig. 1). They must have been held in place by soft tissue.

Considering this mistake, 
much has been made about the value of firsthand observation versus the examination of photographs and illustrations. Paleontologists are fond of dismissing interpretations made in the absence of the fossil itself. They forget that most of the credit or blame for a discovery happens not in the lab, but between the ears. You have to see things correctly from the start or all the dominoes start to fall the wrong way. Mistakes can happen to anyone (including yours truly). Howse and Milner 1995 (Fig. 1) is another example of a firsthand observation that went awry based on one initial mistake. And that was an easy one to make with that odd spoonbill rostrum. It was flat on both sides.

Like Cope vs. Marsh back in the day, I am, once again metaphorically, “putting the skull on the other end of the skeleton” by flipping over the rostrum of Plataleorhynchus. The correct response, of course, should be curiosity or gratitude, not embarrassment, anger or dismissal. However, if anyone out there thinks the rostrum exposure is still palatal, I’d like to hear from you.

References
Howse SCB and Milner AR 1995. The pterodactyloids from the Purbeck Limestone Formation of Dorset. Bulletin of the Natural History Museum London (Geology)51:73-88.

 

What is Orientognathus? Nest it with Changchengopterus and Sordes.

Earlier on January 24, 2015 we looked at a description of Orientognathus chaoyngensis (Lü et al. 2015. Fig.1) a new Late Jurassic rhamphorhynchoid pterosaur known then from a series of comparative descriptions only. No images. Now that I’ve seen a low-resolution photograph (Fig. 1), let’s review the data we had to work with on the 24th of January.

Figure 1. Orientognathus in situ, tracing moved to live position, comparisons to sisters Changchengopterus and Sordes.

Figure 1. Orientognathus in situ, tracing moved to live position, comparisons to sisters Changchengopterus and Sordes. Click to enlarge. More resolution is needed to get more out of this. The wings and tail are not very long here. The sternum is a small triangle.

Data provided:

  1. toothless tip of dentary, slightly pointed – True
  2. mc4/humerus ratio = 0.38 – True and precise
  3. ulna < each individual wing phalanx – False, the ulna is quite long
  4. tibia subequal to femur – False, tibia is longer, both tibia are broken.
  5. deltopectoral crest more developed than in Qinlongopterus – True, but not as much as in Sordes.
  6. anterior teeth stouter and longer than in Pterorhynchus – True, but Pterorhynchus has pretty short anterior teeth.
  7. teeth are straight and longer than in Jianchangnathus Subequal actually. 
  8. pteroid/humerus ratio = 0.21; pteroid has expanded distal end True enough (0.23)
  9. larger than other rhamphorhynchine pterosaurs from Late Jurassic NE China (measurements not indicated). Did not check, but seems pretty big (Fig. 1).

The specimen is nearly complete and partly disarticulated. 
The antebrachium (forearm) is broken. Put them back together and that’s a long forearm.

It turns out the the tibia is not equal to the femur in length
So all of the prior candidates become rejects.

Step two: ulna is not smaller than each individual wing phalanx
Orientognathus has a large antebrachium, subequal to m4.2 and longer than m4.1.

Figure 2. The original nesting of Orientognathus from Lü et al. 2014. Note the lack of resolution in that clade. Changchengopterus is not listed, but should be.

Figure 2. The original nesting of Orientognathus from Lü et al. 2014. Note the lack of resolution in that clade. Changchengopterus is not listed, but should be.

Step three: Phylogenetic Analysis
The prior cladogram lost resolution when Orientognathus was added (Fig. 2) .

However
A new analysis of the large pterosaur tree (not yet updated) nests Orientognathus between Changchengopterus and the primitive specimen of Sordes (Fig. 1) with no loss of resolution.

These three (Sordes, Orientognathus and Changchengopterus) are the metaphorical ‘plain brown sparrows’ among pterosaurs from which all later spectacular specimens are derived. It’s that lack of any ‘distinctive’ traits that is actually their own distinctive trait.

Thus Orientognathus is basal to the several specimens of Sordes and the many specimens of Dorygnathus, from which arise darwinopterids (wukongopterids), scaphognathids and ultimately all the pterodactyloids. Orientognathus may have been hard to nest and caused so little stir because it is indeed plesiomorphic. Getting that antebrachium and tibia right would have helped. If anyone has access to high resolution imagery of the skull and foot, that would be very helpful.

References
Lü J, P H-Y, We X-F, Chan H-L and Kundrat GM 2014. A new rhamphorhynchid pterosaur (Pterosauria) from Jurassic deposits of Liaoning Province, China. http://www.biotaxa.org/Zootaxa/article/view/zootaxa.3911.1.7/0

Bone Wars: Then and Now

Figure 1. Cope and Marsh in their classic poses. These two early paleontologists were combatants in the first "bone wars."

Figure 1. Cope and Marsh in their classic poses. These two early paleontologists were combatants in the first “bone wars” and their story is told on a great PBS video. Click image to see the video.

Cope and Marsh
are famous for their “Bone Wars” also known as the “Great Dinosaur Rush” in the 19th century. Here is a great PBS video on the subject. According to Wikipedia: “Each of the two paleontologists used underhanded methods to try to out-compete the other in the field, resorting to bribery, theft, and destruction of bones. Each scientist also attacked the other in scientific publications, seeking to ruin his credibility and have his funding cut off.”

It all began ‘innocently’ enough when Marsh took the skull off the tail of Cope’s Elasmosaurus and placed it on the neck (Fig. 2). Cope did not take this well.

Figure 2. Elasmosaurus as originally configured with the skull on the end of the short tail (sort of a mosasaur morphology) and on the end of a very long neck, unheard of until then.

Figure 2. Elasmosaurus as originally configured (Cope 1869) with the skull on the end of the short tail (sort of a mosasaur morphology) and on the end of a very long neck, unheard of until then. Click to enlarge.

Mike Everhart at OceansofKansas.com tells the tale in greater detail. Just a few notes here will suffice. Everhart quotes a 28-year-old Cope (1868) who notes the neck was quite unusual, because of the “the presence of chevron-like bones on the inferior surfaces of the cervical vertebrae.”  Then it gets worse. Cope (1869) created a new order, the “Streptosauria” [reversed lizards] for Elasomosaurus. Cope wrote:“Under this name I have characterized a group of high rank among the Reptiles which is allied to the Sauropterygia. The diagnosis will be as follows. The articular processes of the vertebræ, reversed in their directions; viz., the anterior looking downwards, the posterior upwards … The characters of this order are altogether peculiar.”

See how red flags are ignored? 
Even by the authors themselves? We’re all guilty of this, yours truly no exception. Nowadays the “bone wars” are wars of words and manuscript rejections.

The Bird Wars
between Alan Feduccia (and the late L. Martin and S. Czerkas) versus most dinosaur paleontologists began in 1973 and continues today. Originally Feduccia agreed with the long held model for the origin of birds proposed by Gerhard Heilmann (1926) The Origin of Birds arguing against the works of John Ostrom (1970) with his work and insights on Deinonynchus (and countless others who followed), all of whom linked theropod dinosaurs to birds.  With the growing pressure and dozens of new discoveries, after 2002 Feduccia argued that the discovery of the very bird-like theropod dinosaurs, Microraptor and Caudipteryxsuggested an unrecognized radiation of birds that lost flight and secondarily converged on theropods.

Unfortunately that takes the long way around
to get to the point that basal birds share a large suite of traits with bird-like theropods, which is the basis for their phylogenetic relationship. Feduccia never produced an alternate cladorgram of bird origins. Rather in 1999 he wrote, “Although most fields of science are constantly struggling with which methodologies to use, the field of systematics, and espe- cially paleontology, has adopted phylogenetic systematics (cladistic methodology) to the exclusion of other approaches. Despite a barrage of cautions and criticism, cladistics reigns.” Then concluding, Feduccia (1999) wrote, “Perhaps the greatest form of special pleading will be necessary to explain how flight could have originated from the ground up; our present knowledge indicates that there are two requisites for flight origin: small size and high places.” Today it is clear that birds descended from theropod dinosaurs. Experiments have shown that flightless birds run up trees while flapping their wings. That’s all set in stone.

The Large Reptile Tree War
is my attempt at getting paleontologists and referees to consider adding taxa to their family trees to see how more taxa might change their tree topologies. To that end the large reptile tree now has 501 taxa. The large pterosaur tree has 218 taxa. The therapsid tree has 59. All are completely or nearly completely (=deletion of one taxon makes it completely) resolved. These results are repeatable, and all sister taxa look alike. However, they, at times, break with tradition and so raise hackles and doubts.

In a recent rejection letter to manuscript describing a new origin for amniotes, the referee wrote: “I am extremely incredulous of a phylogenetic analysis examining this many taxa that results in a single most parsimonious tree. Rerunning the author’s nexus file in TNT reveals a single most parsimonious tree. TNT collapses zero-length branches more strictly than PAUP* revealing that there are in fact fewer trees supported by unambiguous synapomorphies than reported by the author. The single polytomy present in the strict consensus (Cerritosaurus,Tropidosuchus,Lagerpeton) is the result of how PAUP collapses (or doesn’t) zero length branches than true conflict in the dataset. I must admit that I am extremely incredulous of a phylogenetic analysis examining this many taxa that results in a single most parsimonious tree. I, in fact, cannot think of another published example. The fact that the author does not address this at all is troubling.”

Say…
isn’t this turning a ‘good’ result into a ‘bad’ result?

As we all know, incredulity is a synonym for disbelief.
Why would a scientist elevate ‘belief’ over ‘evidence’ simply because the evidence does not support the traditional paradigm? Some paradigms, as we know from history, are not correct.

BTW, the manuscript was rejected when the large reptile tree had 389 taxa and 228 characters. Today there are 501 taxa and 228 characters. So the situation is worse… or better… now, depending on your outlook.

That manuscript focused on the origin of the Amniota. There were few comments regarding that topic and the included taxa. The supporting document supported and included the large reptile tree. That became the focus of the referee’s comments. Unfortunately manuscripts can only be of a certain length and the number of problems that have to be adequately addressed runs beyond that length (at least to satisfy this referee). I’ve run across this before. Other referees insisted that I visit all 501 specimens, even though this is not standard practice with large trees. In supertree analysis, authors do not have to see a single specimen.

The Pterosaur War
As you all know, I have been promoting new ideas with regard to pterosaur origins, interrelationships, ontogeny, wing shape, launch tactics, etc. etc. always with evidence to demonstrate the hypotheses. And as you all know, evidence is sometimes not believed.

A referee wrote this on my fenestrasaur manuscript submission, “Peters reports here the presence of the whole posterior half of the specimen in Longisquama, tail, pelvic girdle and hind limb included. If the hind limb and posterior trunk were in “plain sight” as written in the manuscript, how could all previous authors (Peters himself included), have missed or blatantly misinterpreted them?”

It happens. Look at the mistakes made with Vancleavea. Mesosaurus. Cosesaurus either with regard to observation or taxon inclusion.

That referee’s complaint is a common one.
Unfortunately Longisquama has been rarely studied and even more rarely written up. Actually there were very few previous authors who described Longisquama and none have produced the sort of precise tracing that I provided (see it here). Others didn’t see what I saw because they didn’t look hard enough. Bottom line: This referee was not going to let me repair my mistakes in print. He was not going to allow more precision come to this enigma taxon. Perhaps he thought it better to keep such ideas safely tucked away from consideration and debate. Better to keep some things cloaked in mystery.

Having been in paleontology for several decades now, it becomes clear that many observations are borrowed from prior workers (I do this myself when it seems safe to do so) and many phylogenies are sometimes uncritically borrowed. Red flags, like the nesting of pterosaurs with parasuchians, are ignored, by the original authors, the manuscript referees and colleagues. Why? Well, I think it’s because they don’t want to rock the boat, which occasionally needs rocking. I can tell you, it’s easier to get data published if it agree with current paradigms.

How did I miss or blatantly misinterpret Longisquama?
Back then I misinterpreted Longisquama because I was naive, a newbie, someone with little to no experience. And Longisquama is arguably one of the most difficult specimens known. Fifteen years later, I not only see things differently, I know what to look for and I know better what I’m seeing.

And the funny thing is…
even if the hind portion of Longisquama was not preserved, phylogenetic bracketing between Sharovipteryx and MPUM 6009 would still give it most of the same traits (the long torso is an autapomorphy, Fig. 2).

Figure 2. The basal fenestrasaur precursors of pterosaurs, including Cosesaurus, Sharovipteryx, Kyrgyzsaurus, Longisquama and a basal pterosaur.

Figure 3. The basal fenestrasaur precursors of pterosaurs, including Cosesaurus, Sharovipteryx, Kyrgyzsaurus, Longisquama and a basal pterosaur.

Pterosaur workers continue to refuse to consider using fenestrasaurs as pterosaur outgroups, preferring instead to use random archosaurs that share few to no pterosaur traits. They certainly don’t use parasuchians, which often nest ancestrally in many cladograms.

Pterosaur workers continue to refuse to consider using tiny pterosaurs (about the size of sparrows and hummingbirds) in phylogenetic analysis, preferring instead to produce cladograms in which transitional taxa don’t share very many traits with precursors and successors.

Pterosaur workers continue to believe that baby to juvenile pterosaurs had traditional ‘cute’ features (short rostrum, large orbit) despite all the evidence to the contrary. I haven’t met one who accepts the fact that pterosaurs developed largely by isometry during ontogeny as discussed here.

Pterosaur workers continue to refuse to consider using multiple specimens of Dorygnathus, Scaphognathus, Pteranodon and other genera that are known from a variety of morphologies. And they reject manuscripts that do.

Why is this so?
I think it’s because, like Cope and Marsh, I metaphorically put the skull on the other end of the skeleton and created an air of embarrassment out there. I discovered that pterosaurs were not archosaurs. That there were four origins for the pterodactyloid grade and each was preceded by a series of phylogenetic miniaturizations. That juvenile pterosaurs developed isometrically. That pterosaur wings had a narrow chord at the elbow. That uropatagia did not extend from leg to leg. These not only don’t go over well. They are avoided and dismissed without a superior hypothesis at every turn.

Sure I’ve made mistakes.
Tens of thousands of them. I discovered all but a few without help. Often the repairs helped cement earlier hypothetical relationships. Sometimes new insights were gained.

Whatever the truth is,
it will all come out sooner or later. It has to — because it’s the truth.

References
Cope ED 1869. Synopsis of the Extinct Batrachia and Reptilia of North America, Part I. Trans. Amer. Phil. Soc. New Series, 14:1-235, 51 figs., 11 pls.
Feduccia A 1973. Dinosaurs as reptiles. Evolution 27 (1): 166–169.
Feduccia A. 1999. 1,2,3 = 2,3,4: Accommodating the cladogram. Proceedings of the National Academy of Science USA. 96:4740-4742.
Ostrom JH 1970. Stratigraphy and paleontology of the Cloverly Formation (Lower Cretaceous) of the Bighorn Basin area, Wyoming and Montana. Bulletin of the Peabody Museum of Natural History 35:1–234.