Chinlestegophis and the origin of caecilia

Yesterday Pardo et al. 2017
described two conspecific and incomplete amphibians in the lineage of caecilians, Chinlestegophis jerkinsi (DMNH 56658, DMNH 39033, Figs. 1, 3). These long-sought specimens were discovered in the late 1990s preserved in Late Triassic burrows.

This is really big news!
Congratulations to the Pardo team!!

From the abstract:
“Here, we report on a small amphibian from the Upper Triassic of Colorado, United States, with a mélange of caecilian synapomorphies and general lissamphibian plesiomorphies. We evaluated its relationships by designing an inclusive phylogenetic analysis that broadly incorporates definitive members of the modern lissamphibian orders and a diversity of extinct temnospondyl amphibians, including stereospondyls. Stem caecilian morphology reveals a previously unrecognized stepwise acquisition of typical caecilian cranial apomorphies during the Triassic. A major implication is that many Paleozoic total group lissamphibians (i.e., higher temnospondyls, including the stereospondyl subclade) fall within crown Lissamphibia, which must have originated before 315 million years ago.”

The diagnosis:
“Small stereospondyl with a combination of brachyopoid and caecilian characteristics.”  Stereospondyls were generally large, flat-skulled aquatic taxa that had simplified and rather weak vertebrae in which the intercentrum was topped by a neural arch and the pleurocentrum was reduced to absent. According to Wikipedia, “All lepospondyls have simple, spool-shaped vertebrae that did not ossify from cartilage, but rather grew as bony cylinders around the notochord.” 

This is the opposite of
Reptilomorphs, in which the pleurocentra are large and the intercentra are smaller. Reptilomorphs generally were smaller and better adapted to terrestrial environments.

In the LRT traditional stereospondyls
(Fig. 5, pink) are mid-sized basalmost tetrapods, aquatic with a weak backbone because they are not far from fish with fins. Temnospondyls have stronger limbs and stronger backbones (Fig. 5, yellow), but typically remain large and aquatic.

Reptilomorphs 
(Fig. 5, orange) tend to be smaller with stronger limbs and vertebrae and reduce their dependence on water. Both lepospondyls (including living amphibians) and reptiles arise from this clade in the LRT.

Few microsaurs
were included in the Pardo et al study (Fig. 4) and the topology of their tree is very different from the present topology. Caecilians nest with lepospondyl microsaurs in the large reptile tree (LRT, 2014).

In addition
several skull bones are identified differently here (Fig. 1) than in the Pardo et al. study (Fig. 3). Pardo et al. identify an otic notch (that hole in the temporal region). Here that appears to be the space left open after the supratemporal has popped out during taphonomy. The supraorbital bones are all re-identified and both the lacrimal and quadratojugal are now listed in the present identification of bones. Based on conversations with Pardo and others, bone identification on several taxa may be the cause of the differing tree topologies.

Figure 1. GIF movie showing the two skulls of Chinlestegophis from Pardo et al. 2017 with DGS colors applied to both along with a revised set of bone labels

Figure 1. GIF movie showing the two skulls of Chinlestegophis from Pardo et al. 2017 with DGS colors applied to both along with a revised set of bone label based on phylogenetic bracketing among the previously excluded microsaurs close to caecilians.

Outgroup taxa should help identify the bones.
Pardo et al. recover Rileymillerus and Batrachosuchus as outgroup taxa within a large clade that includes Eryops and Sclerocephalosaurus at one base and Trimerorhachis and Greererpeton at the very base. By contrast, the LRT recovers Microbrachis and ultimately Utegenia as outgroup taxa. Microsaurs, Microbrachis and Utegenia were not mentioned in the Pardo et al. report.

First step: Learn about Rileymillerus
As usual, I knew nothing about this taxon earlier this week. Now, according to the LRT Rileymillerus nests with Oestocephalus and Ophiderpeton, two other long-bodied microsaurs with round cross-section skulls, not included in the Pardo et all study.  The apparent loss or lack of bones in the temporal region may be homologous with the lateral temporal fenestra in Ophiderpeton. That’s a rare trait among basal tetrapods.

Figure 3. Rileymillerus from Bolt and Chatterjee 2000 with colors applied.

Figure 2. Rileymillerus from Bolt and Chatterjee 2000 with colors applied. Note the lack of bone on both sides of the temples in this specimen, as in Ophiderpeton. The color (DGS) identify of the bones here is not in complete accord with Bolt and Chatterjee. As you can see, the skull has many cracks, which makes finding the sutures that much more difficult.

Unfortunately
Pardo et al. excluded most of the taxa that the LRT found were most closely related to the clade Chinlestephos + (caecilians + lysorophians) That includes Microbrachis and the rest of the microsaurs. They had good reason for doing so (see below).

Figure 3. Chinlestegophis diagram. Drawings produced by Pardo et al. At left bones colored as they labeled them. At right same bone colors rearranged to fit the new interpretation. See figure 1.

Figure 3. Chinlestegophis diagram. Drawings produced by Pardo et al. At left bones colored as they labeled them. At right same bone colors rearranged to fit the new interpretation. See figure 1. The lateral temporal fenestra is interpreted here as the spot on the skull that once held the supratemporal. No related taxa have a lateral temporal fenestra in either cladogram.

The Pardo et al. skull bone labels
differ from the present interpretation (Fig. 3). Even with such massive dissonance, Pardo et al. and the LRT both nest Chinlestegophis with caecilians and not far from Rileymillerus.

How can such a thing happen??
I can’t answer that at present. It’s frankly surprising.

Figure 4. Pardo et al. cladogram nesting caecilians as ultra-derived temnospondyls.

Figure 4. Pardo et al. cladogram nesting caecilians as ultra-derived temnospondyls. Taxa also present in the LRT are highlighted to show the general mixup of taxa that the LRT separates.

The drifting of the postorbital
In most tetrapods the postorbital is one of the circumorbital bones. In caecilians and their relatives the postfrontal takes over that spot and the postorbital drifts posteriorly, still lateral to the parietal. This observation may be one of the issues attending circumorbital and temporal bone identification arguments in this clade.

Figure 5. Basal tetrapod subset of the LRT. This cladogram includes microsaurs. When given the opportunity to nest with microsaurs, caecilians do so.

Figure 5. Basal tetrapod subset of the LRT. This cladogram includes microsaurs. When given the opportunity to nest with microsaurs, caecilians do so.

In their Supplemental Info
Pardo et al. added the traits for Chinlestegophis to the dataset of Maddin et al. 2012 (who earlier described Jurassic Eocaecilia) and found Chinlestegophis nested with Rileymillerus, close to the stem frog Micromelerpeton and strong-legged Acheloma all far from the caecilians and all derived from a sister to giant Eryops. This study did include microsaurs. Lots of them! Other mismatches include nesting the large reptile Limnoscelis between Seymouria and tiny Utaherpeton and Microbrachis, taxa that share few traits with each other in the LRT. Numerous other morphological mismatches also occur In Maddin et al. Evidently no one is using scaled reconstructions in their analyses as a final check on these mismatches. In the LRT caecilians nest with similar long-bodied, tiny-limbed taxa, which some claim is due to convergence. On a similar note, the LRT lumped and separated snakes from amphisbaenids while other trees failed to do this. So perhaps convergence is not the reason here when dealing with burrowing amphibians.

Figure 6. Maddin et al. cladogram featuring only two temnospondyls from the LRT. Here Chinlestegophis does not nest with caecilians.

Figure 6. Maddin et al. cladogram featuring only two temnospondyls from the LRT. Here Chinlestegophis does not nest with caecilians and Rileymllerus nests far from Oestocephalus.

A note from Jason Pardo
restates that the Maddin et al. study “found no close relationship between Eocaecilia and lepospondyls nor did we find a close relationship between Chinlestegophis and those taxa.”

Figure 6. Living caecilian photo.

Figure 7. Living caecilian photo. Lengths range from 6 inches to 5 feet.

All three cladograms
share few major branches in common. As everyone knows by now, the major branches are the more difficult ones to determine. And, if we can’t agree on the identify of the skull bones, of specimens, the tree topologies will have a hard time finding consensus.

Wikipedia reports,
“Currently, the three prevailing theories of lissamphibian (extant amphibians) origin are:

  1. Monophyletic within the temnospondyli
  2. Monophyletic within lepospondyli
  3. Diphyletic (two separate ancestries) with apodans (=caecilians) within the lepospondyls and salamanders and frogs within the temnospondyli.”
Figure 8. Skull of Microbrachis in several views. Here is where the postorbital leaves the orbit margin and drifts posteriorly. Compare to Chinlestegophis above.

Figure 9. Skull of Microbrachis in several views. Here is where the postorbital leaves the orbit margin and drifts posteriorly. Compare to Chinlestegophis above.

So… even the experts have not come to a consensus
on basal tetrapod topologies. The LRT agrees that the lissamphibia are monophyletic within the lepospondyli, matching option #2 above. There are many aspects of caecilians that need to be interpreted in light of their phylogeny. And we’re not coming to a consensus on that. Earlier we looked at the fusion of the cheek bones in caecilians here with the extant taxon Dermophis.

References
Bolt JR and Chatterjee S 2000. A New Temnospondyl Amphibian from the Late Triassic of Texas. Journal of Paleontology 74(4):670-683.
Maddin HC, Jenkins FA, Jr, Anderson JS 2012. The braincase of Eocaecilia micro podia (Lissamphibia, Gymnophiona) and the origin of Caecilians. PLoS One 7:e50743.
Pardo JD, Small BJ and Huttenlocker AK. 2017, Stem caecilian from the Triassic of Colorado sheds light on the origins of Lissamphibia. PNAS: 7 pp. www.pnas.org/cgi/doi/10.1073/pnas.1706752114

 

Reconstruction from jumbled scraps: the squamate, Kuroyuriella

Figure 1. The skull of Kuroyuriella reconstructed from bone scraps (above), most of which are layered on top of one another. Not all elements are identified, but enough are to nest this taxon with Ophisaurus.

Figure 1. The skull of Kuroyuriella (represented by two specimens of different size) reconstructed from bone scraps (above), most of which are layered on top of one another. Not all elements are identified, but enough are known to score and nest this taxon with Ophisaurus.

When provided disarticulated scraps,
start with the easy bones, then fill in the gaps in the puzzle. Sometimes, as in Kuroyuriella mikikoi (Evans and Matsumoto 2015, Early Cretaceous), there are enough parts to more or less recreate the skull most similar (among tested taxa in the large reptile tree) to that of Ophisaurus and basal to Myrmecodaptria and CryptolacertaEvans and Matsumoto nested Kuroyuriella  between Huehuecuetzpalli and the suprageneric clade Rhynchocephalia, both well outside the Squamata.

From the online paper:
“Together, SBEI 1510 and SBEI 1608, as type and referred specimen, characterize Kuroyuriella mikikoi as a small lizard having paired frontals with deep subolfactory processes; a median parietal without a parietal foramen, with sculpture of low relief, and with lateral shelves that restricted the adductor muscle origins to the ventral surface; upper temporal fenestrae that were at least partially closed by expanded postorbitofrontals; an unsculptured maxilla with a strongly concave narial margin; a large flared prefrontal; and a slender, relatively small pterygoid. In the shallow lower jaw, the teeth are closely packed, cylindrical, and pleurodont with lingual replacement; a subdental ridge is present; the dentary bears a tapering coronoid process that braces the coronoid, and has a posterior extension with a curved free margin; the surangular, angular, and splenial are all present and the surangular is shallow; the adductor fossa is open but not expanded; and the articular surface is asymmetrical.

In order to explore the affinities of Kuroyuriella mikikoi, it was coded into the matrix of Gauthier et al. (2012), as extended by Longrich et al. (2012) (184 characters coded out of 622, 70.4% missing data),

The consistent placement of Kuroyuriella on the squamate stem is problematic and probably artifactual, but whether the weighted analysis is giving a more accurate placement is uncertain. Of the derived character states possessed by Kuroyuriella, 76 [1] (postorbital partly occludes upper temporal fenestra), 364 [1] (dentary coronoid process extends beyond level of coronoid apex), 367 [2] (coronoid process of dentary overlaps most of anterolateral surface of coronoid), and 369 [2] (dentary terminates well posterior to coronoid apex) provide some support for placement of Kuroyuriella on the stem of scincids, and 129 [1] (prefrontal extends to mid-orbit), 104 [1] (absence of parietal foramen) and 385 [1] (posterior mylohyoid foramen posterior to coronoid apex) would be consistent with that placement. However, given the considerable difference between the results using equal weighting and Implied Weighting, Kuroyuriella remains incertae sedis pending recovery of more complete material.”

Figure 2. Ophisaurus, the extant glass snake or legless lizard is close to Kuroyuriella in the large reptile tree.

Figure 2. Ophisaurus, the extant glass snake or legless lizard is close to Kuroyuriella in the large reptile tree.

Here
Ophisaurus (Fig. 2) and Kuroyuriella both nest will within the Squamata, not ouside. of it in the large reptile tree. Reconstruction of the skull helps to ‘see’ this lizard as it was. I can’t imagine how difficult it would be to do try to establish traits  with a jumble of disarticulated bones.

As you’ll see, I think the parietal foramen was present. The parietal may have had longer posterior processes, now broken off.

References
Evans SE and Matsumoto R 2015. An assemblage of lizards from the Early Cretaceous of Japan. Palaeontologia Electronica 18.2.36A: 1-36
palaeo-electronica.org/content/2015/1271-japanese-fossil-lizards
http://palaeo-electronica.org/content/2015/1271-japanese-fossil-lizards

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.

Some thoughts on Sineoamphisbaena

One of the strangest (= most unlike its sister taxa) reptiles is Sineoamphisbaena, which nests in the large reptile tree at the base of the burrowing skinks that ultimately gave rise to amphisbaenids like Amphisbaena and Bipes.

Wikipedia reports: Sineoamphisbaena is an extinct genus of squamate of uncertain phylogenetic placement. Wu et al. (1993), Wu et al. (1996) and Gao (1997) proposed and argued that it was the oldest known amphisbaenian; this, however, was challenged by other authors, such as Kearney (2003) and Conrad (2008), who instead assignedSineoamphisbaena to the group of squamates variously known as Macrocephalosauridae, Polyglyphanodontidae or Polyglyphanodontia. A large-scale study of fossil and living squamates published in 2012 by Gauthier et al. did not find evidence for a particularly close relationship between amphisbaenians and Sineoamphisbaena; in their primary analysis Sineoamphisbaena was found to be the sister taxon of the clade containing snakes, amphisbaenians, the family Dibamidae and the American legless lizard. The primary analysis of Gauthier et al. did not support a close relationship between Sineoamphisbaena and polyglyphanodontians either; however, the authors noted that when all snake-like squamates and mosasaurs were removed from the analysis, and burrowing squamates were then added individually to it, Sineoamphisbaenagrouped with polyglyphanodontians. Gauthier et al. (2012) considered it possible that Sineoamphisbaena was a burrowing polyglyphanodontian.”

The large reptile tree agrees with the original Wu et al. (1993) nesting, at the base of a clade of burrowing prehistoric lizards, some of which included amphisbaenids. Their analysis, unfortunately used suprageneric taxa and they recovered all legless taxa (including snakes) in one clade.

Figure 1. The lineage of Sineoamphisbaena with Chalcides as more primitive and Crythiosaurus + Spathorhynchus as more derived. The quadrate is orange.

Figure 1. The lineage of Sineoamphisbaena with Chalcides as more primitive and Crythiosaurus + Spathorhynchus as more derived. The quadrate is orange.

The temporal region of Sineoamphisbaena has been difficult to interpret because of its unique character and bone fusion patterns not quite like any other. Unlike most burrowing lizards, Sineoamphisbaena did not lose any temporal bones. It rearranged them, fusing some. Here (Fig. 2) is the original interpretation and some suggested reinterpretations.

Figure 2. The skull of Sineoamphisbaena as originally interpreted and as reinterpreted here with color coding matched to that of a more "normal" sister, Chalcides guentheri. Note the squamosal forms the posterior border of the upper temporal fenestra of both taxa.

Figure 2. The skull of Sineoamphisbaena as originally interpreted and as reinterpreted here with color coding matched to that of a more “normal” sister, Chalcides guentheri. Note the squamosal forms the posterior border of the upper temporal fenestra of both taxa. And the long jugal is really composed of the jugal + postorbital. It was not a stretch for the squamosal to contact the postfrontal. If it did fuse, then a crack in the specimen has put a question to that.

Distinct from the original interpretation,
the old postorbital is the new squamosal, continuing to border the posterior upper temporal fenestra. The old jugal is the new jugal + postorbital, matching Chalcides. The old squamosal is the new supratemporal, a bone considered missing originally. The old lacrimal is fused to the prefrontal from what I can tell by comparison to Crythiosaurus. The prefrontal and lacrimal fuses to the maxilla in Bipes.

Burrowing lizards,
evolved in a wide variety of ways and all, except Sineoamphisbaena, lose skull (temporal) bones. All appear to have evolved from a variety of the genus Chalcides because some retain a long low rostrum. Others, like Bipes, have a short blocky snout, but Bipes does not rotate its upper teeth medially as Sineoamphisbaena does. So that split likely preceded tooth rotation. It’s a little confusing with lots of convergence in a little clade due to their burrowing niche.

Figure 3. Chalcides, Crythiosaurus and Bipes with bones colored. Note, only the quadrate remains in Bipes. Other bones are lost or fused. Sineoamphisbaena lost the epipterygoid. Crythiosaurus nests basal to Bipes in the large reptile tree, but the extreme reduction of the quadrate is an autapomorphy.

Figure 3. Chalcides, Crythiosaurus and Bipes with bones colored. Note, only the quadrate remains in Bipes. Other bones are lost or fused. Sineoamphisbaena lost the epipterygoid. Crythiosaurus nests basal to Bipes in the large reptile tree, but the extreme reduction of the quadrate is an autapomorphy.

There may be another skink closer to Sineoamphisbaena, but I haven’t found it yet.

References
Gao K 1997. Sineoamphisbaena phylogenetic relationships discussed. Canadian Journal of Earth Sciences. 34: 886-889. online article
Kearney M 2003. The Phylogenetic Position of Sineoamphibaena hextabularis reexamined. Journal of Vertebrate Paleontology 23 (2), 394-403
Müller J, Hipsley CA, Head JJ, Kardjilov N, Hilger A, Wuttke M and Reisz RR 2011. Eocene lizard from Germany reveals amphisbaenian origins. Nature 473 (7347): 364–367. doi:10.1038/nature09919
Wu XC., Brinkman DB, Russell AP, Dong Z, Currie PJ, Hou L, and Cui G 1993. Oldest known amphisbaenian from the Upper Cretaceous of Chinese Inner Mongolia. Nature (London), 366: 57 – 59.
Wu X-C Brinkman DB and Russell AP 1996. Sineoamphisbaena hexatabularis, an amphisbaenian (Diapsida: Squamata) from the Upper Cretaceous redbeds at Bayan Mandahu (Inner Mongolia, People’s Republic of China), and comments on the phylogenetic relationships of the Amphisbaenia. Canadian Journal of Earth Sciences, 33: 541-577.

wiki/Sineoamphisbaena