Triassurus: a tiny Triassic salamander?

Summary for those just skimming:
Including more taxa and using DGS to gather more data from fossils upsets academic results again.

Shoch et al. 2020 discuss the origin of salamanders
by directing their attention to a tiny juvenile Triassic tetrapod, Triassurus (PIN-2584/10, skull length 3.8 mm; Ivakhnenko 1978; Figs. 1–3). The discovery of a larger referred specimen (FG 596/V/20), provided Schoch et al. a reason to reexamine the type.

Science first learned about tiny Triassurus
from Ivakhnenko 1978 (here reproduced in a book, Fig. 1). Not much detail back then.

Figure 1. Illustration and description Triassurus (Ivakhnenko 1978).

Figure 1. Illustration and description Triassurus (Ivakhnenko 1978). Little more than the outline of the skull was illustrated back then.

The Schoch et al. tracing of the tiny holotype
(Fig. 2) likewise offers few details. DGS colors (Fig. 2) provide more and different details.

Figure 3. Triassurus in situ with tracing from Schoch et al. 2020 and DGS color tracing.

Figure 2. Triassurus in situ with tracing from Schoch et al. 2020. DGS color tracing added here. See figure 3 for a reconstruction.

Pushing those DGS details around
to create a reconstruction (Fig. 3) helps one understand the anatomy of Triassurus, enough to score it.

Figure 4. The type specimen of Triassurus in situ and reconstructed.

Figure 3. The type specimen of Triassurus in situ and reconstructed.

Scoring the Middle Triassic Triassurus type
nests it with Early Permian Gerrobatrachus (Fig. 4), one node away from extant salamanders in the large reptile tree (LRT, 1690+ taxa; subset Fig. 5). So, if Triassic Triassurus is the earliest known salamander (as Schoch et al report), then Early Permian Gerobatrachus is one, too. And it is tens of millions of year older. If Gerobatrachus is not a salamander, then both are not salamanders.

Figure 5. Gerrobatrachus adult.

Figure 4. Gerrobatrachus adult.

The LRT tree topology
is distinctly different than the cladogram published by Shoch et al. 2020 (Fig. 6).

Figure 5. Subset of the LRT focusing on basal tetrapods including Triassurus, type and referred specimen FG 596 V 20.

Figure 5. Subset of the LRT focusing on basal tetrapods including Triassurus, type and referred specimen FG 596 V 20.

Unfortunately,
the cladogram employed by Schoch et al. 2020 (Fig. 6) needs more taxa. Currently it nests Proterogyrinus as the outgroup taxon. That creates problems. Relative to the LRT (Fig. 5) one branch of the Schoch et al. cladogram is inverted such that the basalmost tetrapods, Siderops and Gerrothorax, nest as highly derived terminal taxa. The other branch with caecilians, frogs and salamanders is not inverted relative to the LRT, but in the LRT caecilians do not nest with frogs and salamanders. Caecilians nest with microsaurs in the LRT.

Figure 6. Cladogram from Schoch et al. 2020 nests both specimens of Triassurus close to salamanders. Colors match colors in figure 5.

Figure 6. Cladogram from Schoch et al. 2020 nests both specimens of Triassurus close to salamanders. Colors match colors in figure 5.

Schoch et al. 2020 reported on Triassicus,
“to reconstruct crucial steps in the evolution of the salamander body plan, sharing numerous features with ancient amphibians, the temnospondyls. These finds push back the rock record of salamanders by 60 to 74 Ma and at the same time bridge the wide anatomic gap among salamanders, frogs, and temnospondyls.”

In the LRT the salamander body plan goes back to the Early Permian, at least.

From the abstract:
“The origin of extant amphibians remains largely obscure, with only a few early Mesozoic stem taxa known, as opposed to a much better fossil record from the mid-Jurassic on.”

In the LRT the origin of extant amphibians can be traced in detail over several dozen taxa (Fig. 5) back to Cambrian chordates.

Figure 2. Cladogram from Schoch et al. 2020. They insert Eocaecilia here derived from Doleserpeton. The LRT nests Eocaecilia with microsaurs. Note how the morphology does not fit here. Where is Apteon in this cladogram?

Figure 7. Cladogram from Schoch et al. 2020. They insert Eocaecilia here derived from Doleserpeton. The LRT nests Eocaecilia with microsaurs. Note how the morphology does not fit here. Where is Apteon in this cladogram?

From the abstract:
“Yet the most ancient stem-salamanders, known from mid-Jurassic rocks, shed little light on the origin of the clade.Here we report a new specimen of Triassurus sixtelae, a hitherto enigmatic tetrapod from the Middle/Late Triassic of Kyrgyzstan, which we identify as the geologically oldest stem-group salamander.”

“The new, second specimen is derived from the same beds as the holotype, the Madygen Formation of southwestern Kyrgyzstan. It reveals a range of salamander characters in this taxon, pushing back the rock record of urodeles by at least 60 to 74 Ma (Carnian–Bathonian). In addition, this stem-salamander shares plesiomorphic characters with temnospondyls, especially branchiosaurids and amphibamiforms.”

FIgure 8. The FG 596 V20 specimen that Schoch et al. referred to Triassurus does not nest with Triassurus in the LRT. See Figure 9 for reconstruction.

FIgure 8. The FG 596 V20 specimen that Schoch et al. referred to Triassurus does not nest with Triassurus in the LRT. See Figure 9 for reconstruction.

Speaking of that second specimen…
a reconstruction of the narrow-snouted FG 596 V20 specimen (Fig. 8) does not look like the wide-mouth type of Triassurus. In the LRT the second larger FG 596 V20 specimen nests with the CGH129 specimen of the legless microsaur, Phlegethontia (Fig. 9) far from Triassurus and other salamanders.

Figure 9. Reconstruction of the specimen referred to Triassurus, which does not nest with Triassurus in the LRT.

Figure 9. Reconstruction of the specimen referred to Triassurus, which does not nest with Triassurus in the LRT.

What Schoch et al. identified as a large horizontal quadrate (q)
in the FG 596 V20 specimenn(Fig. 8) is re-identified here as a large humerus, larger than the ones they identified. The forelimb goes into the left mouth. The left maxilla is displaced back to the occiput.

Figure 10. Phlegethontia longissima skull (CGH 129) has relatively large temporal plates, a wide flat cranium and a long pointed rostrum.

Figure 10. Phlegethontia longissima skull (CGH 129) has relatively large temporal plates, a wide flat cranium and a long pointed rostrum.

In conclusion, the tiny Triassurus type
nests close to salamanders, but closer to Early Permian Gerobatrachus (Fig. 4). The larger referred FG 596 V20 specimen with legs (Fig. 9) nests with legless Late Carboniferous Phelgethontia (Fig. 10), far from salamanders. Adding taxa and getting deeper into the details using the DGS method upsets the simpler and inaccurate Schoch et al. tracings, tree topology and conclusions.


References
Ivakhnenko M 1978. Tailed amphibians from the Triassic and Jurassic of Middle Asia. Paleontological Journal 1978(3):84-89.
Schoch RR et al. 2020. A Triassic stem-salamander from Kyrgyzstan and the origin of salamanders, Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.2001424117

https://phys.org/news/2020-05-triassurus-sixtelae-fossil-kyrgyzstan-oldest.html

Perryella and convergence in basal tetrapod clades

A recent paper by Schoch 2018,
once again stirs confusion into the phylogeny of basal tetrapods due to taxon exclusion. Schoch reports, “the enigmatic taxon Perryella (Fig. 1) is found to nest just outside Dissorophoidea (phylogenetic defintion), but shares a range of synapomorphies with this clade.” Schoch derives tiny Perryella from the much larger taxa, Trimerorhachis and Sclerocephalus apparently without testing a wide gamut of taxa (as in the LRT), but relying on a wide consensus of tradition, omitting several key taxa.

Figure 1. Perryella is not a transitional taxon in the LRT, but a terminal taxon nesting with Dendrerpeton.

Figure 1. Perryella is not a transitional taxon in the LRT, but a terminal taxon nesting with Dendrerpeton.

A little Perryella history:
In Carlson 1987 the classification of Perryella was uncertain because it shared features with two groups, Trimerorhachidae and Dissorophoidea, which were thought to be distantly related. In the LRT those taxa are indeed distantly related.

In Ruta and Bolt 2006, a phylogenetic analysis placed Perryella between trimerorhachids and other dvinosaurs (basal tetrapod in Ruta and Bolt that includes lepospondyls like Cacops, Fedexia, Dissorophus, frogs, salamanders and caecilians, all taxa nesting in the lepospondyls in the LRT). Here all similarities with trimerorhachids are convergent.

Figure 1. Trimerorhachis and kin to scale. Here are Panderichthys, Tiktaalik, Ossinodus, Dvinosaurus, Acanthostega, Batrachosuchus and Gerrothorax. Maybe those tabular horns on Acanthostega are really supratemporal horns, based on comparisons to related taxa.

Figure 2. Trimerorhachis and kin to scale. Here are the players in today’s blogpost: Panderichthys, Tiktaalik, Ossinodus, Dvinosaurus, Acanthostega, Batrachosuchus and Gerrothorax. Maybe those tabular horns on Acanthostega are really supratemporal horns, based on comparisons to related taxa. These taxa are not related to lepospondyls (including frogs) despite the convergent appearance.

As you’ll note in the cladogram below
Trimerorhachis and Dvinosaurus nest together in the first large (15 tested taxa, Fig. 3) clade of basal tetrapods in the LRT, the trimerorhachids. Meanwhile Perryella nests several nodes away with Dendrerpeton in the lepospondyl clade of the LRT.

Figure 1. Subset of the LRT focusing on basal tetrapods, colorized according to chronology. Note the wide dispersal of Early Carboniferous taxa, suggesting a Late Devonian radiation as yet largely undiscovered.

Figure 3. Subset of the LRT focusing on basal tetrapods, colorized according to chronology. Note the wide dispersal of Early Carboniferous taxa, suggesting a Late Devonian radiation as yet largely undiscovered. Perryella is not listed here, but nests with Dendrerpeton.

By convergence
Trimerorhachis and Perryella both have wide circular interpterygoid vacuities (Figs. 1, 2) and a largely similar set of skull bones. The difference is in the details and you don’t find convergence (if present) unless you test a wide gamut of candidate taxa.

Figure 1. Trimerorhachis was considered a dvinosaurian temnospondyl. Here both Trimerorhachis and Dvinosaurus nest low on the basal tetrapod tree, close to the fin/finger transition.

Figure 4. Trimerorhachis was considered a dvinosaurian temnospondyl. Here both Trimerorhachis and Dvinosaurus nest low on the basal tetrapod tree, close to the fin/finger transition, far from Perryella and the lepospondyls.

A bad traditional paradigm
is at the bottom of this problem. According to Ruta and Bolt (2006), “Whereas the three extant clades (frogs, salamanders, and caecilians) are generally small creatures with feeble skeletons, most of which feed on small invertebrates, their likely stem group, Paleozoic temnospondyls, encompasses 1–2m long, heavily ossified predators. The evolutionary transition between the Paleozoic giants and the dwarfed modern forms has long been sought among the Dissorophoidea, a speciose clade of mainly terrestrial and presumably insect-eating Carboniferous–Triassic temnospondyls that were usually smaller and had less massive skeletons than their fish-eating fellows, but alternative scenarios are still debated.”

Figure 2. Utegenia nests as a sister to Diplovertebron.

Figure 5. Utegenia nests at the base of the Lepospondyli and the Lissamphibia in the LRT. It is also the proximal sister to the Reptilia in the LRT. Do not exclude this taxon from your basal tetrapod studies!

In the LRT
(Fig. 3) there are no huge, heavily ossified ancestors to the lepospondyls and lissamphibians. Rather Ossinodus is the largest ancestor in the lissamphibian line. Ruta and Bolt report, “Watson (1940) wrote a review paper on the origin of anurans in which he sought the ancestry of frogs among amphibamids, notably the tiny, lightly built Amphibamus grandiceps.” This is supported and confirmed by the LRT. They continue, “The discovery of Eocaecilia and Gerobatrachus brought an end to the long-practiced separate treatment of temnospondyls and lissamphibians, because both Eocaecilia and Gerobatrachus retained dermal bones that are not present in any extant lissamphibian, but are well known from temnospondyls.” In the LRT basal lepospondyls, like Utegenia (Fig. 5) which is not a seymouriamorph, but close!) retain dermal bones not present in extant lissamphibians. A keyword search of Ruta and Bolt failed to bring up the taxon, ‘Utegenia.’

Figure 7. Subset of the LRT including Perryella.

Figure 6. Subset of the subset in figure 3 of the LRT that now includes Perryella.

Once again,
that’s taxon exclusion crimping otherwise well-considered and serious studies, like Ruta and Bolt 2006.

References
Carlson KJ 1987. Perryella, a new temnospondylous amphibian from the Lower Permian of Oklahoma. Journal of Paleontology. 61 (1): 135–147.
Ruta M and Bolt JR 2006. A reassessment of the temnospondyl amphibian Perryella olsonifrom the Lower Permian of Oklahoma. Earth and Environmental Science Transactions of the Royal Society of Edinburgh. 97 (2): 113–165.

wiki/Dendrerpeton
wiki/Tersomius
wiki/Perryella

 

SVP 2018: Seeking the origin of living amphibians

Danto et al. 2018 reports,
“Despite increasing knowledge about the fossil record of lissamphibians (frogs,salamanders, and caecilians), their origin is still unresolved and different origins within Paleozoic early tetrapods are proposed.”

By contrast
the large reptile tree (LRT, 1313 taxa; subset Fig. 1) confidently recovers a monophyletic and completely resolved lissamphibia that also includes microsaurs (Fig. 1) and other non-traditional members. Utegina is close to the ancestry of frogs + salamanders + the more distantly related caecilians.

Figure 1. Subset of the LRT focusing on basal tetrapods, colorized according to chronology. Note the wide dispersal of Early Carboniferous taxa, suggesting a Late Devonian radiation as yet largely undiscovered.

Figure 1. Subset of the LRT focusing on basal tetrapods, colorized according to chronology. Note the wide dispersal of Early Carboniferous taxa, suggesting a Late Devonian radiation as yet largely undiscovered. Utegenia is close to the ancestry of all living amphibians (in white).

The Danto team sought the answer
to their enigma not in a phylogenetic analysis, but in a study of developing salamanders. They report, “In this study, we sought to investigate if the ossification sequence of neural arches and centra and the mode of centrum formation in extinct and extant forms could be indicative of phylogenetic relationships.  Here we demonstrate that the mode of centrum formation is highly variable in early tetrapods and lissamphibians and cannot be used to determine the origin of lissamphibians within early tetrapods.”

References
Danto M et al. 2018. The implication of the vertebral development on the origin of lissamphibians. SVP abstract

 

 

 

The origin of Lissamphibia (frogs, salamanders, caecilians)

The origin of modern amphibians has been controversial.
A new paper by Pérez-Ben et al. 2018 seeks to clarify the issue. According to Wikpedia, “Currently, the three prevailing theories of lissamphibian origin are:

  1. Monophyletic within the temnospondyli
  2. Monophyletic within lepospondyli
  3. Diphyletic (two separate ancestries) with apodans within the lepospondyls and salamanders and frogs within the temnospondyli.”

From the Pérez-Ben et al. abstract:
Current hypotheses propose that the living amphibians (lissamphibians) originated within a clade of Paleozoic dwarfed dissorophoid temnospondyls. Morphological traits shared by these small dissorophoids have been interpreted as resulting from constraints imposed by the extreme size reduction, but these statements were based only on qualitative observations. Herein, we assess quantitatively morphological changes in the skull previously associated with miniaturization in the lissamphibian stem lineage by comparing evolutionary and ontogenetic allometries in dissorophoids. Our results show that these features are not comparable to the morphological consequences of extreme size reduction as documented in extant miniature amphibians, but instead they resemble immature conditions of larger temnospondyls. We conclude that the truncation of the ancestral ontogeny, and not constraints related to miniaturization, might have been the factor that played a major role in the morphological evolution of small dissorophoids.

The authors appear to be dividing
tiny (miniaturized) frogs from frogs in general (= immature temnospondyls). And that’s a good start.

The second hypothesis (above)
is supported and recovered in the large reptile tree (LRT (1154 taxa, subset in figure 1) in which Lissamphibians are indeed derived from dissorophids, but dissorophids are lepospondyls (yellow-green clade below), which are derived from reptilomorphs and seymouriamorphs (orange clade below), while temnospondyls are much more primitive and diphyletic (pink and blue clades below). The phylogenetic miniaturization occurred much earlier than Lissamphibia, which is a much larger clade if it is still defined by the inclusion of the more distantly related caecilians, deep within the Microsauria.

FIgure 2. Subset of the LRT has a larger gamut of taxa. Here lepospondyls nest together when more basal tetrapods are added to the taxon list than are present in figure 1.

FIgure 2. Subset of the LRT has a larger gamut of taxa. Here lepospondyls nest together when more basal tetrapods are added to the taxon list than are present in figure 1.

Quantitive approaches
have never trumped phylogenetic approaches.

First: Recover the cladogram.
Let it tell you what happened, and when and how. The dissorophids are indeed derived from more primitive temnospondyls, but several intervening transitional clades must be accounted for. 

References
Pérez-Ben CM, Schoch RR and Báez  AM 2018. Miniaturization and morphological evolution in Paleozoic relatives of living amphibians: a quantitative approach
https://doi.org/10.1017/pab.2017.22Published online: 23 January 2018

Marjanovic and Laurin 2016: Basal tetrapods, continued…

Sorry this took so long…
As you’ll see there was a lot of work and prep involved that has been several weeks in the making. Thank you for your patience.

Earlier I introduced the Marjanovic and Laurin 2016 study
the way they did, by reporting their confirmation of the Ruta and Coats 2007 basal tetrapod topology that they were testing prior to reevaluating the data. I noted then that both studies (Fig. 5) included many so-called pre-reptiles, including  Bruktererpeton, Chroniosaurus, Solenodonsaurus, Limnoscelis, Tseajaia, DiadectesOrobates and Westlothiana,should not be in the pre-amniote inclusion set. Those taxa nest within the Reptilia in the large reptile tree (LRT, subset Fig. 4) with Silvanerpeton and Gephyrostegus at the base of the Reptilia (= Amniota). As reported earlier, those two are the amphibian-like reptiles that first developed the amniotic egg that defines the clade Amniota, a junior synonym of the Reptilia, based on the tree that recovers them at the base of both major branches, the new Archosauromorpha and the new Lepidosauromorpha early in the Viséan.

How can one readily compare two competing cladograms? 
You would not want to sit through a comparison of tens of thousands of scores for competing trees in a short blog like this. But we can compare images of taxa (Figs. 1–3. 6–8) placed in their phylogenetic order, subdivided for clarity into the three major lineages of basal tetrapods:

  1. Basalmost tetrapods and the lineage that led to Reptilia
  2. Members of the Lepospondyli
  3. Members of the Microsauria

These images will serve as a ready reference for today’s topics. As a preview, in summary:

The Marjanovic and Laurin (ML) 2016 tree nests

  1. frogs like Rana and salamanders like Andrias with microsaurs.
  2. small amphibamids, Cacops and Micromelerpeton nest with temnospondyls.
  3. basal Amniota splits into Synapsida (Caseasauria + Archaeovenator) and Sauropsida (Captorhinus, Paleothyris, Petrolacaosaurus) arising from an unknown genus basal to Diadectomorpha + Amniota
  4. The clade Amphibia arises near Solenodonsaurus + the crown-group Tetrapoda
  5. The clade Microsauria is divided into three parts separated by non-microsaurs with origins near Westlothiana.

The LRT nests

  1. frogs and salamanders nest with lepospondyls.
  2. small amphibamids, Cacops and Micromelerpeton nest with lepospondyls.
  3. basal Amniota splits into Archosauromorpha  (several basal taxa, Archaeovenator, Paleothyris and Petrolacaosaurus) and Lepiodosauromorpha (several basal taxa, Caseasauria and Captorhinus) with both major clades arising from Gephyrostegus bohemicus a late-surving Westphalian taxon, and Silvanerpeton, a Viséan taxon.
  4. The clade Amphibia arises near Balanerpeton and the amphibamids.
  5. The clade Microsauria has a single origin near Kirktonecta 

What you should be looking for
is a gradual accumulation of traits in every lineage. And look for taxa that don’t fit in the order presented. This can be done visually with these figures, combining hundreds of traits into one small package. Rest assured that all scoring by ML and the competing analysis in the LRT were done with the utmost care and diligence. So, some biased or errant scoring must have taken place in one study or the other or both for the topologies to differ so great. Bear in mind that ML had firsthand access to fossils and may have bowed to academic tradition, while I had photos and figures to work with and no allegiance to academic tradition.

First
the large reptile tree (LRT) taxa (Figs. 1–3) had two separate origins for limbed vertebrates.

Figure 1. CLICK TO ENLARGE. Basal tetrapod subset according to the LRT. These taxa lead to Reptilia, Lepospondyli and through that clade, the Microsauria. Note the convergent development of limbs and digits arising out of Osteolepis.

Figure 1. CLICK TO ENLARGE. Basal tetrapod subset according to the LRT. These taxa lead to Reptilia, Lepospondyli and through that clade, the Microsauria. Note the convergent development of limbs and digits arising out of Osteolepis.

In both studies
basal tetrapod outgroups are tail-propelled sarcopterygians having muscular fins not yet evolved into limbs with digits. Behind the skull are opercular bones that are lost in taxa with limbs. An exoskeleton of bony scales disappears in taxa with limbs. Snout to tail tip length averages 50 cm.

In the LRT
locomotion switches to the limbs in temnospondyls, which tend to be larger (1m+ and have overlapping dorsal ribs. The Greererpeton branch flattens out the ribs and skull, reducing both the tail and the limbs to likely become sit-and-wait predators. Phylogenetic size reduction and limb elongation is the trend that leads to Reptilia (Gephyrostegus). However an early exception, Crassigyrinus (Fig. 1), elongates the torso and reduces the limbs to adopt an eel-like lifestyle. Kotlassia adopts a salamander-like lifestyle from which Utegenia and the Lepospondyli arise (Fig. 2) alongside Reptilia.

Figure 2. CLICK TO ENLARGE. Subset of the LRT representing lepospondyli leading to frogs.

Figure 2. CLICK TO ENLARGE. Subset of the LRT representing lepospondyli leading to frogs.

In the LRT,
short-tailed, salamander-like Utegenia (derived from the Seymouriamorpha, Fig. 2) is a late-surving basal member of the generally small-sized clade Lepospondyli, which ultimately produces salamanders and frogs. A side branch produces the larger, temnospondyl-like Cacops, which develops a bony ridge atop the dorsal spines. Note the nesting here of Gerobatrachus as a salamander and frog relative, distinct from the ML tree (Fig. 6).

Figure 3. CLICK TO ENLARGE. Subset of the LRT focusing on Microsauria.

Figure 3. CLICK TO ENLARGE. Subset of the LRT focusing on Microsauria.

In the LRT
the Microsauria are derived here from the small basal amphibamids, Caerorhachis and more proximally, Kirktonecta. Microsaurs range from salamander-like to lizard-like to worm-like. The tail elongates to become the organ of locomotion in the Ptyonius clade. The head and torso flatten in the Eoserpeton clade.

Below
is the pertinent subset of the LRT (Fig. 4) with a representative, but not complete or exhaustive set of taxa. A summary of the tree’s differences with the ML tree is presented above. The ML tree is summarized below in three parts (6-8).

Figure 4. Subset of the LRT focusing on basal tetrapods.

Figure 4. Subset of the LRT focusing on basal tetrapods.

The Marjanovic and Laurin 2016 tree
(Fig. 5) presents a topology that is similar to the LRT in parts, but distinct in other parts, as summarized above. I realize this presentation is illegible at this column size due to the large number of taxa. Click on it to enlarge it. At the top and down the right column are basal taxa leading to temnspondyls and reptiles at bottom right. Working from the bottom up the left side are the microsaurs ending with the lissamphibians (frogs and salamanders) at the top/middle of the left column.

Figure 4. CLICK TO ENLARGE. The reevaluated Marjanovic and Laurin tree from which taxa on hand were set to match the tree topology (Figs. 5-7).

Figure 5. CLICK TO ENLARGE. The reevaluated Marjanovic and Laurin tree from which taxa on hand were set to match the tree topology (Figs. 5-7).

The ML tree
subdivides into there parts (Figs 6-8): basal taxa, some leading to temnospondyls and amphibamids; taxa leading to and including Amniota; and finally microsaurs leading to and including extant amphibians.

Figure 5. Basal tetrapods according to Marjanovic and Laurin 2016. Figures 6 and 7 lead to Amniota and Microsauria respectively.

Figure 6. Basal tetrapods according to Marjanovic and Laurin 2016. Figures 6 and 7 lead to Amniota and Microsauria respectively.

In the ML topology,
Ichthyostega, a taxon with a very large pectoral girdle, ribs, and pelvis, gives rise the the altogether smaller and more fish-like Acanthostega, which gives rise to members of the Whatcheeridae, tall-skulled Crassigyrinus and flat-skulled Osinodus. The traditional Colosteidae arise next. They have a variety of long shapes with short-legs. Oddly from this seemingly primitive clade arises small, short-torsoed, long-legged Eucritta followed by long torsoed, short-legged Proterogyrinus followed by a large clade of short-torsoed, long-legged taxa, including the >1m temnospondyls and the <30cm amphibamids.

Figure 7. CLICK TO ENLARGE. These are taxa listed on the Marjanovic and Laurin 2016 that lead to Reptilia (Amniota).

Figure 7. CLICK TO ENLARGE. These are taxa listed on the Marjanovic and Laurin 2016 that lead to Reptilia (Amniota).

In the ML tree
Gephyrostegus arises from the small temnospondyl, Balanerpeton, and and gives rise to Chroniosaurus, Solenodonsaurus, the Seymouriamorpha (including Utegenia) and the Diadectomorpha, nesting as the sister clade to the Amniota. Thus, no phylogenetic miniaturization was present at the origin of the Amniota in the ML tree. Moreover, dozens of taxa were not included here that nest at the base of the Amniota (Reptilia) in the LRT.  Basal amniotes in the ML tree are all Latest Carboniferous to Early Permian, while in the LRT basal amniotes arrived at least 40 million years earlier in the Visean (Early Carboniferous) and had radiated widely by the Late Carboniferous, as shown by the ML taxaon list. No amphibian-like reptiles made it to their Amniota.

FIgure 7. Microsauria according to Marjanovic and Laurin 2016. Here frogs and caecilians nest within the Microsauria.

FIgure 8. CLICK TO ENLARGE. Microsauria according to Marjanovic and Laurin 2016. Here frogs and caecilians nest within the Microsauria.

In the ML tree
the three microsaur clades (Fig. 5) arise from the Viséan taxon, Westlothiana (Fig. 8), which nests as a derived reptile when tested against more amniotes in the LRT. Utaherpeton is a basal microsaur in both trees, but it gives rise to the eel-like Acherontiscus and kin in the ML tree. Westlothiana further gives rise to Scincosaurus and kin, including the larger Diplocaulus. Thirdly, Westlothiana gives rise to lizard-like Tuditanus which gives rise to big-skulled Pantylus and tiny-limbed Microbrachis, shark-nosed Micraroter and Rhynchonkos. In both trees, Batropetes bucks the long-body, short-leg trend. In both trees Celtedens, representing the salamander-like albanerpetontids, gives rise to extant salamanders and frogs

So the possibilities are:

  1. Only one tree is completely correct
  2. Only one tree is mostly correct.
  3. Both trees have some correct and incorrect relationships

Problems

  1. Basal tetrapods tend to converge on several traits. For instance in the LRT, the palate is ‘open’ with narrow pterygoids in both temnospondyls and lepospondyls.
  2. Many small derived taxa lose and fuse skull bones
  3. Many taxa fuse vertebral bones as they evolve away from the notochord-based semi-encircling vertebrae of fish toward more complete vertebrae in which the neural spine, pleurocentrum and intercentrum tend to fuse, sometimes in convergent pattern, as widely recognized in basal reptiles and microsaurs.
  4. In basal tetrapods, fingers are not often preserved. So when four fingers appear their identity has to be ascertained. In the LRT mc5 and digit 5 are absent in Lepospondyls. In the LRT mc1 and digit 1 are absent in the temnospondyls. Five fingers and/or metacarpals are preserved in the few other non-amniote, basal tetrapods that preserve fingers (Proterogyrinus, Seymouria). The ML tree assumes that when four digits are present, they represent digits 1–4.

Ultimately
maximum parsimony and Occam’s Razor should rule unless strong evidence to the contrary is provided. After evidence is presented, it’s up to colleagues to accept or reject or ignore hypotheses.

References
Marjanovic D and Laurin M 2016. Reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates. PeerJ. Not peer-reviewed. 356 pp.
Ruta M and Coates MI 2007
. Dates, nodes and character conflict: addressing the lissamphibian origin problem. Journal of Systematic Palaeontology 5-69-122.

Basal tetrapod cladogram: Marjanovic and Laurin 2016, PeerJ

Recently I added
several basal tetrapod taxa to the large reptile tree (LRT, now 950 taxa) in order to better understand the origin of the clade Reptilia (= Amnlota). Along the way, the software recovered some contra-traditional nestings which revived typically cordial correspondences with Drs. David Marjanovic and Jason Pardo, both of whom have studied basal tetrapods extensively. I don’t have all of the latest literature and I appreciate that these researchers open doors I may not have seen.

Less recently
Marjanovic and Laurin (2016) reexamined a earlier report on lissamphibian origins by Ruta and Coates (2007). Marjanovic and Laurin (ML) report “thousands of suboptimal scores due to typographic and similar errors and to questionable coding decisions: logically linked (redundant) characters, others with only one described state, even characters for which most taxa were scored after presumed relatives. Even continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded.”

Figure 1. Click to enlarge. Wait 10 seconds for animation to begin. Basal tetrapod tree form Marjanovic and Laurin 2016.

Figure 1. Basal tetrapod tree form Marjanovic and Laurin 2016. After 10 seconds those moving lines that appear on the right will make sense when you CLICK TO ENLARGE and see how they connect taxa on competing trees.

ML document and justify all changes
to the earlier matrix, then add 48 taxa to the original 102. They report,  “From the late19th century to now, the modern amphibians have been considered temnospondyls by some (refs omitted), lepospondyls by others and polyphyletic yet others, with Salientia being nested among the temnospondyls, Gymnophionomorpha among the lepospondyls, and Caudata either in the lepospondyls (all early works) or in the temnospondyls (works published in the 21st century).”

“The present work cannot pretend to solve the question of lissamphibian origins or any other of the controversies in the phylogeny of early limbed vertebrates (of which there are many, as we will discuss). It merely tries to test, and explain within the limitations of the dataset, to what degree the trees found by RC07 still follow from their matrix – the largest published one that has been applied to those questions – after a thorough effort to improve the accuracy of the scoring and reduce character redundancy has been carried out to the best of our current knowledge. However, we think this effort forms a necessary step towards solving any of those problems. Further progress may come from larger matrices…”

“Our matrix has only 276 characters, a strong decrease from the 339 of RC07. For the most part, this is due to our mergers of redundant characters and does not entail a loss of information.”

After all that work and all those changes and additions,
ML report their repaired tree “topology is identical to Ruta and Coates 2007.”

Unfortunately that tree is vastly different
from the one recovered in the LRT, which has far fewer taxa, but an equal or greater gamut. Let’s figure out why the topologies differ and are similar. I’ll start slow with the similarities and the metaphorical ‘low-hanging fruit.’ The difficult topics we will handle later. I took the last few weeks (far too little time) to better understand basal tetrapods having zero knowledge of most taxa before starting. I have not been able to cover all the taxa employed by the ML tree.

Similarities:

  1. Both trees include fish and fish-like tetrapods at the base
  2. Both trees include microsaurs, reptiles and extant amphibians as derived taxa
  3. Both trees agree on the inclusion set for microsaurs and holospondyls
Figure 6. Subset of the large reptile tree focusing on basal tetrapods, updated with Gerrothorax.Figure 6. Subset of the large reptile tree focusing on basal tetrapods, updated with Gerrothorax.

Figure 2. Subset of the large reptile tree focusing on basal tetrapods, updated with Gerrothorax.

Differences:

Due to taxon exclusion,
the ML tree nests several reptiles as non-reptiles. These include:

  1. Sivanerpeton – basal reptile/amniote
  2. Gephyrostegus (bohemicus) –  basal reptile/amniote
  3. Bruktererpeton – Lepidosauromorpha
  4. Solenodonsaurus (+ Chroniosaurus, Chroniosuchus) – Archosauromorpha
  5. Tseajaia – Lepidosauromorpha
  6. Limnoscelis – Lepidosauromorpha
  7. Orobates – Lepidosauromorpha
  8. Diadectes – Lepidosauromorpha
  9. Westlothiana – Archosauromorpha

Where each taxon nests in the LRT follows each dash.

Due to taxon exclusion,
the ML tree nests several taxa as ‘Sauropsida’ a clade that no longer has utility based on the new basal reptile dichotomy Archosauromorpha and Lepidosauromorpha. These include:

  1. Captorhinus – Lepidosauromorpha
  2. Paleothyris/Protorothyris – two distinct Archosauromorpha
  3. Petrolacosaurus – Archosauromorpha

Chroniosuchia
ML report, “Chroniosaurus has a fully resolved position one node more crown ward than Gephyrostegidae, Bruktererpeton or Temnospondyli and one node more rootward than Solenodonsaurus.”  This is a similar nesting to the LRT except that all listed taxa other than Temnospondyli nest within the Reptilia. ML are missing several taxa that would have changed their tree topology (see the LRT for that list).

 

Microbrachis
I caught a little heat for not using the latest drawings of Microbrachis earlier. The new tracings (Fig. 3) come from Vallin and Laurin 2004. Note the tracings of the in situ specimen (color) do precisely match the freehand reconstruction they offered. All scoring changes further cemented prior LRT relationships.

Figure 3. Microbrachis images from Vallin and Laurin 2008. Color added here.

Figure 3. Microbrachis images from Vallin and Laurin 2004. Color added here.

More later.

References
Marjanovic D and Laurin M 2016. Reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates. PeerJ. Not peer-reviewed. 356 pp.
Ruta M and Coates MI 2007
. Dates, nodes and character conflict: addressing the lissamphibian origin problem. Journal of Systematic Palaeontology 5-69-122.
Vallin G and Laurin M 2004. Cranial morphology and affinities of Microbrachis, and a reappraisal of the phylogeny and lifestyle of the first amphibians. Journal of Vertebrate Paleontology: Vol. 24 (1): 56-72 online pdf

wiki/Microbrachis

 

Four more basal tetrapods added to the LRT

Spoiler alert:
No basic changes to the large reptile tree topology (LRT, Fig. 1, 938 taxa). The biggest difference from traditional trees continues to be the separation of dissorophoids, including Cacops, from temnospondyls. Cacops and kin are still nesting with the lepospondyls, including all microsaurs and extant amphibians

Figure 1. Subset of the LRT showing basal tetrapods. Four more are added here with no change in tree topology.

Figure 1. Subset of the LRT showing basal tetrapods. Four more are added here with no change in tree topology.

Tomorrow or shortly thereafter
I’ll start reporting some numbers and describing some interesting taxa. For those interested, whenever I add taxa, I revisit and update old taxa including their scores. So if you want an updated .nex file, now is a better time than ever, with errors minimized.

 

The weird skull and affinities of Brachydectes

Before you read any further, check out Jason Pardo’s letter below. He’s the expert. I’m only a freshman when it comes to this very unusual taxon and its kin. 

This post was updated February 8, 2017 with new identifications of several skull bones. This did not change the nesting of Brachydectes with Eocacilia. 

Further updated March 18, 2017 with new skull bone identities for Brachydectes

Brachydectes newberryi (Cope 1868, AMNH 6941; latest Carboniferous; 300 mya; Fig. 1-4) was long considered a lysorophian amphibian with a tiny skull, an extremely long snake-like torso, vestigial limbs and a very short tail. You find them in eastern Kansas.

Figure 1. Brachydectes overall and skull in four views.

Figure 1. Brachydectes overall and skull in four views.

A recent PlosOne article
by Pardo and Anderson (2016) studied the skull of Brachydectes (Fig. 3) using micro CT scanning. They report, “Contra the proposals of some workers, we find no evidence of expected lissamphibian synapomorphies in the skull morphology in Brachydectes newberryi, and instead recognize a number of derived amniote characteristics within the braincase and suspensorium. Morphology previously considered indicative of taxonomic diversity within Lysorophia may reflect ontogenetic rather than taxonomic variation.” Later they wrote, “an expansive phylogenetic analysis is outside the scope of this study and will appear elsewhere.” 

Earlier
in the large reptile tree (LRT), Brachydectes nested between Adelospondylus and Eocaecilia, which also has a long snake-like torso, but composed of far fewer and individually much longer vertebrae and a distinct skull architecture. A large, but not exhaustive, selection of basal amniotes was tested and none attracted Brachydectes as much as the two lissamphibians listed above, given the prior data of a line drawing of the skull (Fig. 2) by Marjanovic and Laurin 2013 derived from Wellstead C F 1991.

Figure 1. Brachydectes skull data from a line drawing produced by Marjanović and Laurin 2013. Most leposponysls have a very narrow parasphenoid process and large interptyergoid vacuities, but eocacaecilians expanded this bone and reduced the vacuities like Brachydectes did. 

Figure 2. Brachydectes skull data from a line drawing produced by Marjanović and Laurin 2013. Most leposponysls have a very narrow parasphenoid process and large interptyergoid vacuities, but eocacaecilians expanded this bone and reduced the vacuities like Brachydectes did.

Figure 1. Brachydectes newberryi has some difficult to identify bones just aft of the orbit due to fusion and reduction. Brachydectes (Laysorophus) elongatus (Fig. 2) provides Rosetta Stone clues as to what is happening in this clade.

Figure 1. Brachydectes newberryi has some difficult to identify bones just aft of the orbit due to fusion and reduction. Brachydectes (Laysorophus) elongatus (Fig. 2) provides Rosetta Stone clues as to what is happening in this clade.

The new data 
(Figs 2,3 ) are not too far off from the Wellstead C F 1991 data. Notably the tabular no longer extends ventrally alongside the squamosal as it does in the larger specimen. Does this represent a break? or fusion? Or phylogenetic difference? Below (Fig. 3) is the new data on KUVP 49541, plus a reinterpretation of skull sutures based on the micro CT scans. The nesting of the new Brachydactes does not shift in the LRT. It is still a lissamphibian close to microsaurs and caecilians. That’s a broad range, indicative of a long list of yet to be found taxa.

Pardo and Anderson’s reconstruction
(Fig. 3) does not include the coronoid or lateral exposure of the splenial.  Pardo and Anderson note the single supraoccipital compares well with that of various basal reptiles, and indeed it does.  The occipital arch of other lissamphibians consists of only paired exoccipitals,.. until you include microsaurs.

More on supraoccipital homologies
According to Pardo and Anderson, “the presence of a well-developed median supraoccipital is restricted to the amniote crown and recumbirostran ‘microsaurs’. Although the supraoccipital of Brachydectes and ‘microsaurs’ has traditionally been considered convergent with the amniote supraoccipital, new data from μCT have demonstrated that the ‘microsaur’ supraoccipital shares a number of morphological details with early amniotes, and early eureptiles in particular, and is likely homologous with the amniote element. This homology does not extend far down the amniote stem, as seymouriamorphs lack a supraoccipital and ‘anthracosaurs’ generally exhibit paired elements within the synoptic tectum.” 

Noteworthy:
In the LRT, microsaurs are sisters to the clade that includes Adeospondylus, Brachydectes and Eocaeceila. That’s a great deal of phylogenetic distance, but not as great as any other pairing in the LRT. Perhaps more taxa will fill the apparent gaps someday.

Figure 4. Four sizes of Brachydectes in situ. Here, unfortunately, the authors have penned in the sutures, negating any possibility of any reviewer to judge whether they were drawn correctly or not.

Figure 4. Four sizes of Brachydectes in situ. Here, unfortunately, the authors have penned in the sutures, negating any possibility of any reviewer to judge whether they were drawn correctly or not.

Pardo and Anderson also report
“neurocranial morphology does not support a close relationship between Brachydectes and lissamphibians.” Admittedly, Brachydectes is indeed quite different from its sisters…yet it is not closer to other tested taxa in the LRT. If you look at various microsaurs and other lissamphibians, you get a wide range of morphologies at every node.

By noting various key features in contention with the traditional relationship. Pardo and Anderson essentially ‘put the cart before the horse.’ They waited to do the phylogenetic analysis, when they should have done that analysis before publishing. Homoplasy is rampant in tetrapods. I think they fell prey to yet another example. Only analysis, at present, settles all issues.

Pardo and Anderson then report, 
“Morphology of the braincase of Brachydectes suggests a close relationship with the brachystelechid ‘microsaurs’ Carrolla craddocki  and Quasicaecilia texana, within the Recumbirostra.” These two are new to me and untested in the LRT. Wikipedia nests them with Batropetes, which has long legs, and a horned-lizard type body, only distantly related to Brachydectes in the LRT. The skull of Quasicaecilia is shown here, but no post-crania is shown. Recumbirostran microsaurs, are considered the earliest known example of adaptation to head-first burrowing in the tetrapod fossil record. I wish the sister candidates offered by Pardo and Anderson were long and snake-like, but they are not. Deletion of post-cranial traits from the LRT does not shift the placement of Brachydectes within the LRT.

Figure 3. Original interpretation of Brachydectes, KUVP 49541, by Pardo and Anderson. Colors added for clarity and to match micro CT scan.

Figure 5. Original interpretation of Brachydectes, KUVP 49541, by Pardo and Anderson. Colors added for clarity and to match micro CT scan.

References
Carroll RL 1967. An Adelogyrinid Lepospondyl Amphibian from the Upper Carboniferous: Canadian Journal of Zoology 45(1):1-16.
Carroll RL and Gaskill P 1978. The order Microsauria. American Philosophical Society, Philadelphia, 211 pp.
Cope ED 1868. Synopsis of the extinct Batrachia of North America. Proc Acad Nat Sci 20: 208–221. doi: 10.5962/bhl.title.60482
Jenkins FA and Walsh M 1993. An Early Jurassic caecilian with limbs. Nature 365: 246–250.
Jenkins FA, Walsh DM and Carroll RL 2007. Anatomy of Eocaecilia micropodia, a limbed caecilian of the Early Jurassic. Bulletin of the Museum of Comparative Zoology 158(6): 285-366.
Marjanović D and Laurin M 2013. The origin(s) of extant amphibians: a review with emphasis on the “lepospondyl hypothesis”. Geodiversitas 35 (1): 207-272. http://dx.doi.org/10.5252/g2013n1a8
Pardo JD and Anderson JS 2016. Cranial Morphology of the Carboniferous-Permian Tetrapod Brachydectes newberryi (Lepospondyli, Lysorophia): New Data from µCT. PLoS ONE 11(8): e0161823. doi:10.1371/journal.pone.0161823. online here.
Wellstead C F 1991. Taxonomic revision of the Lysorophia, Permo-Carboniferous lepospondyl amphibians. Bulletin of the American Museum of Natural History 209: 1–90.

wiki/Eocaecilia
wiki/Brachydectes
wiki/Adelospondylus