Phylogenetic bracketing and pterosaurs – part 2

Two posts ago we looked at part 1 of this topic.

Since pterosaurs (and other tritosaurs) nest between rhynchocephalians and squamates, there are a few traits they likely shared based on phylogenetic bracketing (unless specifically excepted based on fossil evidence). Putting the rhynchocephalians aside for the moment, according to Evans (2003) squamate traits include:

(1)  a specialized quadrate articulation with a dorsal joint typically supplied by the deeply placed supratemporal, reduced squamosal, and distally expanded paroccipital process of the braincase; reduction/loss of pterygoid/quadrate overlap; loss of quadratojugal – all present in basal tritosaurs, but quadrate becomes immobile in Macrocnemus and later taxa.

(2) loss of attachment between the quadrate and epipterygoid, with the development of a specialized ventral synovial joint between the epipterygoid and pterygoid — also present up to Huehuecuetzpalli, but absent in Macrocnemus and later taxa.

(3) subdivision of the primitive metotic fissure of the braincase to give separate openings for the vagus nerve (dorsally) and the perilymphatic duct and glossopharyngeal nerve (via the lateral opening of the recesses scalae tympani ventrally). This leads to the development of a secondary tympanic window for compensatory movements and is associated with expansion of the perilymphatic system and closure of the medial wall of the otic capsule — in fossil tritosaurs these details may not be known and certainly not by me… yet.

(4) loss of ventral belly ribs (gastralia) — Basal tritosaurs, up to Homoeosaurus have gastralia. Then they don’t until Macrocnemus and all later taxa.

(5) emargination of the anterior border of the scapulocoracoid — Basal tritosaurs share this trait. Macrocnemus and tanystropheids refill the emargination. Fenestrasaurs, including pterosaurs expand the emargination resulting in a strap-like scapula and stem-like coracoid, both representing the posterior rims of these bones.

(6) hooked fifth metatarsal with double angulation — shared with tritosaurs and more complex mesotarsal joint – in tritosaurs the mesotarsal joint is simple.

(7a) a suite of soft tissue characters including greater elaboration of the vomeronasal apparatus;

(7b) a single rather than paired meniscus at the knee;

(7c) the presence of femoral and preanal organs;

(7d) fully evertible hemipenes;

(7e) and pallets on the ventral surface of the tongue tip – none of these have been noted in soft tissue fossils.

References
Evans SE 2003. At the feet of the dinosaurs: the origin, evolution and early diversification of squamate reptiles (Lepidosauria: Diapsida). Biological Reviews, Cambridge 78: 513–551.

 

New nesting for Echinerpeton with Secodontosaurus

Figure 1. Just move the mandible forward so the last tooth is anterior to the orbit and Echinerpeton becomes a long snouted pro to-secodontosaur.

Figure 1. Just move the mandible and maxilla forward so the last tooth is anterior to the orbit (as in other pelycosaurs) and Echinerpeton becomes a long snouted proto-secodontosaur. 

Raising my hand to proclaim a nesting error
Earlier (now trashed) I recovered Echinerpeton at the base of the Synapsida and Diapsida, but those elongate dorsal spines seemed odd at that node. Then I noticed that all other pelycosaurs had teeth only in front of the orbit. The skull is largely missing, so there’s no harm in shifting the jaws forward a bit. And suddenly Echinerpeton made more sense.

Echinerpeton intermedium (Reisz 1972), Late Carboniferous, 308 mya. Reisz (1972) tentatively classified Echinerpeton as an ophiacodontid in his initial description, and in 1986 he considered it an indeterminate “pelycosaur“. Benson (2012) could not nest Echinerpeton with certainty, perhaps because he used the wrong outgroups and mistakenly included caseasaurs because he followed tradition without the benefit of a large gamut reptile tree like we have here (Fig. 2).

Figure 1. Secodontosaurus and its ancestors going back to Varanosaurus. Secodontosaurus is the only sphenacodont with a varanopid-like skull.

Figure 1. Secodontosaurus and its ancestors going back to Varanosaurus. Secodontosaurus was the only sphenacodont with a varanopid-like skull. No Echinerpeton has one too.

Here Echinerpeton nests with Secodontosaurus. The snout was long because the last maxillary tooth was in front of the orbit. The maxilla was straight while the dentary was concave dorsally. Both were filled with long teeth.

The dorsal spines were long, but not as long as those of Secodontosaurus.The scapula was small and both the humerus and femur were short and slender. The ankle bones were round elements. Together these point to an aquatic, rather than a terrestrial niche. So Echinerpeton was a crocodile-like sphenacodont pelycosaur.

References
Benson RBJ 2012. Interrelationships of basal synapsids: Cranial and postcranial morphological partitions suggest different topologies. Journal of Systematic Palaeontology: 601-624.
Reisz R 1972. Pelycosaurian reptiles from the Middle Pennsylvanian of North America. Bulletin of the Museum of Comparative Zoology 144 (2): 27–62. online here

 

Darwinopterus: 5 specimens in phylogenetic analysis – part 2

Figure 2. Subset of the large pterosaur tree showing relationships among Darwinopterus and its predecessors among the Wukongopteridae and their predecessors.

Figure 1. Subset of the large pterosaur tree showing relationships among Darwinopterus and its predecessors among the Wukongopteridae and their predecessors.

Yesterday we looked at the phylogenetic ancestors (Fig. 1) of Darwinopterus. Today we’ll take a closer look at the five specimens assigned to this genus.

Lü et al. (2011) noted the alveoli have raised margins, the nasoantorbital fenestra were confluent [not true, if you look closely], inclined quadrate [plesiomorphic], elongate cervical vertebrae with low neural spine and reduced or absent cervical ribs [plesiomorphic], long tail of more than 20 caudals partially enclosed by filiform extensions of the pre- and post-zygopophyses [plesiomorphic] short metacarpus less than 60 percent length of humerus [plesiomorphic] fifth toe with two elongate phalanges [plesiomorphic] and curved second pedal phalanx with the angle of 130 degrees [plesiomorphic].

In the current analysis
the following traits distinguish Darwinopterus from outgroup taxa: Some are equivocal, subject to a change of score by virtue of taphonomic changes and exposure. Only the first two dorsal ribs are robust, not the first three. The humerus shape is straighter. The deltopectoral crest is wider than deep. Manual 1.1 is shorter relative to m2.1. Manual digit 3 is not longer than mt4. The prepubis is putter-shaped. So, really not much. Only 5 steps are added when the outgroup taxa are moved inside the clade.

The most basal taxon
is the female, ZMNH M8802 (Fig. 2) which is crestless, like its ancestors. The mandible tip is bent down.

Figure 2. Darwinoperus ZMNH8802 specimen, the female and most basal member of this genus.

Figure 2. Darwinoperus ZMNH8802 specimen, the female and most basal member of this genus.

On a side note:
The original ischium (Fig. 2a) was misidentified. It is hard to see on top of the right femur (on the left below as seen in ventral view). What was originally identified as a deep left ischium by Lü et al. is instead a second prepubis, identical to the correctly identified prepubis on the opposite side (Fig. 2a, b)

Figure 2a. Original identification by Lü et al. 2011a) of puboischium in Darwinopterus.

Figure 2a. Original identification by Lü et al. 2011a) of puboischium in Darwinopterus.

xx

Figure 2b. Darwinopterus female pelvis (ZMNH 8802) with pelvic bones correctly identified. the ischium is best seen on the left in indigo. The prepubes are red.

Figure 2b. Darwinopterus female pelvis (ZMNH 8802) with pelvic bones correctly identified. the ischium is best seen on the left in indigo. The prepubes are red. The egg has been flattened and deflated, like a balloon. The paired ischia are still deep enough to pass the egg in vivo.

The other four specimens have crests. The other four specimens have a shorter prepubis relative to the pelvis. Again, not much separates them.

The next clade
has two similar members, D. linglongtaensis (Fig. 3) and the YH2000 specimen (Fig. 4). Both are relatively gracile. The orbit is more upright. The mandible is gracile and slightly bent up distally. Some dentary teeth are taller than the mandible. The sacrum is mostly fused. The torso is longer relative to the humerus, separating the elbow from the ilium. The humerus is subequal to the femur. The ulna is longer relative to the humerus. Manual 2.1 and m3.1 are subequal. Manual 3.3 ≥ m3.1 + m3.2. When folded manual 4.1 extends only to the distal ulna, not the half point. Metatarsals 1 and 2 are the longest. Pedal 4.4 is shorter than p4.1.

Figure 3. Darwinopterus YH2000 specimen.

Figure 3. Darwinopterus YH2000 specimen. It has a shorter ilium and a gracile build.

Minor differences, getting into the range of individual variation, separate the YH2000 and IVPP V 16049 specimens. The latter is more robust with a longer ilium and a shorter p5.1.

Figure 4. Darwinopterus linglongtaensis.

Figure 4. Darwinopterus linglongtaensis, IVPP V 16049. This is a robust specimen.

The third clade
has larger members, the Darwinopterus modulars holotype (ZMNH 8782, Fig. 5) and D. robustodens (41HIII-0309A, Fig. 6). The postorbital bar is lower and more robust. The coracoid is less than half the length of the humerus. The humerus is longer relative to the torso. The pubis depth is not shorter than the ischium.

Figure 5. Darwinopterus ZMNH 8782. A taller specimen with a longer neck and larger skull.

Figure 5. Darwinopterus modularis (holotype) ZMNH 8782. A taller specimen with a longer neck and larger skull.

Again, minor differences separate these two, including the length of the neck, distribution of the teeth, a more robust tail in the holotype, and the pelvis shape.

Figure 6. Darwinopterus robustodens at the Henan Geological Museum (41HIII-0309A). The teeth tips are described (Lü et al. 2011) as sharper and are swollen between the crown and root. There are nine tooth pairs in the upper and eleven in the lower jaws, which are smaller than in D. modularis.

Figure 6. Darwinopterus robustodens at the Henan Geological Museum (41HIII-0309A). The teeth tips are described (Lü et al. 2011) as sharper and are swollen between the crown and root. There are nine tooth pairs in the upper and eleven in the lower jaws, which are smaller than in D. modulars. Tomorrow we’ll take a closer look at the naris.

If we concentrate only the feet
We find a gradual evolution and a resulting variety in the pes of the included taxa (Fig. 7). Note the variation in p5.1 vs. mt4, the longest toe from the heel, the variety in metatarsal lengths and the relative lengths of metatarsus to digits.

Figure 6. Darwinopterus feet. If the gracile forms were female, would they have phylogenetically different feet? Or is it more parsimonious to consider the morphologically different forms a clade?

Figure 7. Darwinopterus feet. If the gracile forms were female, would they have phylogenetically different feet? Or is it more parsimonious to consider the morphologically different forms a clade?

The wukongopterids were an interesting clade, evolving some pterodactyloid-grade traits, but not others. The multiple origin of the pterodactyloid-grade is a subject we handled earlier here. If you want to see all the wukongopterids together to scale, click here

References
Lü J, Unwin DM, Jin X, Liu Y and Ji Q 2009. Evidence for modular evolution in a long-tailed pterosaur with a pterodactyloid skull. Proceedings of the Royal Society London B  (DOI 10.1098/rspb.2009.1603.)
Lü J, Unwin DM, Deeming DC, Jin X, Liu Y and Ji Q 2011a. An egg-adult association, gender, and reproduction in pterosaurs. Science, 331(6015): 321-324. doi:10.1126/science.1197323
Lü J, Xu L, Chang H and Zhang X 2011b. A new darwinopterid pterosaur from the Middle Jurassic of Western Liaoning, northeastern China and its ecological implicaitions. Acta Geologica Sinica 85: 507-514.
Lü J-C and Fucha X-H 2010. A new pterosaur (Pterosauria) from Middle Jurassic Tiaojishan Formation of western Liaoning, China. Global Geology 13 (3/4): 113–118. doi:10.3969/j.issn.1673-9736.2010.03/04.01.
Martill DM and Etches E 2012. A new monofenestratan pterosaur from the Kimmeridge Clay Formation (Upper Jurassic, Kimmeridgian) of Dorset, England. Acta Palaeontologica Polonica. in press. doi:10.4202/app.2011.0071.
Wang X, Kellner AWA, Jiang S-X, Cheng X, Meng Xi & Rodrigues T 2010. New long-tailed pterosaurs (Wukongopteridae) from western Liaoning, China. Anais da Academia Brasileira de Ciências 82 (4): 1045–1062.
Wang X-L, Kellner AWA, Jiang S-S, Cheng X, Meng X and Rodriques T 2014. New long-tailed pterosaurs (Wukongopteridae) from western Liaoning, China. Anais da Academia Brasileira de Ciências (2010) 82(4): 1045-1062.
Zhou C-F and Schoch RR 2011. New material of the non-pterodactyloid pterosaur Changchengopterus pani LÜ, 2009 from the Late Jurassic Tiaojishan Formation of western Liaoning. N. Jb. Geol. Paläont. Abh. 260/3, 265–275 published online March 2011.

wiki/Kunpengopterus
wiki/Darwinopterus

Darwinopterus: 5 specimens in phylogenetic analysis – part 1

Earlier we looked at Darwinopterus, of which several specimens (Figs. 1,2) are now known. When the female with the associated egg was found (Lü et al. 2011a) they proposed that some of the differences (pelvis shape, rostral crest, size) could be attributed to gender.

We learned earlier that this would be a unique situation among pterosaurs as all other such candidates for this difference do not indicate gender, but phylogeny when placed under analysis (small crests are derived from no crests and small crests give rise to large crests, for instance). What Lü et al. considered a deep ischium in the female was found to be a deep prepubis here.

Like Pteranodon, Rhamphorhynchus, Pterodactylus, Germanodactylus and other genera, I added the five specimens attributed to Darwinopterus (Fig. 1) to the large pterosaur tree to see how they might be related to one another in a first ever phylogenetic analysis of this genus (Fig. 2).

Figure 1. Click to enlarge. The five specimens of Darwinopterus to scale and in phylogenetic order preceded by six more primitive taxa. The ZMNH 8802 specimen is a female associated with an egg. The others genders shown are guesses by Lü et al. 2011a. Note the skull did not elongate, it actually shrank in the vertical dimension, probably reducing its weight. The female is crestless because it is the most primitive of the five known Darwinopterus specimens. The odds that the remaining four specimens are all males is relatively small.

Figure 1. Click to enlarge. The five specimens of Darwinopterus to scale and in phylogenetic order preceded by six more primitive taxa. The ZMNH 8802 specimen is a female associated with an egg. The others genders shown are guesses by Lü et al. 2011a. Note the skull did not elongate, it actually shrank in the vertical dimension, probably reducing its weight. The female is crestless because it is the most primitive of the five known Darwinopterus specimens. The odds that the remaining four specimens are all males is relatively small. The odd throat sac of Pterorhynchus may represent a normal throat ripped away from its base.

Figure 2. Subset of the large pterosaur tree showing relationships among Darwinopterus and its predecessors among the Wukongopteridae and their predecessors.

Figure 2. Subset of the large pterosaur tree showing relationships among Darwinopterus and its predecessors among the Wukongopteridae and their predecessors.

To give some perspective
Jianchangnathus, at the base of this subset of the large pterosaur tree, also nested between basal Dorygnathus and Scaphognathus. No taxa succeed Darwinopterus. It was a sterile lineage, not a transitional taxon.

Note the very small naris and relatively large skull on Jianchangnathus. More derived taxa, including Darwinopterus, had a skull that was just as long, just not as tall, thereby reducing its weight. So this clade did not have a longer skull than sister taxa.

All more derived taxa, including Darwinopterus, also had a reduced to absent naris. So this is the genesis of that trait.

The long neck of wukongopterids also had its genesis in more basal taxa, like the PMOL specimen attributed to Changchengopterus by Zhou and Shoch 2011.

Earlier we noted the relationship of Pterorhynchus to the wukongopterids. And recently we noted that the new specimen referred to Changchengopterus (Zhou and Schoch 2011) actually nests at the base of the Wukonopteridae, far from the the holotype Changchengopterus, which is half the size.

Kunpengopterus now has a sister taxon in Archaeoistiodactylus (Lü and Fucha 2010) which Martill and Etches (2012) correctly referred to this clade.

Tomorrow we’ll look at the five specimens of Darwinopterus a little more closely.

References
Lü J, Unwin DM, Jin X, Liu Y and Ji Q 2009. Evidence for modular evolution in a long-tailed pterosaur with a pterodactyloid skull. Proceedings of the Royal Society London B  (DOI 10.1098/rspb.2009.1603.)
Lü J, Unwin DM, Deeming DC, Jin X, Liu Y and Ji Q 2011a. An egg-adult association, gender, and reproduction in pterosaurs. Science, 331(6015): 321-324. doi:10.1126/science.1197323
Lü J, Xu L, Chang H and Zhang X 2011b. A new darwinopterid pterosaur from the Middle Jurassic of Western Liaoning, northeastern China and its ecological implicaitions. Acta Geologica Sinica 85: 507-514.
Lü J-C and Fucha X-H 2010. A new pterosaur (Pterosauria) from Middle Jurassic Tiaojishan Formation of western Liaoning, China. Global Geology 13 (3/4): 113–118. doi:10.3969/j.issn.1673-9736.2010.03/04.01.
Martill DM and Etches E 2012. A new monofenestratan pterosaur from the Kimmeridge Clay Formation (Upper Jurassic, Kimmeridgian) of Dorset, England. Acta Palaeontologica Polonica. in press. doi:10.4202/app.2011.0071.
Wang X, Kellner AWA, Jiang S-X, Cheng X, Meng Xi & Rodrigues T 2010. New long-tailed pterosaurs (Wukongopteridae) from western Liaoning, China. Anais da Academia Brasileira de Ciências 82 (4): 1045–1062.
Wang X-L, Kellner AWA, Jiang S-S, Cheng X, Meng X and Rodriques T 2014. New long-tailed pterosaurs (Wukongopteridae) from western Liaoning, China. Anais da Academia Brasileira de Ciências (2010) 82(4): 1045-1062.
Zhou C-F and Schoch RR 2011. New material of the non-pterodactyloid pterosaur Changchengopterus pani LÜ, 2009 from the Late Jurassic Tiaojishan Formation of western Liaoning. N. Jb. Geol. Paläont. Abh. 260/3, 265–275 published online March 2011.

wiki/Kunpengopterus
wiki/Darwinopterus

MorphoBank.org has three new matrices

Okay,
for those interested in getting my matrices from MorphoBank.org rather than from me, the large reptile tree, basal therapsid tree and large pterosaur tree are now available online at Morphobank.org.

Projects 1071, 1072, 1073 

This represents a change from the original project 753 in which all three matrices were in one project.

In total the taxon list is now up to 623 (with a few overlaps due to the three matrices.)

Azendohsaurus postcrania – svp abstracts 2013

From the abstract:
Nesbitt et al. 2013 wrote, “During the Triassic, a number of highly disparate archosauromorphs populated both terrestrial (e.g., Trilophosaurus, rhynchosaurs) and marine ecosystems (e.g., tanystropheids) across Pangea. Unfortunately, the unique and sometimes utterly bizarre body plans of these reptiles (e.g., specialized feeding adaptations) create a major challenge in understanding early archosauromorph relationships and patterns of diversification, as teasing apart homology from homoplasy has been difficult with the current sample of taxa.

“Here we present the postcranial anatomy of Azendohsaurus madagaskarensis, an early archosauromorph from the Middle-Late Triassic of Madagascar. Azendohsaurus madagaskarensis comes from a monotypic bone bed containing an ontogenetically variable sample, with preservation ranging from whole, disarticulated bones, to articulated partial skeletons. From this bonebed, the entire anatomy of the taxon is represented. Azendohsaurus madagaskarensis possessed an elongated neck, short tail, and stocky limbs. The manus and pes have unexpectedly short digits, terminating in large, recurved ungual phalanges. Together with the skull, knowledge of the postcranial skeleton elevates A. madagaskarensis to another highly apomorphic and bizarre Triassic archosauromorph.

“Even so, recovery, description and analysis of the full anatomy of A. madagaskarensis provides clues to understanding the relationships of this species and other problematic and anatomically specialized taxa, including the North American Late Triassic archosauromorphs Trilophosaurus and Teraterpeton. For example, A. madagaskarensis, Trilophosaurus, and Teraterpeton share a dorsally hooked quadrate and enlarged, trenchant unguals, whereas Trilophosaurus and Teraterpeton alone share a number of other character states (e.g., restricted scapular blade, premaxillary beak). We tested these observations in a newly constructed phylogenetic analysis centered on Triassic archosauromorphs and archosauriforms. We find that A. madagaskarensis, Trilophosaurus, Spinosuchus, and Teraterpeton form a clade within Archosauromorpha, but the relationships of this clade to other groups of Triassic archosauromorphs (e.g., archosauriforms, rhynchosaurs, tanystropheids) remains poorly supported. The newly recognized clade containing A. madagaskarensis, Trilophosaurus, and Teraterpeton demonstrates high disparity of feeding adaptations even within a closely related group of basal archosauromorphs.”

The rhynchosaur Hyperodapedon, the protorhynchosaur, Mesosuchus and the two Trlophosaurs, Trilophosaurus and Azendohsaurus are here.

Figure 1. Click to enlarge. On the left, the rhynchosaur Hyperodapedon, the protorhynchosaur, Mesosuchus and the two Trlophosaurs, Trilophosaurus and Azendohsaurus. On the right, basal archosauriforms and Azendohsaurs tucked in the bottom along with a tree segment.

First of all,
its great to hear the postcrania of Azendohsaurus is finally on the table, soon to be published, I presume. The skull nests it as a sister to Trilophosaurus, so the long neck is no surprise and Sapheosaurus. The short tail, short digits and stocky limbs of Azendohsaurus are found phylogenetically nearby in the rhynchosaur Hyperodapedon and the proto-rhynchosaur, Mesosuchus. So, again, no surprise there. This clade has surprising diversity.

Second of all,
Nesbitt et al. 2013 think these taxa are bizarre only because they are under the presumption that they are all archosauromorphs. They are not, as documented by the large reptile tree. It’s no surprise then that Nesbitt et al. report, “relationships remains poorly supported.” Evidently Nesbitt et al. 2013 don’t have a large enough gamut in their reptile tree to recovers their featured taxa as lepidosauromorphs, closer to lepidosaurs than to archosaurs.

When Nesbitt et al. finally do figure out how to nest those taxa, they’ll also find out that their new sister taxa provide a gradual accumulation of traits that lead to all their oddball traits. It’s the same problem Nesbitt 2011 made nesting pterosaurs with archosaurs. In reality, when you don’t exclude the better candidates, tritosaur lepidosaurs provide the gradual accumulation of pterosaurian traits.

Nesbitt 2011 already made the big mistake of nesting Mesosuchus as a basal archosauromorph when it is way closer to sphenodontids. Youngina would have been a better choice as a basal archosauromorph. It’s way more plesiomorphic with regards to proterosuchids, erythrosuchids and choristorderes. 

The exception

Figure 2. Teraterpeton, a former enigma that nests here between  Chanaresuchus and Tropidosuchus.

Figure 2. Teraterpeton, a former enigma that nests in the large reptile tree between Chanaresuchus and Tropidosuchus. While oddballs sometimes nest together, this taxon has little in common with Trilophosaurus.

Teraterpeton is the exception, a pararchosauriform archosaurormorph nesting between Chanaresuchus and Tropidosuchus in the large reptile tree. Earlier we looked at Teraterpeton here. Nesbitt et al. found that Teraterpeton, Trilophosaurus and Azendohsaurus shared a dorsally hooked quadrate and enlarged trenchant unguals. Unfortunately, more that 30 steps are added when Teraterpeton shifts to nest with the other two and the unguals are not really that big in Teraterpeton. They’re actually bigger in the sister taxon, Chanaresuchus. The quadrate often hooks in herbivores. That they have in common.

Gosh,
I hope the Nesbitt team goes to a larger gamut tree and tests their taxa against other candidates before they publish another problem-filled paper like Nesbitt (2011) with strange bedfellows (sisters that don’t share very many traits) all over the place. The nestings of these featured taxa in the large reptile tree are strongly supported.

References
Nesbitt, S, Flynn J, Ranivohrimanina L, Pritchard A and Wyss A 2013.
Relationships among the bizarre: the anatomy of Azendohsaurus madagaskarensis and its implications for resolving early archosauromroph phylogeny. Journal of Vertebrate Paleontology abstracts 2013.

The Early Tetrapod Supertrees of Ruta, Jefferies and Coates 2003

A decade ago, Ruta et al. (2003) produced two distinct phylogenetic supertrees of early tetrapods by combining 50 trees produced by prior workers. That’s 225 taxa in total, an impressive number! The second analysis excluded source trees that had been superceded by more comprehensive studies. Only a very few of the taxa on both trees are found in the large reptile tree (colorized in Figs. 1, 2).

Figure 1. Click to enlarge. Colors added represent taxa listed on the large reptile tree.

Figure 1. Click to enlarge. Colors added represent taxa listed on the large reptile tree.

Since the large reptile tree includes several pre-amniotes listed here (Figs. 1, 2), I thought it would be interesting to compare and contrast these two trees as Ruta et al. (2003) did, “Outstanding areas of disagreement include the branching sequence of lepospondyls and the content of the amniote crown group, in particular the placement of diadectomorphs as stem diapsids.”

Figure 2. The second super tree created by Ruta et al. 2003. Note the several shifts described in the text.

Figure 2. The second super tree created by Ruta et al. 2003. Note the several shifts described in the text.

Figure 1. Microsaurs and other basal non-amniote tetrapods from the large reptile tree.

Figure 1. Microsaurs and other basal non-amniote tetrapods from the large reptile tree.

Ruta et al. (2003) warn in their abstract: “Supertrees are unsurpassed in their ability to summarize relationship patterns from multiple independent topologies. However, we urge caution in using them as a replacement for character-based cladograms and for inferring macroevolutionary patterns.”

They also report, “supertrees can, in certain circumstances, produce spurious groups (i.e. taxon arrangements that are not found in any of the contributory trees.”

[Hone and Benton (2009) know this only too well!!]

In analysis one,
Ruta et al. report, “Authors hypothesize a close relationship between some or all of the lissamphibians and various lepospondyl groups (figure 1). However, analysis I places lissamphibians as a sister group to a clade of lysorophids and microbrachomorph microsaurs. The amniote crown group and total group are coextensive: no amniote stem was found.”

In analysis two, 
Ruta et al. report, “[The] tree shows a deep split within early tetrapods between stem amniotes and stem lissamphibians analysis II includes a stem amniote branch. Anthracosaurs and seymouriamorphs are successive sister groups to a clade of crown amniotes plus diadectomorphs. This larger group is paired with Solenodonsaurus plus lepospondyls. Caerorhachis is placed at the base of the amniote stem (cf. Ruta et al. 2001, 2003). Finally, Casineria and Westlothiana are successive sister taxa to the crown amniotes. Temnospondyls now appear as stem lissamphibians.”

Spurious results,
Ruta et al. report, “Diadectomorphs are polyphyletic in most MPTs, Diadectes and Limnoscelis being nested within the amniote crown, next to stem diapsids. Solenodonsaurus also appears as a crown amniote, as a sister taxon to the diadectomorph, Tseajaia.”

No, that’s good!
The large reptile tree also recovered Solenodonsaurus, TseajaiaDiadectes and Limnoscelis as amniotes. So what’s the problem!

In their summary, Ruta et al. (2003) remind us,
“Supertree methods are the only practical means of generating summaries of primary results.”

Interesting then,
that when Hone and Benton (2009) following Hone and Benton (2007) in their 2-part supertree analysis decided to drop all reference to Peters (2000) and give false credit for the “prolacertiform” hypothesis to Bennett (1996), they must have discovered that inclusion of the primary results from Peters (2000) would give them the same results as Peters (2000). This they were not keen on doing, considering their subsequent deviations. Their mission, as stated in 2007, was to compare the results of Peters (2000) to Bennett (1996). By dropping the former in their 2009 paper (with published analysis), the latter came out victorious, but only by default and not very clearly.

Later Bennett (2013) noted that Hone and Benton (2009) entered typos into their matrix for Peters (2000) then complained they did not get the same results, among many other problems listed here.

Back to Ruta et al. 
Interesting that the Ruta et al. supertree kept Gephyrostegus apart from basal amniotes, perhaps due to the absence of Cephalerpeton, Brouffia and other basal amniotes. Moreover, Gephyrostegus, Silvanerpeton and Proterogyrinus nested in opposite order with the latter nesting as more derived. We found that opposite order also occurring with the Mortimer dinosaur tree here.

Good fodder for good conversation.
Ultimately we’ll all be of one accord.

Bottom line:
You have to appreciate the efforts of Ruta  et al. 2003 because more taxa in large gamut analyses generally aid in understanding relationships… so long as you don’t “drop the ball” by deleting key taxa (as in Hone and Benton (2007, 2009).

References
Ruta M, Jefferey JE and Coates MI 2003. A supertree of early tetrapods. Proceedings of the Royal Society, London B (2003) 270, 2507–2516.
Hone DWE and Benton MJ 2007. An evaluation of the phylogenetic relationships of the pterosaurs to the archosauromorph reptiles. Journal of Systematic Palaeontology 5:465–469.
Hone DWE and Benton MJ 2009. Contrasting supertree and total evidence methods: the origin of the pterosaurs. Zitteliana B28:35–60.