A molecule study that includes ratfish and rats

Here’s a molecule study (Irisarri et al. (10 co-authors)
that includes select members of the Gnathostomata (jawed vertebrates going back to ratfish). Their abstract reports, “Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial.”

At least they are on the right track, with a wide gamut study. The LRT covers very few fish, but a long list tetrapods. Evidently the LRT was not on their radar. (sigh)

“We tested a new bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost-effective. Our analyses emphasize the importance of large, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.”

Importance? Unfortunately you have to be a believer, because their RNA interrelationships can and cannot be verified by a competing analysis of traits (explained in detail below).

“Gene jackknifing of genomic data corroborates the robustness of our tree.”

Unfortunately, genomic data produces several false positives when compared to phenomic data.

Here we’ll compare results
to the large reptile tree (LRT, 1187 taxa), which goes back nearly as far in a morphological study and employs fossil taxa. I have often said that molecules produce false positives over large phylogenetic distances. Here that statement proves to be both true and false, depending on the node.

The LRT includes only bony vertebrates,
so sharks, rays and ratfish are not included as taxa in the LRT. Lungfish and most teleosts are also not included.

Where the Irisarri et al. tree matches the LRT:
Both trees:

1. separate ray fin fish from lobe fin fish
2. separate tetrapods from lobe fin fish
3. separate amniotes from amphibians (only living taxa are tested)
4. separate caecilians from salamanders + frogs
5. separate turtles, mammals, archosaurs and lepidosaurs
6. nest birds with crocs
7. nest Sphenodon with squamates
8. nest all mammals with other mammals, turtles with turtles, birds with birds, etc. etc.
9. nest placental mammals with other placental mammals, apart from non-placental mammals
10. nest palaegnath birds with palaeognath birds, apart from neognath birds
11. nest placental mammals splitting from Monodelphis

Where the Irisarri et al. tree does not match the LRT:
The Isirarri et al. tree:

1. separates mammal reptiles from all other reptiles
2. separates turtles from lepidosaurs, instead nesting turtles with birds and crocs
3. separates iguanids from Sphenodon, instead nesting iguanids and Elgaria (alligator lizard) with snakes
4. separates geckos from snakes, instead nesting geckos with skinks
5. separates the finch (Taeniopygia guttata) from the chicken and turkey, instead nesting the finch as the basalmost neognath

The LRT:

1. nests mammals with birds and crocs, not lepidosaurs
2. nests turtles with lizards, not archosaurs
3. nests geckos with snakes, not skinks
4. nests iguanids at the base of all squamates, therefore closer to Sphenodon
5. nests Elgaria with Cryptolacerta (Eocene) and Ophisaurus (extant, not tested by Irisarri et al)

You might remember
molecules brought us the clade Afrotheria, a clade that includes elephants, aardvarks and golden moles, among a larger list of unrelated taxa

At present a certain amount of faith
attends gene sequencing, a hope that similar genes will translate to the appearance of similar body parts and proportions. Often that faith is rewarded. Other times, it is not. While DNA testing has proven its validity within genera (in crime labs and ancestry searches), the possibility of a ‘false positive’ using gene sequencing over larger phylogenetic distances occurs too often.

Ultimately
if you want to see how evolution works in tetrapods, molecules work for some nodes, not for others, and excludes fossil taxa. For more consistent results that deliver gradual accumulations of traits in derived taxa, using every sort of tetrapod taxa (including fossils), try morphology. It’s the benchmark against which molecules succeed sometimes and fail other times. I cannot yet unravel the pattern of false positives vs. verified positives.

Perhaps the worst aspect of DNA analysis:
it is correct often enough that some well-meaning scientist consider it flawless. At present only one person on the planet has produced a competing trait analysis that shows DNA analysis is flawed…sometimes.

References
Irisarri I et al. 2017. Phylotranscriptomic consolidation of the jawed vertebrate time tree. Nature ecology & evolution 1: 1370–1378. doi:10.1038/s41559-017-0240-5

Pavo, the super chicken!

Actually we’re talking about peafowl today,
(Figs. 1–4) larger and more elaborate sisters to domestic chickens in the LRT (Fig. 5).

Figure 1. Pavo, the peafowl, skull. Compare to Gallus, the chicken.

A very chicken-like skeleton
includes metatarsal spurs on Pavo (Fig. 2). Do these arise from a reinvigorating of pedal digit 5? At least the ‘parts’ (= genes) are in the ‘toolbox’ (cells) to do this. Perhaps this is a new expression of those genes, as in the new expression of digit zero in the manus of the screamer (genus Chauna).

Figure 2. Peafowl skeleton. Select bones colorized.

That giant famous tail on peacocks
does not prevent them from flying (Fig. 3).

Figure 3. Peacock flying.

The whole point of a peacock’s feathers
is to catch the eye of a choosy peafowl who will ultimately allow a suitable suitor to mate with her (Fig. 4).

Figure 4. The point of all those feathers and behaviors: peafowl mating. The males stands crouched upon the back and hips of the female.

Pavo nests with
Gallus (extant) and Eogranivora (Early Cretaceous), between the sparrow (Passer) and the corn crake (Crex) in the large reptile tree (LRT, 1201 taxa).

Figure 5. Subset of the LRT nesting Pavo the peafowl with Gallus the chicken.

Pavo cristatus (Linneaus 1758) The extant Indian peacock (peafowl) nests between Eogranivora and Gallus in the LRT. Only the male carries the extraordinary plumage.

References
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.

wiki/Peafowl

Bird phylogeny: molecules vs. morphology

A not so recent paper in Nature
by Prum 2015, employed phylogenemics (gene sequencing) to recover a cladogram of bird relationships. Earlier here, here and here we looked at problems with results recovered by that study.

Fig. 1. Cladogram from Cloutier et al. 2018 on palaeognath relations based on whole-genome analyses. Compare to figure 2 based on morphology.

A more recent paper
by Coutier 2018, also employed phylogenemics to recover a cladogram of palaeognath bird relationships. This one (Fig. 1) used a chicken (genus: Gallus) as a DNA outgroup.

Figure 2. Basal bird phylogeny based on the LRT (morphology). Palaeognaths are gray lines. Note, none of these early birds are great flyers. Those evolved later.

A manuscript to Nature
pointed out the fallacies of the results and the faith that paleontologists have put in their DNA studies based on comparisons to the trait studies that include fossil taxa in the large reptile tree (LRT, 1087 taxa, illustrated subset Fig. 2). I also reported a certain level of faith that attend all DNA studies. They hope they will recover tree topologies that will result in branches that demonstrate a gradual accumulation of traits (GATs). With birds, DNA studies too often do not produce GATs.

Nature declined to publish
the manuscript. It pointed out previously published errors (e.g. nesting flamingos with grebes, nesting the ostrich at the base of all birds and all paleognaths, nesting chickens and ducks together).

Like many academic publications,
novel discoveries are welcome in Nature. Critical reports that test those hypotheses, exposing overlooked flaws, are not so welcome. Why? Not only did the authors overlook their own flaws, but the editors at Nature and their hand-picked referees/reviewers also overlooked those flaws. Every time a publication or a scientist admits such errors they fear loss of prestige and/or confidence.

Remember when everyone thought
Yi qi had a large extra forelimb bone, and forgot to note the extra bones were actually just a displaced radius and ulna? Sometimes ‘the emperor has no clothes‘ is an apt metaphor. The solution may be plain to see, but some people just don’t see it.

At least now
the editors at Nature have seen that DNA studies should be considered acceptable only if they deliver the expected gradual accumulation of derived traits that is the benchmark by which all phylogenetic and phylogenomic studies must be measured.

You can read that manuscript
in MSWord/PDF format here. I will not submit it elsewhere.

The critical manuscript is titled:
“Bird phylogeny: false positives detected in a gene sequencing study.”

Abstract:
“Traditionally a matrix of taxa and physical traits provides data for phylogenetic analysis. In recent years gene sequencing has taken on a dominant role. Ideally both methods should recover identical family trees that model evolutionary events. Too often they do not. While DNA analysis has proven its validity within genera (e.g. criminal identification), here a competing morphological analysis (the only method that can include fossils) finds several false positives in the results of a recent gene sequencing study of crown clade birds. Unfortunately gene studies have to rely on the hope that they will recover a series of taxa with a gradual accumulation of physical traits that model evolutionary events—without using those physical traits. Based on this benchmark and the present results, it is inappropriate to circumvent direct observation with gene sequencing in bird studies, at least until gene sequencing study results mirror those based on morphology.”

Figure 2. Which taxa share more traits? Phoenicopterus, the flamingo nests with Cariama, the seriema in the LRT, but with Gavia in the Prum et al. DNA study. Gavia nests with Thalasseus, the tern in the LRT.

Bottom line: 
False positives plague DNA studies when tested against morphology. DNA studies can never employ ancient fossils. Why ignore great data?

No matter what your results are, at some time or another you’re going to have to validate DNA studies against trait studies… and HOPE they match.

References
Prum et al. (6 co-authors) 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526:569–573. online
Cloutier A et al. 2018. Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone. bioRxiv doi:10.1101/262949 PDF online

Monodon: THE weirdest skull of all mammals

Today two blogposts are published
because they relate strongly to one another. Here is the post on torsioned tenrec/odontocete skulls.

Figure 1. Distinct from most narwhals, this skull also has right tusk emerging from the canine position. And yes, that’s the maxilla covering most of the skull, even above the orbit! I added an eyeball here to help locate the orbit. The mesethmoid is the red bone that divides the naris (blow hole).

The narwhal (genus Monodon, Fig. 1)
is famous for having one giant spiral tooth sticking out ahead of its skull. Monodon also has one of the most bizarre skulls of all mammals and departs from that of all tetrapods, partly due to the root of the tooth and partly due to the migration of the nares to the back of the skull. Except for its tips, the jugal is missing. The maxilla, lacks teeth (if you don’t count the tusk) and rather than extending below the orbit, extends over the forehead, following the naris on its migration to the back of the skull. The bulbous portion of the skull, the cranium is made of parietals in most mammals, but the parietals are greatly reduced, nearly absent in Monodon.

Figure 2. The beluga, Delphinapterus, is closely related to, though less derived than the narwhal, Monodon. More teeth of a regular shape were present in the jaws. Those two yellow arrows indicate a misalignment of the centerline of the top of the occiput vs. the bottom. Compare to figure 3. The mesethmoid is the red bone in the blow hole. This skull is also bent left, as in the narwhal.

The sister taxon of the narwhal
is the beluga (genus: Delphinapterus). It helps one understand the narwhal a bit better. At least the beluga has a few traditional teeth. These two taxa nest together in the large reptile tree (LRT, 1087 taxa, Fig. 4).

Figure 3. Chonecetus has a more primitive skull with nares closer to the snout tip and no maxilla above the orbit. Not a transitional taxon to baleen whales, which have another separate origin. This drawing lacks any indication of torsion, perhaps because the back half was separated from the front half and the artist ‘repaired’ the twist.

Less derived and more primitive
is Chonecetus (Fig. 3), which has nares closer to the snout tip, and more teeth, and more cranium. This taxon and its sister, Aetiocetus, have been traditionally considered transitional from toothed whales to baleen whales, like Balaenoptera, but baleen whales have an entirely separate ancestry derived from desmostylians, like Desmostylus.

Figure 4. Subset of the LRT focusing on the tenrec/odontocete clade with several whales added.

A recent paper on Monodon tusks (Nweeia et al. 2012)
found “the narwhal tusks are the expression of canine teeth and that vestigial teeth have no apparent functional characteristics and are following a pattern consistent with evolutionary obsolescence.” (See Figs. 5, 6).

Figure 5. Image from Nweeia et al. 2012 showing the unerupted right tusk and the root of the left tusk in the male narwhal along with two unerupted tusks in the female. Note the angle of the posterior skull relative to the anterior midline.

In dorsal or ventral view
it is clear that the the tusk (left) side of the skull is longer than the right side due to angling the posterior skull relative to the rostrum.

Figure 6. CT scans of a female narwhal (Monodon) showing soft tissues and unerupted teeth. Note the angle of the posterior skull relative to the anterior. The left side, the tusk side, is shorter than the right side in figure 5, so the label ‘ventral’ is an error here. This is a dorsal view of the female skull in figure 5. Always test scale bars and labels.

I wonder about the bending of the skull
toward the left in these two whales. Could asymmetry have anything to do with stereo auditory senses? Asymmetry is also found in owl skulls, another taxon that depends strongly on acute hearing for locating prey.

Figure 7. Fetal narwhal skull, here colorized from Nweenia et al. 2012. The jugal disappears in adults. The asymmetry is already apparent here.

Figure 8. Common bottle nose dolphin skull (genus: Tursiops) also displays a bit of asymmetry in dorsal view. Note the yellow arrows on the parietal showing the wee bit of torsion here. 

Update:
With 1187 taxa and 231 traits full resolution was recovered in the LRT after running PAUP FOR 16 minutes and 15 seconds. The single best tree has 16,329 steps.

References
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.’
Nweeia MT et al. (9 co-authors) 2012. Vestigial tooth anatomy and tusk nomenclature for Monodon monoceros. The Anatomical Record 295:1006–1016.
Pallas PS 1766. Miscellanea Zoologica.

wiki/Narwhal
wiki/Beluga_whale

Torsioned odontocete skulls go back to tenrecs

Today two blogposts are published
because they relate strongly to one another. Shortly there will be a post on Monodon, the narwhal, which introduced me to whale skull asymmetry, which I then researched and found the following study from 2011.

Figure 1. Skull asymmetry in odontocete whales from Fahlke et al. 2011.

A paper by Fahlke et al. 2011 reported,
“Eocene archaeocete whales gave rise to all modern toothed and baleen whales (Odontoceti and Mysticeti) during or near the Eocene-Oligocene transition. Odontocetes have asymmetrical skulls, with asymmetry linked to high-frequency sound production and echolocation.” 

This is not true
when more taxa are added to a phylogenetic analysis looking at whales. Archaeocetes are not basal to baleen whales (Mysticeti) in the LRT.

Figure 2. Hemicentetes an extant echolocating tenrec, also has a twisted skull, like its descendants, the odontocete whales. The direction is opposite in this image. Could be a result of the scanning technique (mirroring the image) or a real trait.

Fahlke et al. did not look at tenrecs,
which nest basal to archaeocetes and pakicetids in the large reptile tree (LRT, 1187 taxa). Hemicentetes (Fig. 2) echolocates (Gould 1965) and travels in pods — and it has a torsioned skull (Fig. 2). Baleen whales (mysticetes) had a separate ancestry with desmostylians, apart from archaeocetes.

A torsioned skull further cements tenrecs to archaeocetes and odontocetes. Fahlke et al. did not look at desmostylians either.

Taxa basal to tenrecs
in the LRT, like the elephant shrew, Rhynchocyon, do not have a torsioned skull. So that trait originated with a sister to Hemicentetes.

In an interview, Fahlke reported, 
“This means that the initial asymmetry in whales is not related to echolocation,” said Fahlke, who is working with Philip Gingerich, an internationally recognized authority on whale evolution, at the U-M Museum of Paleontology.

Oh, yes, asymmetry is related to echolocation!
Expand that taxon list to tenrecs, read Gould (1965) and everything will fall into place. The origin of echolocation in the ancestors of whales goes back to the mid-Cretaceous, based on the separation of Madagascar (where tenrecs live) from Pakistan and India (where whale ancestors like the tenrec, Indohyus) are found.

Fahlke’s backstory from the U. of Michigan webpage:
“The actual skull on which the model was based was noticeably asymmetrical, but Fahlke and colleagues at first dismissed the irregularity.

“We thought, like everybody else before us, that this might have happened during burial and fossilization,” Fahlke said. “Under pressure from sediments, fossils oftentimes deform.” To correct for the deformation, coauthor Aaron Wood, a former U-M postdoctoral researcher who is now at the University of Florida, straightened out the skull in the digital model. But when Fahlke began working with the “corrected” model, the jaws just didn’t fit together right. Frustrated, she stared at a cast of the actual skull, puzzling over the problem.

“Finally it dawned on me: Maybe archaeocete skulls really were asymmetrical,” Fahlke said. She didn’t have to go far to explore that idea; the U-M Museum of Paleontology houses one of the world’s largest and most complete archaeocete fossil collections. Fahlke began examining archaeocete skulls, and to her astonishment, “they all showed the same kind of asymmetry?a leftward bend when you look at them from the top down,” she said.”

References
Fahlke JM,  Gingerich PD, Welsh RC and Wood AR. 2011. Cranial asymmetry in Eocene archaeocete whales and the evolution of directional hearing in water. PNAS 108 (35) 14545-14548; https://doi.org/10.1073/pnas.1108927108
Gould E 1965. Evidence for Echolocation in the Tenrecidae of Madagascar
Proceedings of the American Philosophical Society 109 (6): 352-360. online here.
Huggenberger S, Leidenbere S and Oelschläger HHA 2018. Asymmetry of the nasofacial skull in toothed whales (Odontoceti). Journal of Zoology DOI: 10.1111/jzo.12425

https://pterosaurheresies.wordpress.com/2016/07/23/tenrecs-and-echolocation/

U of Michigan story on the Fahlke team’s discovery here

Moloch horridus, the desert thorny devil, has a jungle gliding relative

Is this a case of taxon exclusion?
Perhaps… and yet, given the present taxon list, the thorny devil and the flying dragon are more closely related to each other than to any other taxa in the large reptile tree (LRT, 1087 taxa, Fig. 7).

Figure 1. Moloch in vivo. At present this is the closest relative of the flying dragon, Draco volans, in the LRT. That suggests a few more intervening taxa could be added.

With taxon exclusion, sometimes things like this happen.
The large reptile tree (LRT, 1087 taxa) has just a few agamid iguanids in its taxon list. The addition of the Australian thorny devil, Moloch horridus (Gray 1841), and its nesting with the SE Asian gliding dragon, Draco volans, reminds us that other well-known agamid lizards, like bearded dragons, would probably nest between them.

Figure 2. Skull of Moloch horridus, from Digimorph.org, with bones colored here. Note the maxillary teeth visible through the orbit in DORSAL view. The maxillary teeth are medially oriented. Grayscale image from Digimorph.org and used with permission.

It’s also notable
that the thorny devil does not nest with the similar but more distantly related horned lizard (Phyrnosoma, Fig. 6) of Western North America.

Figure 3. Skeleton of Moloch from Digimorph.org with certain bones colorized here. Note the fewer finger and toe bones. Dermal spikes shown in gray.

 

Figure 4. Draco volans. Note the anterior maxillary fangs, and the antorbital fenestra between the lacrimal and prefrontal, traits shared with Chlamydosaurus (Fig 2). Not the wide prefrontals, as in Moloch.

Lyriocephalus is the last common ancestor
to Draco and Moloch in the LRT. We looked at the skull and skeleton of Lyriocephalus (Fig. 5) earlier here.

Figure 5. Lyriocephalus in vivo.

Curious if the ancestors of Moloch 
experienced a loss of jungle habitat and so adapted to scrub and dessert niches, since sisters and ancestors are jungle iguanids.

Figure 6. Phyronosoma, the horned lizard of North America.

For that matter
desert-dwelling horned lizards are most closely related to jungle-dwelling chameleons, like Trioceros, in the LRT (Fig. 7). Did horned lizards experience a similar loss of jungle? If so, that probably happened before the advent of the odd hands and feet of extant chameleons.

Figure 7. Subset of the LRT focusing on the Iguania. Gray box are extinct taxa.

The clade Iguania
(Fig. 7) goes back to the Early Permian with the MNC TA1045 specimen wrongly attributed to Ascendonanus, which we looked at earlier here and here.

References
Gray JE 1841. Description of some new species and four new genera of reptiles from Western Australia, discovered by John Gould, Esq.: Ann. Mag. Nat. Hist. (1) 7: 86-91.

Avicranium: a 3D drepanosaur skull

Pritchard and Nesbitt 2017
bring us a new Late Triassic drepanosaur, Avicranium renestoi, AMNH FARB 30834, based on CT scanning a crushed skull and reconstructing it digitally (Fig. 1). I added a little distance between the anterior and posterior elements in order to get a rounder orbit. I also restored the missing ascending process of the premaxilla and nasal.

Figure 1. Avicranium from Pritchard and Nesbitt 2017, in situ, original reconstruction and revised with rostral restoration in accord with the plesiomorphic drepanosaur, Vallesaurus. Distinct from Vallesaurus, Avicranium has a concave maxilla and lacks teeth. That long convex squamosal is unique.

The new reconstructed skull
looks like a little oviraptorid (Fig. 2)— strictly by convergence.

Figure 2. Khaan, an oviraptorid, has a skull similar to that of Avicranium.

The closest sister taxon of Avicranium
in the large reptile tree (LRT, 1087 taxa) is the drepanosaur, Vallesaurus based on the skull alone. Pritchard and Nesbitt nested Avicranium as a drepanosaur based on the cervical vertebrae (Fig. 1) and noticed ‘striking similarities’ to birds. The difference includes the crooked jaw line, perhaps related to the absence of teeth in Avicranium.

Figure 2. Vallesaurus is a sister to Avicranium in the LRT.

Pritchard and Nesbitt nested
drepanosaurs uncertainly, reporting “A phylogenetic analysis of Permo-Triassic diapsids supports the hypothesis that drepanosaurs are an archaic lineage that originated in the Permian, far removed from crown group Reptilia.” They did not realize their clade ‘Diapsida’ was actually diphyletic, with lepidosauriformes arising convergently with archosauriformes. The authors did not include taxa that nested basal to drepanosaurs in the LRT including Jesairosaurus, Palaegama and Saurosternon even those these have been on the Internet for several years. In fact, their figure 4 cladogram shows no outgroups for the Drepanosauromorpha, a very dangerous phylogenetic proposition. By contrast the LRT provides certain and verified outgroups back to Devonian tetrapods.

Figure 4. Subset of the LRT focusing on drepanosaurs and Avicranium.

So once again taxon exclusion obscures relationships.
All Pritchard and Nesbitt had to do was to go online for some taxonomic suggestions and their unsolved problem would have been quickly remedied using their own character list. Are paleo-workers trying to avoid taxa offered for testing by the LRT? It would seem so given the present circumstances. Would it tear down the walls if someone knowingly confirmed the present hypothesis of interrelationships?

Well, that’s not going to happen,
except, as we’ve seen, without citation.

References
Pritchard AC and Nesbitt SJ 2017. A bird-like skull in a Triassic diapsid reptile increases heterogeneity of the morphological and phylogenetic radiation of Diapsida. Royal Society Open Science DOI: 10.1098/rsos.170499

wiki/Avicranium

Help fix ‘Dracula’ the giant Romanian pterosaur

This comes from a press release with photos,
not an academic paper. Evidently there is a new giant azhdarchid pterosaur named Dracula, known from ‘a majority of bones’, from which the following museum mount was created (Fig. 1).

Figure 1. Dracula the giant azhdarchid pterosaur museum mount. Hopefully it’s not too late to fix the problems here. Most will just take some twisting, some disassembly and reassembly.

Here are the visible problems:

1. The ridged sternal complex looks like it was created from gastralia. No other sternal complex has such ridges and those from azhdarchids are not big and square.
2. Fingers 1–3 are located laterally. They should be medially.
3. The pteroid should anchor on the radiale (not the ulnare), the pre-axial carpal on the medial side of the distal carpal. And the pteroid should always point back to the deltopectoral crest.
4. In azhdarchids m4.4 is always tiny,
5. This looks like a dinosaur pterygoid.
6. Pedal digit 5 should be on the lateral side of the foot.
7. Twist metacarpal 4 90º laterally so the wing finger extends posterior to the forelimb.

Translated from German:
“In Denkendorf you can now marvel at a bone of “Dracula”, several dozen other bone fragments of the animal are located in Florida, where they are scientifically studied with elaborate technology. A publication on the sensation finding, the researchers have announced for the fall. Until then, “Dracula” remains only the unofficial name of the pterodactyl.”

Maybe it is all based on just the one cervical and some shards. We’ll find out later.

Some links below,
courtesy of Ben Creisler on the Dinosaur Mailing List.

http://www.donaukurier.de/nachrichten/panorama/Denkendorf-DKmobil-Dracula-in-Denkendorf;art154670,3721531

https://www.n-tv.de/wissen/Museum-stellt-Riesensaurier-Dracula-aus-article20350242.html

Colobops and taxon exclusion issues

Too often workers fail to include the closest relatives of new specimens
in analysis and then report they have something new and different in the pantheon of tetrapods. Too often the analysis lacks the correct tree topology, also due to taxon exclusion.

The new genus, Colobops noviportensis
(Pritchard, Gauthier, Hanson, Bever and Bhullar 2018; Fig. 1) was described as a tiny (2.5 cm long skull) saurian reptile from the Triassic of Connecticut, USA. Taxonomically it suffers from taxon exclusion. It was nested by default because more closely related taxa were omitted from a previously published analysis (Pritchard and Nesbitt 2017; Fig. 2), which was an inadequate analysis to work from because it failed to show the basal dichotomy of the Reptilia (Lepidosauromorpha/Archosauromorpha; Fig. 3) revealed by increasing the number of taxa.

Figure 1. Colobops as originally presented and slightly restored. Glad to see other workers are coloring bones or identification. These are from CT scans. The postorbital processes invading the supratemporal fenestrae are unique.

From the abstract
“The taxon possesses an exceptionally reinforced snout and strikingly expanded supratemporal fossae for adductor musculature relative to any known Mesozoic or Recent diapsid of similar size. Our phylogenetic analyses support C. noviportensis as an early diverging pan-archosaur. Colobops noviportensis reveals extraordinary disparity of the feeding apparatus in small-bodied early Mesozoic diapsids, and a suite of morphologies, functionally related to a powerful bite, unknown in any small-bodied diapsid.”

Figure 2. Marmoretta, a basal rhynchocephalian in the lineage of pleurosaurs. Note the variety in the size of the supratemporal (upper) fenestrae, a variety that expands with Colobops.

Unfortunately,
their phylogenetic analysis (Fig. 3) did not include the basal sphenodontid, Marmoretta, more similar to Colobops in the large reptile tree (LRT, 1085 taxa; subset Fig. 4) than any other tested taxon. They are also the same size.

Figure 3. Cladogram from Pritchard et al. failed to include a long list of basal sphenodontians, including Marmoretta, the sister to Colobops in the LRT. Note the shuffling of lepidosauromorph and archosauromorphs in this cladogram, lacking any broad resemblance to the LRT tree topology. Pritchard et al. assume that diapsids are monophyletic, which dooms their analysis. There is so much taxon exclusion here.

Marmoretta oxoniensis (Evans 1991, Waldman and Evans 1994) Middle/Late Jurassic, ~2.5 cm skull length, orginally considered a sister of kuehneosaurs, drepanosaurs and lepidosaurs. Here Marmoretta was derived from a sister to Megachirella and Palaegama. Marmoretta was basal to Gephyrosaurus and the rest of the Sphenodontia = Rhynchochephalia. Two specimens are known (Fig. 2) with distinct proportions in the skull roof (frontal and parietal, see above). Note the variety in the supratemporal fenestrae in these closely related tiny flat-headed taxa, including Colobops.

By the way,
the Wikipedia page on Marmoretta likewise suffers from taxon exclusion.

Figure 4. Cladogram of the Sphenodontia includes Colobops and rhynchosaurs.

Pritchard et al. assumed the monophyly of the Diapsida
which doomed their cladogram to a shuffling of disparate morphologies and by-default nestings (Fig. 3). Several years ago the LRT split the Archosauromorpha from the Lepidosauromorpha at the origin of the Reptilia, and so revealed that the diapsid skull architecture evolved at least twice.

Pritchard et al. nested Colobops
at the base of the Rhynchosauria due to taxon exclusion. In the LRT (subset Fig. 4) rhynchosaurs and Colobops are separated by a long list of taxa. The authors reported, “Two additional steps produce topologies in which C. noviportensis occupies some positions with pan-Archosauria and a position nested within Sphenodontia, a clade that converged anatomically on rhynchosaurs in numerous skull characters.”

If only
Pritchard et al. had used more taxa (or the LRT) they would have known that sphenodontids did not converge with rhynchosaurs, they were basal to rhynchosaurs. The authors report, “Colobops noviportensis represents a combination of morphological traits unknown in extant amniotes, and thus a morphology that would not have been reconstructed in a macroevolutionary analysis based exclusively on extant species.” I don’t see the extant tuatara, Sphenodon. in their taxon list.

Colobops lacks teeth
and lacks alveoli as well. The authors report, “The best insights into the feeding of C. noviportensis come from the general shape of the adductor chamber. In C. noviportensis, the post-temporal process of the parietal is oriented laterally, as in Sphenodontia and Rhynchosauridae, rather than posterolaterally as in most pan-lepidosaurs and pan-archosaurs.” See how they were just peeking in at the insights revealed by the LRT? Yet they followed tradition and previously published phylogenetic analyses beset with problems from the start.

The adductor chambers for jaw muscles in Colobops
are indeed quite large. And the postorbital process that invades the supratemporal fenestra is unique (at present). Sister sphenondontids do not have such a large supratemporal fenestra until Sphenodon. Note that one of the Marmoretta specimens (Fig. 2) had developed a parietal crest, also for the enlargement of the jaw muscles. So they were trying various ways to do this.

Based on the similar sizes of the marmorettid skulls
the skull of Colobops probably represents an adult.

The authors report
“Within individual species, overall skull size appears to correlate strongly with the relative breadth of the adductor chamber; juveniles recapitulate the transition from Permian Diapsida to crown-group with a small supratemporal fossa with small proportionally modest embayments on the parietal giving way to proportionally larger fossae and deeper parietal embayments.” Good to know. Irrelevant in this case.

I’m happy to see these authors have colorize key bones
throughout their paper. That’s the best way to illustrate them.

The final takeaway:
No matter how many co-authors you have with PhDs… no matter how many diagrams you show… no matter how many irrelevant taxa you include… no matter if you have firsthand access to the specimen… no matter if you are published in Nature… if you exclude the most closely related taxa, you’re going to let bloggers report your most basic errors. The LRT is online in order to be freely used. Use it. It’s a good starting point for any new taxon because it minimizes the opportunity for taxon exclusion by including so many taxa.

References
Evans SE 1991. A new lizard−like reptile (Diapsida: Lepidosauromorpha) from the Middle Jurassic of Oxfordshire. Zoological Journal of the Linnean Society 103:391-412.
Pritchard AC and Nesbitt SJ. 2017. A bird-like skull in a Triassic diapsid reptile increases heterogeneity of the morphological and phylogenetic radiation of Diapsida. Royal Society Open Science 4, 170499
Pritchard AC, Gauthier JA, Hanson M, Bever GS and Bhullar B-AS 2018. A tiny Triassic saurian from Connecticut and the early evolution of the diapsid feeding apparatus. Nature Communications open access DOI: 10.1038/s41467-018-03508-1
Waldman M and Evans SE 1994. Lepidosauromorph reptiles from the Middle Jurassic of Skye. Zoological Journal of the Linnean Society 112:135-150.

wiki/Marmoretta

 

 

You heard it here first: Orovenator had diapsid AND varanopid traits—for good reason!

This is a YouTube video of a
talk given by postgraduate David Ford recorded at The 65th Symposium on Vertebrate Palaeontology and Comparative Anatomy, University of Birmingham. His incredibly detailed  observations found diapsid traits AND varanopid traits, which was cause for consternation. Click to view.

Ford used µCT data
to recover in Ororvenator what the large reptile tree (LRT, 1181 taxa) was able to recover from published drawings. Ford nested Orovenator and Synapsida within Diapsida. Although heretical, that’s not the correct solution when you add more pertinent taxa.

By contrast, in the LRT
basal synapsids split at their genesis between Synapsida and Prodiapsida following Vaughnictis, another late-surviving taxon. Ford was unaware of that split at the time. In the LRT, late-surviving early Permian Orovenator was derived from basal synapsids (varanopids) AND ancestral to basal diapsids like Petrolacosaurus in the Late Carboniferous.

We looked at Orovenator relationships earlier
here in 2014 and here in 2017. Key to testing any taxonomic relationships is appropriate taxon inclusion. Let’s hope Ford has expanded his taxon inclusion set appropriately when the paper comes out. He’s got a good handle on the details, but the big picture evidently was not in his ken due to the exclusion of pertinent taxa.

Figure 2. The Prodiapsida now include the holotypes of Ascendonanus and Anningia.