Isistius: the cookie cutter shark, enters the LRT, as a lamprey mimic

The latest addition to the LRT,
Isistius brasiliensis, the extant cookie-cutter shark (Figs. 1–3), was a puzzle to try to figure out, given that the entire skull turned to cartilage and can only be figured out by looking at the bumps and valleys, along with the overall proportions.

To no one’s surprise,
Isistius
nests in the LRT with other small cigar-shaped sharks with large eyeballs, including Carboniferous Falcatus.

Figure 1. Isistius, the cookie cutter shark animated.

Figure 1. Isistius, the cookie cutter shark animated.

Perhaps more importantly,
this taxon addition sparked another look at all the sharks and rays, based on phylogenetic bracketing

Figure 2. Isistius brasiliensis in several views.

Figure 2. Isistius brasiliensis in several views.

But that can only take place
in a valid phylogenetic context, so the shark subset of the large reptile tree (LRT, 1770 taxa) itself came under scrutiny. You might recall, I knew nothing about fish anatomy a year ago when I started posting sharks to the LRT trying to use tetrapod homologs for skull bones. Tinkering remains a good way to learn and not be hamstrung by outdated traditions sometimes found in textbooks.

Figure 3. Isistius skull. Note all the former bones are now fused together into a precise lump of cartilage.

Figure 3. Isistius skull. Note all the former bones are now fused together into a precise lump of cartilage.

Here are the phylogenetic results
subject to further improvements.

Figure x. Subset of the LRT focusing on sharks.

Figure x. Subset of the LRT focusing on sharks.

Isistius brasiliensis
(Quoy and Gaimard 1824) is the extant cookiecutter shark, a living sister to Falcatus. This deep-water shark has light-emiting photophores covering its underside. It migrates to the surface every day to take a circular bite out of giant whales and sharks. In this way it can be seen as a sort of lamprey-mimic. Isistius also consumes smaller free-swimming prey, like squid. Note the anterior nostrils and larger dentary teeth.


References
Quoy JRC and Gaimard JP 1824–1825. des Poissons. Chapter IX”. In de Freycinet, L (ed.). Voyage autour du Monde…exécuté sur les corvettes de L. M. “L’Uranie” et “La Physicienne, pendant les années 1817, 1818, 1819 et 1820. Paris 192–401.

wiki/Isistius

The LRT confirms a 2015 paper: sharks had a semi-bony past

Long et al. 2015
described a few bits and pieces from a Late Devonian shark, Gogoselachus (Fig 1), with a “highly distinctive type of calcified cartilage forming the endoskeleton.”

I came across this 2015 paper a few days ago, long after sharks nested as taxa derived from cartilaginous sturgeon and semi-bony paddlefish ancestors in the Large Reptile Tree (LRT, 1744+ taxa, subset Fig. 2). So having a basal shark with ‘calcified cartilage’ comes as no surprise to the LRT.

Figure 1. Gogoselache restoration based on the few parts shown here.

Figure 1. Gogoselache restoration based on the few parts shown here from Long et al. 2015.

From the Long et al. ‘Background’
“Living gnathostomes (jawed vertebrates) comprise two divisions, Chondrichthyes (cartilaginous fishes, including euchondrichthyans with prismatic calcified cartilage, and extinct stem chondrichthyans) and Osteichthyes (bony fishes including tetrapods).”

This is the traditional view of fish interrelations, the one told in lectures and textbooks. See figure 2 for the more complete LRT view.

“Most of the early chondrichthyan (‘shark’) record is based upon isolated teeth, spines, and scales, with the oldest articulated sharks that exhibit major diagnostic characters of the group—prismatic calcified cartilage and pelvic claspers in males—being from the latest Devonian, c. 360 Mya. This paucity of information about early chondrichthyan anatomy is mainly due to their lack of endoskeletal bone and consequent low preservation potential.”

Figure x. Subset of the LRT focusing on fish.

Figure 2. Subset of the LRT focusing on fish.

From the Long et al. 2015 Methodology/Principal Findings
“Here we present new data from the first well-preserved chondrichthyan fossil from the early Late Devonian (ca. 380–384 Mya) Gogo Formation Lägerstatte of Western Australia. The specimen is the first Devonian shark body fossil to be acid-prepared, revealing the endoskeletal elements as three-dimensional undistorted units: Meckel’s cartilages, nasal, ceratohyal, basibranchial and possible epibranchial cartilages, plus left and right scapulocoracoids, as well as teeth and scales. This unique specimen is assigned to Gogoselachus lynnbeazleyae n. gen. n. sp.”

From the Long et al. 2015 Conclusions/Significance
“The Meckel’s cartilages show a jaw articulation surface dominated by an expansive cotylus, and a small mandibular knob, an unusual condition for chondrichthyans.”

In the LRT the Meckel’s cartilages are scored as fused mandible bones based on ancestral states in which the mandible bones are not fused.

“The scapulocoracoid of the new specimen shows evidence of two pectoral fin basal articulation facets, differing from the standard condition for early gnathostomes which have either one or three articulations.”

“The tooth structure is intermediate between the ‘primitive’ ctenacanthiform and symmoriiform condition, and more derived forms with a euselachian-type base.”

Of special interest is the highly distinctive type of calcified cartilage forming the endoskeleton, comprising multiple layers of nonprismatic subpolygonal tesserae separated by a cellular matrix, interpreted as a transitional step toward the tessellated prismatic calcified cartilage that is recognized as the main diagnostic character of the chondrichthyans.”

In the LRT phylogenetic analysis, rather than a few interesting and traditionally unexpected traits, elucidates interrelationships. Having bony traces in a basal shark skeleton could have been predicted from the LRT, but the fish portion of the LRT came later, this time providing confirmation rather than prediction.

The Long et al. 2015 paper
earned a fair bit of publicity five years ago.

From Phys.org
“Fossil ancestor shows sharks have a bony past.
This study further supports the idea that sharks must have evolved from bony primitive ancestors and lost their bone early on in the race as they acquired their predatory body shape.”

From: theconversation.com
“No bones about it. Sharks evolved cartilage for a reason.
Most people know that sharks have a distinctive, all-cartilage skeleton, but now a fossil from Western Australia has revealed a surprise ‘missing link’ to an earlier, more bony form of the fish.”

“In testing fossil remains discovered by Professor Long in July 2005 at Gogo in the Kimberley in Western Australia, detailed CT scanning analysis has shown that the three-dimensional remnant skeleton contains a small proportion of bone as well as cartilage.”

“Because sharks and rays have entirely cartilaginous skeletons, Professor Long said it was traditionally thought that they were part of a primitive evolutionary pathway, and that bone in other fish was the more advanced condition. But a series of discoveries in recent years has suggested that sharks are “more evolutionarily derived”, and are likely to be descended from bony ancestors.”


References
Long JA, Burrow CJ, Ginter M, Maisey JG, Trinajstic KM, et al. 2015. First Shark from the Late Devonian (Frasnian) Gogo Formation, Western Australia Sheds New Light on the Development of Tessellated Calcified Cartilage.” PLoS ONE10(5): e0126066. DOI: 10.1371/journal.pone.0126066

Was the first dinosaur egg soft?

Norell et al. (8 co-authors) 2020
used phylogenetic bracketing to determine that the first dinosaur egg (still unknown) was soft. They made one mistake that invalidates their phylogenetic bracket (Fig. 1).

Figure 1. From Norell et al. 2020 misleading readers by placing pterosaurs, Lagerpeton and Silesaurus in the lineage of dinosaurs after crocodylomorphs.

Figure 1. From Norell et al. 2020 misleading readers by placing pterosaurs, Lagerpeton and Silesaurus in the lineage of dinosaurs after crocodylomorphs.

From the Norell et al. abstract:
“However, pterosaurs—the sister group to dinosauromorphs—laid soft eggs.”

Simply adding taxa reveals this is wrong.
In the large reptile tree (LRT, 1698+ taxa) pterosaurs nest within Lepidosauria. The pterosaur – dinosaur myth was invalidated by Peters 2000, 2007. So we have to toss out pterosaurs as an invalid nesting. What are we left with?

According to Norell et al.
Crocodylia create rigid calcite eggs. So do members of the Theropoda (including birds). So do members of the phytodinosaur clades, Ornithopoda and Macronaria. Exceptions occur among the highly derived Ceratopsia, which lay soft eggs. Two more exceptions include the primitive sauropodomorphs, Massospondylus and Mussaurus. More importantly, egg shellls remain unknown for basal poposaurs, basal crocodylomorphs, basal theropods and basal phytodinosaurs.

When we use phylogenetic bracketing to make a statement like this
we need to be sure that we have the proper phylogeny. Norell et al. relied on tradition and myth rather than testing. They were wrong. In their claodgram, Norell et al. are hopeful that pterosaurs arose between crocodylomorphs and Lagerpeton (a bipedal proterochampsid also not related to dinosaurs). The Norell et al. cladogram was invalidated by Peters 2000 using four prior phylogenetic analyses. Those citations do not appear in Norell et al. (fufilling Bennett’s curse). In the LRT Silesaurus is a poposaur and thus a dinosaur-mimic, less related to dinosaurs than crocodylomorphs.

When we find eggs for Herrerasaurus and Eoraptor
then we can send a manuscript to Nature. Norell et al. were premature at best, misleading and myth perpetuating at worst. That the referees considered this manuscript okay to publish shows the dinosaur – pterosaur myth is still widespread and deeply entrenched, as discussed earlier here.


References
Norell et al. 2020. The first dinosaur egg was soft. Nature https://doi.org/10.1038/s41586-020-2412-8
Peters D 2000b. A Redescription of Four Prolacertiform Genera and Implications for Pterosaur Phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106 (3): 293–336.
Peters D 2007. The origin and radiation of the Pterosauria. In D. Hone ed. Flugsaurier. The Wellnhofer pterosaur meeting, 2007, Munich, Germany. p. 27.

https://www.cnn.com/2020/06/17/world/soft-dinosaur-eggs-scn/index.html
https://www.cnet.com/news/soft-shelled-dinosaur-eggs-crack-the-mystery-of-missing-fossils/

Helodus: a skull without sutures

Decades prior to PAUP and MacClade,
Professor Moy-Thomas 1936 reasoned that Helodus simplex (Fig. 1; Agassiz 1838; Early Carboniferous, 300mya, 30cm long) ) was close to the ancestry of the clade Holocephalii (ratfish, chimaeras and kin; Fig. 2), which we looked at yesterday. In complete accord, the large reptile tree (LRT, 1641 taxa; subset Fig. 3) fully supports that nesting using modern software: PAUP and MacClade. So… belated well done, Professor Moy-Thomas!

Figure 1. Helodus skull drawings from xxx 1938 show no skull sutures. Colors are applied with blending edges to show were bones are based on tetrapod homologs.

Figure 1. Helodus skull drawings from Moy-Thomas 1936 show no skull sutures. Colors are applied with blending edges to show were bones are based on tetrapod homologs. Gill bars are missing from these diagrams, so were added in light blue here.

In Helodus
the skull bones are all fused together, so suture estimates are provided here (Fig. 1) based on phyogenetic bracketing. Note the tiny premaxillary teeth and complex maxillary teeth. Tabulars appear to be absent. Note the coosified cervicals / anterior dorsals extending to the notochord and first dorsal spine.

Moy-Thomas 1936
considered the anatomy of Helodus in detail. From the abstract:

  1. “The skull is found to be holostylic, and to have many characters in common with the skull of the Holocephali, but in some respects is less specialized.
  2. The pectoral fins, with their long metapterygium, small propterygium, and fused anterior radials, resemble very closely those of the Holocephali.
  3. The pelvic and unpaired fins, and general body shape are found to resemble those of the Holocephali.
  4. It is concluded that the Cochliodonts are almost certainly closely related to the ancestors of the Holocephali, and the relatively unspecialized condition of the teeth gives support to the view that the holostylic condition of the jaws is primitive for the group. It is suggested that all the Bradyodonts were holostylic, that the hyomandibular may never have been suspensory, and that they may have diverged from the true Selachii before the hyomandibular played a part in the jaw suspension.”
FIgure 1. Ratfish (chimaera) and Heterodontus to scale.

FIgure 2. Ratfish (chimaera) and Heterodontus to scale.

 

Taking one phylogenetic step further back from Helodus,
yesterday we looked at Heterodontus (Fig. 2), the Chondrichthyes taxon phylogenetically ancestral to Helodus and the Holocephalii.

Figure 5. Subset of the LRT focusing on basal chordates, vertebrates and bony fish not related to tetrapods. Scomber and Istiophorus are new additions to the gold clade.

Figure 5. Subset of the LRT focusing on basal chordates, vertebrates and bony fish not related to tetrapods. Scomber and Istiophorus are new additions to the gold clade.

References
Agassiz L 1838. Recherches Sur Les Poissons Fossiles. Tome III (livr. 11). Imprimérie de Petitpierre, Neuchatel 73-140.
Moy-Thomas JA 1936. On the Structure and Affinities of the Carboniferous Cochliodont Helodus simplex. Cambridge University Press. 73(11):488–503.

wiki/Chondrichthyes
wiki/Chimaera
wiki/Cladoselache
wiki/Chondrosteus
wiki/Symmoriida
wiki/Horn_shark
wiki/Helodus not listed in English

New Champsosaurus paper perpetuates old myths

Whenever taxon exclusion mistakes are made and reviewed here,
I try to write to the lead author of the paper. Below is a recent email directed to Professor Dudgeon et al. 2020 on their recent review of the well-preserved skull of Champsosaurus (Figs. 1, 3), which they re-examined using computed tomography analysis.

Figure 1. Champsosaurus from Dugeon et al. Here the nasal is the ascending process of the premaxilla. The prefrontal is the nasal fused to the prefrontal. The postorbital is the postfrontal and vice versa.

Figure 1. Champsosaurus from Dugeon et al. Here the nasal is the ascending process of the premaxilla. The prefrontal is the nasal fused to the prefrontal. The postorbital (pro) is the postfrontal (pof) and vice versa.

Dear Dr. Dudgeon:

It’s always good to see new studies on old skulls.

Based on phylogenetic bracketing the bone traditionally identified as the ‘nasal’ is the ascending process of the premaxilla. That makes the purported ‘prefrontal’ a fused nasal + prefrontal. The postorbital and postfrontal are mislabeled with the other bone identity based on Tchoria (Fig. 2), a taxon not mentioned in your text. See attached.

Choristoderes are not ‘neodiapsid reptiles.’ Phylogenetically they are archosauriformes arising from Proterosuchus, Elachistosuchus and Tchoria. Phylogenetic miniaturization in that lineage lost the antorbital fenestra. See links below.

https://pterosaurheresies.wordpress.com/2013/08/13/champsosaurus-and-its-snorkel-nose/
http://reptileevolution.com/reptile-tree.htm
http://reptileevolution.com/champsosaurus.htm
http://reptileevolution.com/youngina-bpi2871.htm
http://reptileevolution.com/hyphalosaurus.htm
http://reptileevolution.com/lazarussuchus.htm

Best regards,

Figure 1. Tchoria and phylogenetic bracketing help identify bones in the skull of Champsosaurus (Fig. 2).

Figure 2. Tchoria and phylogenetic bracketing help identify bones in the skull of Champsosaurus (Fig. 2).

So, the Dudgeon et al. paper
is yet another great example of a situation in which phylogenetic analysis and bracketing (= comparing related taxa) sheds more light on a specimen than high-resolution micro-computed tomography scanning and/or adding characters (= looking more deeply into one taxon to the exclusion of others).

Figure 2. Champsosaurus skull with premaxilla in yellow.

Figure 3. Champsosaurus skull with premaxilla in yellow, nasal + prefrontal in pink. Bone identities determined by phylogenetic bracketing with Tchoria. See figure 2.

The greatest benefit 
available from the large reptile tree (LRT, 1631 taxa) is this sort of phylogenetic bracketing based on the validated nesting of sisters that have never been tested together in prior studies. You can look more deeply into one skull, as Dudgeon et al. did. Or you can examine many skulls, as ReptileEvolution.com and the LRT enable workers to do (Figs. 2, 4). In this case, using computed tomography on one skull did not put an end to traditional myths regarding the identity of bones in Champsosaurus.

Note to readers who like to harp on these issues:
More characters were not needed to resolve these problems. More taxa were needed.

Firsthand access + computed tomography did not help Dudgeon et al. Rather, a century-old drawing (Brown 1905, Fig. 3), access to several sister taxa for comparison (Figs. 2, 4) and Adobe Photoshop were the tools needed to resolve this issue.

It helps to know what you are dealing with.
Only a wide-gamut phylogenetic analysis that minimizes taxon exclusion can tell you where a specimen nests in the cladogram. Too often workers like Dudgeon et al. rely on vague citations, rather than running tests themselves or citing ongoing and self-repairing studies like the LRT. Publishing a mistake is to be avoided no matter how trivial.

Figure 2. Dorsal, lateral and palatal views of BPI 2871 with bones colorized above. Below, reconstructed images of BPI 2871 tracings. It is more complete than illustrated by Gow 1975. Click to enlarge. Note the tiny remnant of the antorbital fenestra. The squamosal has been broken into several parts.

Figure 4. Dorsal, lateral and palatal views of Late Triassic BPI 2871 with bones colorized above. Below, reconstructed images of BPI 2871 tracings. It is more complete than illustrated by Gow 1975. Note the tiny remnant of the antorbital fenestra and the long ascending process of the premaxilla.  The squamosal has been broken into several parts. This is a tiny phylogenetically miniaturized sister to the ancestor of Champsosaurus.

Champsosaurus annectens (Cope 1876, Brown 1905) ~1.5 m in length, Late Cretaceous to Eocene. Champsosaurus was derived from a sister to Tchoiria, and was a sister to other choristoderes, such as Cteniogenys and Lazarussuchus. This clade must have originated in the Late Permian or Early Triassic, but fossils are chiefly from late survivors, hence the wide variety in their morphology.


References
Brown B 1905. The osteology of Champsosaurus Cope. Memoirs of the AMNH 9 (1):1-26. http://digitallibrary.amnh.org/dspace/handle/2246/63
Cope ED 1876.
On some extinct reptiles and Batrachia from the Judith River and Fox Hills beds of Montana: Proceedings of the Academy of Natural Sciences, Philadelphia. 28, p. 340-359.
Dudgeon TW, Maddin HC, Evans DC & Mallon JC 2020. 
Computed tomography analysis of the cranium of Champsosaurus lindoei and implications for choristoderan neomorphic ossification. Journal of Anatomy (advance online publication)
doi: https://doi.org/10.1111/joa.13134
https://onlinelibrary.wiley.com/doi/10.1111/joa.13134

http://reptileevolution.com/champsosaurus.htm

Ferrodraco, a new Aussie ornithocheirid with gracile wings

Most ornithocheird pterosaurs have robust wings
(Figs. 1–3). This new one from Australia (Pentland et al. 2019) has gracile cervicals and wing bits relative to the normally proportioned crested rostrum, a fact overlooked by the authors. Ferrodraco (Early Cretaceous) has small and gracile cervicals and wing elements relative to other ornithocheirids.

FIgure 1. Apparently overlooked by all eight authors, Ferrodraco has a gracile post-crania compared to its rostrum.

FIgure 1. Apparently overlooked by all eight authors, Ferrodraco has a gracile post-crania compared to its rostrum and relative to related pterosaurs. It is possible that this taxon was another flightless pterosaur, but the distal wing phalanges remain unknown.

It was skinny, but was it flightless?
We don’t have the distal wing phalanges. So whether Ferrodraco was flightless or not cannot be definitively answered. This specimen is extremely gracile compared to sister taxa (Figs. 1-3). Only one other pterosaur, Raeticodactylus (Late Triassic) had such gracile wing elements, but the distal elements were normally proportioned.

The holotype described in situ:
“Several elements, including the skull and mandible and many of the appendicular elements (based on key-fits between adherent matrix on anatomically adjacent elements) were clearly articulated post-fossilisation; however, erosion and soil rotation led to fragmentation of the specimen prior to its excavation.”

Figure 2. Ferrodraco scaled to Arthurdactylus. Note the robust antebrachium in Arthurdactylus vs. the gracile antebrachium in Ferrodraco.

Figure 2. Ferrodraco scaled to Arthurdactylus. Note the robust antebrachium in Arthurdactylus vs. the gracile antebrachium in Ferrodraco.

The new ornithocheirid has been nicknamed ‘Butch’
(AODF 876, Australian Age of Dinosaurs Fossil, Winton, Queensland, Australia).

FIgure 3. Ferrodracto compared to Coloborhynchus to the same scale.

FIgure 3. Ferrodracto compared to Coloborhynchus to the same scale. Note the difference in cervical size.

Every new pterosaur specimen
continues to be amazing in its own way. Fortunately ReptileEvolution.com provides a ready reference for easy comparison within hours of publication for new specimens.

Figure 5. Added late. The cervicals restored and to scale creating a neck of appropriate length.

Figure 4. Added late. The cervicals restored and to scale creating a neck of appropriate length.

Added later the same day:
Here (Fig. 4) are the cervicals restored to scale and 5x larger for detail.


References
Pentland AH et al. (seven co-authors) 2019.
Ferrodraco lentoni gen. et sp. nov., a new ornithocheirid pterosaur from the Winton Formation (Cenomanian–lower Turonian) of Queensland, Australia. Nature.com/scientificreports 9:13454 https://doi.org/10.1038/s41598-019-49789-4

Electric eels and anglerfish? They don’t look similar…

Updated January 15, 2021
with the addition of more taxa the electric eel nests with the bowfin, Amia, while the goosefish, Lophius, nests with the tripod fish, Bathypterois.

…and yet
the large reptile tree (LRT, 1514 taxa; subset Fig. 4) continues to nest Electrophorus and Lophius together with every additional fish taxon ever since they entered the LRT, not quite on the same day, but close.

Either something is wrong…
or something is right. These two are such odd bedfellows. Why do they continue to attract one another. My curiosity was raised, so I dived into the candidate sister taxon list!

Traditionally
catfish, like Clarias, have been associated with the electric eel, Electrophorus, but the LRT separates them by a great morphological gap, as we learned earlier here.

There is an electric catfish
with small eyes, thick lips and a cylindrical body. Unfortunately, Malapterurus is indeed a catfish, not close or even transitional to Electrophorus.

Figure 1. Lophius in vivo. The pelvic fins are hidden from view beneath the large pectoral fins. So Lophius is all mouth and tail. Inset shows a larva/hatchling not to scale.

Figure 1. The goosefish Lophius in vivo. The pelvic fins are hidden from view beneath the large pectoral fins. This does not look much like an electric eel, but the two nest together in the LRT. Let’s search for a suitable, reasonable and valid transitional taxon. The inset hatchling goosefish does not provide a clue to the identity of the transitional taxon.

Figure 1. Bathypterois, the deep sea tripod fish, shown with diagram of jaws and palate from Sulak 2006, then colored and matched to the in vivo specimen.

Figure 1. Bathypterois, the deep sea tripod fish, shown with diagram of jaws and palate from Sulak 2006, then colored and matched to the in vivo specimen.

At times like this
my guess is to go looking for a long, narrow angler fish relative (if there is one) to bridge the morphological gap that currently separates the wide-mouth goosefish, Lophius (Fig. 1), from its elongate LRT sister, the electric eel Electrophorus (Fig. 2).

It turns out a good candidate 
is Forbesichthys (Fig. 2; Putnam, 1872; 9cm in length) the spring cave fish of Missouri, USA. Yes, that’s a long way from the Amazon, where Electrophorus is found, AND a long way from both sides of the North Atlantic, where Lophius is found.

de Santana, Vari and Wosiacki 2013 determined
“that Electrophorus possesses a true caudal fin formed of a terminal centrum, hypural plate and a low number of caudal-fin rays.”

Figure 1. Forbesichthys an apparent sister taxon to Electrophorus along with other sisters to the blind cave fish, Typhlichthys subterraneus. When I find skull material for Forbesichthys, I will enter it in the LRT.

Figure 2. Forbesichthys an apparent sister taxon to Electrophorus along with other sisters to the blind cave fish, Typhlichthys subterraneus. When I find skull material for Forbesichthys, I will enter it in the LRT. That’s the mandible of Typhlichthys superimposed on the skull of the electric eel, the only comparable data at present. Image from Armbruster, Niemiller and Hart 2016.

Figure 1. Amia juvenile with DGS colors added. Image from Digimorph.org and used with permission.

Figure 1. Amia juvenile with DGS colors added. Image from Digimorph.org and used with permission.

Unfortunately skull material for Forbesichthys agassizii
cannot be located at present, so its addition to the LRT will have wait until those data arrive. Wikipedia reports, “The head is sloped, and it has a protruding lower jaw” similar to the electric eel. “It has a well-developed sensory system. This system occurs in clusters on the head.” Like the electric eel, eyesight is poor in all cave fish, many of which are not related to Forbesichthys. Note the similar arrangement of all fins on cave fish (Fig. 2) to the goosefish (Fig. 1).

Figure 4. Electrophorus, the electric eel, in vivo.

Figure 3. Electrophorus, the electric eel, in vivo from de Santana et al. 2013.

Radiation and distribution
Given the present phylogenetic topology, the last common ancestor of Forbesichthys, Lophius and Electrophorus was in North American rivers before some descendants radiated along the coast to South America, while still others radiated along the perimeter of the then reduced North Atlantic. That primitive last common ancestor probably looked like Forbesichthys and sought dark and murky environments that it was already suited to. Both goosefish and electric eels are clearly derived.

I’m not sure how cave fish got into caves
in the first place, or how many thousands or tens of millions of years they have been there, but cave fish probably arrived from nearby rivers and lakes seeping into limestone fissures a long time ago, given that their non-cave sisters no longer inhabit North American lakes and rivers. (Let me know if this is incorrect!)

Figure 3. Revised subset of the LRT focusing on ray fin fish and kin.

Figure 3. Revised subset of the LRT focusing on ray fin fish and kin.

Interesting factoid:
Many cave fish are cannibals, not only to sustain themselves in low prey environments, but also to avoid overpopulating such environments.

Further updates will come
if and when skull data for Fobesichthys arrives.

If anyone knows
that this hypothesis of relationships was published earlier, please cite the reference and let me know so I can provide proper credit.


References
Armbruster JW, Niemiller ML and Hart PB 2016. Morphological Evolution of the Cave-, Spring-, and Swampfishes of the Amblyopsidae (Percopsiformes). Copeia 194(3):763–777,
deSantana CD, Vari RP and Wosiacki 2013. The Untold Story of the Caudal Skeleton in the Electric Eel (Ostariophysi: Gymnotiformes: Electrophorus). PLoS ONE 8(7): e68719. https://doi.org/10.1371/journal.pone.0068719
Putnam FW, 1872. The blind fishes of the Mammoth Cave and their allies. American Naturalist v. 6 (no. 1): 6-30. Also published in:
Packard, Jr. and Putnam 1872. Life in the Mammoth Cave, etc. chapter 3, pp. 29-54.

wiki/Spring_cavefish
wiki/Electrophorus
wiki/Lophius

The nomenclature of skull bones in primitive lungfish

Campbell, Barwick and Pridmore 1995
labeled the many small bones of the lungfish skull in response to perceived nomenclature issues.

Unfortunately,
the authors continued the traditional practice of labeling the skull bones with letters and numbers (Fig. 1), thereby ignoring homologies with other vertebrates in which the skull bones have traditional names, like maxilla, frontal, etc.

Their abstract:
“An attempt is made to examine the problem of the nomenclature of the roofing bones in the most primitive dipnoans, which is still a matter of contention. The letter and number system that has been in use for the last half century was based on Dipterus, a Middle Devonian genus that has a reduced number of bones and a greatly shortened cheek in comparison with the Early Devonian Dipnorhynchus. Several attempts have been made to expand the Dipterus nomenclature to accommodate the more primitive condition in Dipnorhynchus and Uranolophus, but none has yet been generally accepted. The most recent attempt by Westoll (1989), which involves errors of reconstruction and interpretation, is discussed in this paper. The matter is of importance because assessment of the relationships of primitive dipnoans to other groups depends to a substantial extent upon these homologies.”

Figure 1. The Middle Devonian lungfish, Howidipterus, with subdivided skull bones colorized here to match those in the placoderm Entelognathus (Fig. 2).

Figure 1. The Middle Devonian lungfish, Howidipterus, with subdivided skull bones colorized here to match those in the placoderm Entelognathus (Fig. 2).

Schultze 2008 responded by
homologizing the skull bones of actinoperygians with those of sarcopterygians (as I just found out… learning as I go.) Not sure what the latest practice is.

Figure 4. Subset of the LRT updated with new basal vertebrates.

Figure 4. Subset of the LRT updated with new basal vertebrates.

We’ve already seen the breakup of skull bones in lungfish
into many little bones. These need to be homologized with those of other vertebrates, as shown at ReptileEvolution.com and at this prior blogpost. The way to do this is by way of phylogenetic bracketing.


References
Campbell KSW, Barwick RE and Pridmore PA 1995. On the nomenclature of the roofing and cheekbones in primitive dipnoans. Journal of Vertebrate Paleontology 15(1):28–36.
Schultze H-P 2008 (2007). Nomenclature and homologization of cranial bones in actinopterygians. Nomenclature and homologization of cranial bones in actinopterygians. In Mesozoic Fishes 4 – Homology and Phylogeny. Editors: Arratia G, Schultze H-P and MVH Wilson, Verlag Dr. F. Pfeil.

Mapping the rabbitfish (Chimaera) skull

Updated December 14, 2020
because so many more chondrichthyes and chimaera have been added to the LRT.

Chimaera monstrosa (Linneaus 1758; Figs. 1–3), the extant rabbitfish, a type of ratfish, nests between sharks and sturgeons in the large reptile tree (LRT, 1467 taxa).

The fish’s quadrate
shifts anteriorly to below the orbit. The mouth is largely ventrally oriented. The teeth are transformed and fused to plates and beaks. The large pectoral fins provide propulsion while the tail is reduced to a whip.

Figure 1. Chimaera monstrosa in vivo.

Figure 1. Chimaera monstrosa in vivo.

No one, it seems, has attempted to map the skull before.
The rabbitfish skull is an apparently suture-less cartilaginous shape, almost as if it had been 3D printed (Fig. 2). Check out the academic literature and you’ll see skull shape outlines, and that’s about it. Not many workers call ratfish their specialty. Figuring out where the likely boundaries of the bones are is best left to phylogenetic bracketing (comparisons with putative and traditional sister taxa). Digital graphic segregation (coloring the bones) seems to help, especially in the presentation.

Figure 2. Ratfish skull with 'bones' (actually precursor cartilage' colored and labeled.

Figure 2. Ratfish skull with ‘bones’ (actually precursor cartilage’ colored and labeled.

Most ratfish
have a extended soft rostrum (Fig. 3). This one does not (or it was cut off (Fig. 2).

Figure y. Basal Gnathostomata with the addition of Rhinochimaera.

Figure 3. Basal Gnathostomata with the addition of Rhinochimaera.

Most workers
recognize the relationship of chimaeras with sharks and rays, but apparently none add sturgeons and spoonbills to that list, despite the fact that chimaeras also have gill covers and similar morphologies overall (Fig. 3). As we learned earlier here, acanthodians are not related to sharks.

Figure 5. Shark skull evolution according to the LRT. Compare to figure 1.

Figure 4. Shark skull evolution according to the LRT. Compare to figure 1.

PS.
For those interested in the controversial basal bird Ambopteryx,
a closeup of the radius in question is presented here. I can’t think of anything in science more exciting than to be published in Nature. I can’t think of anything more haunting than to have a mistake published in Nature.


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/Chimaera

Tiny Abdalodon: a basal cynodont, drags in Lycosuchus

Today’s blogpost returns to basal Therapsida,
after several years of ignoring this clade.

Kammerer 2016 reidentifies an old Procynosuchus skull 
as an even more basal cynodont, now named Abdalodon (Fig. 1). The problem is: cynodonts arise from basal theriodonts (Therocephalia) and Abdalodon nests with another flat-head taxon, Lycosuchus (Fig. 1), a traditional therocephalian in every other cladogram, but not the Therapsid Skull Tree (TST, 67 skull-only taxa, Fig. 2), a sister cladogram to the LRT.

So, where is the cynodont dividing line?
(= which tested taxon is the progenitor of all later cynodonts and mammals?)

It would help if we knew the phylogenetic definition
of Cynodontia because we should never go by traits (which may converge), but only by taxon + taxon + their last common ancestor and all descendants to determine monophyletic clades.

From the Kammerer 2016 abstract:
“Phylogenetic analysis recovers Abdalodon as the sister‐taxon of Charassognathus, forming a clade (Charassognathidae fam. nov.) at the base of Cynodontia. These taxa represent a previously unrecognized radiation of small‐bodied Permian cynodonts. Despite their small size, the holotypes of Abdalodon and Charassognathus probably represent adults and indicate that early evolution of cynodonts may have occurred at small body size, explaining the poor Permian fossil record of the group.”

Figure 1. Abdalodon nests with the many times larger therocephalian Lycosuchus in the LRT.

Figure 1. Abdalodon nests with the many times larger therocephalian Lycosuchus in the LRT.

Hopson and Kitching 2001 defined  Cynodontia
(Fig. 2) as the most inclusive group containing Mammalia, but excluding Bauria. In the TT Abdalodon nests with Lycosuchus on the cynodont side of Bauria.

Figure 4. TST revised with new data on Patranomodon and sister taxa.

Figure 4. TST revised with new data on Patranomodon and sister taxa.

So that makes Lycosuchus a cynodont,
by definition.

Figure 2. Procynosuchus, a basal cynodont therapsid synapsid sister to humans in the large reptile tree (prior to the addition of advanced cynodonts including mammals).

Figure 3. Procynosuchus, a basal cynodont therapsid synapsid sister to humans in the large reptile tree (prior to the addition of advanced cynodonts including mammals). This skull has been overinflated dorsoventrally based on the preserved skull, which everyone must have thought was crushed in that dimension.

Earlier we looked at
some Wikipedia writers when they stated, “Exactly where the border between reptile-like amphibians (non-amniote reptiliomorphs) and amniotes lies will probably never be known, as the reproductive structures involved fossilize poorly…” 

Contra that baseless assertion,
with phylogenetic analysis and clades defined by taxa it is easy to determine which taxa are the last common ancestors, sisters to the progenitors of every derived clade in the TT, LRT or LPT. We can tell exactly which taxon was the first to lay amniotic eggs, without having direct evidence of eggs, simply because all of its ancestors in the LRT laid amniotic eggs. In the same way, we can figure out which taxon, among those tested, is the basalmost cynodont. Adding Bauria to the LRT made that happen today.

Let’s talk about size
The extreme size difference between Abdalodon and Lycosuchus (Fig. 1) brings up the possibility of cynodonts going through a phylogenetic size squeeze… retaining juvenile traits into adulthood… neotony… essentially becoming sexually mature at a tiny size for more rapid reproduction, reduced food needs, ease in finding shelters, etc. We’ve seen that before in several clades here, here and here, to name a few.

Figure 4. Charassognathus does not share more traits with Abdalodon than other taxa, like Bauria and Promoschorhynchops in the TT.

Figure 4. Charassognathus does not share more traits with Abdalodon than other taxa, like Bauria and Promoschorhynchops in the TT.

Kammerer 2016 mentioned another small taxon,
Charassognathus (Fig. 4). In the TST (Fig. 2) Charassognathus nests with Bauria and Promoschorhynchops, within the Therocephalia, distinct from, and not far from Abdalodon and the Cynodontia. So no confirmation here for Kammerer’s proposed clade, ‘Charassognathidae’ (see above).


References
Hopson JA and Kitching JW 2001. A Probainognathian Cynodont from South Africa and the Phylogeny of Nonmammalian Cynodonts” pp 5-35 in: Parish A, et al.  editors, Studies in Organismic and Evolutionary biology in honor of A. W. Crompton. Bullettin of the Museum of Comparative Zoology. Harvard University 156(1).
Kammerer CF 2016. A new taxon of cynodont from the Tropidostoma Assemblage Zone (upper Permian) of South Africa, and the early evolution of Cynodontia. Papers in Palaeontology 2(3): 387–397. https://doi.org/10.1002/spp2.1046

wiki/Bauria
wiki/Abdalodon
wiki/Lycosuchus