Extant Palaeonisciformes

According to Wikipedia,
“The Palaeonisciformes (Palaeoniscida) are an extinct order of early ray-finned fishes (Actinopterygii). Palaeonisciformes sensu lato first appeared in the fossil record in the Late Silurian and last appeared in the Late Cretaceous.”

Adding taxa upsets this hypothesis. Now both hypotheses need to be tested.

Figure 1. Subset of the LRT focusing on Palaeonisciformes, including extant taxa like Malacosteus, Engraulis and Coilia. The uncolored taxa are traditional palaeonisciforms.

Recent housekeeping
to the fish portion of the large reptile tree (LRT, 2262 taxa, Fig 1) recovered three extant taxa that arose directly from the Palaeonisciformes. These three (Malacosteus, Engraulis, and Coilia (Figs 2, 3) shifted out of the Actionopterygia (ray-fin fish) when facial bones in two taxa, Birgeria and Kalops (Figs 2, 3), were correctly identified based on tetrapod homologies.

Another traditional ray-fin fish, Late Triassic Birgeria (Figs 2, 3), now nests between the traditional Carboniferous palaeonisciform, Kalops (Fig 2) and the three newly identified Palaeonisciformes. That makes extinct Birgeria and Kalops pertinent parts of this previously untold story of macroevolution by way of microevolution.

Earlier three members of the extinct Onychodontiformes
(Selenodus, Onychodus and Strunius) moved into the Palaeonisciformes (Fig 1). They don’t have lobe fins. Their two-part skull roof turns out to be convergent with Sarcopterygii. Let the software sort your taxon list into clades and let us know what you recover.

Figure 2. Extant palaeonisciformes in the LRT include Engraulis, Malacosteus and Coilia. All three share the trait of a large lateral orbit close to the short rostral tip extending even slightly beyond the jaws, convergent with sharks.

When Kalops was first described
(Poplln and Lund 2002;) the authors reported, “It was decided not to perform a cladistic analysis herein to search for the interrelationships of Kalops. Moreover there is not yet any established classification of lower actinopterygians resulting from an inclusive, uncontested general phylogenetic analysis. We believe such an analysis would have been based on too
limited a suite of species; it seems somewhat derisory to try narrow cladistic efforts each time a few or single new genus or species is described. Thus we have taken a more global approach to discuss the systematic status of this new genus. As in previous articles (e.g., Poplin and Lund, 2000), we use the term “Palaeoniscimorpha” (Lund et al., 1995) as a strict synonym of “Basal Actinopteri” sensu Patterson, 1982.”

We might have to wait awhile for ‘uncontested‘. The LRT provided the required ‘inclusive‘.

Figure 3. Once considered ray-fin fish, these four taxa, Birgeria, Malacosteus, Engraulis and Coilia, now nest as descendants of Kalops within the monophyloetic Palaeonisciformes in the LRT. See figure 1. Note the slender, angled operculum (lavender) and the nasals (pink) extending beyond the premaxilla (yellow).

The LRT documents several clades of fish that evolved ray fins,
just as several clades evolved lobe fins and two clades evolved fingers and toes.

Convergence. Add more taxa so you won’t be fooled by convergence.

Convergence is rampant in the Chordata.
So don’t cherry-pick a short list of taxa while omitting others based on one, two or a dozen traits. Textbooks can be out-of-date. Always test several hundred traits in your own LRT and let the software tell you which taxa from a wide gamut list belong to novel or established clades.

Taxon exclusion remains the number one problem in paleontology. Let’s fix that.

The use of standard DGS colors
(Fig 3) helps to establish and understand tetrapod homologies in all tested taxa. Labels and arrows become superfluous. Keep your graphics simple.

If you’re not part of this revolution in chordate phylogeny
stop sitting on your hands and start building your own LRT with DGS methods. The LRT started with just 240 taxa. As in any and every scientific endeavor, replicating this experiment is essential because the current LRT hypothesis requires confirmation, refutation or modification from independent studies employing a similar taxon list and your own set of 200+ multi-state characters.

This appears to be a novel hypothesis of interrelationships.
If not please provide a citation so I can promote it here.

References
Ayres WO 1848. pp. 64–73. In: Proceedings of the Boston Society of Natural History, Vol. 3. Proceedings of the Boston Society of Natural History, Boston.
Ayres WO 1849. Description of a new genus of fishes, Malacosteus. Boston Journal of Natural History 6:53–64.
Figueroa RT et al (6 co-authors) 2023. Exceptional fossil preservation and evolution of the ray-finned fish brain. Nature https://doi.org/10.1038/s41586-022-05666-1
Gray JE 1830. : Illustrations of Indian Zoology 1, (pl. 85).
Kenaley CP 2007. Revision of the Stoplight Loosejaw Genus Malacosteus (Teleostei: Stomiidae: Malacosteinae), with Description of a New Species from the Temperate Southern Hemisphere and Indian Ocean. Copeia. 2007 (4): 886–900. 
doi:10.1643/0045-8511(2007)7[886:
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Poplin CM and Lund R 2002. Two Carboniferous fine-eyed palaeoniscoids (Pisces, Actinopterygii) from Bear Gulch (USA). Journal of Paleontology 76(6):1014–1028.
Romano C and Brinkman W 2009. Reappraisal of the lower actinopterygian Birgeria stensioei ALDINGER, 1931 (Osteichthyes; Birgeriidae) from the Middle Triassic
of Monte San Giorgio (Switzerland) and Besano (Italy). Neues Jahrbuch für Geologie und Paläontologie – Abhandlungen. 252: 17–31.
Xu G-H, Ma X-Y and Zhao L-J 2018. A large peltopleurid fish (Actinopterygii: Peltopleuriformes) from the Middle Triassic of Yunnan and Guizhou, China. Vertebrata PalAsiatica 56(4):106–120.

wiki/Birgeria
wiki/Malacosteus
wiki/European_anchovy
wiki/Coilia
wiki/Engraulinae
wiki/Palaeonisciformes
wiki/Kalops – not yet listed
wiki/Bluefieldius – not yet listed

Strunius, Onychodus and Selenodus move to the Palaeoniscidae, far from the Sarcopterygii (pre-tetrapod lobe-fins)

Scaphognathus counterplate and soft tissue preservation

From the Henkemeir, Jäger and Sander 2023 abstract
“The description of the holotype of the non-pterodactyloid pterosaur Scaphognathus crassirostris from the Upper Jurassic Solnhofen Formation by the German palaeontologist Georg August Goldfuß in 1831 was the basis for the first published scientific life reconstruction of a pterosaur.

Ironically since then, Scaphognathus (Figs 1, 2) has been the subject of only a few works of art. It is the archetypal ‘plain brown sparrow‘ of pterosaurs. To its credit, in the large pterosaur tree (LPT, 267 taxa) Scaphognathus was basal to two clades of ‘pterodactyloid’-grade pterosaurs. Transitional taxa (Fig 3) first went through a strong phase of phylogenetic miniaturization.

Figure 1. Images from Henkemeier, Jáger and Sander 2023. Colors added here. The stains are not as interesting here as the textures.

From the Henkemeir, Jäger and Sander 2023 abstract
“In this study, reflectance transformation imaging (RTI) was used to investigate fine surface details of the S. crassirostris type specimen. The observations of Goldfuß concerning the existence of different preservational patterns of the hair-like integumentary structures (pycnofibres) in this specimen were confirmed.”

Information on RTI can be found here and here.

As the authors explain, their focus was on tiny hairs identified 190 years ago. Apparently less attention was paid to the gular sac, wing membranes and other interesting hard and soft parts. Those are highlighted here (Figs 1, 2) by digitally putting the counterplate back on top of the plate, then registering them, decreasing color saturation and increasing contrast. No RTI was used, only Adobe PhotoShop.

Figure 2. Scaphognathus holotype plate and counterplate. Note the curved stripe impressions over the right femur and pelvis. These impressions could be parasagittal dorsal frills, as in Longisquama and Jeholopterus. Note the curve behind the knee, representing the slender uropatagium.

Phylogenetic analysis
in the LRT nests pterosaurs with Longisquama, a flightless taxon famous for its dorsal and cranial frlls, also seen in Jeholopterus (Fig 4).

Fig. 3. The descendants of Scaphognathus. Note the size reduction followed by a size increase.

Like all pterosaurs.
the Scaphognathus wing membrane (Fig 1) had a narrow chord and stretched between the elbow and wing tip, enabling complete disappearance during wing folding, as in birds. As often happens, the membrane on Scaphognathus is torn away from the wing finger during burial.

Figure 4. Reconstruction of Jeholopterus. This owl-like bloodslurper was covered with super soft pycnofibers to make it a silent flyer.

References
Goldfuss GA 1830. Pterodactylus crassirostris. Isis von Oken, Jena pp. 552–553.
Goldfuß GA 1831. Beiträge zur Kenntnis verschiedener Reptilien der Vorwelt. Nova Acta
Physico-Medica Academiae Caesareae Leopoldino-Carolinae Naturae Curiosorum, 15:61-
128.
Henkemeier N, Jáger KRK and Sander PM 2023. Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuß, 1831) using reflectance transformation imaging. Palaeontologia Electronica26(2):a16. https://doi.org/10.26879/1070
Wellnhofer P 1975a. Teil I. Die Rhamphorhynchoidea (Pterosauria) der Oberjura-Plattenkalke Süddeutschlands. Allgemeine Skelettmorphologie. Paleontographica A 148: 1-33. 1975b. Teil II. Systematische Beschreibung. Paleontographica A 148: 132-186. 1975c. Teil III. Paläokolgie und Stammesgeschichte. Palaeontographica 149: 1-30.

wiki/Scaphognathus

http://reptileevolution.com/scaphognathus.htm

Moray eel hatchlings look like Middle Triassic Ctenognathichthys

Some fish change shape as they grow up.
The skull of a moray eel hatchling (Fig 1, genus: Gymnothorax) becomes longer, lower, and with shorter teeth as it transforms into an adult (Fig 2).

Figure 1. Gymnothorax (moray eel) hatchling compared to a similarly toothy Middle Triassic ancestor, Ctenognathichthys. See figure 4 for an enlargement of the skull.

A look-alike Middle Triassic fish,
Ctenognathichthys bellottii (Fig 1, 3–5), essentially has the skull of a moray eel hatchling (Fig 1). This extinct ‘comb-jaw-fish’ entered the large reptile tree (LRT, 2261 taxa) alongside coeval Feroxicthys (Fig 6) just prior to the bony-fish split that produced ray-fins on one branch and lobe-fins on the other.

Moray eels are basal ray-fins in the LRT.

Figure 3. Gymnothorax (aka Lycodontis) funebris, a type of moray eel. Compare to the larva in figure 1.

Superficially the comb-jaw-fish
is an example of convergence with moray eels. However, since Ctenognathichthys (Figs 1, 3–5) nests in the ancestry of Gymnothorax, instead this may be an example of reversal as moray eel ontogeny recapitulates this stage of phylogeny.

Figure 3. Ctenognathichthys bellottii in situ.

Xu 2021 wrote,
“During feeding, it used its long and sharp teeth to grasp and tear the prey from the substrate or to bite a piece from a larger prey item. Louwoichthys (a relative of Ctenognathichthys) might have fed on marine organism debris (e.g. dead fish and other animals). Other potential prey could have included fish eggs, arthropod larvae or small crustaceans (e.g. mysidaceans or isopods).”

Oddly, Xu 2021 did not mention Feroxichthys (Fig 6), which he had described a year earlier.

Figure 4. Skull of Ctenognathichthys bellottii in situ.

A related species, Ctenognathichthys revista
(Fig 5), had a relatively smaller face and a deeper body with tiny, barely visible fins. This lack of large lateral fins is interesting because the moray eel totally lacks lateral fins. Even so, transitional taxa between these taxa had larger fins and more fusiform shapes.

Figure 5. Ctenognathichthys revista is a deeper bodiied congeneric relative. Not a fast-swimmer.

Xu 2021
held tight to the traditional view of fish systematics, writing, “Neopterygii is a taxonomically diverse group of ray-finned fishes, including Teleostei, Holostei and their closely related fossil taxa.”

With more taxa the LRT does not recognize a monophyletic Holostei or Neopterygii (= the remainder of Actinopterygii sans Holostei).

Figure 6. Feroxicthys (lower right) added to skull diagrams of taxa related to Ctenognathichthys from Mickle 2012. Colors and Feroxichthys (a Xu 2020 taxon) added here.

On a tangential note, Mickle’s 2012 PhD dissertation
urged the adoption of a standard nomenclature for fish facial bones. She wrote, “Currently, there is no standardized nomenclatural scheme for identifying and naming the bones of the snout in lower actinopterygian fishes. This creates a situation where the same bone names are used to identify very different bones. This is problematic because it makes comparing taxa described by different scientists difficult and presents potential pitfalls for building character matrices for phylogenetic analyses. Because of the problems the absence of a standardized nomenclature scheme presents, a new set of rules for the identification of the bones of the snout of lower actinopterygians is proposed here.”

I agree. Mickle’s proposal is needed, but did not go far enough. Here (Figs 1–6) all facial bones are colored with tetrapod homologies, enabling the common ‘nomenclature’ necessary to score traits and build the LRT. The use of standard colors dispenses with the need to label individual fish face bones, which tend to split and fuse.

References
De Alessandri G 1910. Studii sui pesci triassici della I-ombardia. Mem. S!oc. 1t Sc. Nat., 3(1): 1-145, Milano.
Mickle K 2012. Unraveling the Systematics of Palaeoniscoid Fishes–Lower Actinopterygians in Need of a Complete Phylogenetic Revision. Mickle_ku_0099D_12123_DATA_1.pdf (9.926Mb)
Tintori A 1998. Ctenognathichthys bellottii (de Alessandri, 1910): Nomenclature problems and stratigraphical importance of this Middle Triassic actinoopterygian fish. Rivista Italiana di Paleontologia e Stratigrafia 104(3)417–422.
Xu G-H. 2020. Feroxichthys yunnanensis gen. et sp. nov. (Colobodontidae, Neopterygii), a large durophagous predator from the Middle Triassic (Anisian) Luoping Biota, eastern Yunnan, China. PeerJ 8:e10229 DOI 10.7717/peerj.10229
Xu G-H 2021. A new stem-neopterygian fish from the Middle Triassic (Anisian) of Yunnan, China, with a reassessment of the relationships of early neopterygian clades. Zoological Journal of the Linnean Society 191, 375–394.

https://en.wikipedia.org/wiki/Ctenognathichthys

The thresher shark, Alopias, enters the LRT

Alopias vulpinus
(Rafinesque 1810, up to 6m, Figs 1, 2) is the extant common thresher shark, known for its extra-long caudal fin.

Figure 1. The thresher shark, Alopias, in vivo.

Other than that tail…
The orbit is longer than the rostrum or temple. The prefrontal contacts the maxilla. The premaxilla angles down (Fig 2) and the anal fin of Alopias is a mere vestige.

Figure 2. Alopias skull in two views from Simon De Marchi of Elasmo-Morph. Colors added here.

Here
in the large reptile tree (LRT, 2260 taxa) Alopias nests with Isurus, the mako shark, which has a longer skull, larger teeth and, obviously, a shorter caudal fin.

References
Rafinesque CS 1810. Caratteri di alcuni nuovi generi e nuove specie di animali e piante della sicilia, con varie osservazioni sopra i medisimi. Per le stampe di Sanfilippo: Palermo, Italy. pp. 105, 20 fold. Pl., online

wiki/Shortfin_mako_shark – Isurus
wiki/Great_white_shark – Charchardon
wiki/Thresher shark – Alopias

White et al 2023 report: marsupial birth no longer intermediate

Unfortunately
White et al based their phylogeny on genomics and skull morphology. Omitting fossil taxa is not a good method for determining phylogeny. Overlooking transitional taxa (Fig 1) is likewise not good. Trusting genes in deep time studies will also lead you astray.

In a paper devoted to marsupial reproduction you might find it ironic that White et al do not mention the words ‘pouch’ or ‘marsupium’ in their text.

From the White et al summary:
“Within mammals, different reproductive strategies (e.g., egg laying, live birth of extremely underdeveloped young, and live birth of well-developed young) have been linked to divergent evolutionary histories.”

This is oversimplified and misleading. Basal placentals in the trait-based large reptile tree (LRT, 2260 taxa) are also underdeveloped, while derived placentals (e.g. odontocetes, mysticetes, ungulates) are well-developed.

“How and when developmental variation across mammals arose is unclear.”

Perhaps because White et al eschew trait-based analysis and omit fossil taxa.

“While egg laying is unquestionably considered the ancestral state for all mammals, many long-standing biases treat the extreme underdeveloped state of marsupial young as the ancestral state for therian mammals (clade including both marsupials and placentals), with the well-developed young of placentals often considered the derived mode of development.

The LRT supports the traditional hypothesis, deriving basal placentals from taxa near Monodelphis, a marsupial without an enclosing pouch (Fig 1). White et al mention Monodelphis only once and then in regard to a skull bone, the supraoccipital.

Figure 1. Monodelphls and pups exposed as no pouch is present in this basal placental taxon. Note the tail is not bushy.

From the White et al summary:
‘Here, we quantify mammalian cranial morphological development and estimate ancestral patterns of cranial shape development using geometric morphometric analysis of the largest comparative ontogenetic dataset of mammals to date (165 specimens, 22 species).

Why stop at cranial shape? Why ‘estimate’ ancestral patterns when the fossil record is available? Why not just run a trait-based phylogenetic analysis, like the LRT?

“We identify a conserved region of cranial morphospace for fetal specimens, after which cranial morphology diversified through ontogeny in a coneshaped pattern.

Put away your genomics. Just run a trait-based phylogenetic analysis.

“Cranial morphological variation was found to be significantly associated with the level of development (position on the altricial-precocial spectrum) exhibited at birth.

Even if true, it doesn’t matter. If you’re looking at the cranium, you’re overlooking the pouch. Just run a trait-based phylogenetic analysis.

“Estimation of ancestral state allometry (size-related shape change) reconstructs marsupials as pedomorphic relative to the ancestral therian mammal.

No need to estimate ancestral states when fossils are available. Use fossils in a trait-based phylogenetic analysis. And when you do you will find many instances of pedomorphy (= phylogenetic miniaturization) at the genesis of novel clades. Speaking of which, the most glaring example, Hadrodium, is not mentioned in the text.

Figure 2. Subset of the LRT focusing on marsupials, color-coded according to size. Smaller derived from larger = pedomorphosis.

From the White et al summary:
“In contrast, the estimated allometries for the ancestral placental and ancestral therian were indistinguishable. Thus, from our results, we hypothesize that placental mammal cranial development most closely reflects that of the ancestral therian mammal, while marsupial cranial development represents a more derived mode of mammalian development, in stark contrast to many interpretations of mammalian evolution.”

From the introduction
“All living mammals shared a common ancestor that lived at least 165 million years ago.”

White et al don’t name that last common ancestor, Megazostrodon (Fig 1), in the text.

“The mammalian crown group is defined by the divergence of monotremes from therians, which themselves diverged into the modern lineages of marsupials and placentals approximately 160 million years ago.”

That’s incorrect. A crown group is defined by a last common ancestor of all living clade members. Again, that would be the fossil, Megazostrodon. The Therian crown group would omit monotremes and thus mark the divergence of monotremes from therians.

Bottom line:
If White et al wanted to learn more about marsupial reproduction, the pouch and its absence in placentals is the place to start, not the skull shape.

I’ll say it again, White et al do not mention the words ‘pouch’ or ‘marsupium’ in their text.

References
White HE et al (8 co-authors) 2023. Paedomorphosis in the ancestry of marsupial mammals. Current Biology https://doi.org/10.1016/j.cub.2023.04.009

Publicity
phys.org/news/2023-05-marsupials-evolved-mammals.html

Lead author online bio
kcl.ac.uk/people/heather-white

Three reasons why you should never use genes to establish clades

Raven’s PhD thesis on armored dinosaurs published as a co-authored paper

Raven et al 2023 wrote in a recently published paper:
“The armoured dinosaurs (Thyreophora) were a significant component of Mesozoic terrestrial ecosystems, appearing in the earliest Jurassic and surviving until the latest Cretaceous, and fossils of the group have been found on all continents, including Antarctica.”

This is assuming there is a monophyletic clade Thyreophora. After all, that is what is in the textbooks and so that is what PhDs teach at the university level. This needs to be tested.

Rave 2021 wrote in an earlier PhD thesis:
“The armoured dinosaurs (Thyreophora) are an iconic group of dinosaurs, owing to the bizarre and eponymous covering of osteoderms on the heads, backs and tails of the members of the group.”

By contrast the large reptile tree (LRT, 2260 taxa, subset Fig 1) recovers two clades of armored dinosaurs, both with unarmored ancestors basal to later ornithopods and ceratopsians. So an untested assumption, elevated to tradition and supported by current university textbooks, undermines this study from its inception.

Don’t let this happen to you. Add taxa, especially to your outgroup list.

Figure 1. Subset of the LRT focusing on the Phytodinosauria in September 2022. Note the separation of the Scelidosaurus (ankylosaurs) clade from the Lesothosaurus (stegosaurs) clade.

Rave 2021 wrote:
“They [thyreophorans] are an early-diverging clade of bird-hipped ornithischian dinosaurs and include some of the most recognisable dinosaurs such as Ankylosaurus and Stegosaurus.”

By contrast the LRT (Fig 1) does not indicate an early divergence.

“A surprisingly poor understanding of the group therefore undermines the evolutionary and historical significance of Thyreophora.”

Ironic statement, especially so since the LRT does not recognize the traditional clade, ‘Thyreophora’ unless it also includes ornithopods and ceratopsians, which was not the intention of the author, Nopsca 1915. The invalidation of this clade has been online since 2018.

“Due to a patchy fossil record and dramatically different osteologies compared to their ornithischian relatives, there are still outstanding questions remaining about the evolution of the group. In this thesis, I aim to correct several of these issues using a multi-faceted approach. I redescribe the morphology and taxonomy of the British Wealden Supergroup ankylosaurs Hylaeosaurus and Polacanthus.”

“I then incorporate these key taxa into a new anatomical dataset for a species-level phylogenetic analysis of the thyreophoran dinosaurs. This is the largest dataset to date for Thyreophora, with 340 morphological characters and 91 taxa, and it was analysed using equal- and implied-weights parsimony and Bayesian inference.”

Laudable. Good to see a large and new (= not borrowed) dataset.

“This reveals a novel hypothesis for thyreophoran relationships, and the hitherto accepted ankylosaurian dichotomy is not supported.”

This thesis and paper dig much deeper into ankylosaurs than the LRT does at present.

“This thesis offers an overview of the evolution of the thyreophoran dinosaurs, incorporating key taxonomic, phylogenetic, biogeographic and macroevolutionary analyses that are fundamental to the study of palaeontology, and it represents a step-change in our understanding of these iconic dinosaurs.”

Unfortunately, Raven cherry-picked his outgroup taxa, Lesothosaurus and Laquintasaura, instead of testing a wider gamut of taxa (Fig 1) to let the cladogram tell him which taxa were outgroup taxa. In the LRT (Fig 1) Early Jurassic Lesothosaurus is a basal member of the Stegosauria. Early Jurassic Laquhttp://reptileevolution.com/hexinlusaurus.htmintasaura is a basal member of the Ceratopsia.

This is the sort of mistake that can be made
when you follow vertpaleo textbooks. When you build your cladograms, start with a clean slate, without assumptions and traditions.

“Assume nothing, question everything.” – Richard Feynman.

References
Nopcsa F 1915. Die Dinosaurier der siebenbürgischen Landesteile Ungarns. Mitteilungen aus dem Jahrbuche der königlich ungarischen Geologischen Reichsanstalt 23: 1–24.
Raven TJ 2021. The taxonomic, phylogenetic, biogeographic and macroevolutionary history of the armoured dinosaurs (Ornithischia: Thyreophora). A thesis submitted in partial fulfilment of the requirements of the University of Brighton for the degree of Doctor of Philosophy.
Raven T et al (3 co-authors) 2023. The phylogenetic relationships and evolutionary history of the armoured dinosaurs (Ornithischia: Thyreophora). Journal of Systematic Palaeontology 21(1): article 2205433 pp. DOI: 10.1080/14772019.2023.2205433

wiki/Thyreophora

Klug et al 2023 describe Maghriboselache – part 2 of 2

A new cladoselachian shark,
Maghriboselache mohamezanei (Klug et al 2023, Late Devonian, 365mya, Figs 1–3), was considered unique due to its snout, but was not unique. Taxon exclusion was to blame.

Yesterday we looked at the comparative anatomy of Maghriboselache. Today: a fair amount of criticism for the Klug et al 2023 cladogram.

Figure 1. Although superficially similar (both were old, flat and wide) the pre-gnathostome placoderm Xiushanosteus cannot be closely related to the lobe-fin bony fish, but that’s what the borrowed cladogram of Klug et al 2023 indicates. In the LRT Entelognathus is basal to Chondrichthyes. This is what taxon exclusion delivers. Colleagues, please, add taxa. Your topologies too often make no sense.

From the Klug et al 2008 introduction
“Our understanding of chondrichthyan phylogeny has been vastly improved in recent years by the addition of anatomical information from three-dimensional crania (including endocasts) and enriched sampling of postcrania.”

In addition, the large reptile tree (LRT, 2259 taxa, subset Fig 2) includes extant and extinct taxa and thus minimizes the too often problem of taxon exclusion.

Figure 2 Subset of the LRT focusing on sharks, ratfish and their relatives. Here chimaeriformes are a clade within Elasmobranchii with an Early Devoian origin or earlier.

From the Klug et al 2008 introduction
“Emerging consensuses include the wholesale movement of acanthodians on to the chondrichthyan stem, and, more contentiously, recognition of numerous Paleozoic clades as stem holocephalans.”

By contrast by simply including more taxa
the LRT moves acanthodians on the osteichthyan stem and several osteichthyans evolved apart from others directly from several different acanthodians. The LRT moves the traditional small Early Silurian placoderm, Entelognathus, to the base of the Chondrichtheys. In similar fashion the tiny Early Silurian placoderm, Shenacanthus, nests in the LRT at the base of the Acanthodii + Osteichthyes. Both follow the deeply established pattern of phylogenetic miniaturization at the genesis of novel clades.

“With this change has come increasing recognition that total group Chondrichthyes and thus all crown gnathostomes, originated at least as far back as the early Silurian.”

This is confirmed by the LRT.

“Among the stem holocephalans, the Symmoriiformes are an important group, comprising a series of bizarre species, several of which bear unusual fin spines.”

This is not confirmed by the LRT. Stem holocephalans arise from the clade of Isurus, the mako shark. Elasmobranchii was erected by Bonaparte in 1838. So Chondricthyes (Huxley 1880) is the junior synonym. Symmoriiformes (Fig 2) are a more primitive grade, not a real clade in the LRT.

“However, alternative hypotheses remain current, and these posit Symmoriiformes as either stem chondrichthyans or stem elasmobranch.”

Definitions are important. Wikipedia defines Elasmobranchii as all members of the Chondrichthyes other than holocephalans, assuming a basal dichotomy within Chondricthyes. The LRT refutes that hypothesis. In the LRT holocephalans arise from mako sharks (Isurus) and various skates and ray clades arise independently and convergently from other sharks. So adding taxa resolves this traditional problem, too.

Adding taxa resolves all phylogenetic problems.
Don’t borrow your cladogram from prior authors. Build your own wide gamut cladogram so you will know the A-B-Cs of evolution and can relate them to your readers with authority and certainty. Bring paleontology up to higher standards. Add taxa.

References
Dean B 1894a. Contributions to the morphology of Cladoselache (Cladodus). Journal of Morphology 9:87–114.
Dean B 1894b. A new cladodont from the Ohio Waverly, Cladoselache newberryi, n.sp. Transactions of the New York Academy of Science, 13: 115–119.
Garman S 1884. An Extraordinary Shark. Bulletin of the Essex Institute: 47–55.
Klug C et al  (8 co-authors) 2023. Broad snouted cladoselachian with sensory specialization at the base of modern chondrichthyans. Swiss Journal of Palaeontology. 142 (1): 2. doi:10.1186/s13358-023-00266-6

wiki/Cladoselache
wiki/Maghriboselache

Klug et al 2023 describe Maghriboselache – part 1 of 2

A new cladoselachian shark,
Maghriboselache mohamezanei (Klug et al 2023, Late Devonian, 365mya, Figs 1–3), was considered unique due to its wide snout, as the authors report: uniquely broader than the large eyeballs (Fig 2, Klug et al 2023 their figure 15).

But was it? Did the authors overlook anything?

As you’ll see, this study is about longer than typical optic nerves (= eye stalks), an old, borrowed cladogram and taxon exclusion.

Figure 1. Cladoselache (male and female) compared to scale with a smaller Maghriboselache (from Klug et al 2023).

Klug et al. reported,
“In Pucapampella and Gydoselache (Maisey et al., 2018), the pila support an optic pedicel (eye stalk) but no pedicel is evident in Maghriboselache.”

A pedical is a small stalklike structure connecting an organ to the body.

Klug et al support their hypothesis
by providing a selection of shark crania and large eyeballs that fill their orbit (their figure 14). Rhincodon, the whale shark (Fig 2), is not among those examples. That’s a mistake rectified here. Note the broad rostrum (Fig 2 pink) of Rhincodon, a living relative of Cladoselache and Maghriboselache in the large reptile tree (LRT, 2259 taxa, subset Fig 3).

Figure 2. At right, the eyestalk (optic nerve) of Rhincodon, the extant whale shark. At left: figure 15 from Klug et al 2023) of Maghriboselache, here modified in frame 2 with wider eyes supported by a short hypothetical eyestalk (Fig 5).

Maghriboselache is known from
several pretty well-preserved complete cartilage skeletons, some male (with dorsal fin spines). others female (without dorsal fin spines, Fig 1).

Figure 3. Subset of the LRT focusing on Chondrichtheys, distinct from all prior shark cladograms due to taxon inclusion. Sharks radiated during the Silurian.

Distinct from Cladoselache,
in Maghriboselache the premaxillary teeth are fused to form a parasymphysal tooth (Figs 4, 5).

Perhaps accidentally, this middle tooth was not shown in the authors’ illustratration (Fig 2 = Figure 15 in Klug et al 2023), which is shown with Cladoselache teeth.

In Maghriboselache the cranium
was raised as a parasagittal crest. A jugal was present and labial cartilages were not (Figs 4, 5).

Figure 4. Skull of Maghriboselache from Klug et al 2023, their figure 5). This is a µCT scan with some, but not all eleemnts colorized. Compare to DGS method in figure 3.

The skull of Maghriboselache
was µCT scanned and partly colorized by Klug et al (Fig 4). That’s a great first draft, but more colors and a more logical layout (Fig 5) would have been easier to read and understand.

When elements are given tetrapod homologies (Fig 5) the traditional ‘palatoquadrate’ (Fig 4) becomes the tetrapod lacrimal (Fig 5 tan) with thin strips of the premaxilla (yellow) and maxilla (green) along the ventral rim. Homologs of the tetrapod quadrate, palatine and pterygoid are not present in sharks.

Figure 5. Skull of Maghriboselache using DGS methods. Note the placement of the eyeballs on long optic nerve stalks, as in living sharks. Let’s start creating layouts of skulls in this simple, easy-to-read fashion with standardized colors. One of those labial cartilages, the middle one, could be and likely is a displaced jugal.

Getting back to eye stalks (= optic nerves)
In the clade Chondrichthyes basal members (Fig 6) had small eyes, small brains and long eye stalks. This morphology was overlooked by Klug et al, but could have been established with the LRT (subset Fig 3).

Figure 6. Several basal chondrichthyes demonstrate the early appearance of long eye stalks to connect eyeballs to tiny brains. Also note the ventral view of Cladoselache here demonstrating the presence (at bottom) of a wide rostrum (pink), as found in Maghriboselache (Figs 4, 5).

In part 2 of 2, tomorrow,
we’ll look at advances in our understanding of gnathostome phylogeny (Fig 3) unfortunately not yet present in Klug et al 2023 due to taxon exclusion.

References
Dean B 1894. Contributions to the morphology of Cladoselache (Cladodus). Journal of Morphology 9:87–114.
Dean B 1894. A new cladodont from the Ohio Waverly, Cladoselache newberryi, n.sp. Transactions of the New York Academy of Science, 13: 115–119.
Garman S 1884. An Extraordinary Shark. Bulletin of the Essex Institute: 47–55.
Klug C et al  (8 co-authors) 2023. Broad snouted cladoselachian with sensory specialization at the base of modern chondrichthyans. Swiss Journal of Palaeontology. 142 (1): 2. doi:10.1186/s13358-023-00266-6

wiki/Cladoselache
wiki/Maghriboselache

Archaeomene enters the LRT between Wadeichthys and Tarrassius, all three basal to moray eels

Archaeomene tenuis
and Archaeomene robustus (originally Madariscus robustus Woodward 1895, Bean 2021, Latest Jurassic, 150mya, Fig 1) was originally and traditionally considered a member of the Pholidophorus clade.

By contrast
here in the large reptile tree (LRT, 2259 taxa) this genus nests between Wadeichthys and Tarrasius (Fig 2) and the rest of the moray eel (Fig 2) clade. Prior authors determined the robustus species was the adult of the tenuis juvenile. Note the transition to an eel-like morphology with smaller lateral fins and a straighter tail fin.

Note the tiny premaxilla, shallow dentary and large orbit. These traits are autapomorphies (= restricted to this taxon).

Figure 1. Archaeomene robustus (adult, above) and A tenuis (juvenile, below).

Tarrasius problematicus
(Traquair 1881; Sallan 2012; Viséan, Early Carboniferous, 340mya; 10cm) was considered similar to the bichir, Polypterus, but phylogenetically close to Eusthenopteron and Phanerosteon.

That’s not the way it worked out in the LRT,
which was created to minimize taxon exclusion.

Figure 2. The moray eel, Gymnothorax, compared to Tarrasius. Archaeomene, Wadeicthys and other relatives.

In the LRT
Tarrasius nests with the moray eels, basal to Gymnothorax. The DGS tracing and skull reconstruction are different than the Sallan 2012 reconstruction (Fig 2). The postorbital was fused to the postfrontal. The teeth were blunt.

Distinct from other fish,
the vertebral column of Tarrasius was morphologically divided into cervical, dorsal, lumbar, sacral and caudal regions, despite lacking pelvic fins. This vertebral morphology division is retained in moray eels, which have a much longer caudal region.

Superficiallly similar
Paratarrasius is also considered a member of the tarrasiids, but is more closely related to the spiny shark, Brachyacanthus, in the LRT based chiefly on skull traits.

This appears to be a novel hypothesis of interrelationships.
If not, please provide a citation so I can promote it here.

References
Bean L B 2021. Revision of the Mesozoic freshwater fish clade Archaeomaenidae. Alcheringa: An Australasian Journal of Palaeontology. 45 (2): 217–259.
Egerton P de MG 1860. Report of the British Association for Science for 1859.
Transactions of the Sections. 116.
Giebel CGA 1848. Fauna der Vorwelt, 1 (3) mit steter Berücksichtigung der lebenden Thiere: Fische. Couverture online
Lund R and Poplin C 2002. Cladistic Analysis of the Relationships of the Tarrasiids (Lower Carboniferous Actinopterygians). Journal of Vertebrate Paleontology 22(3):480–486.
Traquair RH 1881. Report on the fossil fishes selected by the Geological Survey of Scotland in Eskdale and Liddesdale. I. Ganoidei. Trans. R. Soc. Edin. 30,
14–71.
Woodward AS 1895. The fossil fishes of the Talbragar Beds (Jurassic?). Memoirs of the Geological Survey of New South Wales 9:1-31.

wiki/Tarrasius
wiki/Archaeomaene
wiki/Paratarrasius – not yet posted

The Krebs cycle and the origin of life at the atomic level YouTube video

Fascinating and informative.
Highly recommended if you want to know this cutting edge of biochemistry.

Lots of info in a little time. You’ll probably benefit from a second viewing.

References
Nick Lane’s personal website.