Scutosaurus modeled by computer

Romano et al. 2021 created
a digital version of the iconic pareiasaur, Scutosaurus (Fig. 1).

Figure 1. Scutosaurus model created by Romano et al. 2021. Note the nearly vertical ribs of this pareiasaur, distinct from the more lateral ribs of Bunostegos and its turtle descendants. Note how the hind limbs appear erect in lateral view and sprawling in posterior view.

From the abstract:
“In this contribution we provide a possible in vivo reconstruction of the largest individual of the species Scutosaurus karpinskii and a volumetric body mass estimate for the taxon, considering that body size is one of the most important biological aspects of organisms. The body mass of Scutosaurus was calculated using a 3D photogrammetric model of the complete mounted skeleton PIN 2005/1537 from the Sokolki locality, Arkhangelsk Region, Russia, on exhibit at the Borissiak Paleontological Institute, Russian Academy of Sciences (Moscow).”

Romano et al. wrote:
“Pareiasaurs are classified as members of the clade Parareptilia, a group of basal amniotes with no living representatives.”

Figure 1. Carbonodraco enters the LRT alongside another recent addition, Kudnu, at the base of the pareiasaurs + turtles.
Figure 1. Carbonodraco enters the LRT alongside another recent addition, Kudnu, at the base of the pareiasaurs + turtles.Figure 1. Carbonodraco enters the LRT alongside another recent addition, Kudnu, at the base of the pareiasaurs + turtles.

the large reptile tree (LRT, 1938+ taxa) does not recover the clade Parareptilia. In the LRT pareiasaurs arose from Stephanospondylus, Carbanodraco and Kudnu, taxa not mentioned in Romano et al. A knobby-skulled Late Permian Sahara pareiasaur, Bunostegos, is the closest pareiasaur to two clade of turtles, hard shell and soft shell.

None of this affects the results of the Romano et al. study,
but it does falsifiy certain traditional, yet mythological phylogenetic statements reported by the team. If this is what they are teaching at universities around the world, you might want to rethink how you spend your tuition dollars.


Romano M, Manucci F, Rubidge B and Van den Brandt MJ 2021. Volumetric Body Mass Estimate and in vivo Reconstruction of the Russian Pareiasaur Scutosaurus karpinskii.
Front. Ecol. Evol. 9:692035. doi: 10.3389/fevo.2021.692035

Tapejarid ‘composite’ Kariridraco will not enter the LPT

Cerquiera et al. 2021 reported,
“Mechanical preparation revealed that the original concretion bearing the fossil was a composite, in which the rostral ends of the premaxillae and dentaries of a second pterosaur specimen was glued to the holotype. In order to avoid misinterpretations, we choose to only illustrate those elements that safely belong to a single individual. The exact location where MPSC R 1056 was found is, unknown, since the specimen was donated to MPSC by local workers.”

I wonder if this was before or after the threat of arrest?
Apparently the local workers wanted to sell this specimen on their own and attempted to make it look more marketable before ‘realizing the error of their ways’ and ‘donating’ their poorly prepared specimen to the MPSC (Museu de Paleontologia Plácido Cidade Nuvens, Santana do Cariri, Brazil). If their intentions were honorable, as soon as the local workers found the specimen they would have asked their boss to find a museum paleontologist pronto!

You find this sort of thing
wherever there is a market for pterosaur skeletons and skulls.

The authors reported
MPSC R 1056 as a 2-part chimaera (Fig. 1), but illustrated it as a 3-part chimaera. They gave the small (Fig. 2) specimen a name: Kariridraco dianae based on what appears to be glued together AND taphonomically damaged and scattered specimen.

Figure 1a. Kariridraco as originally found a 3-part chimaera. The authors considered the pink portion of the specimen genuine. Here even that is called into question based on the ‘blueprint’ of a complete tupuxuarid juvenile (see figure 2) with adult proportions.
Figure 1b. Same as 1a, but enlarged and rotated to show details. What looks like a mandible fenestra is the inside of the mandible, with surangular missing.

Given that part of the specimen is recognized as chicanery,
should musuem specialists be giving the rest of this specimen their ‘blessing’ based on what is apparently more chicanery and/or overlooked taphonomic scattering?

the whole Sordes fiasco was based on workers not recognizing the displaced bones and wing membranes. And they still haven’t confessed to their misdeeds. Read that sordid story here.

The authors report,
“The unusually steep premaxillary crest and the fact that the rostrum anterior to this structure was adulterated by fossil dealers led us to raise concerns about the crest authenticity. Careful examination of the fossil and surrounding matrix revealed that, although there are signs of a breakage close to the base of the crest (where it contacts the main body of the premaxillomaxilla), the two resulting counterparts fit together, with no signs of add-ons or other modifications. Bone surface at the base of the crest was eroded off, so that trabecular bone is exposed at that portion.”

If the mid-portion of the specimen had normal proportions,
it would be more acceptable. But it doesn’t have typical, traditional proportions. That’s a red flag. That signals more chicanery. The crest base is not firmly attached to the jaws, as recognized by the authors. The unusually high crest angle is the result of taphonomic damage mistakenly accepted as a real trait. The matrix may be undisturbed because taphonomic shifting on a broken up fossil is not the same as preparator chicanery. This is why you have to be on the lookout for both and a reconstruction is so important before scoring traits.

Figure 1. Ontogenetic skull and crest development in Tupuxuara. Note the eyes are small and the rostrum is long in juveniles. Only the crest expands and only posteriorly.
Figure 2. Ontogenetic skull and crest development in Tupuxuara. Note the eyes are small and the rostrum is long in juveniles. Only the crest expands and only posteriorly.

The bone break that is most interesting
is the one close to the anterior of the antorbital fenestra. This is the one that greatly shortens the skull (Figs. 1a, 1b). When separated to normal proportions based on the underlying blueprint all the bones are still the correct size for a juvenile tupuxuarid (Fig. 2).

The authors did not mention the small overall size of the specimen.
Nor did the term ‘juvenile’ enter the text. Nor did they mention the Goshura (Japan) specimen. The complete, 3D juvenile tupuxuarid serving as the blueprint (Fig. 1) may not be in a museum. I saw it at a fossil expo in Arizona several decades ago.

Figure 3. Cladogram from Cerqueira et al. 2021. Here pterosaurs arise from a tiny croc with vestigial fingers, Scleromochlus. This is a myth that continues to be found in university textbooks written by the author of that myth.

The pterosaur cladogram provided by Cerqueira et al. was borrowed,
and borrowed and borrowed again. Outgroup taxa include three very un-pterosaurian taxa and the basal pterosaur is a highly derived anurognathid. Embarrassing to see this as professional output. We’ve known more parsimonious pterosaur outgroup taxa for twenty years. We’ve had more complete pterosaur cladograms for a decade or more.

The lessons for today,
1. Be wary of composite (some call these ‘fake’) fossils. 2. Try to describe new genera on the basis of better preserved specimens. 3. Create reconstructions and compare them to known, more complete taxa. 4. No need to include Scleromochlus and other archosauriforms in a pterosaur cladogram that focuses on tapejards and tupuxuarids. A series of Germanodactylus and dsungaripterids will do.

Figure 4. Tapejaridae in the LPT.
Figure 4. Tapejaridae in the LPT. Click here to enlarge.

Some specimens just belong in the back, on the shelves,
until someone is willing to put in the effort required to understand the chicanery and taphonomy by creating a reconstruction that can be properly scored using the tools of comparative anatomy.

Cerqueira GM, Santos MA, Marks MF, Sayão JM and Pinheiro FL 2021. A new azhdarchoid pterosaur from the Lower Cretaceous of Brazil and the paleobiogeography of the Tapejaridae. Acta Palaeontologica Polonica. 66. doi:10.4202/app.00848.2020


The cichlid Labeotropheus: fish eater? Or algae grazer?

Conith and Albertson 2021
illustrated a series of three images (Fig. 1, here animated) to show a schematic “cichlid” that looks that looks like Labeotropheus (Fig. 2), a genus also mentioned in their text. The caption reads, “C – Schematic illustrating the relative positions of the oral (red) and pharyngeal (blue) jaws within the skulls of cichlid fishes. D – Schematic illustrating the relative roles of each jaw complex in prey capture and prey processing.”

So, we’re left guessing which one of 500 to 1000 species of cichlid from three African lakes we’re looking at in the authors’ diagram. Labeotropheus (Fig. 2) seems reasonably close if not right on the money.

Figure 1. Labeotropheus animation from three images in Conith and Albertson 2021, eating a fish. According to Wikipedia Labeotropheus is an algae grazer.

Wikipedia reports on Labeotropheus,
“These cichlids are popular ornamental fish and are ideally suited to the cichlid aquarium. Like many Malawi cichlids, these species are algal grazers.”

So… which is correct? Fish-eater? Or algae grazer? Or were the authors purposefully being nebulous when writing their caption?

Figure 2. Labeotropheus x-ray and graphic from Conith and Albertson 2021, colorized here. Circumorbital ring added. Note the position of the mandible in the x-ray. Compare to figure 1.

Evidently diet is not germane.
Conith and Albertson wrote: “Ray-finned fishes have broken functional constraints by developing two jaws (oral-pharyngeal), decoupling prey capture (oral jaw) from processing (pharyngeal jaw). It is hypothesized that the oral and pharyngeal jaws represent independent evolutionary modules and this facilitated diversification in feeding architectures. Here we test this hypothesis in African cichlids. Contrary to our expectation, we find integration between jaws at multiple evolutionary levels.”

It would have been ideal to show the fish eating type of cichlid eating the fish, rather than the algae grazer eating the fish, but their point was made. Some cichlids do eat little fish. And when one body part changes, so do others (contra the modular hypothesis).

Conith and Albertson wrote,
“Cichlids that hunt elusive prey typically pair slender, mobile oral jaws with gracile pharyngeal jaws, while cichlids that feed on algae or other tough foods typically pair robust, compact oral jaws with strong pharyngeal jaws.”

Gracile or robust? (Fig. 1) You be the judge. There’s no doubt a fish eating a fish is more interesting than an algae grazer. Remember, professors sometimes play by different rules. In academia you gotta get published! Or perish. Or so the saying goes…

Or headline grabber? Co-author Conith was quoted in, “Remember the movie ‘Alien,’ when the alien is about to eat Sigourney Weaver’s character? It opens its mouth and out comes a second set of jaws. Fast forward twenty years, and here I am, studying animals that have jaws in their throats.”

Quoting Conith,It opens its mouth and out comes a second set of jaws.” Funny. Their own diagram (Fig. 1) shows the second set of ‘jaws’ remaining way back in the throat. My guess is reporters for might not have published this report if the subject was a 30cm algae grazer, “best kept in aquariums with volumes greater than 120L or 31.5 gallons.”

Albertson concludes, “This tells us that we need to rethink the fundamentals of evolutionary mechanisms.”

Do we? Or should we just be more specific when writing captions? Or less hyperbolic when speaking with reporters. Science is science, not show business. Stick with the fundamentals.

The first cichlid, Labeotropheus, entered
the large reptile tree (LRT, 1937 taxa) today nesting alongside Paleocene Massamorichthys and extant Monocentris. It is derived from an ancient sister to extant Polydactylus. Labeotropheus fuelleborni (Ahi 1926; 30cm) is the blue mbuna, endemic to Lake Malawi in eastern Africa.

Ahi E 1926. Einige neue Fische der Familie Cichlidae aus dem Njassa-See. Sber. Ges. naturf. Freunde, Berl. : 51-62.
Conith AJ and Albertson RC 2021. The cichlid oral and pharyngeal jaws are evolutionarily and genetically coupled. Nature Communications



Alligator and Deinosuchus enter the LRT

One is a large extant icon of Florida, famous for crossing golf courses. The other is a Cretaceous giant of coastal North America. Today Alligator (Fig. 1) and Deinosuchus (Fig. 2) enter the large reptile tree (LRT, 1936+ taxa; subset Fig. 3).

This started with an online NPR story (link below):
“There’s this concept out there that crocodylians are unchanging forms,” Brochu said. “That they appear way back in the distant past and haven’t changed since the days of the dinosaurs. That is simply not true.” Dr. Chris Brochu was a co-author on the paper: Cosette AP and Brochu CA 2020, a systematic review of Deinosuchus, which prompted the NPR story.

Figure 1. Alligator skull colorized here.

Alligator mississippiensis (Holbrook 1842; originally Crocodilius mississippiensis, Daudin 1802; up to 4.6m) is the American alligator. Derived (through a long chain of transitional taxa) from a sister to Middle Cretaceous Isisfordia (Fig. 4), these aquatic archosaurs have shifted the internal nares to the rear of the pterygoid enabling breathing while eating, like mammals.

Figure 2. Deinosuchus riograndensis assembled and colorized from Cosette and Brochu 2020. Lateral view of 3D model from the Langston lab. It doesn’t quite match the fossil. Note the lack of deep pterygoids in the model.

Deinosuchus riograndensis
(Colbert and Bird 1954, originally Phobosuchus riograndensis, TMM 43620-1), original genus: (Deinosuchus hatcheri (Holland 1909 CM963; Late Cretaceous; approaching 10m in length) is a coastal giant of North America. Premaxillary fenestrae are found on the anterior dorsally expanded premaxilla, as in Crocodylus niloticus, but not Alligator. The confluent nares open dorsoposteriorly along the parasagittal plane. Note the model lateral view does not quite match the fossil dorsal view with regard to the anterior extent of the quadratojugal.

Figure 3. Subset of the LRT focusing on Crocodylomorpha with the addition of Alligator and Sebecus. Many scores were rescored with this addition. This is part of the LRT process: review.

The cladogram by Cosette and Brochu 2020
focused solely only the species surrounding Deinosuchus and do not extend to the base of the Crocodylomorpha and beyond. When you deal at the species level, like that, you may need more characters or you may not, but you will need more pertinent characters to separate taxa at the specimen and species level, while eliminating irrelevant characters and states.

Figure 4. Isisfordia was a Middle Cretaceous precursor to later alligator and crocodiles in the LRT.
Figure 4. Isisfordia was a Middle Cretaceous precursor to later alligator and crocodiles in the LRT.

In the LRT,
working at the generic level, 238 multi-state characters have, so far, done the job of separating one fish from another, one croc from another, etc. Calls for more characters in the LRT are not based on experience and fact, but on out-of-date hypotheses still found in university textbooks and lectures. Not sure why academics are adamant about adding traits and equally adamant about not adding taxa. That’s why the LRT experiment exists.

Figure 5. Sebecus with a new premaxilla based on Deinosuchus (Fig. 2).

Sebecus icaeorhinus
(Simpson 1937, Pol et al. 2012, Eocene; Fig. 5) is a land croc from South America. Like a theropod dinosaur, the teeth were laterally compressed and serrated. Sebecus was earlier nested with Baurusuchus, but now nests more closely to living crocs with conical teeth.

This hypothesis of interrelationships appears to be novel.
If there is a prior citation, please let me know so I can promote it here.

Cosette AP and Brochu CA 2020. A systematic review of the giant alligatoroid Deinosuchus from the Campanian of North America and its implications for the relationships at the root of Crocodylia. Journal of Vertebrate Paleontology 40(1):e1767638
Daudin FM 1801-2. Histoire Naturelle, Générale et Particulière des Reptiles; ouvrage faisant suit à l’Histoire naturell générale et particulière, composée par Leclerc de Buffon; et rédigee par C.S. Sonnini, membre de plusieurs sociétés savantes. Vol. 2. F. Dufart, Paris, 432 pp.
Hollbrook JE 1842. North American Herpetology; or, A description of the reptiles inhabiting the United States. Vol II (2nd ed.). J. Dobson, Philadelphia, 142 pp.
Simpson GG 1937. An ancient eusuchian crocodile from Patagonia. American Museum Noviates 965: 19–20.


Are whales artiodactyls? No.

Prothero and 15 co-authors 2021
report the clade name Cetioartiodactylia “is a junior synonym for Artiodactylia.” That confirms Spauling, O’Leary and Gatesy (2009), but that’s not the point. In Prothero et al. 16 PhDs think whales are monophyletic and evolved from either small, deer-like taxa… or, according to Graur and Higgins 1994, Irwin and Arnason (1994) and Gatesy et al. (1996): hippos, universally and mistakenly considered to be artiodactyls (see Fig. 3). All prior workers overlooked, omitted, ignored and excluded mysticete and ondontocete precursor taxa with legs recovered in the LRT (Figs. 1–3).

From the abstract:
“The name “Cetartiodactyla” was proposed in 1997 to reflect the molecular data that suggested that Cetacea is closely related to Artiodactyla. Since then, that taxon has spread in popularity, even outside the scientific literature. However, the implications of the name are confusing, because Cetacea and Artiodactyla are not sister-taxa.

Cetacea and Artiodactyla are also not sister-taxa in the large reptile tree (LRT, 1936+ taxa; subset Fig. 3) because Cetacea is an invalid clade. Members of the Odontoceti arise completely separate from Mysticeti (Figs. 1, 2) and apart from Artiodactyla.

Are hippos artiodactyls? No. In the LRT (subset Fig. 3) hippos nest outside the Artiodactyla, between oreodonts + mesonychids and anthracobunids + desmostylians + mysticetes.

“Instead, the evidence clearly shows that cetaceans are a group embedded within Artiodactyla, not a sister-taxon of equal rank. It has long been accepted practice that systematists do not modify the names of higher groups when new subgroups are added to them. For example, Owen’s original concept of Artiodactyla did not change its name when more and more disparate taxa were added to it. Dinosauria did not become “Avedinosauria” when it became clear that birds are a subgroup of dinosaurs, nor did Reptilia become “Avereptilia”. In the interests of taxonomic priority and stability, and especially because the name is inherently misleading, we recommend that the name “Cetartiodactyla” be abandoned. If one wishes to make a reference to the fact that whales are now considered to be a subgroup of artiodactyls, they could be referred to informally as “whales and other artiodactyls” or “whales and terrestrial artiodactyls” without using a formal taxonomic name that is confusing and misleading.”

Curious why 16 authors signed their names to this nomenclature paper? It seems to be an opportunity for 15 PhDs to stamp their approval on this junior synonym effort led by Dr. Prothero. Unfortunately this turns out to be too small a bandage for such a large wound.

Figure 8. Odontoceti (toothed whale) origin and evolution. Here Anagale, Andrewsarchus, Sinonyx, Hemicentetes, Tenrec Indohyus and Leptictidium precede Pakicetus. Maiacetus and Orcinus are aquatic odontocetes.
Figure 8. Odontoceti (toothed whale) origin and evolution. Here Anagale, Andrewsarchus, Sinonyx, Hemicentetes, Tenrec Indohyus and Leptictidium precede Pakicetus. Maiacetus and Orcinus are aquatic odontocetes.

Vislbokova 2013
wrote on the origin of Cetartiodactyla. “The data on phylogeny and early evolution of Cetartiodactyla are analyzed and a model for the initial stage of their history is proposed. It is shown that the roots of Cetartiodactyla go back to generalized Cretaceous terrestrial Eutheria, and a hypothetical basal group of Cetartiodactyla was probably ancestral to the orders Artiodactyla and Cetacea. The Artiodactyla-Cetacea divergence and adaptive radiation of Artiodactyla, which gave rise to the suborders Ruminantia, Tylopoda, and Suiformes, apparently occurred in the pre-Eocene time, earlier than 55 Ma. Molecular similarity between Hippopotamidae and Cetacea is evidence of common origin of Artiodactyla and Cetacea and adaptation to aquatic environment.”

This 2013 paper also suffers from taxon exclusion and dependence on deep time molecular studies. Note the lack of specific taxa and the use of “generalized Cretaceous terrestrial Eutheria’. Just add taxa to find out where whales really came from (Figs. 1–3), all the way back to Ediacaran worms.

Figure 1. Taxa in the lineage of right whales include Desmostylus, Caperea and Eubalaena. The tiny bit of jugal posterior to the orbit (in cyan) is found in all baleen whales tested so far. The frontals over the eyes are just roofing the eyeballs in Desmostylus, much wider in Caperea and much, much longer in Eubalaena.
Figure 1. Taxa in the lineage of right whales include Desmostylus, Caperea and Eubalaena. The tiny bit of jugal posterior to the orbit (in cyan) is found in all baleen whales tested so far. The frontals over the eyes are just roofing the eyeballs in Desmostylus, much wider in Caperea and much, much longer in Eubalaena.

Prothero et al. 2021 report:
“The relationship of Cetacea and Hippopotamidae has since been confirmed by all the studies already cited and is now well established by paleontological studies that demonstrate the origin of hippos from a common ancestor with whales within the paraphyletic group Anthracotheria,
which most systematists regard as the sister-group of whales and hippos.”

This is incorrect when you add even a few pertinent taxa (Figs. 1–3).

Figure 3. Subset of the LRT focusing on placentals. Note the separation of Odontoceti from Mysticeti. Note the splitting of the two Vulpavis species. Note the placement of Hippopotamus close to Mesonychus, not within Artiodactyla. Simply adding taxa gives you this family tree topology. Taxon exclusion spoils prior efforts at understanding whale origins.

Spauliding, O’Leary and Gatesy 2009
ran their own analysis and likewise omitted desmostylians, anthracobunids, tenrecs and anagalids. They recovered a monophyletic Cetacea with toothless Mysticeti (= baleen whales) nesting by default between Basilosaurus and Physeter, two toothed whales. This is an untenable association given the competing hypothesis that includes more taxa that demonstrate a gradual accumulation of derived traits, leading to convergence between Mysticeti and Odontoceti. The LRT was able to lump and separate these taxa with the present character list.

As demonstrated here, you can learn more
by simply doing the work yourself rather than sitting in university lecture halls and reading university textbooks on vertebrate paleontology. Professors continue to promote taxon exclusion even though it spoils efforts at understanding whale origins, turtle origins, snake origins, pterosaur origins, shark origins, etc.

Prothero et al. 2021 relies on several molecule studies.
Colleagues in paleontology: Let’s get back to bones, lots and lots of bones from lots and lots of taxa. Molecules and taxon exclusion are providing false positives and leading to very sketchy conclusions. You were inspired to get into paleontology because you thought bones were fascinating. Get back to that original inspiration.

Gatesy J, Hayashi C, Cronin MA, and Arctander P 1996. Evidence from milk casein genes that cetaceans are close relatives of hippopotamid artiodactyls. Mol Biol Evol 13(7):954-963.
Graur D and Higgins DG 1994. Molecular evidence for the inclusion of cetaceans within the order Artiodactyla. Mol Biol Evol 11(3):357-364.
Irwin DM and Árnason U 1994. Cytochrome b gene of marine mammals: Phylogeny and evolution. J Mamm Evol 2(1):37-55.
Prothero et al. (15 co-authors) 2021. On the Unnecessary and Misleading Taxon “Cetartiodactyla”. Journal of Mammalian Evolution.
Spaulding M, O’Leary MA and Gatesy J 2009. Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolution. PLoS One 4(9): e7062.
Vislobokova IA 2013. On the Origin of Cetartiodactyla: Comparison of Data on Evolutionary Morphology and Molecular Biology. Palaeontological Journal 47(3):321–334.

Rejected by referees including P. Gingerich:
Peters D 2013. The triple origin of whales.

Snakes and the K-Pg extinction event

Klein et al. 2021 “combined an extensive molecular dataset with phylogenetically and stratigraphically constrained fossil calibrations to infer an evolutionary timescale for Serpentes.

Once again: molecules. Beware of molecules. They deliver false positives in deep time studies due to endemic, geographic viruses that invade the ‘molecules’. You don’t have to trust traits. You can see them, measure them, watch them evolve. Molecules make you recover foolish cladograms and send them off to the editors of Nature… where they get approved and published!!!

Klein et al. test 115 snake taxa and 54 outgroups (see below).

Even though
the large reptile tree (LRT, 1936+ taxa; subset Fig. 1) currently includes very few extant terrestrial snake taxa, it does have a very long list of snake ancestors and a pretty good list of fossorial taxa.

So let’s see how things match up: traits vs. molecules in snakes,
remembering always that snake fossils are extremely rare on this planet.

Figure 3. Subset of the LRT focusing on geckos and their sister snake ancestors.
Figure 1. Subset of the LRT focusing on geckos and their sister snake ancestors.

Klein et al. report,
“Historically, squamates were believed to have experienced minimal extinction at the K-Pg boundary. However, analysis of the K-Pg transition in western North America found evidence for high rates of extinction among squamates, although it remains unclear whether this pattern holds on a global scale.”

“The early fossil record of crown group snakes is fragmentary, often restricted to vertebrae and
afflicted by relatively high rates of homoplasy.”
As noted above.

“So far, molecular divergence time analyses of snakes recover conflicting patterns. Most
studies (they cite four) suggest that the majority of extant snake clades diverged in the Cretaceous, although several analyses (they cite three) hint at a more recent diversification of the major subclade Alethinophidia
[= all snakes other than blind snakes and thread snakes].”

By contrast,
in the LRT (subset Fig. 1) blind snakes and thread snakes are the most derived fossorial snakes and they arise from members of the Alethinophidia like Loxocemus and Xenopeltis. So Alethinophidia, as defined, is paraphyletic in the LRT. The problem is: in Klein et al. highly derived blind snakes (Figs. 2, 3) are basal to more plesiomorphic terrestrial snakes. This makes the Klein et al. cladogram upside-down phylogenetically.

“Our results suggest a potential diversification of snakes near the time of the K-Pg transition. We find a pattern of increasing vertebral disparity in the aftermath of the extinction, with concurrent increases in average and maximum body size, and dispersal to previously unoccupied landmasses.”

Figure 3. Tetrapodophis and Barlochersaurus at full scale when seen on a monitor at 72 dpi.
Figure 1. Tetrapodophis and Barlochersaurus at full scale when seen on a monitor at 72 dpi.

Insert: a bit of backstory.
Tiny four-legged Early Cretaceous Tetrapodophis (16cm; Fig. 1) and and even tinier Barlochersaurus (1.5cm; Fig. 1) are proximal outgroups to all extant snakes in the LRT. So they start small, phylogenetically miniaturized. Snakes split immediately into terrestrial and semi-fossorial forms with Late Cretaceous Dinilysia (88mya, 1.8m in length est) at the base of ‘terrestrial’ snakes.

Older (95mya), smaller (1m) and swimming, Pachyrhachis also nests among the paucity of ‘terrestrial’ snakes in the LRT.

Much smaller Najash (Late Cretaceous, 90mya; 2cm skull) nests at the base of the fossorial snakes in the LRT.

These dates are probably much later than that initial dichotomy and radiation.
Instead these dates more likely represent maximum dispersal. With a sample of one, anything can happen statistically.

The authors used 169 taxa in their analysis.
They chose (= cherry-picked) ten non-squamate amniote and 44 non-snake squamate outgroups, rather than letting the software recover three or four actual proximal outgroups. Included among the 44 were Homo, the human, Gallus, the chicken, Chelydra, the turtle, and Mus the mouse. This is sad. Trait analysis would never have to use these unrelated taxa in a snake analysis.

Technical note on the published cladogram:
In order to read the illegible p39 SuppFig consensus tree of Klein et al. you have to open the page in Photoshop using a 300 dpi setting and still the type is fuzzy from over-magnification. They did not use vector graphics, which enable unlimited magnification.

Distinct from the LRT, highly derived geckos are recovered by Klein et al. at the basal node for squamates. As you’ll note above (Fig. 1) when traits and fossils are employed, geckos are not the most primtive squamates, but are the closest extant snake relatives in the LRT.

Distinct from the LRT, chameleons and anolids are proximal snake outgroups recovered by Klein et al.

Distinct from the LRT, the most derived blind snakes nest as basal snake taxa recovered by Klein et al. And these give rise to less derived, more plesiomorphic fossorial snakes. And these give rise to less derived, more plesiomorphic terrestrial and aquatic snakes.

Distinct from the LRT Klein et al. nest arboreal chameleons with burrowing blind snakes (with no transitional taxa between them).

Figure 2. Liotypholps skull from and used with permission. Unlike related taxa, a prefrontal shows up here (reversal) to anchor a tall, mobile, tooth palatine.
Figure 2. Liotypholps skull from and used with permission. Unlike related taxa, a prefrontal shows up here (reversal) to anchor a tall, mobile, tooth palatine. If you think this skull is highly derived, you are correct. Even the jaws don’t work like typical jaws do here. They eyes don’t work either. This is a blind snake.

Because Klein et al. trusted deep time molecules, their cladogram is upside-down.
Apparently no one on their team, or the editors at Nature, or the PhD referees objected to the bizarre results. Folks, this is the paleo-university system in a nutshell. If this is what you want, go for it, pay for it, have your professors tell you what they want you to study. If not, then collect your own trait-based data, run your own analysis, and see for yourself how snakes evolved. Ironically, for budding paleontologists, molecular studies omit the fossils they want to study.

Without a valid, sensible trait-based cladogram that includes fossils
all the work that follows (and there was a lot of work that followed in Klein et al.) is not dubious, or suspect, but a waste of time. Apparently they are teaching university students that molecules deliver better results than traits and fossils. They don’t. Study the bones and study the fossils and learn something.

Leptotyphlops jaws movie
Figure 3. Click to animate. Leptotyphlops jaws move medially, not up and down. For this reason alone, and there are many others, Leptotyphlops is one of the most derived burrowing snakes, not the most primitive one.

The cladograms on SuppData pp. 42–44 are also nearly illegible due to the amount of data and the standard page size. Question: why are digital data restricted to page size? It’s illegible when printed. Why not increase the digital page size? The LRT is 25 inches tall and has vector-based PDF files that support it. PDF images can be enlarged to any size without degradation.

Klein CG et al. (5 co-authors) 2021. Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction. Nature Don’t forget to download the SuppData, which has at least 29 figures and 6 tables.

Weird Petrocephalus enters the LRT between piranhas and elephantfish

Odd looking Petrocephalus (Fig. 2) has an unexpected ancestry (Fig. 1) and even odder progeny (Fig. 3).

Figure 1.  On the piranha, Serrasalmus, the premaxilla (yellow) does not extend to the tooth row. Instead the maxilla (green) carries all the upper teeth. Serrasalmus skeleton image courtesy of ©Steve Huskey and used with permission.
Figure 1.  On the piranha, Serrasalmus, the premaxilla (yellow) does not extend to the tooth row. Instead the maxilla (green) carries all the upper teeth. Serrasalmus skeleton image courtesy of ©Steve Huskey and used with permission.
Figure 2. Petrocephalus, a type of elephantfish without a trunk, nests between Serrasalmus (figure 1) and Gnathonemus (figure 3).
Figure 3. Gnathonemus, the elephant fish, for obvious reasons, has been traditionally considered a sister to Osteoglossum. Here it nests with Hippocampus, the seahorse. Image from Gregory 1938.

Evolution at work, starting with the piranaha, Serrasalmus:
In Petrocephalus the circumorbital ring is reduced.
In Gnathonemus the circumorbital ring is absent.

In Petrocephalus the jaws and teeth are much smaller.
In Gnathonemus the jaws are smaller on an extended, curved rostrum and the teeth are smaller still.

In Petrocephalus the posterior crest is reduced.
In Gnathonemus the posterior crest is smaller still.

In the LRT the relationship between the piranha and elephantfish
was already established. The addition of Petrocephalus (Fig. 2) makes it one of many transitional taxon between the piranha, Serrasalmus (Fig. 1), and the elephantfish, Gnathonemus (Fig. 3). The less lethal Brycon, the South American trout or Sabalo barracuda (Fig. 4), currently nests at the base of this clade. These are basal ray fin fish with an ancestry that probably extends back to the Devonian.

Figure 4. Brycon, the extant South American trout, is basal to the piranha and the mormyrids.
Figure 4. Brycon, the extant South American trout, is basal to the piranha and the mormyrids.

Petrocephalus bane
(Lacepède 1803; 20cm) is considered a mormyrid, like Mormyrops,and a species of elephant fish, despite lacking a ‘trunk’. Here it nests between Serrasalmus and Gnathonemus. The mandible is smaller than the orbit. Crests appears on the front and on the posterodorsal skull, but they do not show up outside the skin in vivo.

de Lacepéde BG 1803. Histoire naturelle des poissons. Tome Cinquieme. 5(1-21):1-803 + index.


The roughshark, Oxynotus, enters the LRT. The anal fin exits 13 times. Plus the many origins and ends of spines on fins.

The traditional family, Oxynotidae,
includes only one genus and 6 species. In the large reptile tree (LRT, 1936+ taxa, subset Figs. 3,4) Oxynotus (Fig. 1) nests basal to two LRT taxa, Isistius, the cookiecutter shark, and Dalatias, the kitefin shark, both with smaller fins. So… by the rules these two must also be members of the Oxynotidae. Shark experts (Kriwet and Klug 2009) don’t see it that way. More taxonomic issues below.

Figure 1. Oxynotus centrina in several views. Skull elements estimated.
Figure 1. Oxynotus centrina in several views. Skull elements estimated. Here the dorsal spines start in the middle, not on the leading edge, distinct from most other spine fin taxa.

Oxynotus centrina
(Linneaus 1758; up to 1.5m; Fig. 1) is the extant angular roughshark. Ridges appear over the eyes and between the pectoral and pelvic fins. The anal fin is absent, as in other clade members. A dorsal spine is present on both dorsals, but not at the leading edge. These chimaera-like sharks feed on small bottom-dwelling prey, like worms, crustaceans and molluscs. The ventral nares are enormous.

Figure 1. Gregorius descends from Hybodus, the shark and is ancestral to Prohalecites at the base of the ray-fin bony fish. Gregorius is also ancestral to Homalacanthus at the base of the spiny sharks leading to lobefins, placoderms, catfish and a variety of other taxa.
Figure 2. Gregorius descends from Hybodus, the shark and is ancestral to Prohalecites at the base of the ray-fin bony fish. Gregorius is also ancestral to Homalacanthus at the base of the spiny sharks leading to lobefins, placoderms, catfish and a variety of other taxa.

The origin and evolution of spines on fins
Academic fish workers think spiny fins on spiny sharks (= acanthodians, Fig. 2) have no clear ancestors and no clear descendants. The LRT (Figs. 3,4) recovers a long set of spiny shark ancestors (like (Oxynotus, Fig. 1) and descendants (like like lobe fins and vertebrates).

Figure 3. Subset of the LRT focusing on basal vertebrates. Colors indicate spiny fins, lobe fins, etc. Note the basal nesting of Squalus, likely an Early Silurian taxon based on chronological bracketing. The catfish, Hoplosternum, has plats and spines.

The origin and evolution of the anal fin
The absence of the anal fin on Oxynotus brings up the subject of anal fin disappearance in vertebrates. In LRT (Fig. 4), the anal fin appears early (Fig. 4 lavender) and then disappears 13x (Fig. 4 amber), ultimately lost forever in Panderichthys + tetrapods.

Figure 4. Appearance (lavender) and disappearance (amber) of the anal fin in vertetbrates.

Traditionally (= in textbooks)
Oxynotus (Fig. 1) is considered a member of the Squaliformes (dogfish sharks). The
last common ancestor in the LRT (subset Fig. 4) is the extant dogfish, Squalus (Fig. 5).

Kriwet and Klug 2009 wrote,
“Dogfish sharks (the Squaliformes) are a highly diverse group of neoselachian sharks occurring in coastal and oceanic, cool temperate, and deep tropical waters worldwide.”

There’s that phrase, “highly diverse” again. This time, however, if Squaliformes are indeed monophyletic, Kriwet and Klug grossly underestimate the diversity of this clade, which includes the authors themsevles!

Figure 2. The spiny dogfish, Squalus acanthi as, in vivo.
Figure 5. The spiny dogfish, Squalus acanthi as, in vivo. Note the anal fin is absent in this taxon and all traditional squaliform sharks. The anal fin disappears 13x in the LRT.

LRT taxonomy
In the LRT (Fig. 2) Squalus (Fig. 5) is the last common ancestor of a small clade that includes chimaera (ratfish).

In the LRT (Fig. 2) Squalus is close to the last common ancestor of a much larger clade that includes ratfish, all more derived sharks, all bony fish (including tetrapods).

In the LRT (Fig. 2) Oxynotus and other sharks that look like Squalus are currently separated from Squalus by traditional non-squaliform taxa, like Isurus, a traditional lamniform alongside the CMNH 9280 specimen from the Late Devonian.

More taxa in the LRT will probably solve this issue. Either Lamniformes arise from squaliformes or some phylogenetic definitions need to change.

Figure 4. Daliatias, the extant kitefin shark, has relatively large labial cartilages.
Figure 6. Dalatias, the extant kitefin shark, has relatively large labial cartilages.

According to Kriwet and Klug 2009
the fossil record of Squaliformes consists predominantly of isolated teeth that date back to the Barremian (Early Cretaceous), ca. 125 million years ago. Full body fossils are found in Late Cretaceous strata.

In the LRT chronological bracketing hypothetically moves that record back to the Silurian.

According to Kriwet and Klug 2009
“The supertree resulting from combining published partial phylogenetic hypotheses the most inclusive estimate of squaliform interrelationships to date showing 23 out of about 35 known fossil and extant genera. The results presented here are in general agreement with most published phylogenetic hypotheses and differ only slightly from others. According to our hypothesis, Squaliformes is composed of six monophyletic groupings of family rank; Squalidae (Squalus and †Protosqualus) is separated at the deepest branching level from all other squaliforms according to this reconstruction.”

Kriwet and Klug did what most shark experts did and do: they cherry-picked only those taxa that look like Squalus. Their cladogram includes no rays, ratfish, higher sharks, bony fish and tetrapod descendants of Squalus. In the LRT (Figs. 3, 4) taxon inclusion sheds new light on hypothetical interrelationships.

Let your software tell you which taxa to include and exclude.
Don’t cherry-pick taxa based on obvious traits. Monophyly is a powerful concept that needs to be utilized at all nodes.

Kriwet J and Klug 2009. Fossil record and origin of squaliform sharks. (Chondrichthyes, Neoselachii. Pp. xx –xx. (Gallucci, McFarlane and Bargmann eds.) In Biology and Management of dogfish sharks. Chapter: Fossil record and origin of squaliform sharks (Chondrichthyes, Neoselachii). American Fisheries Society, Maryland.
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/Angular_roughshark – Oxynotus

First Rhamphorhynchus from Gondwana (Chile)

This is exciting news.
Rhamphorhynchus is known chiefly from Solnhofen Limestones (Tithonian, 150mya). This specimen is from the earlier Oxfordian (160mya) in the Atacama Desert of northern Chile, formerly a coast of Gondwana.

Figure 1. Three views of the Gondwana humerus together with comparative taxa on frame Alarcon-Munoz et al. 2021. On frame two elements are two scale with a matching specimen, though half size, YPM 1778.
Figure 1. Three views of the Gondwana humerus together with comparative taxa on frame #1 of this figure from Alarcon-Munoz et al. 2021. The authors sprinkle those three views: A, H and K on this graphic. On frame #2 the same elements are shown ‘to scale’ and arranged according to genus. All three tracings of the Gondwana humerus are collected together and boxed at upper left. Added to frame #2 is a more closely matching specimen, YPM 1778, overlooked by the authors. It is half the size of the Chilean specimen. Two frames change every 5 seconds.

From the abstract:
“We describe partial remains of a non-pterodactyloid pterosaur from Upper Jurassic levels of the Atacama Desert in northern Chile. The material includes a left humerus, a possible dorsal vertebra, and the shaft of a wing phalanx, all preserved in three dimensions and likely belonging to a single individual. The humerus has a hatchet-shaped deltopectoral crest, proximally positioned, and its shaft is markedly anteriorly curved, which are characteristic features of the clade Rhamphorhynchidae.

Three views of the Chilean humerus
were provided by Alarcón-Muñoz et al. (Fig. 1) together with cherry-picked humeri of various Rhamphorhynchus and Dorygnathus specimens. In frame 2 (Fig. 1) these are also shown to scale, flipped to a common view (deltopectoral crest left) rearranged generically. Unfortunately the authors did not include the specimen with the humerus presently closest to the Gondwana specimen: the YPM 1778 specimen (n33 in Wellnhofer’s 1975 catalog) of Rhamphorhynchus shown here in situ (Fig. 2).

Figure 1. The Yale specimen of Rhamphorhynchus phyllurus with preserved wingtip ungual highlighted. See figure 2 for closeup.
Figure 2. The Yale specimen (YPM 1778) of Rhamphorhynchus phyllurus with preserved wingtip ungual highlighted. This humerus of this specimen is a close match to the Chilean humerus, but half the size.

From the abstract, continued:
In addition, the presence of a groove that runs along the caudal surface of the phalanx, being flanked by two asymmetric crests, is a distinctive feature of the clade Rhamphorhynchinae, which includes such genera as Rhamphorhynchus and Nesodactylus.

In the LRT Nesodactylus nests within Campylognathoides prior to the genesis of Rhamphorhynchus, which first appeared following phylogenetic miniaturization (Fig. 3).

“Previous to this research, known records of Rhamphorhynchinae were restricted to Laurasia; thus, the specimen studied here represents the first evidence of this group found to date in Gondwana. Associated ammonoids allow us to assign the material to a middle Oxfordian age, which makes this specimen the oldest known pterosaur found in Chile, and the first of Oxfordian age in Gondwana. This discovery suggests that the clade Rhamphorhynchidae had a global distribution during the Late Jurassic.”

Figure 2. Rhamphorhynchus specimens to scale. The Lauer Collection specimen would precede the Limhoff specimen on the second row.
Figure 3. Rhamphorhynchus specimens to scale. Click here to enlarge.

Global distribution for Rhamphorhynchus is excellent news,
and serves to emphasize the pure luck we have with fossil formation and fossil discovery. Fossil beds and localities can be extremely tiny pinpricks on the surface of the Earth. Even so, the LRT documents no large gaps in the fossil record. All included taxa look like close relatives.

Figure 4. Portion of the Rudolph Zallinger mural at the Yale Peabody Museum featuring Morrison Formation dinosaurs of North America and a European Rhamphorhynchus at upper left. The Gondwana Rhamphorhynchus makes this hypothesis of association more likely.

Alarcón-Muñoz J, et al (5 co-authors) 2021. First record of a Late Jurassic rhamphorhynchine pterosaur from Gondwana. Acta Palaeontolgica Polonica 66:
Wellnhofer P 1975a-c. Teil I. Die Rhamphorhynchoidea (Pterosauria) der Oberjura-Plattenkalke Süddeutschlands. Allgemeine Skelettmorphologie. Paleontographica A 148: 1-33. Teil II. Systematische Beschreibung. Paleontographica A 148: 132-186. Teil III. Paläokolgie und Stammesgeschichte. Palaeontographica 149: 1-30.


Goodbye, Osteoglossomorpha: It’s polyphyletic in the LRT

Hilton and Lavouvé 2018
review the suspiciously varied traditional ‘clade’ Osteoglossomorpha.

From the abstract:
“The bony-tongue fishes, Osteoglossomorpha, have been the focus of a great deal of morphological, systematic, and evolutionary study, due in part to their basal position among extant teleostean fishes.”

That’s only partly true. Turns out, only some members of this traditional ‘clade’ are basal telostean taxa in the LRT. And none are the most basal. Ironically, the most derived one, Hiodon (Figs. 1, 2), looks more like a traditional fish than any of the more basal taxa.

Hilton and Lavouvé say traditional Osteoglossomorpha members include:

1. Mooneyes (= Hiodon – Hiodontidae)
2. Knifefish (= featherbacks like Notopterus – Notopteridae)
3. Abus (= African knifefish = Gymnarchus – Gymnarchidae)
4. Elephantfishes (= Mormyrus – Mormyridae)
5a. Arowanas (= Osteoglossum – Osteoglossidae)
5b. Pirarucu (= Arapaima – Osteoglossidae)
6. African butterflyfish (= Pantodon – Pantodontidae)

Figure 1. Traditional osteoglossomorphs according to Hilton and Lavouvé 2018. Note the variety. In the LRT only two of these nest together and not with Osteoglossum.

The traditional smaller clade, Osteoglossiformes
includes all the above sans Hiodon. The presence of teeth on the parasphenoid and tongue bones (hyoids) traditionally unite these taxa. The forward part of the gastrointestinal tract passes to the left of the esophagus and stomach distinct from all other fish. Unfortunately these traits (and apparently others not listed) are not enough to attract them together in the LRT, and apart from their LRT sisters and cousins. The LRT tests only skeletal and other hard parts that typically fossilize, like ganoid scales. The LRT tells us the presence of teeth on the parasphenoid and tongue bones are convergent. That’s why it is so important to run the scores for 238 traits and not “Pull a Larry Martin” by relying on a few to a few dozen traits.

Remember, clades are based on a last common ancestor basis,
not the possession of a short list of possibly convergent traits. (e.g. Amia, the bowfin, also has parasphenoid teeth, but is not considered a traditional osteoglossomorph).

Figure 2. Traditional osteoglossomorph skulls according to Hilton and Lavouvé 2018. Note the variety. In the LRT only two of these nest together and not with Osteoglossum.

From the abstract:
“This morphologically heterogeneous group also has a long and diverse fossil
record, including taxa from all continents and both freshwater and marine deposits.
In this paper we review the state of knowledge for osteoglossomorph fishes.”

As usual, whenever you see the phrase, ‘morphologically heterogeneous’
it’s a fair bet the clade is not monophyletic. Tested in the large reptile tree (LRT, 1936+ taxa; subset Fig. 1) only two sets nest with each other (Pantodon nests with Arapaima and Mormyrops nests with Gymnarchus). The rest do not. The traditional ‘Osteoglossomorpha’ falls apart when more taxa are added. So does the traditional Osteoglossiformes and the traditional Osteoglossidae (Arapaima does not nest with Osteoglossum in the LRT).

Figure 3. Subset of the LRT focusing on bony fish. Light red boxed taxa are traditional members of the Osteoglossomorpha and they are not monophyletic here. Far from it.

Hilton and Lavouvé 2018 report
“Osteoglossomorpha – the bony-tongue fishes – have been the focus of a great deal of morphological, systematic, and evolutionary study, due in part to their basal position among
extant teleostean fishes.”

This is not recovered by the LRT (Fig. 1). Members of the traditional Osteoglossomorpha nest in a scattershot pattern (= not together) when more taxa are added.

Hilton and Lavouvé 2018 report
“In their pivotal classification, Greenwood et al. (1966) formally established the modern conceptualization of crown-group Osteoglossomorpha, although all families had been more or less associated with one another by ichthyologists for some time. “

Greenwood et al. wrote:
“Results indicate the necessity of a major regrouping of teleostean orders, and this also is attempted. Traditionally, studies such as ours have been based on morphology, especially the
skeleton, which is the only complete organ system available for detailed comparison with

Exactly. That’s why the LRT tests skeletal elements.

“However, with the variety of both primitive and advanced teleosts living today, we are most emphatically of the opinion that approaches other than morphological ones would be exceedingly fruitful in the investigation of teleostean interrelationships.”

Let’s not go with opinions. The software that recovered the LRT does not have an opinion.

For the Osteoglossomorpha,
Greenwood et al. listed 9 traits either always or often seen in member taxa. They were Pulling a Larry Martin. But in 1966, what else could one do? Back then you could not build a matrix then run the data through analysis. Science marches on.

Greenwood et al. did not employ fossil taxa.
Hilton and Lavoué did emply fossil taxa, but those taxa were cherry-picked. What you need is a wide gamut of taxa so each one will find its closest sisters, the ones sharing the most traits.

Let’s strive to minimize taxon exclusion. It’s the number one problem in paleontology. Whoever thought pterosaurs would nest with tanystropheids? Or that Vancleavea would nest with thalattosaurs? Or that bats and pangolins would be closely related? Or that toothed and baleen whales would have separate ancestries in tenrecs and desmostylians? Take the cherry-picking, textbooks and opinions out of your analyses and just keep adding taxa.

Greenwood PH, Rosen DE, Weitzman SH and Myers GS 1966. Phyletic studies of teleostean fishes, with a provisional classification of living forms. Bull Am Mus Nat Hist. 1966; 131(4):339-456.
Hilton EJ and Lavoué S 2018. A review of the systematic biology of fossil and living bony-tongue fishes, Osteoglossomorpha (Actinopterygii: Teleostei). Neotropical Ichthyology, 16(3): e180031, 2018 DOI: 10.1590/1982-0224-20180031