Portunatasaurus almost enters the LRT with dolichosaurs, not mosasaurs

Too few traits are present
for Portunatasaurus (Figs. 1–3) to be entered into the LRT without loss of resolution, but that shouldn’t stop us from figuring out what it is and what it isn’t.

Figure 1. Portunatasaurus compared to stem mosasaur, Aigialosaurus and to marine stem snake, Aphanizocnemus.

Figure 1. Portunatasaurus compared to stem mosasaur, Aigialosaurus and to marine stem snake, Aphanizocnemus.

From the Mekarski et al. 2019 abstract:
“A new genus and species of plesiopedal mosasauroid, Portunatasaurus krambergeri, from the Cenomanian–Turonian (Late Cretaceous) of Croatia is described.”

Ooops. Taxon exclusion rears its ugly head again. In the large reptile tree (LRT, 1823+ taxa) Portunatasaurus (Fig. 1) is closer to aquatic snake ancestors, like Aphanizocnemus (Fig. 1), than a “plesiopedal mosasaurid.” Even with so few traits to test, moving Portunatasaurus closer to mosasaurs and aigialosaurs adds 4 steps. In the LRT Aphanizocnemus nests as a snake ancestor: a marine varanoid dolichosaur scleroglossan squamate.

Figure 2. Portunatasaurus diagram with corrections.

Figure 2. Portunatasaurus diagram with corrections. Note the robust ribs, as in dolichosaurs. Mosasaurs and aigialosaurs have gracile ribs, a trait not tested in the LRT.

Mekarski et al. 2019 continue:
“An articulated skeleton, representing an animal roughly a meter long was found in 2008 on the island of Dugi Otok. The specimen is well represented from the anterior cervical series to the pelvis.”

There is no lumbar area in the Mekarsi et al. diagram (Fig. 2). Moving the pelvic area posteriorly to give Portunatasaurus a lumbar area agrees with other clade members. Note the robust ribs in Portunatasaurus, as in dolichosaurs. Mosasaurs and aigialosaurs (Fig. 1) have gracile ribs, a trait not tested in the LRT.

Figure 3. Portunatasaurus manus (right) and reconstructed with PILs (left).

Figure 3. Portunatasaurus manus (right) and reconstructed with PILs (left).

Mekarski et al. 2019 continue:
“Preserved elements include cervical and dorsal vertebrae, rib fragments, pelvic fragments, and an exquisitely preserved right forelimb. The taxon possesses plesiomorphic characters such as terrestrial limbs and an elongate body similar to that of basal mosasauroids such as Aigialosaurus or Komensaurus, but also shares derived characteristics with mosasaurine mosasaurids such as Mosasaurus.”

Note: the authors appear to have omitted dolichosaurs from consideration. Dolichosaurs are not mentioned in the abstract. Let me know if this is an error. I have contacted Mekarski for a PDF.

“The articulated hand exhibits a unique anatomy that appears to be transitional in form between the terrestrially capable aigialosaurs and fully aquatic mosasaurines, including 10 ossified carpal elements (as in aigialosaurs), intermediately reduced pro- and epipodials, and a broad, flattened first metacarpal (as in mosasaurines).

Note: the authors appear to be not looking at dolichosaurs. Whenever an author uses the word “unique” it is a good bet that pertinent taxa have been omitted because nothing in “unique” in evolution. What is unique for one clade is commonplace in another.

“The new and unique limb anatomy contributes to a revised scenario of mosasauroid paddle evolution, whereby the abbreviation of the forelimb and the hydrofoil shape of the paddle evolves either earlier in the mosasaur lineage than previously thought or more times than previously considered.”

Authors rarely consider the number one problem in paleontology: taxon exclusion. They prefer those headline-grabbing words like “unique” so they can postulate newer hypotheses ‘than previously considered.” Well, don’t we all… but these authors/PhDs are paid to do this and not make mistakes in taxon exclusion that an amateur with an online cladogram can pick apart without actually seeing the specimen.

“The presence of this new genus, the third and geologically youngest species of aigialosaur from Croatia, suggests an unrealized diversity and ecological importance of this family within the shallow, Late Cretaceous Tethys Sea.”

I assume it is a coincidence that mosasaur ancestors and unrelated snake ancestors were both found in the earliest Late Cretaceous strata surrounding today’s Mediterranean Sea. Let me know of Mekarski et al. tested dolicohosaurs in their cladogram. I had access only to the abstract and some figures.

The paper [PDF] just arrived.
No phylogenetic analysis is provided. Aphanizocnemus is not mentioned. Other dolichosaurs are compared.


References
Mekarski MC et al. 2019. Description of a new basal mosasauroid from the Late Cretaceous of Croatia, with comments on the evolution of the mosasauroid forelimb. Journal of Vertebrate Paleontology. 39: e1577872. doi:10.1080/02724634.2019.1577872.

wiki/Portunatasaurus

Atractaspis: a burrowing snake not related to other burrowing snakes

Snake origins have traditionally perplexed paleontologists,
but not the large reptile tree (LRT, 1745+ taxa; Fig. 2). In the LRT snakes arise from tiny Tetrapodophis and Barlochersaurus (both with tiny vestigial limbs) following a series of aquatic taxa and a basal split from geckos. At their LRT genesis, snakes split into terrestrial and fossorial (burrowing) taxa.

Then along comes the burrowing viper, Atractaspis
(Fig. 1) studied in µCT scans by Strong, Palci and Caldwell 2020. “The genus Atractaspis, known commonly as the burrowing asp, is a fossorial lineage within the Colubroidea (= cobras, vipers and rattlesnakes), the most deeply nested clade of extant snakes.”

Figure 1. Atractaspis skull µCT scan from Strong, Palci and Caldwell 2020.

Figure 1. Atractaspis skull µCT scan from Strong, Palci and Caldwell 2020. Note the immature fangs ready to take the place of the main fangs and otherwise toothless jaws.

While sharing many traits with traditional burrowing snakes,
Atractaspis nests with the rattlesnake, Croatlus in the LRT. So, no big surprises here. The LRT confirms traditional snake topology, that is, once they lose their limbs and become snakes. Prior to that, taxon exclusion has made snake origins the enigma it remains in the traditional academic literature.

From the Strong, Palci and Caldwell abstract:
“Comparative osteological analyses of extant organisms provide key insight into major evolutionary transitions and phylogenetic hypotheses. This is especially true for snakes, given their unique morphology relative to other squamates and the persistent controversy regarding their evolutionary origins.”

re: Persistent controversy? Click here.

“However, the osteology of several major snake groups remains undescribed, thus hindering efforts to accurately reconstruct the phylogeny of snakes. One such group is the Atractaspididae, a family of fossorial colubroids. We herein present the first detailed description of the atractaspidid skull, based on fully segmented micro‐computed tomography (micro‐CT) scans of Atractaspis irregulars.”

See figure 1.

“The skull of Atractaspis presents a highly unique morphology influenced by both fossoriality and paedomorphosis. This paedomorphosis is especially evident in the jaws, palate, and suspensorium, the major elements associated with macrostomy (large‐gaped feeding in snakes).”

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

Figure 2. Subset of the LRT focusing on geckos and their sister snake ancestors. Atractaspis (not listed here) nests with Croatlus among the terrestrial snakes.

Continuing from Strong, Palci and Caldwell:
“Comparison to scolecophidians—a group of blind, fossorial, miniaturized snakes—in turn sheds light on current hypotheses of snake phylogeny. Features of both the naso‐frontal joint and the morphofunctional system related to macrostomy refute the traditional notion that scolecophidians are fundamentally different from alethinophidians (all other extant snakes). Instead, these features support the controversial hypothesis of scolecophidians as “regressed alethinophidians,” in contrast to their traditional placement as the earliest‐diverging snake lineage.”

In the LRT, fossorial (burrowing) snakes follow tradition and diverge from all other snakes at the genesis of snakes. Therefore, Atractaspis is convergent with fossorial snakes, but keeps that wide-gape elongate quadrate (red in figure 1) from its viper ancestors.

The origin of snakes alongside the origin of mosasaurs and the origin of Lanthanotus, all in phylogenetic order. Not to scale. Note the branching off of burrowing snakes.

Figure 3, From 2015, prior to the insertion of Tetrapodophis: The origin of snakes alongside the origin of mosasaurs and the origin of Lanthanotus, all in phylogenetic order. Not to scale. Note the branching off of burrowing snakes at the origin of snakes near Dinilysia and Pachyrhachis.

Continuing from Strong, Palci and Caldwell:
“We propose that Atractaspis and scolecophidians fall along a morphological continuum, characterized by differing degrees of paedomorphosis. Altogether, a combination of heterochrony and miniaturization provides a mechanism for the derivation of the scolecophidian skull from an ancestral fossorial alethinophidian morphotype, exemplified by the nonminiaturized and less extreme paedomorph Atractaspis.”

“The phylogeny of scolecophidians is uncertain, due in large part to disagreement between morphological and molecular data.”

Suggestion based on evidence: Ignore molecular data.

Continuing from Strong, Palci and Caldwell:
“Interestingly, a recent morphological phylogeny (Garberoglio et al., 2019) focussing on extinct snakes recovered scolecophidians as nested within Alethinophidia in stark contrast to the more orthodox placement of this group as basally divergent among Serpentes. These results strongly highlight the importance of continued morphological and phylogenetic analyses of this group, including a renewed examination of potential alethinophidian affinities of scolecophidians.”

A valid set of outgroup taxa (Fig. 2) should settle this issue. Just add taxa to find out for yourself.


References
Strong CRC, Palci A and Caldwell MW 2020. Insights into skull evolution in fossorial snakes, as revealed by the cranial morphology of Atractaspis irregularis (Serpentes: Colubroidea). Journal of Anatomy. https://doi.org/10.1111/joa.13295

Tiny Late Cretaceous Najash: basal to burrowing snakes

Garberoglio et al. 2019
bring us long awaited skull data and several new partial skeletons of a Late Cretaceous snake with legs, Najash rionegrina (Figs. 1, 2). It must be said, the only evidence of legs supplied by the current authors was a caption labeled tibia on a tiny straight bone near the edge of the matrix. Nevertheless, legs and hips were described earlier in other headless specimens of Najash (Apesteguía and Zaher 2006; Fig. 1).

Figure 2. The pelvis of the protosnake with legs, Najash, compared to Heloderma (burrower) and Adriosaurus (swimmer). Heloderma appears to share more traits with Najash.

Figure 2. The pelvis of the protosnake with legs, Najash, compared to Heloderma (burrower) and Adriosaurus (swimmer). Heloderma appears to share more traits with Najash.

Most of the new specimens
were found in layered sandstone related to migrating aeolian dunes, along with abundant rhizoliths (root systems encased in desiccated mineral matter) and burrows.

Figure 1. Najash compared to Tetrapodophis (the last snake with legs) and Loxocemus, an extant burrowing snake without legs.

Figure 2. Najash compared to Tetrapodophis (the last snake with legs) and Loxocemus, an extant burrowing snake without legs.

From the authors’ abstract:
“the evolutionary versatility of the vertebrate body plan, including body elongation, limb loss, and skull kinesis. However, understanding the earliest steps toward the acquisition of these remarkable adaptations is hampered by the very limited fossil record of early snakes.”

That’s not true.
In the large reptile tree (LRT, 1602+ taxa, subset Fig. 3) snakes have a well documented ancestry back to Cambrian lancelets. The cladogram presented by the nine co-authors was steeped in tradition and lacking in appropriate outgroup taxa. Contra Garberoglio et al. 2019, Varanus and its monitor lizard kin are not part of snake ancestry in the LRT.

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

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

Garberoglio et al. continue:
“These new Najash specimens reveal a mosaic of primitive lizard-like features such as a large triradiate jugal and absence of the crista circumfenestralis, derived snake features such as the absence of the postorbital, as well as intermediate conditions such as a vertically oriented quadrate. The new cranial data also robustly resolve the phylogenetic position of this crucial snake taxon, along with other limbed snakes.”

  1. The authors’ cladogram did not nest Najash with burrowing snakes, as in the LRT, but at a much more primitive node.
  2. Perhaps this is so because Tetrapodophis and Barlochersaurus were not mentioned in the text.
  3. The quadrate was sharply bent posteriorly at a right angle, a trait only found in burrowing snakes.
  4. I found no primitive lizard-like features here, other than legs and hips, traits found in Tetraphodophis and Barlochersaurus, the last common ancestors of all living snakes.
  5. Najash is a crown-group snake in the LRT until additional untested taxa move it out.

Najash rionegrina (Apesteguía and Zaher 2006; Garberoglio FF et al. 2019; Late Cretaceous) is a tiny burrowing snake that retained a pelvis and hind limbs, transitional between Tetrapodophis and Loxocemus. The premaxilla was tiny, as in terrestrial snakes. The mandible rose anteriorly, as in burrowing snakes. The jugal and vomers were retained.


References
Apesteguía S and Zaher H 2006.A Cretaceous terrestrial snake with robust hindlimbs and a sacrum. Nature. 440 (7087): 1037–1040.
Garberoglio FF et al. (eight co-authors) 2019.
New skulls and skeletons of the Cretaceous legged snake Najash, and the evolution of the modern snake plan. Science Advances 2019(5):eaax5833, 8pp.

wiki/Najash

Snake origin paper fails due to genomics and fakes an ancestral snake skull

Watanabe et al. 2019
“demonstrate that highly diverse phenotypes, exemplified by lizards and snakes, can and do arise from differential selection acting on conserved patterns of phenotypic integration.”

To build their phylogenetic tree, Watanabe 2019 report,
“To conduct comparative phylogenetic methods, we constructed a time-calibrated phylogenetic tree by using a published time calibrated molecular phylogeny of extant squamates (Zheng and Weins 2016) and incorporating extinct taxa based on previous systematic work and fossil occurrence data from the Paleobiology Database (paleobiodb.org). We grafted extinct taxa onto the extant tree by applying the equal-branching method based on the mean of first occurrence age range. Although the phylogenetic placement of Mosasauria within squamates remains ambiguous, Plotosaurus was placed within the molecular phylogeny as a sister taxon to Serpentes (“Pythonomorpha hypothesis”) and Polyglyphanodon as sister to iguanians in accordance with the phylogeny based on combined molecular and morphological data.”

Taxon exclusion is once again the problem here.
Too few fossil taxa appea in the Watanabe et al. cladogram. The keyword ‘outgroup’ is not found in the text or SuppData. Watanabe et al. report, Sphenodon was not included in analyses with the exception of morphospaces.” As a result the highly derived legless amphisbaenid, Dibamus, was chosen as the outgroup. That is wrong, according to the large reptile tree (LRT, 1524 taxa) in which iguanids are plesiomorphic basalmost squamates. Sphenodontids and tritosaurs are outgroups in the LRT, are not represented.

Mosasaurs, like Plotosaurus, arise from varanids in the LRT. The clade Pythonomorpha is not recovered by the LRT.

Snake ancestors (none of which appear in Watanabe et al.) arise from Jurassic gekko-like ancestors, like Tchingisaurus and ending with tiny Tetraphodophis (Fig. 1). The list of snake ancestors includes terrestrial taxa, like Ardeosaurus, and aquatic taxa, like Pontosaurus. Fossorial (burrowing) snakes arise as derived taxa, not primitive forms. 

Figure 1. Hypothetical ancestral snake skull compared to real ancestral snake skull.

Figure 1. Hypothetical ancestral snake skull compared to real ancestral snake skull. Watanabe et al. 2019 should have stayed away from fiction.

Quoting the NHM.AC.UK press release,
“Prof Goswami says, ‘There is a lot of debate about how snakes evolved, but we think we have traced the ancestral skull shape. Lots of scientists have speculated that maybe snake ancestors lived in water, which made them lose their legs. So it’s surprising that the patterns we saw led us to a semi-fossorial animal.’” 

There is no debate
when you use the last common ancestor approach based on phenomic (trait-based) phylogenetic analyses. Following in the footsteps of those who imagined pterosaur ancestors, the Watanabe team imagined a snake ancestor for no reason, because the LRT provides a long list of snake ancestors going back to Silurian jawless fish.

Gene studies
work well in criminal identification closely related taxa within a genus. Genomics fail for various reasons in deep time studies. This is something paleontologists and biologists need to realize. If you want results in which all derived taxa demonstrate gradually accumulating traits, you have to use trait-based studies and fossil taxa. Why turn your back on proven results in favor of a method you hope works, but never does?


References
Watanabe A, Fabre A-C, Felice RN, Maisano JA, Müller J, Herrel A and Goswami A 2019. Ecomorphological diversification in squamates from conserved pattern of cranial integration. www.pnas.org/cgi/doi/10.1073/pnas.1820967116
Zheng Y and Wiens JJ and 2016. Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Mol. Phylogenet. Evol. 94, 537–547.

National History Museum News

 

 

A new extremely tiny pre-snake: Barlochersaurus

Just out,
Daza et al.. 2018 describe a privately-owned, Mid-Cretaceous, teeny-tiny, ‘enigmatic’ lizard preserved in amber, Barlochersaurus winhtini (Figs. 1, 3; 1.5 in total length). The authors report, “The fossil is one of the smallest and most complete Cretaceous lizards ever found, preserving both the articulated skeleton and remains of the muscular system and other soft tissues. Despite its completeness, its state of preservation obscures important diagnostic features.We determined its taxonomic allocation using two approaches: we used previously identified autapomorphies of squamates that were observable in the fossil; and we included the fossil in a large squamate morphological data set.”FIgure 1. From Daza et al. 2018 and color overlays applied here. FIgure 1. From Daza et al. 2018 and color overlays applied here.

FIgure 1. From Daza et al. 2018 and color overlays applied here.Phylogenetically the authors report,
“Results from the phylogenetic analysis places the fossil in one of four positions: as sister taxon of either Shinisaurus crocodilurus or Parasaniwa wyomingensis, at the root of Varanoidea, or in a polytomy with Varanoidea and a fossorial group retrieved in a previous assessment of squamate relationships.”

Figure 2. Subset of the LRT showing stem snakes, snakes and their sister group, the geckos.

Figure 2. Subset of the LRT showing stem snakes, snakes and their sister group, the geckos.

Unfortunately this lack of resolution is due to taxon exclusion.
In the large reptile tree (LRT, 1318 taxa; subset Fig. 2) Barlochersaurus nests between the stem snakes Pontosaurus (Fig. 5) and tiny Tetrapodophis (Figs. 3, 4) neither of which is listed in the text of the Daza et al. paper.

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

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

According to Wikipedia
“Anguimorpha include the anguids (alligator lizardsglass lizardsgalliwasps and legless lizards)They are characterized by being heavily armored with non-overlapping scales, and almost all having well-developed ventrolateral folds (excluding Anguis). Anguidae members can, however, be somewhat difficult to identify in their family, as members can be limbed or limbless, and can be both viviparous and oviparous.” The LRT tests several anguids. They do not attract Barlochersaurus as well as Tetrapodophis and Pontosaurus.

Figure 4. The skull of Tetrapodophis, the proximal outgroup taxon to living snakes.

Figure 4. The skull of Tetrapodophis, the proximal outgroup taxon to living snakes.

Pontosaurus
(Fig. 5) has a longer tail and is much larger overall. The manus and pes of Pontosaurus are similar in proportion and detail to those of Barlochersaurus.

Figure 2. Pontosaurus and its parts. Data from Caldwell 2006. This is one of the last taxa we know in the snake lineage that still had a pectoral girdle.

Figure 2. Pontosaurus and its parts. Data from Caldwell 2006. This is one of the last taxa we know in the snake lineage that still had a pectoral girdle.

The Daza team printed 3D replicas,
blown up to 10 times the original size. These are publicly available at Florida’s Museum of Natural History and Harvard’s Museum of Comparative Zoology.

Earlier
we looked at a more primitive pre-snake with legs (JKZ-Bu267) also found in amber here.

And, oh, yeah… did I forget to mention?
Phylogenetic miniaturization at the genesis of major and minor clades in the LRT strikes again! This time, to the extreme!

References
Daza JD, Bauer AM, Stanley EL, Bolet A, Dickson B and Losos JB 2018. A enigmatic miniaturized and attenuate whole lizard from the Mid-Cretaceous amber of Myanmar. Breviora 563: 18pp.

https://www.pbs.org/wgbh/nova/article/paperclip-lizard/

More DNA results for worm-snake interrelationships

Aurélien et al. 2018 bring us
molecular evidence for the paraphyly of Scolecophidia (burrowing miniaturized worm-snakes, Fig. 2), which they claim “represent the earliest branching clades within the snake tree.” Like others making the same claim before, this is a preposterous statement given the highly derived skulls of various burrowing snakes and the major lack of fossil stem snakes in their cladogram. The Aurélien et al. cladogram includes Varanus, Lacertidae and Anolis sp. as progressively more distant outgroup taxa, omitting (as in all DNA studies) even more fossil taxa.

We looked at
the previous DaSilva et al. 2018 study that took on the origin of snakes using DNA  and a few fossils earlier here (and see figure 1.)

The LRT ancestors of snakes
were recovered here (subset Fig. 1) five years ago.

Figure 1. Subset of the LRT focusing on squamates and snakes. Note how many key taxa in the origin of snakes have been omitted by the DaSilva et al. study.

Figure 1. Subset of the LRT focusing on squamates and snakes. Note how many key taxa in the origin of snakes have been omitted by the previous DaSilva et al. study.

Distinct from DNA studies 
the large reptile tree (LRT, 1308 taxa; subset in Fig. 1) employs fossil taxa and skeletal traits. In doing so burrowing snakes are recovered as a derived monophyletic clade displaying a gradual accumulation of derived traits in derived taxa (Fig. 2). And that makes sense. We expect a gradual accumulation of derived traits in derived taxa, and that’s exactly what you get in the snake section of the LRT. We learned earlier to distrust DNA studies when dealing with distantly related tetrapods, and this is yet another case of the same problem.

Figure 2. Heloderma, Lanthanotus, Anilius, Cylindrophis, Uropeltis, and Leptotyphlops to scale. Boxed scales are enlarged.

Figure 2. Heloderma, Lanthanotus, Anilius, Cylindrophis, Uropeltis, and Leptotyphlops to scale. Boxed scales are enlarged. The first two are not related to the worm snakes.

Leptotyphlops jaws movie

Figure 3. Click to animate. Leptotyphlops jaws move medially, not up and down. For this reason alone, Leptotyphlops is the most derived snake, not the most primitive one. A long list of other traits support that nesting.

References
Aurélian M et al. (5 co-authors) 2018. Molecular evidence for the paraphyly of Scolecophidia and its evolutionary implications. Journal of Evolutionary Biology DOI: 10.1111/jeb.13373 online here.
DaSilva FO et al. (7 co-authors) 2018. The ecological origins of snakes as revealed by skull evolution. Nature.com/Nature Communications (2018)9:376  1–11. DOI: 10.1038/s41467-017-02788-3 pdf

What would snakes be, if Pan-ophidians were not known?

This is lesson 2 in taxon exclusion…
to see where select clades would nest in the absence of their proximal taxa.

Ophidians (Pan-serpentes) are all squamates closer to snakes (clade = Serpentes) than to other living groups of lizards. More narrowly, according to Wikipedia, “Ophidia was defined as the “most recent common ancestor of Pachyrhachis and Serpentes (modern snakes), and all its descendants” by Lee and Caldwell (1998: 1551).”

We’re going to introduce the term to Pan-Ophidia
for all clade members in the lineage of snakes (= closer to snakes than to other living groups of lizards). Clade members of the Ophidia are somewhat different in the large reptile tree (LRT, 1142 taxa, subset Fig. 1). Here the Ophidia currently begins with Norellius and includes Ardeosaurus, Eichstaettisaurus, Pontosaurus, Tetrapodophis, Dinilysia and their kin, with a sister clade among the ancestors to geckos.

Figure 2. Subset of the large reptile tree focusing on lepidosaurs and snakes are among the squamates.

Figure 1. Subset of the large reptile tree focusing on lepidosaurs and snakes are among the squamates.

Since we have access to the large reptile tree
(LRT, 1242 taxa) which lets us play around with deletions (taxon exclusion) let’s see where snakes (Dinilysia + Pachyrhachis + living snakes) would nest in the absence of ophidians (and Archosauromorpha). At the base of snakes is the basal burrowing snake, Loxocemus. Outgroups include the clade Heloderma + Lanthanotus and the clade Anniella + Gobiderma. This clade nests between Shinisaurus and the Ophisaurus clade + skinks. Moreover, the rest of the Squamata breaks into 14 clades without resolution, among them the geckos and varanids.

Deleting all geckos (sisters to the Pan-Ophidia in the LRT) returns complete resolution to the remainder of the tree, and snakes still nest with the clades listed above, not with varanids or mosasaurs.

Deleting Dinilysia + Pachyrhachis
not only loses resolution within snakes, all proximal outgroup taxa also lose resolution. Outgroups also include the skinks + amphibaenids

When the gekko clade is included again,
does not improve the situation. No wonder snakes have been so difficult to nest, in the absence of the proximal taxa listed in figure 1.

Taxon exclusion
has been the number one problem in traditional paleontology. That’s why the LRT includes such a wide gamut of taxa. The result is a minimizing of taxon exclusion and the problems that attend it.

More traditionally (and due to taxon exclusion)
Wikipedia reports, “There is fossil evidence to suggest that snakes may have evolved from burrowing lizards, such as the varanids (or a similar group) during the Cretaceous Period. This hypothesis was strengthened in 2015 by the discovery of a 113m year-old fossil of a four-legged snake in Brazil that has been named Tetrapodophis amplectus. It has many snake-like features, is adapted for burrowing and its stomach indicates that it was preying on other animals.”

Taxon exclusion
has been the number one problem in traditional paleontology. That’s why the LRT includes such a wide gamut of taxa. The result is a minimizing of taxon exclusion and the problems that attend it.

References

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

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

Primitivus: a new marine pre-snake, dolichosaur

There are those
who practice taxon exclusion in their search for taxon ancestors. Now, Paparella et al. 2018 can be counted among them as they bring us a wonderful new find, Primitivus manduriensis from the Late Cretaceous of Italy. They correctly nest it as a pre-snake and a dolichosaur (Fig. 1). Primitivus also preserves snake-like scales.

Figure 1. Like the LRT, Paparella et al. 2018 nest Primitivus with Pontosaurus, but this cladogram is missing several taxa that attract snakes away from mosasaurs.

Figure 1. Like the LRT, Paparella et al. 2018 nest Primitivus with Pontosaurus, but this cladogram is missing several taxa that attract snakes away from mosasaurs.

Unfortunately, due to taxon exclusion
the Paparella team nest Primitivus with the invalid clade ‘Pythonomorpha‘ (mosasaurs  + snakes) rather than the more broadly tested pre-dolichosaurs (= ardeosaurs): Ardeosaurus, Eichstättisaurus and tiny Jucaraseps, none of which are mentioned in the text. These taxa are ancestral to the dolichosaurs leading to snakes in the large reptile tree (LRT, 1236 taxa, Fig. 2). The LRT tests all these candidates and finds mosasaurs and varanids nest elsewhere, apart from snakes, dolichosaurs, ardeosaurs and geckos. Deletion of the ardeosaurs makes no change in the LRT tree topology. This is a strong nesting.

The Paparella team also nest tiny Tetrapodophis
at the stem of Mosasauroidea + Dolichosauridae and apart from snakes (Fig. 1), rather than basal to snakes, as in the LRT (Fig. 2).

Figure 2. Subset of the large reptile tree focusing on lepidosaurs and snakes are among the squamates.

Figure 2. Subset of the large reptile tree focusing on lepidosaurs and snakes are among the squamates. Primitivus nests with Pontosaurus here, but is not shown here. See it in the LRT.

Sadly,
an otherwise excellent paper has this fatal flaw due to taxon exclusion. Sometimes I wonder why workers don’t test taxa that years ago were found relevant in the LRT. That’s why the LRT is online, available 24/7 worldwide.

Figure 3. Primitivus skull in visible and UV light from Paparella et al. They did not identify bones, so DGS colors were added here.

Figure 3. Primitivus skull in visible and UV light from Paparella et al. They did not identify bones, so DGS colors were added here.

As we learned earlier,
phylogenetic miniaturization gave us both aquatic dolichosaurs (via tiny Jucaraseps) and later, terrestrial snakes (via tiny Tetrapodophis).

Figure 4. Primitivus in situ from Paparella et al. 2018 in visible light. UV images is distorted to match.

Figure 4. Primitivus in situ from Paparella et al. 2018 in visible light. UV images is distorted to match.

There is very little difference, apart from size,
between the larger Pontosaurus and the smaller Primitivus. Not sure why the Paparella team did not present skull identification in their primary publication.

Figure 3. Primitivus hand and foot from Paparella et al. 2018, DGS colors added here.

Figure 3. Primitivus hand and foot from Paparella et al. 2018, DGS colors added here.

References
Paparella I, Palci A, Nicosia U and Caldwell MW 2018. A new fossil marine lizard with soft tissues from the Late Cretaceous of southern Italy. Royal Society Open Science 5: 172411. http://dx.doi.org/10.1098/rsos.172411

Publicity including in vivo restorations:
https://www.cbc.ca/news/canada/edmonton/pretty-amazing-alberta-researchers-spot-new-fossil-species-and-its-lunch-1.4715056

https://phys.org/news/2018-06-scientists-species-ancient-marine-lizard.html

The identity of the ‘supratemporal’ in snakes

Adding the rattlesnake
Cortalus (Fig. 1), to the large reptile tree (LRT, 1226 taxa) nested it with Boa, the boa constrictor. A typical review of snake skull bones ensued, since it had been awhile since I looked at snakes.

Interestingly
some traditions (but not all, see Fig. 2) anchor the quadrate on a bone identified as the supratemporal (Fig. 3). Others label that bone a squamosal.

In the LRT
several snake-ancestor taxa, including Pontosaurus (Figs. 3, 4), show the squamosal (magenta) remains the quadrate anchor, as in all other tetrapods. The more medial supratemporals become vestiges and disappear in higher snakes.

Figure 2. Crotalus the timber rattlesnake in two views. The light blue dot is the last remains of the jugal.

Figure 1. Crotalus the timber rattlesnake in two views. The light blue dot is the last remains of the jugal.

So, is that anchor bone
the supratemporal? or is it the squamosal? Some authors label it one way (Figs. 2, 8). Others label it the other. The problem is, despite what other tetrapods do with that bone, it lies close to the parietal in snakes, like the supratemporal. Squamosals usually frame the upper temporal fenestra. Validated ancestral taxa with both bones provide the solution.

Figure 3. Is the anchor bone for the quadrate a supratemporal or squamosal? See text for discussion.

Figure 2. Is the anchor bone for the quadrate a supratemporal or squamosal? Some authors go one way. Others go the other (see figure 8). The LRT indicates the squamosal is correct. So do ontogenetic studies. See text for discussion.

Pontosaurus has both
bones (Fig. 4) and nests basal to snakes. Pontosaurus lesinensis  (Gorjanovic-Kramberger 1892; Caldwell 2006) was a larger sister to Adriosaurus with a longer, deeper tail.

Figure 4. Pontosaurus skull in situ with relevant bones labeled. Note the squamosal leans into the parietal.

Figure 3. Pontosaurus skull in situ with relevant bones labeled. Note the squamosal leans into the parietal.

A reconstruction of Pontosaurus
(Fig. 4) clarifies the position and size of the squamosal, jugal, postorbital and supratemporal, matching those of other related taxa. Note the squamosals are pinched medially, the first step toward making those bones line against the cranium (parietal and other bones), as in snakes.

Figure 5. The skull of Pontosaurus reconstructed. Here the squamosal leans in, reducing the size of the upper temporal fenestra, which is absent/confluent with the lateral temporal fenestra in living snakes.

Figure 4. The skull of Pontosaurus reconstructed. Here the squamosal bends medially, reducing the size of the upper temporal fenestra, which is absent/confluent with the lateral temporal fenestra in living snakes. This taxon is basal to Tetrapodophis, Dinilysia and Pachyrhachis.

So where did the supratemporal identification come from?
I have not found the original source yet. Perhaps it came from the hypothesis that snakes are derived from mosasaurs (Fig. 6), but it is not easy to see how this happened.

The blogging professor, Darren Naish (1998-2009), wrote online hereMosasauroids (mosasaurids and all of their close relatives) are platynotan lizards that, in the most recent analyses, share 40 shared derived characters with snakes (Ophidia) – therefore they share a single ancestor and form the clade Pythonomorpha Cope, 1869.”

Figure 5. Tylosaurus and other mosasaurs. Note the small supratemporal and large squamosal.

Figure 5. Tylosaurus and other mosasaurs. Note the small supratemporal and large squamosal. Workers, like ED Cope and Darren Naish, found many similarities between mosasaurs and snakes, all by convergence according to other workers and the LRT.

According to Wikipedia
“Pythonomorpha was originally proposed by paleontologist ED Cope (1869) as a reptilian order comprising mosasaurs, which he believed to be close relatives of Ophidia (snakes). [However] Many recent authors demonstrate a closer relationship between mosasaurs and varanid lizards, like Varanus.” The latter relationship is supported by the LRT, which derives snakes from a long list of long-bodied taxa not related to mosasaurs and not tested by earlier workers, including tiny, four-legged Tetradophis (Fig. 6).

Figure 5. Snake skull evolution from Adriasaurus to Crotalus.

Figure 6. Snake skull evolution from Adriasaurus to the rattlesnake, Crotalus. Given the lack of a coronoid in Dinilysia and its presence in sister taxa makes me wonder if it has been displaced. The yellow bone, labeled the pterygoid, is a good candidate, but making judgements like that from a drawing is risky.

Pachyrhachis (Fig. 7) is a basal snake
with an expanded cranium, either reducing the twin posterior parietal processes or perhaps filling the space between them (because the cranium is relatively longer). Such a cranium appears to be inherited from tiny Tetrapodophis, which is preserved flat. In both taxa the squamosals lie upon the expanded cranium. The postorbital is fused to the postfrontal and no longer contacts the squamosal. The upper temporal fenestra is thus absent and/or confluent with the lateral temporal fenestra at the pre-snake/snake transition.

Figure 7. Pachyrhachis, a basal snake.

Figure 7. Pachyrhachis, a basal snake in which the postorbital no longer contacts the squamosal, which lies close to the parietal, losing the upper temporal fenestra.

Ontogeny
Werneburg and Sánchez-Villagra 2015 tested homology hypotheses by examining snake and lizard embryos then reported, “The ‘supratemporal’ of snakes could be homolog to squamosal of other squamates, which starts ossification early to become relatively large in snakes.” The authors wrongly reported, “We included for the first time Varanus, a critical taxon in phylogenetic context.” Varanus is not related to snakes in the LRT. The authors did not include Pontosaurus, Tetrapodophis and several other snake ancestors listed in the LRT. Without these taxa, the correct phylogenetic framework was not present in their study.

Figure 7. Snake skull form Andjelkovic et al. 2017 mislabeling the squamosal as a supratemporal.

Figure 8. Snake skull form Andjelkovic et al. 2017 mislabeling the squamosal as a supratemporal.

 

Longtime readers may remember
I took a stab at this issue several years ago, but that was before the present tree topology of snake relations was established. Once I realized that I followed an invalid tradition back then, I trashed that post to avoid further confusion. I discover errors all the time, most often in my own work. I then repair those errors and misconceptions, which is the basis of good science, as everyone knows. Sadly, not every paleontologist follows this dictum.

On that note…
You might remember another traditional bone I-D mistake was also found in turtles,
in which the supratemporal was misidentified as the squamosal. So, yes, widespread misidentification can happen, and a wide gamut phylogenetic analysis illuminates such problems. So, bottom line, once again taxon exclusion is the single source of this long-standing problem. 

References
Caldwell MW 2006. A new species of Pontosaurus (Squamata, Pythonomorpha) from the Upper Cretaceous of Lebanon and a phylogenetic analysis of Pythonomorpha. Memorie della Società Italiana di Scienze Naturali e del Museo Civico di Storia Naturale di Milano 34: 1–42.
Cope ED 1869. On the reptilian orders Pythonomorpha and Streptosauria. Proceedings of the Boston Society of Natural History 12:250–266.
Gorjanovic-Kramberge D 1892. O fosilnih cetaceih hrvatske i kranjske. Rad. Jugoslavenske Akademije Znanosti i Umjetnosti 111:1-21.
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Werneburg I and Sánchez-Vilagra MR 2015. Skeletal heterochrony is associated with the anatomical specializations of snakes among squamate reptiles. Evolution 69(1):254-63. doi: 10.1111/evo.12559. Epub 2014 Dec 17.

wiki/Crotalus
wiki/Boa_constrictor
wiki/Pontosaurus
wiki/Pythonomorpha

Bipedal Cretaceous lizard tracks

These are the oldest lizard tracks in the world…
(if you don’t consider Rotodactylus (Early Triassic) strictly a ‘lizard’ (= squamate). One rotodactylid trackmaker, Cosesaurus, is a tiny lepidosaur).

Figure 1. Bipedal lizard tracks from South Korea in situ.

Figure 1. Bipedal lizard tracks from South Korea in situ. They are tiny.

From the abstract
“Four heteropod lizard trackways discovered in the Hasandong Formation (Aptian-early Albian), South Korea assigned to Sauripes hadongensis, n. ichnogen., n. ichnosp., which represents the oldest lizard tracks in the world. Most tracks are pes tracks that are very small. The pes tracks show “typical” lizard morphology as having curved digit imprints that progressively increase in length from digits I to IV, a smaller digit V that is separated from the other digits by a large interdigital angle. The manus track shows a different morphology from the pes. The predominant pes tracks, the long stride length of pes, narrow trackway width, digitigrade manus and pes prints, and anteriorly oriented long axis of the fourth pedal digit indicate that these trackways were made by lizards running bipedally, suggesting that bipedality was possible early in lizard evolution.”
Actually, the lizard was not running.
Typically in running tracks the prints are very far apart and these tracks are sometimes left toe to right heel.

Figure 2. Original and new tracings of the bipedal lizard tracks from South Korea. PILs are added,

Figure 2. Original and new tracings of the bipedal lizard tracks from South Korea. PILs are added. Manual digit 4 and 5 appear to have shifted.

 The authors did not venture who made the tracks.
They reported, “based on the palaeobiogeographic distribution of facultative extant families, the lizard that produced S. hadongensis tracks could well have been a member of an extinct family or stem members of Iguania, which was present in the Early Cretaceous.”
Actually the closest match among tested taxa
is with Eichstaettisaurus (Fig. 1), a basal member in the lineage of snakes. And this clade is close to the origin of geckos. ReptileEvolutiion.com and the large reptile tree would have been good resources for the authors to use. Lots of lizard pedes were illustrated and scored there.

Figure 3. Originally pictured as a generic lizard (below), here Eichstattsaurus scaled to the track size walks upright.

Figure 3. Originally imagined  as a generic lizard (below), here Eichstattsaurus matched and scaled to the track size walks upright.

 Based on a phylogenetic analysis of the tracks
the closest match in the LRT is with Eichstaettisaurus, so a slightly larger relative made them. Distinct from the skeletal taxon, the trackmaker had a longer p2.1 than 2.1 and pedal digit 1 was quite short. Otherwise a good match in all other regards.
So why walk bipedally?
It was walking, not running, so escape from predation can be ruled out. Elevating the upper torso and head, like a cobra, can be intimidating to rivals, or just offer a better view over local plant life. This sort of flexibility could have helped them get into the trees and then to move to higher branches.
References
Lee H-J, Lee Y-N, Fiorillo AR &  LÃ J-C 2018. Lizards ran bipedally 110 million years ago. Scientific Reports 8: 2617. doi:10.1038/s41598-018-20809-z