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

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

Snake evolution: new paper suffers from taxon exclusion

DaSilva et al. 2018
bring us a new perspective on snake evolution that employs molecules, physical traits, embryos, fossils, CT scans… a huge amount of data and labor… perhaps all for nought because they excluded so many pre-snake taxa (Fig. 2). And their results do not produce a gradual accumulation of derived traits (Fig. 1), even when they omit the mosasaur skulls listed at their base of snakes. Here I added that missing mosasaur skull.

Figure 1. Figure 1 from DaSilva et al. 2018 with mosasaur skull added here. Note the complete lack of a gradual accumulation of traits leading to snakes and the very derived snake skull placed at the base of all snakes.

Figure 1. Figure 1 from DaSilva et al. 2018 with mosasaur skull added here. Note the complete lack of a gradual accumulation of traits leading to snakes and the very derived snake skull placed at the base of all snakes. No wonder they omitted adding the mosasaur skull to the parade of pre-snakes. IF you were part of this study and failed to raise your hand at this RED FLAG, then do better next time.

The DaSilva et al. abstract:
“The ecological origin of snakes remains amongst the most controversial topics in evolution, with three competing hypotheses: fossorial; marine; or terrestrial. Here we use a geometric morphometric approach integrating ecological, phylogenetic, paleontological, and developmental data for building models of skull shape and size evolution and developmental rate changes in squamates. Our large-scale data reveal that whereas the most recent common ancestor of crown snakes had a small skull with a shape undeniably adapted for fossoriality, all snakes plus their sister group derive from a surface-terrestrial form with non-fossorial behavior, thus redirecting the debate toward an underexplored evolutionary scenario. Our comprehensive heterochrony analyses further indicate that snakes later evolved novel craniofacial specializations through global acceleration of skull development. These results highlight the importance of the interplay between natural selection and developmental processes in snake origin and diversification, leading first to invasion of a new habitat and then to subsequent ecological radiations.”  Fossorial = burrowing.

The DaSilva et al. Supplementary Data reports:
“To include a large dataset of squamate specimens, including extant, fossil, and embryonic taxa (see details below as well as Fig. 1 (main text) and Supplementary Fig. 1), we used a composite phylogenetic hypothesis based on the most recent molecular as well as combined molecular and morphological studies on squamate evolution.”

As readers know by now,
molecular data fails at large phylogenetic distances. It produces false positives. Even so, their large number of physical traits (691 morphological characters and 46 genes) should have given them a good cladogram… unless they omitted huge swaths of taxa.

Which is what they did (Fig. 2).

Even though they used fossil and embryological data,
their results do not produce a gradual accumulation of traits (Fig. 1). Nor do they employ appropriate outgroup taxa, either for squamates or for snakes (Fig. 2).

Without these key transitional taxa,
the authors have no idea what the basalmost squamates and snakes should look like. Here’s what the large reptile tree (LRT, 1152 taxa) recovered (Fig. 1):

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 DaSilva et al. study.

If nothing else,
I hope readers gain a critical and skeptical eye toward published material. Sometimes it’s not what they say, but what they omit that spoils their results.

The LRT is a good base
to begin more focused studies in tetrapod evolution. It covers virtually all the possible candidates so workers can have high confidence that their more focused studies include relevant taxa and exclude irrelevant taxa.

For more information on snake origins
click here and/or here, along with links therein.

References
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

Snake origins according to DNA studies

Figure 1. Cladogram of squamates from Streicher and Wiens 2017 highlighting the origin of snakes based on DNA. Unfortunately, only the closely related taxa are correctly nested here. See figure 2 for gradual accumulations of traits in all related taxa.

Figure 1. Cladogram of squamates from Streicher and Wiens 2017 highlighting the origin of snakes based on DNA. Unfortunately, only the closely related taxa are correctly nested here. See figure 2 for gradual accumulations of traits in all related taxa.

 

Why would Streicher and Wiens 2017
(Fig. 1) want to do this? They can’t use fossils. They’ll never find a gradual accumulation of traits, starting from ‘snakes with legs’. And… DNA does not work over large phylogenetic distances. They put their faith in DNA. They believed they would get an answer. Their prayers were answered, but the answer does not make sense. Their cladogram cannot be verified with morphological studies (Fig. 2). Morph studies can and do use fossils and do produce a gradual accumulation of traits. Morphology is, and will always be, the gold standard of phylogenetics.

We have to stop wasting time
on methods that do not work over large phylogenetic distances. Rant. Rant. Rave. Rave.

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.

Here’s how you know, at first glance,
how the Streicher and Wiens cladogram produces odd, mismatching sisters.

  1. Derived taxa usually do not appear at the base of major clades: Dibamus, Typhlops
  2. Mismatches usually do not nest close to one another: Bipes & Lacerta, Python & Typhlops, Dibamus & Sphenodon

Streicher and Wiens will never find out
that snake ancestors had legs using DNA. Those just never shows up in molecules. Their paper’s title: “Phylogenomic analyses of more than 400 nuclear loci resolve the origin of snakes among lizards families” do not resolve the origin of snakes.

Snakes arise
from near the very beginning of a rapidly diversifying Scleroglossa. The snake clade split from the gekko clade shortly after the origin of the Squamata. Derived burrowing snakes with jaws that pull prey items in appear in derived taxa, not as basal plesiomorphic forms. When basal taxa are bland and plesiomorphic, that’s a good sign that you’re doing something right.

References
StreicherJW and Wiens JJ 2017. Phylogenomic analyses of more than 400 nuclear loci resolve the origin of snakes among lizards families. Biology Letters 13: 20170393.
http://dx.doi.org/10.1098/rsbl.2017.0393

 

 

News at the genesis of snakes: Tetrapodophis ‘highly suggestive’ as aquatic

A year ago
Martill et al. 2015 described the stem snake, Tetrapodophis (Fig. 1) and considered it a burrowing squamate. A new paper by Lee et al. 2016 reports that Tetrapodophis had aquatic adaptations.

Figure 2. Tiny Tetrapodophis at full scale if your monitor produces 72 dpi images (standard on many monitors).

Figure 1. Tiny Tetrapodophis at full scale if your monitor produces 72 dpi images (standard on many monitors).

This new study confirms 
what you read here, here and here when we nested Tetrapodophis with the following aquatic pre-snaketaxa: PontosaurusAdriosaurus and Aphanziocnemus in the large reptile tree (subset Fig. 2).

From the Lee et al abstract
“The exquisite transitional fossil Tetrapodophis – interpreted as a stem-snake with four small legs from the Lower Cretaceous of Brazil – has been widely considered a burrowing animal, consistent with recent studies arguing that snakes had fossorial ancestors [not so here]. We reevaluate the ecomorphology of this important taxon using a multivariate morphometric analysis and a reexamination of the limb anatomy. Our analysis shows that the body proportions are unusual and similar to both burrowing and surface-active squamates. We also show that it exhibits striking and compelling features of limb anatomy, including enlarged first metapodials and reduced tarsal/carpal ossification – that conversely are highly suggestive of aquatic habits, and are found in marine squamates. The morphology and inferred ecology of Tetrapodophis therefore does not clearly favour fossorial over aquatic origins of snakes.”

Figure 2. Scleroglossan subset of the large reptile tree. Generalists taxa duplicated in the Yi and Norell tree are shown in bright green. Burrowers shared in the Yi and Norell tree are in dark green. Legless taxa are black. Vestiges are in gray. Unknown are striped.

Figure 2. Scleroglossan subset of the large reptile tree. Generalists taxa duplicated in the Yi and Norell tree are shown in bright green. Burrowers shared in the Yi and Norell tree are in dark green. Legless taxa are black. Vestiges are in gray. Unknown are striped.

Wonder why 
prior workers have not performed a phylogenetic analysis on this taxon that includes the above named aquatic squamates and Jucaraseps?

References
Lee MSY, Palci A, Jones MEH, Caldwell MW, Holme JD & Reisz RR 2016. Aquatic adaptations in the four limbs of the snake-like reptile Tetrapodophis from the Lower Cretaceous of Brazil. Cretaceous Research (advance online publication)
doi:10.1016/j.cretres.2016.06.004 online for sale
Martill DM, Tischlinger H and Longrich NR 2015. A four-legged snake from the Early Cretaceous of Gondwana. Science 349 (6246): 416-419. DOI: 10.1126/science.aaa9208

Dinilysia and the burrowing(?) origin of snakes

A recent paper
by Yi and Norell 2015 attempted to answer the controversy whether ancestral snakes were terrestrial burrowers or marine swimmers while looking at their ear vestibules. They looked at the stem snake Dinilysia (1.8m in length) along with other reptiles and noted that the spherical vestibule portion of the inner ear was large (Fig. 1), like those of other burrowing reptiles.

Then they put together a cladogram (Fig.1) that was missing pertinent taxa in the ancestry of snakes, as determined by the large reptile tree (Fig. 2).

Figure 1. Colored chart originally published in Yi and Norell 2015 with their cladogram of snake origins tied to burrowing, aquatic and generalst niches, I have added black bars for legless taxa and gray bars for vestigial leg taxa. The inner ear of Dinilysia is shown at the bottom.

Figure 1. Colored chart originally published in Yi and Norell 2015 with their cladogram of snake origins tied to burrowing, aquatic and generalst niches, I have added dark green bars for burrowers and light green for other taxa, black bars for legless taxa and gray bars for vestigial leg taxa. The inner ear of Dinilysia is shown at the bottom. It does resemble the inner ear of burrowers. Note the large number of legless taxa preceding leg taxa, revealing this as an untenable family tree. See figure 2 for a cladogram that makes more sense.

 

Legless taxa
are primitive in the Yi and Norell tree (Fig. 1). That marks their cladogram as untenable or at best, unlikely because legs would have to redevelop in Varanus and Heloderma in the Yi and Norell tree. By contrast, legless taxa are largely derived in the scleroglossan subset of the large reptile tree (Fig. 2, Bipes is a notable exception).

Figure 2. Scleroglossan subset of the large reptile tree. Generalists taxa duplicated in the Yi and Norell tree are shown in bright green. Burrowers shared in the Yi and Norell tree are in dark green. Legless taxa are black. Vestiges are in gray. Unknown are striped.

Figure 2. Scleroglossan subset of the large reptile tree. Generalists taxa duplicated in the Yi and Norell tree are shown in bright green. Burrowers shared in the Yi and Norell tree are in dark green. Legless taxa are black. Vestiges are in gray. Unknown are striped. Here legless taxa are largely derived/

The cladogram of Yi and Norell 
cannot tell us whether ancestral (= pre-Dinilysia) snakes were burrowers or not because Yi and Norell did not include any pre-Dinilysia ancestral snakes in their cladogram. That’s a major oversight.

By contrast,
the large reptile (Fig. 2) tree indicates that many pre-snakes, like Adriosaurus, were not burrowers — BUT BUT BUT — teeny tiny Tetrapodophis was a likely burrower, derived from a series of much larger swimmers, like AdriosaurusTetrapodophis was the size and shape of living burrowing snakes AND Dinilysia was the proximal descendant taxon in the large reptile tree. No one has yet revealed what sort of inner ear vestibule Tetrapodophis had. But IF it followed the pattern shown by Yi and Norell and had a burrowing-type large vestibule, it would follow that its proximal descendant, Dinilysia, might have shared that trait, no matter what its niche was. So the large inner ear vestibule of Dinilysia indicates that it could have been a burrower (at least until other data, like its large size, trumps the Yi and Norell results) or it could have been the descendant of a burrower.

Unfortunately, the large vestibule of Dinilysia cannot tell us whether or not pre-Dinilysia taxa were burrowers or not. We should look at the vestibule in those taxa from the large reptile tree. IMHO tiny Tetrapodophis was a likely burrower and Dinilysia was not by virtue of its much greater size.

Remember when we wondered if pterosaurs were quadrupeds or bipeds? 
And then we discovered they were both!

Were pre-snakes aquatic or burrowing?
Again, they were likely both!

References
Yi H and Norell MA 2015. The burrowing origin of modern snakes. Research Article Science Advances 2015;1:e1500743  27 November 2015

 

 

SVP 9 – Origin of snakes: Da Silva

Da Silva 2015 takes on the origin of snakes using skull shape. Notes follow (*):

From the abstract:
“The origin of snakes is a contentious topic with three competing hypotheses: aquatic, terrestrial or fossorial*. The snake fossil record is poor with a few preserved complete skulls dated back to the Cretaceous**. Phylogenies using discrete morphological data and including fossils are contradictory regarding the ophidian ancestor***. Thus, alternative approaches that aid tracking down the lizard-snake ancestral transition are necessary****. Comparisons of quantitative data such as skull shape of extant and fossil taxa but also ontogenetic trajectories of skull development are relevant alternative approaches. In this study, we analyzed for the first time more than 600 extant and extinct taxa representative of all major Squamata families using two- and three-dimensional landmarked-based geometric morphometrics. We also mapped a consensus phylogeny onto the morphospace and estimated ancestral shapes with Parsimony. Lastly, we traced 61 skull
ontogenetic trajectories with principal component analysis. We first found that snakes and lizards occupy different parts of the morphospace, except for many convergent fossorial forms. Shape transitions are gradual and strongly linked with ecology. The first axis of variation largely accounts for changes in the braincase and quadrate. Interestingly, ancestral estimations recovered the most common ancestor of snakes as a small fossorial similar to Anomochilus*****, while Cretaceous snakes show intermediate skull shapes similar to boas and pythons. Ontogenetic trajectories of snakes and lizards are linear and  overall parallel phylogeny in snakes. Young embryos of Alethinophidia have similar shape to terrestrial adult lizards and trajectories are clearly peramorphic. Adults and embryos of Scolecophidia are located at the base of lizard ontogenetic trajectories, likely indicating neoteny. Altogether, our data indicate that skull shape and ecology are strongly connected, supporting the hypothesis that modern snakes lineages originated from a fossorial snake ancestor through an early transition from terrestrial lizards. Lastly, natural selection fine-tuned skull ecological function upon variation generated by heterochrony.”

*The large reptile tree solved this problem. The answer is secondarily terrestrial from aquatic ancestors. For more information, start here.
** Not so. the record is wonderfully complete. Da Silva just did not recognize it yet.
*** True. But then, none but the large reptile tree employ Jucaraseps and Tetraopodophis.
**** Not so. Just taxon inclusion and phylogenetic analysis will solve the problem.
***** No. Anomochilus is a highly derived burrowing form, not a basal snake in the large reptile tree.

References
Da Silva FO 2015. Skull shape supports a terrestrial – fossorial transition in the early evolution of snakes through heterochrony. Journal of Vertebrate Paleontology abstracts.