Burrowing squamates: Ebel et al. 2020 examines bone micro-anatomy

From the Ebel et al 2020 abstract:
“We reconstructed the acquisition of a fossorial lifestyle in 2813 lepidosaurs and assessed the skull roof compactness from microCT cross-sections in a representative subset (n = 99). We tested this and five macroscopic morphological traits for their convergent evolution. We found that fossoriality evolved independently in 54 lepidosaur lineages. Furthermore, a highly compact skull roof, small skull diameter, elongate cranium, and low length ratio of frontal and parietal were repeatedly acquired in concert with a fossorial lifestyle.”

Unfortunately the Ebel team relied on a genomic cladogram. By contrast the large reptile tree (LRT, 1772+ taxa, subset Fig. 2) found only 6 lepidosaur fossorial clades. Perhaps this is so because the LRT is a phenomic (trait-based) cladogram in which fossorial and legless Dibamus is a highly derived skink, alongside Bipes and Amphisbaena, not a basalmost squamate nesting alone. In the LRT, basalmost squamates have legs, fingers and toes, traits many derived squamates retain then lose.

Figure 1. Cladogram of burrowing (fossorial) squamates from Ebel et al. 2020. Compare to figure 2 from the LRT.

Figure 1. Cladogram of burrowing (fossorial) squamates from Ebel et al. 2020. Compare to figure 2 from the LRT.

Ebel et al 2020 abstract continues:
“We report a novel case of convergence that concerns lepidosaur diversity as a whole. Our findings further indicate an early evolution of fossorial modifications in the amphisbaenian ‘worm-lizards’ and support a fossorial origin for snakes.”

By contrast the LRT employs a wider gamut of taxa, including fossils, and finds a basal dichotomy at the genesis of snakes. One branch remained terrestrial while the other branch became fossorial. The morphologically weirdest burrowing snakes are the most derived. That’s how evolution works: from simple and plesiomorphic to bizarre and derived.

The latest LRT addition to snakes, Atractaspis, is a burrowing venomous snake arising from terrestrial snakes. That taxon would have been overlooked prior to addition to the LRT, so there may be other squamate burrowers not yet tested by the LRT.

Figure 2. Subset of the LRT focusing on Squamata. Compare to Ebel et al. 2020 in figure 1.

Figure 2. Subset of the LRT focusing on Squamata. Compare to Ebel et al. 2020 in figure 1.

The LRT finds only six clades
of burrowing squamates (Fig. 2) and an entirely different tree topology that includes fossils and protosquamates, and, need I say it, tritosaurs.


References
Ebel R, Müller J, Ramm T, Hipsley C and Amson E 2020. First evidence of convergent lifestyle signal in reptile skull roof micro anatomy. BMC Biology 18…185. https://doi.org/10.1186/s12915-020-00908-y

SVP abstract 20: Squamate variability within a single species

Petermann and Gauthier 2020 bring us their views on the 
“potential consequences of our inability to assess intraspecific variability in growth rates.”

From the Petermann and Gauthier abstract:
“An investigation of life-history parameters in the extant iguanian lizard Sauromalus ater (the Common Chuckwalla), a sexually dimorphic species from the SW U.S.A., revealed remarkable intraspecific variability.”

“We found expected differences in growth strategies between males and females, but also within each sex, relating to body size and the timing of sexual maturity. Males and females can grow rapidly to size-at-sexual-maturity, producing above-average adult body sizes. Or, they can grow slowly to size-at-sexual-maturity, yielding adults at or below average body sizes. Neither growth strategy influences longevity. As a result, we found that body size of similar-aged individuals varied by 53% for males and 38% for females, and maximum differences in ‘adults’ of 64% for males and 38% for females.”

Further ranging results were found here earlier in the large pterosaur tree (LPT, 251 taxa) for the lepidosaur pterosaurs, Pteranodon (Fig. 1) and Rhamphorhynchus (Fig. 2). These both became fully resolved in phylogenetic analysis.

Figure 2. The DMNH specimen is in color, nesting between the short crest KS specimen and the long crest AMNH specimen.

Figure 2. The DMNH specimen is in color, nesting between the short crest KS specimen and the long crest AMNH specimen.

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

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

Continuing from the Petermann and Gauthier abstract:
“Our results add to previous reports of intraspecific variability in extant and extinct vertebrates. High levels of intraspecific size-variability have multiple implications for vertebrate paleontology.

  1. Morphologically similar specimens from the same locality could belong to the same species even if the size difference among adult individuals exceeds 50%, which is a higher level than previously thought.
  2. Specimens that have been analyzed skeletochronologically and have been found to be similar or identical in chronological age, may not exhibit similar sizes.
  3. Variability in growth strategies may lead to mistaking males and females (especially among sexual dimorphs), or individuals using different growth strategies, as belonging to separate species.”

This is the way evolution works in all vertebrate communities, including humans, where some are taller, some are robust, some are more colorful or sexier, some are brilliant, distinct from the others. In both Rhamphorhynchus and Pteranodon, no two specimens are alike.

“We previously presented evidence that a sequence of sub-terminal skeletal suture fusions relates to maximum body size in squamates, and not to chronological age. This indicates that late-ontogenetic, suture-fusion events could be used to evaluate whether two or more specimens of similar morphology and chronological age are differently-sized conspecifics. Likewise, skeletal suture fusions may aid discerning different growth strategies within a single species, as opposed to the presence of two morphologically similar, but nonetheless separate, species in a single taphonomic assemblage.”

This follows the work of Maisano 2002, who found fusion patterns were phylogenetic in lepidosaurs. a pattern continued in pterosaurs, where fusion patterns are also phylogenetic, distinct form archosaur growth patterns.


References
Maisano JA 2002. 
Terminal fusions of skeletal elements as indicators of maturity in squamates. Journal of Vertebrae Paleontology 22: 268–275.
Petermann H and Gauthier JA 2020. Intrespecific variability in an extant squamate and its implications for use in skeletochronology in extinct vertebrates. SVP abstracts 2020.

 

The three-eyed lizard enters the LRT alongside the monkey lizard

The extant, omnivorous Madagascar sand lizard,
Chalarodon madagascariensis (Peters 1854; 22cm long; Figs. 1, 2), enters the large reptile tree (LRT, 1747+ taxa) today. No surprises here. It nests with iguanid squamates between Eocene Koidosaurus and extant Pristidactylus + Basiliscus.

Figure 1. The three-eyed lizard, Chalarodon, in vivo.

Figure 1. The three-eyed lizard, Chalarodon, in vivo.

Figure 2. Chalarodon skull in 5 views. Images from Digimorph.org and used with permission.

Figure 2. Chalarodon skull in 5 views. Images from Digimorph.org and used with permission. Colors added. Note the tiny postfrontal, a vestige fused to the frontal.

The extant bush anole or monkey lizard
Polychrus marmoratus (Linneaus 1758, Figs. 3, 4) also enters the LRT, alongside Chalarodon. This arboreal jungle lizard has a very long prehensile tail and eyes that rotate independently.

Figure 3. The monkey lizard, Polychrus, in vivo.

Figure 3. The monkey lizard, Polychrus, in vivo.

Figure 3. Polychrus marmoratus skull in 4 views from Digimorph.org and used with permission. Colors added.

Figure 4. Polychrus marmoratus skull in 4 views from Digimorph.org and used with permission. Colors added.

References
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Peters WCH 1854. Diagnosen neuer Batrachier, welche zusammen mit der früher (24. Juli und 17. August) gegebenen Übersicht der Schlangen und Eidechsen mitgetheilt werden. Ber. Bekanntmach. Geeignet. Verhandl. Königl.-Preuss. Akad. Wiss. Berlin 1854: 614-628.

wiki/Chalarodon_madagascariensis
wiki/Polychrus

Kopidosaurus: no longer an enigmatic iguanian

Scarpetta 2020 bring us a tiny new Eocene lizard,
Kopidosaurus perplexus (YPM VP 8287) known from most of a disarticulated skull still in the matrix, but carefully presented in several views as µCT scans (Fig. 1).

Scarpetta warns his readers,
“Fossil identifications made in a phylogenetic framework are beholden to specific tree hypotheses. Without phylogenetic consensus, the systematic provenance of any given fossil can be volatile. Pleurodonta (Squamata: Iguania) is an ancient and frequently-studied lizard clade for which phylogenetic resolution is notoriously elusive.

Scarpetta reports,
“I address the effects of three molecular scaffolds on the systematic diagnosis of that fossil. I use two phylogenetic matrices, and both parsimony and Bayesian methods to validate my results, and perform Bayesian hypothesis testing to evaluate support for two alternative hypotheses of the phylogenetic relationships of the new taxon.”

Scarpetta did not provide a reconstruction of the skull. That is remedied here (Fig. 1).

Unfortunately Scarpetta’s three molecular scaffolds are based on genes, so they are completely useless for deep time studies, as documented several times in vertebrates. None of the three genomic studies in Scarpetta 2020 agree with each other. None agree with the LRT (Fig. 2).

Unfortunately Scarpetta’s phylogenetic analyses result in lists of suprageneric taxa, not genera, as in the LRT. Scarpetta reports, “The uncertainty of the relationships of Kopidosaurus is due in part to the mosaic morphology of the fossil and the problematic nature of pleurodontan phylogeny.”

There is no such thing as mosaic evolution. So stop using that excuse.

It doesn’t have to be this complicated. Use the LRT. It’s simple. Just Plug ‘n’ Play.

Figure 1. Kopidosaurus perplexus in situ and µCT scans from Scarpetta 2020. Reconstruction added here.

Figure 1. Kopidosaurus perplexus in situ and µCT scans from Scarpetta 2020. Reconstructions in lateral and palatal views added here.

Scarpetta reports,
“YPM VP 8287 preserves no morphological feature or combination of features that would allow clear referral to any member of Pleurodonta.” And that’s why he shouldn’t be “Pulling a Larry Martin” (relying on key traits that might converge). Instead: drop the new taxon into a comprehensive cladogram, like the LRT (Fig. 2), and let the software nest the enigma.

Definition according to Wikipedia:
Pleurodonta (from Greek lateral teeth, in reference to the position of the teeth on the jaw) is one of the two subdivisions of Iguania, the other being Acrodonta (teeth on the top [of the jaw]). Pleurodonta includes all families previously split from Iguanidae sensu lato (CorytophanidaeCrotaphytidaeHoplocercidaeOpluridaePolychrotidae, etc.), whereas Acrodonta includes Agamidae and Chamaeleonidae.”

The frontal and parietal are incomplete
and the skull is small at <2cm. Am I the first to wonder if this was a juvenile skull? Scarpetta does not bring up the subject. The large orbit relative to skull length supports that hypothesis. Otherwise this could be an adult in the process of phylogenetic miniaturization, common at the genesis of many clades (Fig. 2).

Scarpetta concluded,
“Given the phylogenetic volatility of Kopidosaurus, I refrain from favoring any biogeographic or divergence hypothesis based on the identification of the fossil and advise similar caution for other systematically enigmatic fossils, lizard or otherwise.”

Don’t give up! Use the LRT.

Here 
in the large reptile tree (LRT, 1740+ taxa) Eocene Kopidosaurus nests at the base of a clade of living iguanians (Fig. 2). It is a plesiomorphic taxon, but that doesn’t matter to the LRT. Only a suite of characters is able to nest Kopidosaurus with this level of confidence by minimizing taxon exclusion.

Figure 2. Subset of the LRT focusing on basal Squamata. Here Kopidosaurus nests at the base of a clade of living iguanians including Pristidactylus and Anolis.

Figure 2. Subset of the LRT focusing on basal Squamata. Here Kopidosaurus nests at the base of a clade of living iguanians including Pristidactylus, Basisliscus and Anolis.

As a reminder,
the LRT is still using just 238 traits, most of which were not used here due to the lack of a premaxilla, vomer and post-crania. Paleontologists still don’t want to accept the fact that the LRT continues to lump and separate with so few multi-state characters. Even those taxa previously tested without resolution, as described by Scarpetta 2020.


References
Scarpetta SG 2020. Effects of phylogenetic uncertainty on fossil identification illustrated
by a new and enigmatic Eocene iguanian. Nature.com/scientifcreports 10:15734.
https://doi.org/10.1038/s41598-020-72509-2

The Solomon Islands skink (genus Corucia) enters the LRT

Today the extant Solomon Islands skink
(Corucia zebrata, Gray 1855; Figs. 1, 2) enters the large reptile tree (LRT, 1714+ taxa). It nests basal to Gymnophthlamus + Vanzosaura and between Chalcides and Sirenoscincus.

Figure 1. The Solomon Islands skink (Corucia zebrata) is the largest skink on the planet, gives birth with a placenta and lives in communities.

Figure 1. The Solomon Islands skink (Corucia zebrata) is the largest skink on the planet, gives birth with a placenta and lives in communities.

This nesting comes as no surprise.
After all, skeletally Corucia is just another widely recognized skink, albeit with some unique reproductive and social qualities (see below).

Figure 2. The skink, Corucia zebrata with DGS colors added.

Figure 2. The skink, Corucia zebrata with DGS colors added.

Do not confuse Corucia with Carusia
(Fig. 3). The two are not the same, nor are they closely related.

Figure 1. Carusia intermedia, a basal lepidosaur close to Meyasaurus now, but looks a lot like Scandensia. Note the primitive choanae and broad palatal elements. None of the data I have shows the caudoventral process of the jugal, so I added it here from the description. Same with the epipterygoid.

Figure 3. Carusia intermedia, a basal lepidosaur close to Meyasaurus now, but looks a lot like Scandensia. Note the primitive choanae and broad palatal elements. None of the data I have shows the caudoventral process of the jugal, so I added it here from the description. Same with the epipterygoid.

Corucia zebrata
(Gray 1855, Figs. 1, 2) is the extant Soloman Islands skink, the largest known extant species of skink. Long chisel teeth distinguish this herbivorous genus. The tail is prehensile. This is one of the few species of reptile to live in communal groups. Rather than laying eggs, relatively large young are born after developing within a placenta. Single babies are typical. Twins are rare according to Wikipedia.

Removing all Carusia sister taxa in the LRT
fails to shift Carusia from its traditionally overlooked node basal to squamates.

The Wikipedia entry
on the ‘clade’ Carusioidea excludes great swathes of taxa relative to the LRT, so it mistakenly suggests that extinct Carusia is a member of the Squamata. Adding pertinent taxa solves that problem, as the LRT demonstrates.


References
Gray JE 1855. (1856). New Genus of Fish-scaled Lizards (Scissosaræ), from New Guinea. Annals and Magazine of Natural History, Second Series 18: 345–346.

wiki/Solomon_Islands_skink
wiki/Carusia
wiki/Carusioidea
http://www.markwitton.com
http://tetzoo.com

https://www.researchgate.net/publication/328388754_A_new_lepidosaur_clade_the_Tritosauria

Uma, the fringe-toed lizard, enters the LRT

Uma is the extant fringe-toed lizard
(Fig. 1). This California desert specimen has a large orbit, much larger than the eyeball.

Figure 1. Skull of Uma, the fringe-toed lizard, plus face and in situ photo.

Figure 1. Skull of Uma, the fringe-toed lizard, plus face and in situ photo.

Uma inornata (Baird 1859) is the extant fringe-toed lizard, an insectivore. Flaps and interlocking scales prevent sand from entering the nose, mouth, eyes and ears. In the large reptile tree (LRT, 1707+ taxa) Uma nests with another desert lizard, Phrynosoma (Fig. 2). This clade nests with chameleons within the Iguania within the Squamata. No surprises here. Everyone agrees to this.

Figure 6. Phyronosoma, the horned lizard of North America.

Figure 2. Phyronosoma, the horned lizard of North America.

The addition of Uma to the LRT
and the few corrections made to scores in nearby taxa moved the following three former Early Cretaceous protosquamates to the squamates: Indrasaurus, Hoyalacerta, and Meyasaurus. These now nest basal to Yabeinosaurus within Scleroglossa. So generalized are these three taxa, they now also nest as sisters to the gekko + snakes and their ancestors clade.

This is how the LRT nests taxa
without bias, myth or tradition.


References
Baird SF 1859. Description o new genera an species of North American lizards in the Museum of the Smithsonian Institution. Proceedings of the Academy of Natural Science: 253–256.

wiki/Fringe-toed_lizard
digimorph./Uma_scoparia/

Megaevolutionary dynamics in reptiles: Simoes et al. 2020

Simoes et al 2020 discuss
“rates of phenotypic evolution and disparity across broad scales of time to understand the evolutionary dynamics behind the origin of major clades, or how they relate to rates of molecular evolution.”

“Here, we provide a total evidence approach to this problem using the largest available data set on diapsid reptiles.”

Unfortunately not large enough to understand that traditional ‘diapsid’ reptiles are diphyletic, splitting in the Viséan and convergently developing two

“We find a strong decoupling between phenotypic and molecular rates of evolution,”

Yet another case of gene-trait mismatch in analysis.

“and that the origin of snakes is marked by exceptionally high evolutionary rates.”

Taxon exclusion is the reason for this exclusion.

Figure 1. Cladogram from Simoes et al. 2020. Gray tones added to show Lepidosauromorpha in the LRT.

Figure 1. Cladogram from Simoes et al. 2020. Gray tones added to show Lepidosauromorpha in the LRT.

“Here, we explore megaevolutionary dynamics on phenotypic and molecular evolution during two fundamental periods of reptile evolution: i) the origin and early diversification of the major lineages of diapsid reptiles (lizards, snakes, tuataras, turtles, archosaurs, marine reptiles, among others) during the Permian and Triassic periods,”

In the LRT the new archosauromorphs split from new lepidosauromorphs in the Viséan (Early Carboniferous).

“as the origin and evolution of lepidosaurs (lizards, snakes and tuataras) from the Jurassic to the present.”

In the LRT lepidosaurs had their origin in the Permian and the Simoes team ignores the Triassic radiation of lepidosaurs leading to tanystropheids and pterosaurs.

So without a proper and valid phylogenetic context,
why continue? How can they possibly discuss ‘rates of change’ if they do not include basal taxa from earlier period?

“Our results indicating exceptionally high phenotypic evolutionary rates at the origin of snakes further suggest that snakes not only possess a distinctive morphology within reptiles,  but also that the first steps towards the acquisition of the snake body plan was extremely fast.”

In the LRT many taxa are included in the origin of snakes from basal geckos. These are missing from Simoes list of snake ancestor.

Figure 1.  Subset of the LRT focusing on lepidosaurs and snakes are among the squamates.

Figure 1.  Subset of the LRT focusing on lepidosaurs and snakes are among the squamates.

In the LRT all sister taxa resemble one another
and document a gradual accumulation of derived traits.

If you have any particular evolutionary questions,
they were probably answered earlier in previous posts. Use the keyword box at upper right to seek your answer.

 

Squamate tooth complexity: Lafuma et al. 2020

Updated July 7, 2020
the LRT moves Meyasaurus, Indrasaurus and Hoyalacerta to the base of the Yabeinosaurus + Sakurasaurus clade within the Scleroglossa and Squamata.

This blogpost builds slowly. 
If you are short of time, drag down to the final paragraphs.

Lafuma et al. 2020 report,
“Complexity increase through cusp addition has dominated the diversification of many mammal groups.”

Be careful with blanket statements like that. What they wrote may be true of pre-mammal cynodonts (adding cusps), but teeth decrease in complexity in the lineage of pangolins, edentates, odontocetes and mysticetes. Carnivores have fewer teeth. So do elephants and manatees.

“However, studies of Mammalia alone don’t allow identification of patterns of tooth complexity conserved throughout vertebrate evolution.”

That sentence needs a re-write. It does not make sense.

“Here, we use morphometric and phylogenetic comparative methods across fossil and extant squamates (“lizards” and snakes) to show they also repeatedly evolved
increasingly complex teeth, but with more flexibility than mammals.”

Starting to sound iffy here knowing that Iguana (Fig. 1) is a basal squamate in the large reptile tree (LRT, 1669+ taxa, subset Fig. 2) and it has complex multi-cusp teeth. In the LRT varanids, sea-going mosasaurs and all legless lizards (including snakes) are all highly derived — and they have simple cones for teeth.

Pet Peeve: The authors don’t discuss lepidosaur pterosaurs that likewise had multi-cusp teeth in the Triassic, and only one cusp or no teeth in derived taxa.

Figure 2. The basalmost tested iguanid, Iguana. Note the resemblance to basalmost scleroglossans.

Figure 2. The basalmost tested iguanid, Iguana, one of the basalmost squamates in the LRT, contra Lafuma et al. who omitted so many outgroup taxa that their cladogram was upside-down.

Lafuma et al. 2020 continue,
“Since the Late Jurassic, six major squamate groups independently evolved multiple-cusped teeth from a single-cusped common ancestor.”

And those six in their phylogenetic order are:

  1. Scincoidea
  2. Polyglyphanodontia
  3. Lacertoidea
  4. Mosasauria
  5. Anguimorpha
  6. Iguania

Sophineta and three members of the Rhynchocephalia are outgroups to Squamata in the Lafuma et al. cladogram. That’s reasonable, but far from complete, and with disastrous consequences (see below).

“Unlike mammals reversals to lower cusp numbers were frequent in squamates, with varied multiple-cusped morphologies in several groups resulting in heterogenous evolutionary rates.”

See above.

The Lafuma et al. 2020 cladogram
lists the following clades of Squamates in this order (LRT order in parentheses).

  1. Gekkota (4th in the LRT and they share an ancestry with Serpentes in the LRT)
  2. Dibamia (last in the LRT, within skinks)
  3. Scincoidea (last in the LRT)
  4. Polyglyphanodontia (third in the LRT)
  5. Lacertoidea (second in the LRT)
  6. Mosasauria (fourth to last in the LRT)
  7. Serpentes (4th and they share an ancestry with Gekkota in the LRT)
  8. Anguimorpha (second to last in the LRT)
  9. Iguania (first in the LRT)

Due to taxon exclusion
the Lafuma et al. 2020 cladogram is inverted (upside-down) compared to the LRT (Fig. 2). As a result, so is their conclusion.

But let’s dig deeper trying to figure out how
this inversion happened. The authors report, “For topology we followed the total evidence phylogeny of Simões et al. – the first work to find agreement between morphological and molecular evidence regarding early squamate evolution.” Take a second look, dear readers. Borrowing a cladogram, taxon exclusion and genomics has given these workers an upside-down topology.

Figure 1.  Subset of the LRT focusing on lepidosaurs and snakes are among the squamates.

Figure 2.  Subset of the LRT from 2019 focusing on lepidosaurs including squamates.

Lafuma et al. 2020 list several hundred more squamate taxa
than the LRT includes, but this is where outgroups become important. Here is a list of missing Protosquamata taxa from the Lafuma et al. taxon list. Adding these taxa would bring much needed polarity to the Lafuma et al. cladogram:

  1. Lacertulus
  2. Schoenesmahl
  3. Fraxinisaura
  4. Hoyalacerta
  5. Indrasaurus
  6. Homoeosaurus
  7. Dalinghosaurus
  8. MFSN 19235
  9. Scandensia
  10. Calanguban
  11. Liushusaurus
  12. Purbicella
  13. Hongshanxi
  14. Euposaurus

But that’s not all… add to that list:
Tetraphodophis, Jucaraseps and Ardeosaurus. These three taxa link Norellius, Eichstaettisaurus and geckos to basal snakes. In the Lafuma cladogram Norellius, Eichstaettisaurus and geckos nest apart from Pontosaurus + Adriosaurus. For some reason, the basalmost gekko in the LRT, Tchingisaurus, nests with the basal amphisbaenan, Sineoamphisbaena in the Lafuma et al. tree. A sister, Sineoscincus, is omitted from the Lafuma et al. tree. Bahndwivici and Yabeinosaurus, nest basal to varanids and mosasaurs in the LRT, but are not listed by Lafuma et al.

If you’re going to report on the order of acquisition of traits,
you have to have your phylogenetic order established correctly. To do that you have to include more outgroup taxa, something that was not done in the Lafuma et al. study. By contrast, the LRT includes outgroup taxa back to Cambrian headless chordates, just to be sure all the bases are covered.


References
Lafuma F, Corfe IJ, Clavel J and Di-Pol N 2020. Multiple evolutionary origins and losses of tooth complexity in squamates. biRxiv preprint: https://doi.org/10.1101/2020.04.15.042796

Squamate genes show ‘no support’ for key traditional morphological relationships

If squamate genes showed ‘no support’
for key traditional morphological relationships, that was a red flag that Burbrink et al. 2019 chose to ignore. Instead they put their faith in genes instead of the measurable evidence of traits. As we’ve seen many times before, something is wrong with deep time genetic testing, hobbled from the starting blocks by not including fossil taxa. No gene test has ever revealed that a jugal is absent or present, that a metatarsal is longer than the toe or shorter. Whenever those things happen, we’ll review genomic tests again.

Burbrink et al. 2019 report with great confidence,
“Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups.

The opposite is true, as we’ve seen before.
Genomics is providing false positive family trees that do not match phenomic trees (Fig. 1)… not all the time, but often enough not to trust deep time genomics.

Figure 1.  Subset of the LRT focusing on lepidosaurs and snakes are among the squamates.

Figure 1.  Subset of the LRT focusing on lepidosaurs and snakes are among the squamates. This cladogram includes fossil taxa and documents a gradual accumulation of traits across all taxa. 

Burbrink et al. 2019 report with great confidence,
“Here, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome scale data.

Genomic studies cannot and do not include fossil taxa,
which also puts genomic studies at a great disadvantage. How do you test genomic studies? You test genomic studies with phenomic studies, not the other way around.

Burbrink et al. 2019 report with great confidence,
“We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata.

According to Wikipedia and Variety of Life:
Toxicofera =  proposed clade Serpentes (snakes), Anguimorpha (monitor lizards, gila monster, and alligator lizards) and Iguania (iguanas, agamas, and chameleons). None of this is supported by the LRT.

Scleroglossa = includes anguimorphs, geckos, autarchoglossans (scincomorphs and varanoids), and amphisbaenians. For the most part this is supported by the LRT, but snakes are not listed here and they are related to geckos. Amphisabaenians are scincomorphs.

Macrostomata = non-fossorial snakes. In the LRT (subset Fig. 1) fossorial (= burrowing snakes) are a clade within the non-fossorial snakes. In other words, Burbrink’s team got it backwards, perhaps because no fossil snakes and pre-snakes were included.

“We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; and between the three toxiferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).”

Don’t trust the results recovered by Burbrink et al. 2019. 
Genomic tests in lizards are not supported by validated phenomic tests. Only the LRT (at present) documents a gradual accumulation of traits across extinct and extant lepidosaur and squamate taxa that goes back to jawless Silurian fish.

Sorry guys, no matter how much effort went into creating Burbrink et al. and its supplementary data with 15 co-authors, it turned out not to provide any insights into squamate evolutionary events and therefore, was a waste of time. Worse yet, it promoted false positives as good science.

Next time,
before promoting genomics above phenomics, test genomics against phenomics.  Yesterday we looked at a possible reason why genomic tests do not replicate phenomic tests.


References
Burbrink FT et al. (14 co-authors) 2019. Interrogating genomic-scale data for Squamata (lizards, snakes, and amphisbaenians) shows no support for key traditional morphological relationships. Systematic Biology, syz062 (advance online publication)
doi: https://doi.org/10.1093/sysbio/syz062
https://academic.oup.com/sysbio/advance-article-abstract/doi/10.1093/sysbio/syz062/5573126

Hongshanxi: just barely NOT a squamate

Updated July 7, 2020
the LRT moves Meyasaurus, Indrasaurus and Hoyalacerta to the base of the Yabeinosaurus + Sakurasaurus clade within the Scleroglossa and Squamata.

Dong, Wang, Mou, Zhang and Evans 2019 bring us
Hongshanxi xidi, a tiny, new and rare, complete, articulated and flattened Oxfordian (earliest late) Jurassic lepidosaur the authors had difficulty nesting with both traits and molecules.

In happy contrast,
the large reptile tree (LRT 1578 taxa) recovers Hongshanxi as the proximal outgroup to the clade Squamata, between Liushusaurus (Evans and Wang 2010) Early Cretaceous, ~10 cm) and IguanaEuposaurus cirinensis (Lortet 1892, MHNL 15681, Late Jurassic, Kimmeridgian, 155 mya, 3.5cm snout vent length) without firsthand observations.

Figure 1. Hongshanxi in situ with DGS colors added to pectoral region.

Figure 1. Hongshanxi in situ with DGS colors added to pectoral region.

From the abstract
It [Hongshanxi] is distinguished from other Jurassic-Cretaceous lizards by a unique combination of derived characters, notably a long frontal with posterior processes that clasp the short parietal; cranial osteoderms limited to the lower temporal and supraocular regions; and an elongated manus and pes. Phylogenetic analysis using morphological data alone places the new taxon on the stem of a traditional ‘Scleroglossa’, but when the same data is run with a backbone constraint tree based on molecular data, the new taxon is placed on the stem of Squamata as a whole. Thus its position, and that of other Jurassic and Early Cretaceous taxa, seem to be influenced primarily by the position of Gekkota.”

Figure 2. Hongshanxi skull with DGS colors added.

Figure 2. Hongshanxi skull with DGS colors added.

Unfortunately
Dong et al. were using an outdated and incomplete taxon list, that of Gauthier 2012 (610 characters, 192 taxa) with maybe a dozen additional Early Cretaceous taxa described since then. The authors report, “However, as with many other Jurassic and early Cretaceous taxa (e.g. Scandensia, Yabeinosaurus, Hoyalacerta, Liushusaurus), the phylogenetic position of Hongshanxi n. gen. cannot be clearly resolved.”

That may be because the authors do not understand that a series of lepidosaurs preceded the Squamata. These predecessors include the pterosaur clade, Tritosauria. In the LRT the Lepidosauria is completely resolved with high Bootstrap values at nearly all nodes with the addition of Hongshanxi, which looks quite a lot like its nearly coeval sister taxa and is similar in size and location.

Figure 3. Hongshanxi pelvic region in situ with DGS colors added

Figure 3. Hongshanxi pelvic region in situ with DGS colors added

The authors also do not realize
they cannot rely on molecular studies to clarify relationships in deep time. The solution to these problems is online, the LRT, ready for anyone to use. If workers want to continue ‘spinning their wheels’ recovering no clear solutions, that’s to the detriment of our science.

Oddly
the hands and feet of Hongshanxi are elongate, like their arboreal sisters, but the penultimate phalanges are shorter than the more proximal phalanges, distinct from their arboreal sisters. The torso is short relative to the femur length. The authors correctly note the very odd lack of a straight frontal-parietal suture. Also very odd is the open acetabulum (hip joint), which was overlooked by the authors.


References
Dong L, Wang Y, Mou L, Zhang G and Evans SW 2019. A new Jurassic lizard from China in Steyer J.-S., Augé M. L. & Métais G. (eds), Memorial Jean-Claude Rage: A life of paleo-herpetologist. Geodiversitas 41 (16): 623-641. https://doi.org/10.5252/geodiversitas2019v41a16.

http://geodiversitas.com/41/16