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

Flatfish origin no longer ‘uncertain’ ca. 2008

We took an earlier look
at flatfish origins here. Today, more taxa and a look at earlier hypotheses proposing a dual origin for flatfish.

Friedman 2008 wrote, “The evolutionary origins of flatfish asymmetry are uncertain because there are no transitional forms linking flatfishes with their symmetrical relatives. Here I show that Amphistium (Fig. 4) and the new genus Heteronectes (Fig. 3), both extinct spiny-finned fishes from the Eocene epoch of Europe, are the most primitive pleuronectiforms known. The orbital region of the skull in both taxa is strongly asymmetrical, as in living flatfishes, but these genera retain many primitive characters unknown in extant forms. Most remarkably, orbital migration was incomplete in Amphistium and Heteronectes, with eyes remaining on opposite sides of the head in post-metamorphic individuals.”

Friedman 2008 was a major discovery supported by the LRT in 2019.
But it did not go as deep as the LRT (Fig. 9, see below).

If you’re interested in seeing how flatfish operate in vivo,
here’s a video from YouTube:

Here
in the large reptile tree (LRT, 1579 taxa, subset Fig. 9) we can trace the origin of flatfish immediately to the tuna (Thunnus, Fig. 1) and thread fin (Polydactylus, Fig. 2) and then further back to jawless Silurian fish.

Figure 3. Thunnus, the tuna, skeleton and skin.

Figure 1. Thunnus, the tuna, skeleton and skin. More primitive than traditional cladograms recover it.

Thunnus thyrnnus (Linneaus 1758; 4.6m long; Fig. 1) is the extant Atlantic tuna. Traditionally it is considered a member of the perch family. Here it nests following the Late Carboniferous Coccocephalichthys wildi. The jugal is retained. The squamosal is absent. The maxilla appears to retain one tiny tooth. Note the lacrimal contacts the ventral jugal, creating an orbit not confluent with a lateral temporal fenestra. The tip of the premaxilla descends and carries tiny teeth.

Figure 1. The thread fin, Polydactylus, enters the LRT close to flatfish + tuna.

Figure 2. The thread fin, Polydactylus, enters the LRT close to flatfish + tuna.

Polydactylus oxtonemus (Girard 1858; up to 23cm, some species up to 2m; Fig. 2) is the extant Atlantic threadfin. Traditionally considered a Perciforme (perch family) here Polydactylus is shallows-dwelling transitional taxon from free-swmming Thunnus (tuna) to flattened Heteronectes and the later flatfish. Note the five thread-likerays/feelers anterior to the pectoral fin arising from the gular bone. These drag along the sea floor similar to sea robins, like Prionotus.

Figure 3. Heteronectes is transitional between Polydactylus and flatfish.

Figure 3. Heteronectes is transitional between Polydactylus and flatfish.

Heteronectes chaneti (Friedman 2008, 2012) is an Eocene fish with an assymetric face originally considered basal to extant flatfish. Note the retention of circumorbital bones. It is transitional between Polydactylus (Fig. 2) and Amphistium (Fig. 4).

Figure 4. Amphistium is transitional between Heteronectes and flatfish.

Figure 4. Amphistium is transitional between Heteronectes and flatfish.

Amphistium paradoxum (Agassiz 1835) is an Eocene fish with an asymmetric face, transitional to extant flatfish. It also has the flatfish shape, so it probably swam broadside down.

Figure 6. Psettodes is the most primitive living flatfish. Note the dorsal position of the right eye.

Figure 6. Psettodes is the most primitive living flatfish. Note the dorsal position of the right eye.

 

FIgure 6. Cynoglosses is the extant tongue sole, a flatfish so derived that the pectorals are absent, the tail is continuous with the dorsal and anal fins, the mouth is no longer terminal and both eyes are in the ventral half of the left side of whatever remains of the skull.

FIgure 6. Cynoglosses is the extant tongue sole, a flatfish so derived that the pectorals are absent, the tail is continuous with the dorsal and anal fins, the mouth is no longer terminal and both eyes are in the ventral half of the left side of whatever remains of the skull.

Flatfish
are found over sand or mud flats and beaches, and among mangroves. They feed mostly on crustaceans, as well as chaetognaths, polychaetes, fishes, and some plant material. The common presence of small juveniles throughout the year suggests a prolonged spawning season. The reproduction of a few related species has been studied and they appear to be protandrous, sex changing from male to female with growth (Motomura 2004). I mean, with all the other changes… why not?

For awhile fish workers were thinking
“Flatfish can be divided into two groups: the three species of spiny turbot that make up the family Psettodidae, and the much larger suborder Pleuronectoidei.  Unsurprisingly, fish biologists long assumed that both groups of flatfish evolved from a single common ancestor; it is hard to imagine such a bizarre adaptation having evolved multiple times.”

“Recently however, this common-sense assumption has come under attack. Several studies have found support for the distinct flatfish adaptation having evolved on two separate occasions. Is the flatfish body-plan not as unique as it appears?” (Fig. 7).

Figure 1. Eight cladograms printed by Harrington et al. 2016, four of which recover a monophyletic clade of flatfish. Four others recover a diphyletic split. None of these duplicate the diphyletic results recovered in the LRT.

Figure 7. Eight previously published genomic cladograms printed by Harrington et al. 2016, four of which recover a monophyletic clade of flatfish. Four others recover a diphyletic split. None of these duplicate the diphyletic results recovered in the LRT. This becomes the question Harrington et al. wanted to answer.

 

Harrington et al. 2016 report,
“Here, we recovered significant support for flatfish monophyly and relationships among carangimorphs through analysis of over 1,000 UCE loci.”

Figure 2. Friedman et al. genomic study puts flatfish together (orange and yellow added).

Figure 8. Harrington et al. 2014 genomic study puts flatfish together (orange and yellow added). Again, this tree is not replicated by the LRT.  Scombroides is related to Thunnus.

Figure 3. Subset of the LRT focusing on ray fin fish.

Figure 9. Subset of the LRT focusing on ray fin fish.

The LRT employs fossil taxa
(Fig. 9) and, like Harrington 2014 (Fig. 8) does not find a dual origin for flatfish. So, finally a genomic study matches a phenomic study!


References
Bloch ME and Schneider JG 1801.Systema Ichthyologiae Iconibus cx Ilustratum. Post obitum auctoris opus inchoatum absolvit, correxit, interpolavit Jo. Gottlob Schneider, Saxo. Berolini. Sumtibus Auctoris Impressum et Bibliopolio Sanderiano Commissum. i-lx + 1-584, Pls. 1-110.
Friedman M 2008.
The evolutionary origin of flatfish asymmetry. Nature 454:209–212.
Friedman M 2012. Osteology of †Heteronectes chaneti (Acanthomorpha, Pleuronectiformes), an Eocene stem flatfish, with a discussion of flatfish sister-group relationships. Journal of Vertebrate Paleontology (32) 4: 735-756; doi: 10.1080/02724634.2012.661352
Girard CF 1858. Notes upon various new genera and new species of fishes, in the museum of the Smithsonian Institution, and collected in connection with the United States and Mexican boundary survey: Major William Emory, Commissioner. Proceedings of the Academy of Natural Sciences of Philadelphia. 10: 167-171.
Harrington RC, et al. (6 co-authors) 2016. Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye. BMC Evolutionary Biology 16 (224).
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
McCoy F 1855. A synopsis of the classification of the British Palaeozoic rocks, with a systematic description of the British Palaeozoic fossils. Fasciculus 3, Mollusca and Palaeozoic fishes. British Palaeozoic Fossils, Part II. Palaeontology 407-666.

Solution to genomic/phenomic divergence

We’ve been wondering why
phenomic (trait-based) studies do not completely match genomic (molecule-based) studies in phylogenetic analyses with similar taxon lists.

For instance,
the large reptile tree is a phenomic study of vertebrates that includes extinct and extant birds as a subset/clade. Prum et al. 2015 is a genomic study of extant birds. The bird parts of their topologies do not match.

Here is one answer @ 8:29 in.
“It quickly became clear that most traits in a human being aren’t caused by a single gene or a handful of genes. They often arise out of the complex interaction of hundreds or thousands or even tens of thousands of genes and other bits of DNA working in concert.”

“So the challenge sort of shifted. It wasn’t about finding a single gene or mutation for any one thing. It was about mapping these huge swaths of the genome and looking for variations.”

For example, they found,
“20,000 spots in the genome affect height.”

Of course,
only phenomic studies can include a wide gamut of fossil taxa.

And,
only phenomic studies let you see and document the gradual accumulation of traits in all sister taxa, echoing actual events in the family tree of vertebrates.

Bonus YouTube video!

Here is a demonstration
for the use of wings/winglets before flight was possible in both pre-pterosaurs and pre-birds. Originally I was thinking only of using wings to impress potential mates. Here defending eggs or young from intruders is also a possibility. While these bird parents are keeping their wings outstretched and relatively still, flapping them vigorously and coming down on the lizard’s back would only add to the lizard’s dilemma.


References
Prum et al. 2015

 

New pterosaur skull from China: Nurhachius luei

Riley Black (formerly Brian Switek) wrote:
in the subhead of her Scientific American blogpost, “New pterosaur was fossilized with a ridiculous grin.”

Well… maybe,
but in situ (Fig. 1) it’s not the first or only one. And when reconstructed (Fig. 2) the grin is gone.

On the plus side,
the Aptian (Early Cretaceous) skull attributed to Nurhachius is complete, which is always wonderful, especially for such fragile skulls.

Figure 1. New Nurhachius skull in situ. Bone colors added using DGS methods. BPMC-0204

Figure 1. New Nurhachius skull in situ. Bone colors added using DGS methods. BPMC-0204. The little curved pink ridge ventral to the jugal is the displaced descending nasal process found in sister taxa. Tiny cervical ribs are present, but overlooked.

Then Black’s subhead reports, 
“A skull found in China reveals a previously unknown flying reptile.” Well, if you read the text, not really. The authors consider the new specimen congeneric with the holotype Nurhachius (Fig. 3).

FIgure 2. New Nurhachius reconstruction. Sorry,Riley, no grin. The tiny, slit-like nostril and anterior extensions of the nasal and jugal following it are shown here.

FIgure 2. New Nurhachius reconstruction. Sorry,Riley, no grin. The tiny, slit-like nostril and anterior extensions of the nasal and jugal following it are shown here.

The teeth are like those of other istiodactylids in shape and distribution,
but when you put the two Nurhachius skulls together (Fig. 3), the two are not congeneric, so far as can be determined from available data. The mandible is not as robust in the new specimen, the rostrum is not as long. There in indication of the broader rostral tip found in Istiodactylus and other istiodactylids, nor is the orbit subdivided by circumorbital processes. The referred specimen preserves post orbital and cranial bones unknown in the holotype.

Figure 3. Nurhachius ignaciobritol reconstructed to scale alongside N. luei skull. These two do not look congeneric. The authors should have shown the two together like this.

Figure 3. Nurhachius ignaciobritol reconstructed to scale alongside N. luei skull. These two do not look congeneric. The authors should have shown the two together like this.

 

The genus holotype is
Nurhachius ignaciobritoi 
(Wang, Kellner, Zhou & Campos 2005; Fig. 3) IVPP V-13288, Early Cretaceous, skull length ~30 cm, ~2.5 m wingspan). The wings are long. The free fingers and toes are tiny. The sternum portion of the sternal complex is deep.

From the abstract:
“A revised diagnosis of the genus Nurhachius is provided, being this taxon characterized by the presence of a slight dorsal deflection of the palatal anterior tip, which is homoplastic with the Anhangueria and Cimoliopterus. N. luei sp. nov. shows an unusual pattern of tooth replacement, with respect to other pterodactyloid species.”

Istiodactylus model by David Peters

Figure 4. Istiodactylus model

The phylogenetic analysis presented by Zhou et al. 2019
is not worth showing or discussing due to the inclusion of Scleromochlus (a basal bipedal croc) and the exclusion of dozens of relevant pterosaur and fenestrasaur taxa. The new Nurhachius nests in the large pterosaur tree (LPT, 240 taxa), basal to other istiodactylids, next to, but not with Nurhachius. Proximal outgroup taxa include Coloborhynchus and Criorhynchus.


References
Zhou X, Pegas RV, Leal MEC and Bonde N 2019. Nurhachius luei, a new istiodactylid pterosaur (Pterosauria, Pterodactyloidea) from the Early Cretaceous Jiufotang Formation of Chaoyang City, Liaoning Province (China) and comments on the Istiodactylidae. PeerJ 7:e7688 DOI 10.7717/peerj.7688

https://peerj.com/articles/7688/

scientificamerican.com/laelaps/new-pterosaur-was-fossilized-with-a-ridiculous-grin

Styracocephalus x2 enters the TST

Fraser-King et al. 2019
bring us new data on Styracocephalus (Fig. 3), a purported dinocephalian therapsid from Late Permian South Africa. Unfortunately the Fraser-King et al. phylogenetic analysis (Fig. 1) excludes relevant taxa (like Phthinosuchus) and includes one unrelated taxon, Tetraceratops. The authority for this criticism is a larger study, the therapsid skull tree (TST, 72 taxa, subset Fig. 2) a side branch of the large reptile tree (LRT, 1579 taxa). It includes the relevant taxa in the Fraser-King et al. study, and many more excluded from Fraser-King et al.

Figure 1. Cladogram from Fraser-King et al. 2019. Compare to figure 2 where many more taxa are included.

Figure 1. Cladogram from Fraser-King et al. 2019. Compare to figure 2 where many more taxa are included. Tetraceratops is not related to any therapsid, but nests closer to Limnoscelis.

FIgure 2. TST with the addition of two specimens attributed to Styracocephalus and Raranimus. Compare to fewer taxa in figure 1.

FIgure 2. TST with the addition of two specimens attributed to Styracocephalus and Raranimus. Compare to fewer taxa in figure 1. Here Styracocephalus is not related to tapinocephalids. The TST is fully resolved.

Both the holotype of Styracocephalus
and the new referred specimen nest together in the LRT despite their many morphological differences (Fig. 3). Even so, I think the differences are strong enough to erect a new genus for the new specimen. The two nest with the Phthinosuchus clade in the LRT, a taxon not included in the Fraser-King et al. study.

Figure 1. At left, the holotype of Sclerocephalus SAM PK 8936. At right the distinctly different referred specimen to scale BPI I 7141.

Figure 3. At left, the holotype of Sclerocephalus SAM PK 8936. At right the distinctly different referred specimen to scale BPI I 7141.

So, in this case,
I’m a splitter, not a lumper. And I wish Fraser-King et al. had included a few more taxa.

PS
Raranimus also entered the TST because Fraser-King included that taxon. Raranimus nested with Ictidorhinus, and ironically, could be congeneric given how little is known of Raranimus.


References
Fraser-King S, Benoit J, Day MO and Rubidge BS 2019. Cranial morphology and phylogenetic relationship of the enigmatic dinocephalian Styracocephalus platyrhynchus from the Karoo Supergroup, South Africa. Palaeontologia africana 54: 14–29.

 

Allenypterus enters the LRT

Earlier we looked at another strange Bear Gulch fish,
the small chimaeirid, Belantsea. Today, we add another small specimen, Allenypterus (Fig. 1), this time from the coelacanth clade. Like Belantsea, Allenypterus is distinct from other members of its clade (e.g. Latimeria), yet not enough to nest it in another clade.

Figure 1. Allenypterus nests with the coelacanth lobefins in the LRT and elsewhere.

Figure 1. Allenypterus nests with the coelacanth lobefins in the LRT and elsewhere. At a typical monitor resolution of 72dpi, this specimen is shown close to natural size.

The specimen was apparently preserved
(Fig. 1) with the premaxilla and maxilla detached from the skull, but still occluding with the dentary.

Allenypterus montanus (Melton 1969; Lund and Lund 1984; 15cm long; Late Carboniferous) is a small, early coelocanth with a distinct tear-drop shape. The dorsal fins and anal fin do not have lobes. This is a derived trait.


References
Lund R and Lund W 1984. New genera and species of coelacanths from the Bear Gulch Limestone (Lower Carboniferous) of Montana (U.S.A.). Geobios. 17 (2): 237–244.
Melton WG 1969. A new dorypterid fish from central Montana. Northwest Science 43:196-206.

wiki/Allenypterus

The Times (UK) declares: proof for ‘winged dinosaurs’ vaulting

According to The Times.co.uk,
“Isle of Wight find proves winged dinosaurs took off by ‘vaulting’ into the air. Following the discovery of a fossilised giant pterosaur, scientists may have resolved how the 650lb beasts took flight. The sheer size of such creatures has long baffled scientists because they seem too heavy to take off. Now research with a computerised 3D model suggests they used their massive leg and wing muscles to catapult themselves into the air.”

Figure 1. Image from The Sunday Times (UK) showing the Isle of Wight and an ornithocheird filled with helium on a smaller planet taking off by vaulting.

Figure 1. Image from The Sunday Times (UK) showing the Isle of Wight and an ornithocheird filled with helium on a smaller planet taking off by vaulting. See figure 2 for the 650 lb Hatzegopteryx. The human silhouette (gray at left) is way too small for this ornithocheirid, so they got their pterosaurs mixed-up.

“Robert Coram, a professional fossil hunter who made the find, said: “It might have been the largest flying creature that had ever lived up to that time.”

“Mr Habib explained: “Mathematical modelling indicates that launching from a quadrupedal stance — pushing off first with the hind limbs and then with the forelimbs — would have provided the leaping power giant pterosaurs required for takeoff.”

FIgure 2. From The Sunday Times (UK) showing a human to scale with a restoration of Hatzegopteryx.

FIgure 2. From The Sunday Times (UK) showing a human to scale with a restoration of Hatzegopteryx.

This article appears to follow a Witton 2019 SVPCA abstract
(coincidence?) discussing the flight capabilities of the giant azhdarchid, Hatzegopteryx, using Graphic Double Integration and Principal Component Analysis. AND this article coincides with a Scientific American cover story on pterosaurs by Dr. Habib, discussed earlier here.

The pterosaur experts talking to The Times are still not discussing
the much smaller phylogenetic ancestors of azhdarchids with longer wings, nor do they consider the reduced to vestigial distal phalanges that essential clip the wings of azhdarchids over 1.8 m (6 ft) tall, nor do they recognize the traits that attend small flightless pterosaurs.

Let’s stop promoting giant volant pterosaurs
until these objections are met and resolved. Perhaps a little backtracking and apologizing for earlier grand standing is in order here.

Figure 1. Estimating giant azhdarchid weight from estimated height and comparables with similar smaller taxa.

Figure 3. Estimating giant azhdarchid weight from estimated height and comparables with similar smaller taxa.

Let’s define giant pterosaurs
as those at least 2m or 7ft tall at the eyeball (sans crest if present). The rest are large (more or less human-sized) pterosaurs (comparable to Pelagornis, Fig. 4) or smaller pterosaurs comparable to some other extant bird (e.g. goose-, robin- or hummingbird-sized).

Figure 1. Click to enlarge. The largest flying and non-flying birds and pterosaurs to scale.

Figure 4. Click to enlarge. The largest flying and non-flying birds and pterosaurs to scale.

You might remember
an earlier post featuring a classified ad from U of Leicester, (UK) seeking a student to prove the vaulting pterosaur hypothesis by finding appropriate pterosaur tracks. The Isle of Wight includes several strata with dinosaur tracks. Perhaps someday they will deliver giant pterosaur tracks that suddenly end. Then we can argue if the pterosaur flew from that point on and how it did so.


References
Witton M 2019. You’re going to need a bigger plane: body mass and flight capabilities of the giant pterosaur. SVPCA abstracts.
Counter arguments based on facts appear here: