Pappochelys: STILL not the ancestor of turtles, no matter what you read in Nature

Schoch et al. 2019 rehash an old trope.
suffering from overlooked taxon exclusion and convergence revealed by a wider gamut phylogenetic analysis, the large reptile tree (LRT, 1542 taxa).

From their abstract:
“Unlike any other tetrapod, turtles form their dorsal bony shell (carapace) not from osteoderms, but by contribution of the ribs and vertebrae that expand into the dermis to form plate-like shell components. Although this was known from embryological studies in extant turtles, important steps in this evolutionary sequence have recently been highlighted by the Triassic taxa Pappochelys, Eorhynchochelys and Odontochelys, and the Permian Eunotosaurus. The discovery of Pappochelys shed light on the origin of the ventral bony shell (plastron), which formed from enlarged gastralia. A major question is whether the turtle shell evolved in the context of a terrestrial or aquatic environment. Whereas Odontochelys was controversially interpreted as aquatic, a terrestrial origin of turtles was proposed based on evidence of fossorial adaptations in Eunotosaurus. We report palaeohistological data for Pappochelys, a taxon that exemplifies earlier evolutionary stages in the formation of the bony shell than Odontochelys. Bone histological evidence reveals (1) evolutionary changes in bone microstructure in ribs and gastralia approaching the turtle condition and (2) evidence for a predominantly amphibious or fossorial mode of life in Pappochelys, which support the hypothesis that crucial steps in the evolution of the shell occurred in a terrestrial rather than fully aquatic environment.”

Figure 2. Shoch and Sues compared Pappochelys to Odontochelys and Proganochelys, but deleted the more primitive Eunotosaurus. And it's easy to see why. Eunotosaurus has wider ribs than its two purported successors. That and the LRT tell you its not a turtle, but a turtle mimic. Note the inaccuracy Schoch and Sues applied to their Odontochelys. The version from ReptileEvolution.com appears in frame 2 of this GIF animation.

Figure 1. Shoch and Sues compared Pappochelys to Odontochelys and Proganochelys, but deleted the more primitive Eunotosaurus. And it’s easy to see why. Eunotosaurus has wider ribs than its two purported successors. That and the LRT tell you its not a turtle, but a turtle mimic. Note the inaccuracy Schoch and Sues applied to their Odontochelys. The version from ReptileEvolution.com appears in frame 2 of this GIF animation.

We’ve explored such possibilities
earlier here, here and here. A wider gamut (1542 taxa) competing cladogram of vertebrate interrelationships recovers Pappochelys close to the ancestry of placodonts, and Eunotosaurus + Eorhynochelys close to Acleistorhinus. Neither are close to turtles. Odontochelys is close to the origin of soft shell turtles. The small horned pareiasaur, Sclerosaurus, is closer. Proganochelys is close to the origin of hard shell turtles. Meiolania and the small horned pareiasaur, Elginia, are closer. Convergence and taxon exclusion seem to be the trouble here.

Figure 2. Another gap is filled by nesting E. wuyongae between Bunostegos and Elginia at the base of hard shell turtles in the LRT.

Figure 2. Another gap is filled by nesting E. wuyongae between Bunostegos and Elginia at the base of hard shell turtles in the LRT.

Back to the Schoch et al. question:
“A major question is whether the turtle shell evolved in the context of a terrestrial or aquatic environment.” 

Answer:
Both. See dual origin of turtles from pareiasaurs and notes above. Schoch et al. are not working within the correct phylogenetic context. When they get the same results while including the turtle ancestors recovered by the wide gamut LRT, let me know. For now, apparently, they appear to be content to play in their little corner ignoring data that has been online for several years.

See and read:
https://www.researchgate.net/publication/328388481_The_dual_origin_of_turtles_from_pareiasaurs

Online cladogram here:


References
Schoch RR, Klein N, Scheyer TM and Sues H-D 2019. Microanatomy of the stem-turtle Pappochelys rosinae indicates a predominantly fossorial mode of life and clarifies early steps in the evolution of the shell. Nature Scientific Reports 9:10430 online here

 

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The flying fish (Exocoetus) enters the LRT alongside the swordfish

Nesting flying fish (Exocoetus) with swordfish (Xiphias)
(Figs. 1–3) in the large reptile tree (LRT, 1542 taxa; subset Fig. 4) seems like an odd pairing. Even so, no tested taxon is closer to swordfish than flying fish…

Figure 1. Flying fish (Exocoetus) skull.

Figure 1. Flying fish (Exocoetus) skull.

…until you add the needlefish (Tylosurus),
(Fig. 5) and then it all seems to make more sense visually.

Figure 2. Flying fish (Exocoetus volitans) line drawing.

Figure 2. Flying fish (Exocoetus volitans) line drawing.

Exocoetus volitans (Linneaus 1758; up to 30m ) is the extant blue flyingfish, here related to the swordfish, XiphiasExocoetus travels in schools or schoals. Sometimes they exit the water to avoid predators. Juveniles have a relatively shorter torso. Hatchlings are slow-moving and tiny. Note the antorbital fenestra and large lacrimal, as in Xiphias. Distinctly flying fish have a jaw joint directly below the orbit. The coracoid is larger than the scapula, raising the pectorl fins.

Figure 1. Extant swordfish (Xiphias) to scale with Eocene swordfish (Blochius).

Figure 3. Extant swordfish (Xiphias) to scale with Eocene swordfish (Blochius).

Xiphias gladius (Linneaus 1758; Gregory and Conrad 1937; up to 4.5m in length) is the extant swordfish, derived from the barracuda, Sphyraena. 1cm long hatchlings more closely resembled little barracudas, then little sailfish before reducing the long dorsal fin. The sword is not used to spear, but to slice and maim smaller fish traveling in schools. The pelvic fins are absent. Larger females produce more eggs, up to 29 million.

Please compare the juvenile swordfish, with Lepisosteus, the long-nose gar, which nests as a sister and shares many traits, including long toothy jaw and an elongate body.

Figure 4. Subset of the LRT focusing on basal vertebrates (fish) with the addition of Tylosurus, the needlefish.

Figure 4. Subset of the LRT focusing on basal vertebrates (fish) with the addition of Tylosurus, the needlefish.

Tylosurus acus (Lacépéde 1803) is the extant needlefish, a long-snouted, toothy sister to the flying fish, Exocoetus, in the LRT and other cladograms. Note the divided naris and new bone identities compared to the Gregory 1938 drawing. Distinct from related taxa, the pectoral fins are set further posteriorly on the torso. This speedy taxon somewhat bridges the gap between flying fish and swordfish. Compare this adult to the juvenile swordfish (above) and to the ancestral barracudas and pikes, Sphyraena, and Esox.

Figure 5. Tylosurus, the needlefish, in several views. This taxon links swordfish to flying fish and links this clade to barracudas + pikes and to garfish (Lepisosteus).

Figure 5. Tylosurus, the needlefish, in several views. This taxon links swordfish to flying fish and links this clade to barracudas + pikes and to garfish (Lepisosteus).

Readers may recall
an unrelated, though convergent, Late Triassic flying fish, Thoracopterus, which earlier nested with extinct Xiphactinus and extant anchovies, like Engraulis, in the LRT.

Iniopteryx, an odd chimaera/ratfish from the Late Carboniferous, also had large elevated pectoral fins, but those were made for display, not for gliding. That fish entered the LRT here.

Traditional fish classification
considers swordfish, needlefish and flying fish members of the broad clade Percomorpha (which one might imagine are perches and their descendants, but actually include cusk eels and their descendants. Otherwise traditional cladograms do not lump flying fish and swordfish together between pikes and garfish, as recovered in the LRT (subset Fig. 4).

If I missed a citation that predates this one
that supports this hypothesis of interrelationships, please send me the citation. It does not appear to be matched by genomic (gene/molecule) studies.


References
Gregory WK and Conrad GM 1937. The comparative anatomy of the swordfish (Xiphias) and the sailfish (Istiophorus). The American Museum Novitates, 952:1-25.
de Lacepéde BG 1803. Histoire naturelle des poissons. Tome Cinquieme. 5(1-21):1-803 + index.
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.

wiki/Xiphias
wiki/Exocoetus_volitans
wiki/Tylosurus

Testing for bipedalism in archosaurs (and pterosaurs)

Grinham, VanBuren and Norman 2019
looked at the origin of bipedalism in the archosaur and pre-archosaur ancestors of birds.

They report, “We test whether facultative bipedality is a transitionary state of locomotor mode evolution in the most recent early archosaur phylogenies using maximum-likelihood ancestral state reconstructions for the first time. Across a total of seven independent transitions from quadrupedality to a state of obligate bipedality, we find that facultative bipedality exists as an intermediary mode only once, despite being acquired a total of 14 times. We also report more independent acquisitions of obligate bipedality in archosaurs than previously hypothesized, suggesting that locomotor mode is more evolutionarily fluid than expected and more readily experimented with in these reptiles.”

The authors used the cladograms of Ezcurra 2016 and Nesbitt 2011,
both of which are riddled with inappropriate taxon inclusion and exclusion problems as reported earlier here and here. Therefore comparisons regarding the number of times obligate bipedality in archosaurs occurred is useless lacking a consensus phylogenetic contaxt. In the large reptile tree (LRT, 1542 taxa) bipedality occurs only once in archosaurs. It just precedes the origin of the archosaurs (crocs + dinos only). Ezcurra, Nesbitt and Grinham et al. include a long list of inappropriate taxa in their inclusion set according to the LRT that skews results (e.g. the lepidosauromorphs: Jesairisosaurus, Macrocnemus, Mesosuchus, Gephyrosaurus, Planocephalosaurus, Eudimorphodon, Dimorphodon).

Grinham, VanBuren and Norman 2019
follow Nesbitt 2011 who listed the pterosaurs Eudimorphodon and Dimorphodon as archosauriforms. Grinham et al. 2017 considered both to be quadrupeds without explanation. The only pterosaur paper cited by Grinham et al. is Padian 2008. Peters 2007 recovered pterosaurs with lepidosaurs like Huehuecuetzpalli, later validated, expanded and published online in LRT. Peters 2000, 2011 reported on bipedal pterosaur tracks and restricted most cited pterosaur ichnites to flat-footed beach-combing pterosaur clades. Use keyword “bipedal pterosaur tracks” in the SEARCH box to see prior samples of digitigrade and bipedal tracks reported by this blogpost along with their citations.

Padian 2008 reported
“Peters (2000) also reached the conclusion that pterosaurs were not ornithodirans, and found instead that they were nested within what is traditionally considered the Prolacertiformes. It remains to be seen whether other workers can duplicate this result, but a recent analysis by Hone and Benton (2007) failed to find support for Peters’ analyses. For the present, because five different analyses have found that pterosaurs are ornithodirans, and the systematic community seems to have largely accepted this, the present paper will proceed with this provisional conclusion, without discounting other possible solutions.”

We looked at the bogus results
of Hone and Benton 2007 earlier here. They dropped taxa proposed as pterosaur ancestors by Peters 2000 because their inclusion would have tilted their supertree toward the topology recovered by Peters 2000, who tested four previously published cladograms by adding novel taxa to them. One year earlier than Peters 2000, co-author Benton 1999 had proposed Scleromochlus as a pterosaur sister/ancestor, which Peters 2000 invalidated. Evidently professor Benton did not appreciate that and succeeded, at least in Padian’s eyes, to dismiss Peters 2000 as an unacceptable and suppressible minority view.

Note that none
of Padian’s “five different analyses” used novel taxa proposed by Peters 2000. Padian’s report, “The systematic community seems to have largely accepted this,” demonstrates that Padian and his community were adverse to testing the novel taxa of Peters 2000 on their own terms, preferring the cozy comfort of tradition and orthodoxy — and they did this after Peters 2000 invalidated earlier efforts simply by adding a few taxa. Very easy to do. Even today it remains impossible to explain the origin of pterosaurs as archosaurs in a phylogenetic context because they are not archosaurs. In the world of academics, taxon exclusion remains a useful tool. We should all fight against this practice.

Later Padian 2008 reports, 
“Alternatively, if we consider that pterosaurs evolved from quadrupedal basal archosauromorphs such as Prolacertiformes (Peters, 2000), a rather different model of limb evolution must be proposed. In prolacertiforms the humerus is longer than the forearm and the femur is longer than the tibia; the glenoacetabular length is also long, as in most terrestrial quadrupeds. To attain the proportions seen in basal pterosaurs, the relative lengths of humerus and forearm and of femur and tibia would have to have been reversed, and the vertebral column would have had to shorten considerably (or the limb segments increase). These changes are independent of the extensive reorganization of the joints for erect posture and parasagittal gait, for which there is no evidence so far in prolacertiforms.”

Figure 1. Click to enlarge. The origin of the pterosaur wing and the migration of the pteroid and preaxial carpal. A. Sphenodon. B. Huehuecuetzpalli. C. Cosesaurus. D. Sharovipteryx. E. Longisquama. F-H. The Milan specimen MPUM 6009, a basal pterosaur.

Note: Padian 2008 chose to ignore the limb proportions
of Longisquama (Figs. 1, 2) another taxon proposed by Peters 2000 with a humerus shorter than the forearm, as in pterosaurs. He also ignored Sharovipteryx, another taxon proposed by Peters 2000, with a femur shorter than the tibia. In the world of academics, taxon exclusion remains a useful tool. We should all fight against this.

Padian 2008 also chose to ignore the evidence for bipedalism
in Cosesaurus (Fig. 2) matching facutatively bipedal Rotodactylus tracks (Peters 2000) and Sharovipteryx (Fig. 2), an obligate biped based on proportions. Both have the short torso relative to the limb length sought for and purposefully overlooked by Padian 2008 (see above quotation). In the world of academics, taxon exclusion remains a useful tool. We should all fight against this.

Figure 3. The origin of pterosaurs now includes Kyrgyzsaurus, nesting between Cosesaurus and Sharovipteryx.

Figure 2. The origin of pterosaurs now includes Kyrgyzsaurus, nesting between Cosesaurus and Sharovipteryx.

Students of paleontology:
I’m sorry, this is just the way it is.

Getting back to bipedalism in archosaurs,
the LRT, subset Fig. 4) documents the patterns and possibilities of bipedal locomotion in taxa preceding dinosaurs. The topology here employs more taxa, pushes pterosaurs over to lepidosaurs (Peters 2007) and nests only Crocodylomorpha + Dinosauria within the Archosauria. Poposauria is the proximal outgroup. This is where bipedalism in archosaurs first appeared. Other bipedal taxa achieved this ability by convergence. Secondary quadrupedalism occurred several times in archosaurs, and by convergence in certain derived pterosaurs (e.g. ctenochasmatids and azhdarchids), as evidenced by their backward pointing manual digit 3 in ichnites.

Figure 3. Subset of the LRT focusing on the archosauromorph synapsid-grade taxa and diapsid-grade taxa with color added to bipedal taxa.

Figure 3. Subset of the LRT focusing on the archosauromorph synapsid-grade taxa and diapsid-grade taxa with color added to bipedal taxa.

As documented here and elsewhere
It does not matter if certain hypotheses are peer-reviewed and published or not.
Academic authors can choose to omit pertinent taxa and papers knowing that ‘friendly’ academic referees and editors will likewise choose to overlook such omissions. Apparently all academics seek and work to maintain the orthodox line, no matter how invalid it may be.

That’s why this blogpost and ReptileEvolution.com came into being.
We’re talking about hard science. Ignoring and omitting hard evidence cannot be tolerated or coddled. I ask only that academic workers rise to the professionalism they seek to inspire in their own students. History will put this all into perspective. Professional legacies may end up in shame unless they take action soon. Just test the taxa. 


References
Benton MJ 1999. Scleromochlus taylori and the origin of the pterosaurs. Philosophical Transactions of the Royal Society London, Series B 354 1423-1446. Online pdf
Ezcurra MD 2016 The phylogenetic relationships of basal archosauromorphs, with an emphasis on the systematics of proterosuchian archosauriforms. PeerJ 4, e1778. (doi:10.7717/peerj.1778)
Grinham LR, VanBuren CS and Norman DB 2019. Testing for a facultative locomotor mode in the acquisition of archosaur bipedality. R. Soc. open sci. 6: 190569. http://dx.doi.org/10.1098/rsos.190569
Hone DWE and Benton MJ 2007. An evaluation of the phylogenetic relationships of the pterosaurs to the archosauromorph reptiles. Journal of Systematic Palaeontology 5:465–469.
Hone DWE and Benton MJ 2008. Contrasting supertree and total evidence methods: the origin of the pterosaurs. Zitteliana B28:35–60.
Nesbitt SJ 2011. The early evolution ofArchosaurs: relationships and the origin of major clades. Bull. Am. Museum Nat. Hist. 352, 1–292. (doi:10.1206/352.1)
Padian K 2008. Were pterosaur ancestors bipedal or quadrupedal? Morphometric,
functional, and phylogenetic considerations. Zitteliana R. B Abhandlungen der Bayer.
Staatssammlung fur Palaontologie und Geol. 28B, 21–28.
Peters D 2000a. Description and Interpretation of Interphalangeal Lines in Tetrapods.  Ichnos 7:11-41.
Peters D 2000b. A Redescription of Four Prolacertiform Genera and Implications for Pterosaur Phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106 (3): 293–336.
Peters D 2002. A New Model for the Evolution of the Pterosaur Wing – with a twist. – Historical Biology 15: 277–301.
Peters, D 2007. The origin and radiation of the Pterosauria. Flugsaurier. The Wellnhofer Pterosaur Meeting, Munich 27
Peters D 2011. A Catalog of Pterosaur Pedes for Trackmaker Identification. Ichnos 18(2):114-141. http://dx.doi.org/10.1080/10420940.2011.573605

Indrasaurus and Microraptor: the inside story

O’Connor et al. 2019 report on
a small pre-squamate lizard, Indrasaurus wangi (Fig. 1; STM5-32), ingested just before the untimely death of its feathered predator, Microraptor (Fig. 3, STM5-32). Both were added to the large reptile tree (LRT, 1542 taxa). O’Connor et al. note, “This is the fourth specimen of Microraptor described with ingested remains preserved in the abdominal cavity, with enantiornithine birds, mammals, and fish previously documented.”

Figure 1. Indrasaurus reconstructed.

Figure 1. Indrasaurus reconstructed. Sister taxa do not have an antorbital fenestra, so the one that appears here is suspect, but possible.

From their abstract:
“Phylogenetic analysis suggests Indrasaurus wangi gen. et sp. nov. is a basal scleroglossan closely related to the slightly older Liushusaurus. Comparison of ingested remains preserved across Paraves suggests that dromaeosaurids retained the plesiomorphic condition in which ingested prey were fully digested, rather than egested, as has been demonstrated was the case in the probable troodontid Anchiornis.”

In the LRT Liushusaurus is an outgroup taxon to the Squamata, a clade defined by extant taxa. Liushusaurus nests six nodes apart from Indrasaurus.

FIgure 3. Hoyalacerta in situ nests close to Indrasaurus in the LRT. Note the similarly long torso and short, small limbs.

Figure 2. Hoyalacerta in situ nests close to Indrasaurus in the LRT. Note the similarly long torso and short, small limbs.

O’Connor et al. remarked,
“Phylogenetic relationships in fossil squamates are difficult to determine with currently available matrices. Given the uncertainty regarding squamate relationships at this time, we do not find it unusual that our results add to the current disparity.” O’Connor et al. did not realize the clade Protosquamata enclosed the clade Squamata. The LRT was the first to recover this clade and another previously overlooked lepidosaur clade, the Tritosauria, nesting between Sphenodontia and Squamata.

Figure 2. Indrasaurus and Microraptor to scale.

Figure 3. Indrasaurus and Microraptor to scale. Despite what appear to be jaw tips, those are separated dentaries an the skull is preserved in dorsal view, lacking premaxillae and nasals.

In the LRT,
Indrasaurus (STM5-32) nests close to the coeval Hoyalacerta (Fig. 2) in the Protosquamata, a more primitive clade than Squamata that includes Squamata and otherwise no extant taxa. O’Connor et al. are mistaken, according to the LRT, when they consider Indrasaurus a scleroglossan squamate.

Antorbital fenestra?
Indrasaurus sister taxa do not have an antorbital fenestra, so the one that appears here (Fg. 1) is suspect, but possible.

FIgure 6. Ornitholestes nests as a sister to Sciurumimus, between Compsognathus and Microraptor.

FIgure 4. Ornitholestes nests as a sister to Sciurumimus, between Compsognathus and Microraptor.

The STM5-32 specimen of Microraptor (Fig. 3) nests as the basalmost tested Microraptor derived from a sister to Sciurumimus and Ornitholestes (Fig. 4), convergent with and distinct from pre-bird clades. Traditional cladograms, like the recently published Hartman et al. 2019, do not associate these three taxa apart from birds. O’Connor et al. consider Microraptor to be a dromaeosaurid. The LRT rejects that hypothesis of interrelationships.

Three Microraptor species
Since the three tested Microraptors nest apart from one another with high Bootstrap scores, two need to be given new specific names, not lumped under Microraptor zhaoianus, as O’Connor et al. do.

Was Microraptor volant?
O’Connor et al. consider all specimens of Microraptor to be volant (capable of flight). The short, nearly disc-like shape of the coracoid (Fig. 2) argues against this, despite the presence of large feathers in this genus. The key difference between Late Jurassic birds and pre-bird anchiornithids is the elongation of the locked-down coracoid, which marks the genesis of flapping in pterosaurs and birds. Like their ancestor, Ornitholestes, Microraptor had small, disc-like coracoids that slid like those of most tetrapods with coracoids. Based on the elongation and locking down of coracoids, evidently flapping occurred before forelimb elongation in pterosaurs, afterwards in basalmost birds, like the basal Archaeopteryx specimens. Microraptor was a glider at best, not a flapper, which requires locked-down elongate coracoids.

Figure 4. Subset of the LRT focusing on the theropod-bird transition, distinctly different than in Hartman et al. 2019. Here in a fully resolved cladogram, birds and anchiornithids are monophyletic. Taxon inclusion resolves cladistic issues raised by Hartman et al.

Figure 4. Subset of the LRT focusing on the theropod-bird transition, distinctly different than in Hartman et al. 2019. Here in a fully resolved cladogram, birds and anchiornithids are monophyletic. Taxon inclusion resolves cladistic issues raised by Hartman et al.

I am in the heretical minority
when I say giant azhdarchids and small microraptors were not capable of flight. I report from the evidence, not the feeling, the authority or tradition.


References
O’Connor et al. (six co-authors) 2019. Microraptor with ingested lizard suggests non-specialized digestive function. Current Biology 29, 1–7. https://doi.org/10.1016/j.cub.2019.06.020

This month: 8 years of PterosaurHeresies and ReptileEvolution.com

PterosaurHeresies.Wordpress.com
has been the daily blogpost for additions and changes to ReptileEvolution.com, a growing, illustrated, and sometimes animated online study of vertebrate morphology and interrelationships. This month marks eight years online.

At the core
of this ongoing published (but not peer-reviewed study) is the large reptile tree (LRT, 1540 taxa) and it’s two branching subsets: the large pterosaur tree (LPT, 238 taxa) and the therapsid skull tree (TST, 69 taxa). With every new taxon these three studies become more inclusive, more comprehensive, and better able to nest all included taxa because nearly all possible candidates are tested. The complete gamut is sampled.

Figure 1. Bat embryo wing shape compared to Pterodactylus. Note the ability to fold (relax) the wings until they virtually disappear in both cases. Also note the origin of bat wings paralleling those of pterosaur wings in that during embryology the bat wing also has a narrow chord that more deeply develops long after birth.

Figure 1. Bat embryo wing shape compared to Pterodactylus. Note the ability to fold (relax) the wings until they virtually disappear in both cases. Also note the origin of bat wings paralleling those of pterosaur wings in that during embryology the bat wing also has a narrow chord that more deeply develops long after birth.

Except for a few very incomplete and deletable taxa,
all three trees are fully resolved with high Bootstrap scores (when scored as smaller subsets due to computer limitations). No other comprehensive studies make that claim.

All taxa are illustrated,
often with colors identifying skull bones, overlays and animations—so pertinent data is shown ask if in vivo. No other comprehensive studies provide such a large percentage of reconstructions.

Figure 1. Rorqual evolution from desmostylians, Neoparadoxia, the RBCM specimen of Behemotops, Miocaperea, Eschrichtius and Cetotherium, not to scale.

Figure 1. Rorqual evolution from desmostylians, Neoparadoxia, the RBCM specimen of Behemotops, Miocaperea, Eschrichtius and Cetotherium, not to scale.

Against current paradigms
the three cladograms employ relatively few multi-state characters, too few according to the experts. Plenty enough, however, according to the full resolution results of the LRT. This is an example of one small fact ruining a widely accepted hypothesis.

Similar to every other paleontologist on the planet,
I knew literally nothing about every added taxon. That means no expertise or academic bias was brought to bear on the initial observations. I did not trust previously published cladograms and matrices, as most other paleontologists do. They too often add their taxon to an trusted, untested tree topology, and too often to the ruin of their results.

Figure 2. Eusauropleura to scale with ancestral and descendant taxa including Eucritta, Utegenia, Silvanerpeton and Gephyrostegus, the last common ancestor of all reptiles.

Figure 1. Eusauropleura to scale with ancestral and descendant taxa including Eucritta, Utegenia, Silvanerpeton and Gephyrostegus, the last common ancestor of all reptiles.

Over the last eight years
I have learned about and conveyed to you fresh insights about birds, fish and everything in between. No doubt, tens of thousands of scoring and illustrative errors occurred along the way. I know this because I have made that many corrections over the last eight years… some new ones just yesterday. So, it’s a continuing process. Those who have attempted to dissuade readership several years ago have watched from the sidelines as paradigm-busting discoveries were announced month after month over the past eight years. Several of those discoveries were discovered again years later by academics, confirming the validity of the LRT. I will let you know the first time one of those professors acknowledges the citation omission.

Figure 1. Animation of the mandible of the multituberculate Kryptobaatar showing the sliding of the jaw joint producing separate biting and grinding actions, just like rodents, their closest relatives in the LRT.

Figure 1. Animation of the mandible of the multituberculate Kryptobaatar showing the sliding of the jaw joint producing separate biting and grinding actions, just like rodents, their closest relatives in the LRT.

Published studies
lacking pertinent taxa were criticized. Artists were celebrated. Misidentified bones in reptiles like Yi qi and Ambopteryx where re-identified (see below). Traditions were ignored. Authority was challenged. Data was celebrated.

Figure 1. Ambopteryx nests midway and is phylogenetically midway between the larger Yi and the smaller Scansoriopteryx. None of these taxa have an extra long bone in the arm.

Figure 1. Ambopteryx nests midway and is phylogenetically midway between the larger Yi and the smaller Scansoriopteryx. None of these taxa have an extra long bone in the arm.

First post: July 12, 2011.
The Dinosaur Heresies (Bakker 1986) opened chapter one with the statement, “I remember the first time the thought struck me! ‘There’s something very wrong with our dinosaurs.” In turn, by convergence, I opened with this blogpost with the statement, There is also something very wrong with our pterosaurs. Examining and correcting those errors is the reason for this blog.” Little did I realize there was also something wrong with birds, fish, turtles and many of the major vertebrate clades, almost always due to taxon exclusion. 

Since that first post,
the growing online LRT, LPT and TST have recovered novel interrelationships in bats, whales, mammals, reptiles, creodonts, turtles, snakes, pterosaurs, dinosaurs, archosaurs, archosauriforms, diapsids, anapsids, mesosaurs, synapsids, birds, pre-birds, fish, and dozens more. Use the keyword box to search for your favorites.

Figure 2. Another gap is filled by nesting E. wuyongae between Bunostegos and Elginia at the base of hard shell turtles in the LRT.

Figure 2. Another gap is filled by nesting E. wuyongae between Bunostegos and Elginia at the base of hard shell turtles in the LRT.

Thank you for your readership,
your questions, your comments, your interest in this subject. I have learned so much over the last eight years. Discoveries are fun. I hope this 8-year-long ongoing presentation leads to more focused studies in a data-driven, validated phylogenetic context. And I hope it leads to the rejection of old, invalidated traditions, most of which continue to hang on without evidence, like tail-dragging dinosaurs.

Feathers and fangs: What is Hesperornithoides?

Answer:
Hesperornithoides miessleri (Figs. 1, 2; Late Jurassic, Wyoming, USA; Hartman et al. 2019; WYDICE-DML-001 (formerly WDC DML-001)) is the newest fanged anchiornithid theropod dinosaur to be described, compared and nested (Figs. 3, 4).

From the Hartman et al. abstract
“Limb proportions firmly establish Hesperornithoides as occupying a terrestrial, non-volant lifestyle. Our phylogenetic analysis emphasizes extensive taxonomic sampling and robust character construction, recovering the new taxon most parsimoniously as a troodontid close to Daliansaurus, Xixiasaurus, and Sinusonasus.” [see Figure 3, note: Xixiasaurus is not listed in their cladogram].

“All parsimonious results support the hypothesis that each early paravian clade was plesiomorphically flightless, raising the possibility that avian flight originated as late as the Late Jurassic or Early Cretaceous.” [this is an old hypothesis dating back to the discovery of Late Jurassic Archaeopteryx in the 1860s and it remains a well-established paradigm.]

Figure 1. Published reconstruction of Hesperornithes from Hartman et al. 2019, to scale with Caihong, a similar, though smaller, taxon and Sinusonasus, another sister based on very few bones, but look at that canine fang!

Figure 1. Published reconstruction of Hesperornithes from Hartman et al. 2019, to scale with Caihong, a similar, though smaller, taxon preserved with a complete set of bird-like feathers, and Sinusonasus, another sister based on very few bones, but look at that canine fang!

The cladogram by Hartman et al. 2017
(Fig. 3) is similar to one published by Lefevre et al. 2017 in nesting birds (Avialae) as outgroups to the Dromaeosauridae + Troodontidae, the opposite of the large reptile tree (LRT, 1540 taxa, subset Fig. 4).

Today
we’ll compare the Hartman et al. nesting (Fig. 3) to the one recovered by the LRT (Fig. 4).

Figure 2. Tentative restoration of the skull of Hesperornithes alongside to scale skull of Caihong. The maxillae are similar and both have a distinct fang.

Figure 2. Tentative restoration of the skull of Hesperornithes alongside to scale skull of Caihong. The maxillae are similar and both have a distinct fang.

The Hartman et al. cladogram
(Fig. 3) nested Hesperornithoides with Sinusonasus (IVPP V 11527, Xu and Wang 2004; Early Cretacaceous, Fig. 1), as in the LRT (Fig. 4).

The Hartman et al. cladogram included several taxa not previously included in LRT, 1540 taxa, subset Fig. 4), so I added five to the LRT.

  1. Hesperornithoides (Fig. 1) – sister to Sinusonasus in both cladograms
  2. Sinusonasus (Fig. 1) – sister to Hesperornithoides in both cladograms
  3. Daliansaurus (Fig. 5) – nearby outgroup taxon in both cladograms
  4. Alma (Fig. 6) – more distant outgroup taxon in both cladograms
  5. Protarchaeopteryx (Fig. 7) – primitive oviraptorid in both cladograms
Figure 3. Cladogram published by Hartman et al. 2019, colors added to more or less match those in the subset of the LRT (Fig. 4), a distinctly different topology. Here birds and troodontids/anchirornithids are polypheletic.

Figure 3. Cladogram published by Hartman et al. 2019, colors added to more or less match those in the subset of the LRT (Fig. 4), a distinctly different topology. Here birds and troodontids/anchirornithids are polypheletic.

Issues arise in the Hartman et al. cladogram

  1. Birds arise from the proximal outgroup, Oviraptorosauria
  2. Archaeopteryx is not in the lineage of modern and Cretaceous birds
  3. Anchiornithid troodontids are scattered about
  4. Balaur nests with birds
  5. Microraptors and basal tyrannosaurs nest with dromaeosaurids
  6. The outgroup taxon in figure 3 is: Compsognathus; in the SuppData: Dilophosaurus. Neither is a Triassic theropod.
  7. Running the .nex file results in thousands of MPTs (most parsimonious trees), even when pruned down to well-known, largely articulated taxa. Their phylogenetic analysis included 700 characters (and that means hundreds of less-than-complete taxa) tested against 501 taxa. Changing the outgroup taxon to Sinocalliopteryx resulted in far fewer MPTs, but see here for more validated outgroup taxa. Hartman et al. reported, “The analysis resulted in >99999 most parsimonious trees.” Essentially useless… and they knew that attempting to publish their report.
Figure 4. Subset of the LRT focusing on the theropod-bird transition, distinctly different than in Hartman et al. 2019. Here in a fully resolved cladogram, birds and anchiornithids are monophyletic. Taxon inclusion resolves cladistic issues raised by Hartman et al.

Figure 4. Subset of the LRT focusing on the theropod-bird transition, distinctly different than in Hartman et al. 2019. Here in a fully resolved cladogram, birds and anchiornithids are monophyletic. Taxon inclusion resolves cladistic issues raised by Hartman et al.

By contrast,
in the LRT (Fig. 4):

  1. The cladogram is fully resolved (1 MPT).
  2. Birds, including Archaeopteryx and 12 other Solnhofen bird-like taxa arise from anchiornithids, which arise from troodontids (including dromaeosaurids), which arise from Ornitholestes and kin, which arise from the CNJ79 specimen attributed to Compsognathus and kin (including therzinosaurs + oviraptorids), which arises from the holotype Compsognathus and kin (including ornithomimosaurs and tyrannosaurs).
  3. Double killler-clawed Balaur nests with Velociraptor, not with birds.
  4. The outgroup taxa in the LRT include the Triassic dinosaurs, Herrerasaurus, Tawa and a long list going back to Silurian jawless fish.
  5. Hesperornithoides (Fig. 1) and Sinusonasus (Fig. 1) nest with another anchiornithid with fewer teeth and one elongated canine, Caihong (Fig. 1) and a long list of other shared traits. Caihong has a full set of bird-like feathers, so less well-preserved Hesperornithoides likely shared this trait. Caihong nests closer to Archaeopteryx in the Hartman et al. cladogram.
Figure 6. Daliansaurus reconstructed from the original tracing.

Figure 5. Daliansaurus reconstructed from the original tracing. In the Hartman et al. cladogram, this taxon nests close to Hesperornithoides. In the LRT it nests at the base of the Hesperornithes clade.

A few suggestions for Hartman et al. 2019

  1. Build your tree with fewer, but more complete taxa in order to achieve full resolution
  2. Choose a plesiomorphic Triassic theropod or dinosaur outgroup for your outgroup
  3. Practice more precision in your reconstructions. Do not freehand anything. Do not add bones where bones are not known.
  4. Try not to borrow cladograms (like the TWiG dataset) from others, but build your own, especially when the results are so demonstrably poor (>99,999 MPTs)
  5. Include both Compsognathus specimens. They are different from one another and, apparently, key to understanding interrelationships.
  6. Include as many of the 13 Solnhofen birds and pre-birds that you can and show reconstructions so we know you understand the materials. Checking individual scores is like going to Indiana Jones’ government warehouse. Note how the Solnhofen birds split apart and nest at the bases of all the derived bird clades in the LRT (Fig. 4).
FIgure 5. Alma reconstructed and restored (gray).

FIgure 6. Alma reconstructed and restored (gray).

Hartman et al. report, 
“We follow the advice of Jenner (2004) that authors should attempt to include all previously proposed characters and terminal taxa, while explicitly justifying omissions. To this end we have attempted to include every character from all TWiG papers published through 2012, with the goal to continually add characters.”

As their results demonstrate, such efforts are a waste of time.
Pertinent taxa and suitable outgroup taxa were overlooked. The goal is full resolution and understanding. If incomplete taxa and too many characters prevent you from reaching this goal, start pruning, or start digging into the data. There is only one tree topology in Deep Time. Our job is to find it.

Figure 9. Protarchaeopteryx traced in situ, reconstructed a bit and the skull of Incisivosaurus for comparison.

Figure 7. Protarchaeopteryx traced in situ, reconstructed a bit and the skull of Incisivosaurus for comparison. This taxon nests with oviraptorids in both cladograms, basal to Archaeopteryx and birds in Hartman et al. 2019. Not sure if that is all the tail there is, or if more is buried or missing. Probably the latter, according to phylogenetic bracketing.

I sincerely hope this review of Hartman et al. 2019
is helpful. The LRT confirms their nesting of Hesperornithoides with Sinusonasus. Outside of that the two cladograms diverge radically and only one of these two competing cladograms is fully resolved with a gradual accumulation of traits at every node.


References
Hartman S, Mortimer M, Wahl WR, Lomax DR, Lippincott J and Lovelace DM 2019. A new paravian dinosaur from the Late Jurassic of North America supports a late acquisition of avian flight. PeerJ 7:e7247 DOI 10.7717/peerj.7247
Lefèvre U, Cau A, Cincotta A,  Hu D-Y, Chinsamy A,Escuillié F and Godefroit P 2017. A new Jurassic theropod from China documents a transitional step in the macrostructure of feathers. The Science of Nature, 104: 74 (advance online publication). doi:10.1007/s00114-017-1496-y
Xu X and Wang X-l 2004. A New Troodontid (Theropoda: Troodontidae) from the Lower Cretaceous Yixian Formation of Western Liaoning, China”. Acta Geologica Sinica 78(1): 22-26.

wiki/Sinusonasus
wiki/Troodontidae
wiki/Hesperornithoides
wiki/Xixiasaurus
wiki/Anchiornthidae
wiki/Origin_of_birds

The other clade descending from speedy jacks includes slower eels and anglers

Earlier, and with fewer taxa,
the large reptile tree (LRT, 1535 taxa, subset Fig. 1) nested European eels (Anguilla) with pikes (Esox) and barracuda (Sphyraena). With the addition of new taxa the transitions between the earlier forms become smoother, easier to understand and more complete.

Figure 1. Subset of the LRT focusing on basal vertebrates (fish) and the clade that gave rise to eels and frogfish.

Figure 1. Subset of the LRT focusing on basal vertebrates (fish) and the clade that gave rise to eels and frogfish.

You might ALSO remember,
earlier we looked at a species of amberjack, Seriola rivoliana, which nests basal to pufferfish, molas, triggerfish and mudskippers. Another species of speedy Seriola (Fig. 2) is the focus of today’s blogpost.

Figure 2. Seriola zonata, the banded rudder fish, is basal to cusk eels and frogfish in the LRT.

Figure 2. Seriola zonata, the banded rudder fish, is basal to cusk eels and frogfish in the LRT.

Today, with additional taxa
European eels are moved away from pikes with intervening, transitional taxa, including a second species of amberjack, the banded rudder fish, Seriola zonata (Valenciennnes 1833). In the LRT S. zonata is basal to eels, frogfish, anglers, knife fish and electric eels (Fig. 1). Notably, none of these derived taxa are speedy, open-water predators distinct from S. zonata. Aparently all derived taxa have slower lifestyles and thus many became bottom dwellers. Note the almost identical skulls shown in figures 2 and 3, despite their postcranial differences.

Seriola zonata (Valenciennnes 1833; commonly 50cm, up to 75cm) is the extant banded rudderfish. Here it nests basal to the European eel (Fig. 4) and cusk eel (Fig. 3). Large individuals (over 10 inches) have no bands. This fish, though commonly caught, is rarely identified. Large ones, with a raccoon-stripe on the eye and an iridescent gold stripe on the side, are usually called amberjacks when caught, and juveniles are called pilotfish.

Figure 3. Dicrolene, the cusk eel, nests close to S. rivoliana in the LRT.

Figure 3. Dicrolene, the cusk eel, nests close to S. rivoliana in the LRT.

Dicrolene nigracaudis (Goode and Bean 1883, Alcock 1899, Dicrolene introniger shown below) is a rare species of deep sea cusk eel, family Ophidiiformes. Distinct from true eels, cusk eels have pelvic fins transformed into barbels below the pectoral fins. The lower half of each long pectoral fin is transformed into a set of bottom feeling rays.

European eels
are longer-skulled versions of cusk eels in the LRT.

 

Figure 2. The skull of Anguilla from Gregory 1936, with bones colored here and matched to an invivo photo. This is a revised illustration.

Figure 5. The skull of Anguilla from Gregory 1936, with bones colored here and matched to an invivo photo. This is a revised illustration.

Anguilla anguilla (Linneaus 1758; up to 80cm in length, 1.5 exceptionally) is the extant European eel, a sister to the cusk eel in the LRT. Like DicroleneAnguillal acks several facial bones, pelvic fins and the tail has reverted to a straight tail. The life cycle includes breeding and young hatching in the mid-Atlantic with migration back to European rivers before the adults return to the mid-Atlantic. Bones are relabeled here based on sister taxa.

This appears to be a novel hypothesis of interrelationships
that links previously unlinked taxa. If I missed a citation that predates this one that supports this hypothesis of interrelationships, please send me the citation.

Figure 4. Antennarius, the frogfish, nests basal to anglerfish, derived from S. rivoliana.

Figure 4. Antennarius, the frogfish, nests basal to anglerfish, derived from S. rivoliana.

Antennarius sp. (Daudin 1816) is the extant frogfish, a bottom-dwelling sit-and-wait predator with a lure and an enormous gape. The pelvic fins are anterior to the pectoral fins. Both are used to walk on the sea floor. Note the separation of the parietals by the postparietals. Although Antennarius superficially resembles an angler, it is as sister to Seriola zonata (above).

Earlier we looked at the connection between the remaining clade members: anglers, cave fish and electric eels.

Figure 7. Lophius, the anglerfish, nests between frogfish and electric eels in the LRT.

Figure 5. Lophius, the anglerfish, nests between frogfish and electric eels in the LRT.

Lophius americanus (Rafinesque 1810; up to 1.5m in length) is the extant goosefish or monkfish. The closest relative in the LRT is the electric eel, Electrophorus. The pelvic fins are small and anteroventral to the pectoral fins.

The LRT continues to bring diverse clades of fish together,
reducing the number of clades and illuminating interrelationships.

Figure 5. Skull of the electric eel (Electrophorus) distinct from the moray eel (Fig. 4) and European eel (Fig. 2).

Figure 6. Skull of the electric eel (Electrophorus) distinct from the moray eel (Fig. 4) and European eel (Fig. 2).

Electrophorus electricus (originally Gymnotus electricus, Linneaus 1766; Gill 1864; up to 2m in length) is the extant electric eel, an obligate air breather nesting between Lophius and Gymnotus (Fig. 7). Electric organs that deliver shocks to enemies and prey make up 80% of the body.

Figure 6. Gymnotus, the knife fish.

Figure 7. Gymnotus, the knife fish.

Gymnotus carapo (Linneaus 1758; up to 100cm in length) is the extant banded knifefish, a nocturnal small prey predator with essentially no dorsal, caudal or pelvic fins. The anal fin undulates for slow propulsion. The electric signal is weak.

Figure 8. Skull of Gymnotus.

Figure 8. Skull of Gymnotus.

I never knew fish could be so fascinating.
And I never thought I would be among the first to employ phylogenetic skeletal traits to recover this branch of the tree of life. There has been too much dependence on gene studies, which likewise don’t produce a gradual accumulation of derived traits for all sister taxa for other vertebrate clades over deep time. Soon we will take a look at the differences between a genomic fish tree and a phenomic fish tree. You’ll see.


References
Alcock AW 1899. A descriptive catalogue of the Indian deep-sea fishes in the Indian Museum. International Publisher, USA 87 pp.
Cubelio SS, Joseph J, Venu S, Deepu AV and Kurup BM 2009. Redescription of Dicrolene nigracaudis (Alcock, 1899) a rare species of deep sea cusk eel (Ophidiiformes; Ophidiidae) from Indian EEZ. Indian Journal of Marine Sciences 38(2):166–169.
Daudin FM 1816. Antennarius. In: Dictionaire des sciences naturelles.
Goode GB and Bean TH 1883. Reports on the results of dredging under the supervision of Alexander Agassiz, on the east coast of the United States, during the summer of 1880, by the U. S. coast survey steamer Blake, C, Bulletin of the Museum of Comparative Zoology at Harvard College 10 (5), pp. 183-226: 202 .
Linnaeus C von 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Valenciennnes A in Cuvier G and Valenciennes A 1833. Histoire naturelle des poissons. Tome neuvième. Suite du livre neuvième. Des Scombéroïdes. 9: i-xxix + 3 pp. + 1-512. Pls. 246-279.,

wiki/Seriola
wiki/Amberjack
wiki/Antennarius

wiki/Cusk-eels
wiki/Dicrolene
wiki/European_eel