Megachirella: Not at the origin of squamates. Lacertulus is older.

We looked at Lacertulus and the origin of the Squamata in the Late Permian
here in October 2011.

We looked at the splitting of the Tritosauria from the Protosquamata
here in December 2014.

Siimòes et al. 2018
proposed to nest Megachirella watchtleri (Fig. 1) at the origin of squamates in the Middle Triassic, 75 million years earlier than the previously known oldest squamate fossils. They reported, “For the first time, to our knowledge, morphological and molecular data are in agreement regarding early squamate evolution, with geckoes—and not iguanians—as the earliest crown clade squamates. Divergence time estimates using relaxed combined morphological and molecular clocks show that lepidosaurs and most other diapsids originated before the Permian/Triassic extinction event, indicating that the Triassic was a period of radiation, not origin, for several diapsid lineages.”

Figure 1. New µCT scans of Megachirella from Simoes et al. 2018.

Figure 1. New µCT scans of Megachirella from Simoes et al. 2018.

Unfortunately
|they did not include relevant taxa. According to the large reptile tree (LRT, 1224 taxa, www.reptileevolution.com/reptile-tree.htm) Megachirella nests at the base of the Rhynchocephalia (= Sphenodontia) along with Pleurosaurus (excluded from the Simoes team study) when many more relevant taxa are included.

Figure 2. Megachirella nests in the middle of this cladogram, that also nests turtles between rib gliders and choristoderes.

Figure 2. Megachirella nests in the middle of this cladogram, that also nests turtles between rib gliders and choristoderes.

 

Lacertulus is older (Late Permian) and more directly related to squamates.

FIgure 2. Megachirella (Renesto and Posenato 2003) is a sister to the BSRUG diapsid.

FIgure 3. Megachirella (Renesto and Posenato 2003) is a sister to the BSRUG diapsid and reconstructed here.

Nesting turtles with rib gliders
(Coelurosauravus) only hints at major flaws in the Simoes et al. cladogram topology. Nesting Sophineta and Palaegama close to and basal to Megachirella confirms findings made years earlier by the LRT. Marmoretta is also close, but nests within the Rhynchocephalia in the LRT.

Figure 2. Pleurosaurus and Palaeopleurosaurus skulls compared to those of sister taxa.

Figure 2. Pleurosaurus and Palaeopleurosaurus skulls compared to those of sister taxa.

Tijubina (which Simoes redescribed in 2012) is also missing from the Simoes et al. 2018 study.

Figure 1. Palaegama is basal to Coelurosauravus ('rib' gliders), Megachirella (rhynchocephalians), Lacertulus (protosquamates) and Tijubina (tritosaurs)

Figure 5. Palaegama is basal to Coelurosauravus (‘rib’ gliders), Megachirella (rhynchocephalians), Lacertulus (protosquamates) and Tijubina (tritosaurs)

 

 

References
Simòes T, and 8 co-authors 2018. The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps. Nature 557: 706â709 (2018)

Publicity
https://www.livescience.com/62693-mother-of-lizards-fossil.html

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Elgin 2014 PhD dissertation: nits and picks, part 2

Yesterday we looked at
a misidentified pterosaur specimen from the State Museum of Natural History Karlsruhe (SMNK) that wasn’t a Tupuxuara, as originally considered by then PhD candidate, now Dr. Ross Elgin. Consider that blogpost an unlabeled part 1.

Today, in part 2,
we’ll take a look at several other aspects of the Ross Elgin 2014 PhD dissertation that deserve credit and discredit. 

FIgure 1. GIF animation of image from Elgin 2014 comparing wing membrane configurations and a more accurate rendition of what Peters 2002 proposed. See text for list of issues here.

FIgure 1. GIF animation of image from Elgin 2014 comparing wing membrane configurations and a more accurate rendition of what Peters 2002 proposed and Elgin distorted. See text for list of issues here. In reality, like birds, the wings and hind limbs are decoupled. Most pterosaur workers don’t believe the data.

Elgin mistakenly reported,
“The primary flight membrane is reconstructed with an ankle attachment of the trailing edge, a configuration that was never fundamentally altered throughout the evolutionary history of the group.” Elgin ignored the bipedal origin of the Pterosauria, and ignored the narrow-chord wing membrane data that attends every pterosaur fossil that preserves wing membranes, perhaps on the advice of his mentors. And he ignored, or distorted, what Peters 2000 actually proposed for a wing membrane and bone orientation in pterosaurs (Fig. 1).  This may be what happens when you have to feed the fever dreams of a teacher rather than recording actual data. Elgin reported, “I am indebted to both David Hone and Eberhard “Dino” Frey for the opportunity to undertake this project and continue my work on the enigmatic and curious group of animals known as pterosaurs.”

Solutions to problems with Figure 1.

  1. The scapula/coracoid should rotate laterally, as in all articulated fossils
  2. The elbow should angle further posteriorly, as in all articulated fossils (+ in birds and bats)
  3. The pteroid should point to the deltopectoral crest, as in all articulated fossils
  4. The free fingers should point ventrally (in flight). Crushing typically rotates the narrow claws anteriorly.
  5. Metacarpals 1-3 should line up anteriorly, not stack themselves against mc4
  6. Manual 4.4 should articulate at an angle to m4.3, deepening the wing tip
  7. The propatagium should extend only to the deltopectoral crest
  8. The brachiopatagium should stretch between the wingtip and elbow with a fuselage fillet to distal thigh, as in all articulated fossils
  9. The thigh should be more meaty based on the long anterior ilium
  10. The femur should extend laterally to form a horizontal stabilizer (and note the sprawling lepidosaur orientation!)
  11. The femur should be flipped, as shown in Elgin’s figure 3 below.
  12. The uropatagia do not extend to the tiny tail, as in all articulated fossils. Elgin’s essentially creates a single uropatagium, which is a decades-old false paradigm.

If the above illustration by Elgin 2014 looks familiar
it’s because we looked at it earlier here, after publication of Elgin, Hone and Frey 2011. Also check out all the images on this ReptileEvolution page. You might remember these authors employed the fiction of ‘wing membrane shrinkage’ to explain the data, instead of just accepting the data, as is. We have evidence of pterosaur ancestors with wings decoupled from the hind limbs, so there was never a gliding transitional phase. Flapping preceded flying.

Along the same lines
Hone and Benton (2007, 2008); and Nesbitt and Hone (2010a, b) preferred to see things their own way, rather than strict adherence to the data. So, maybe young Elgin was unduly influenced by his professors and mentors.

Elgin introduced us to
Microtuban altivolan, which he described as a non-azhdarchid azhdarchoid. In the large pterosaur tree (LPT, 1189 taxa) Microtuban indeed nests at the base of the azhdarchid clade, arising from certain dorygnathids, a relationship Elgin never tested.

Elgin suggested a possible sexual dimorphism,
“where the pelvic girdle lacks a symphysis and remains open even in large adults is observed within Coloborhynchus robustus.” (Fig. 2) Let’s blame this one partly on his teachers, and partly on sloppiness. The base of the pterosaur pelvis opens and closes in phylogenetic patterns, not gender patterns. That tricked up Bennett, too, and Elgin’s teachers followed Bennett’s mistakes. On the sloppiness point, the open pelvis of C. robustus is missing its ventral and posterior borders, exactly the bones needed to join the ischia together (Fig. 2). It doesn’t look like Elgin was cheating. He must have thought he was not cheating. But he was cheating by changing points of view, changing scales and not adding back missing bone to follow generic patterns. This was all resolved with a little tracing in Adobe Photoshop, the paleontologists’ best friend.

Figure 1. Elgin compared these two Coloborhynchus pelves together, but failed to align them, scale them and add back missing bone.

Figure 2. Elgin compared these two Coloborhynchus pelves together, but failed to align them, scale them and add back missing bone.

Elgin was also tricked by
traditional archosaur patterns and paradigms in ontogeny. He expected sutures to close at adulthood. This tricked up Bennett, too. Instead, since pterosaurs are lepidosaurs, sometimes they do, sometimes they never do, and sometimes they fuse sutures before maturity and reading their final size. It’s all phylogenetic, not ontogenetic with lepidosaurs, including pterosaurs.

Figure 2. Coloborhynchus robustus (bones and outlines from Elgin 2014) compared to C. spielbergi (b&w). Notes added.

Figure 3. Coloborhynchus robustus (bones and outlines from Elgin 2014) compared to C. spielbergi (b&w). Notes added.

Elgin described and did not illustrate the missing wing finger:
“The wing finger phalanges in almost all pterosaurs are similar in form with expanded proximal and distal margins, the shafts of which show various degrees of curvature. Those preserved in SMNK PAL 1133 are not exception and agree well with other descriptions of pterodactyloids.” This description can only be the result of naiveté and inexperience. In reality phalanx proportions change between genera and species. It would have been helpful to see the wing finger of C. robustus since the C. spielbergi wing finger is missing.

Elgin 2014 mistakenly considered

  1. pterosaurs to be archosauromorphs.
  2. anurognathids to be basal pterodactyloids
  3. Darwinopterus to be ‘an animal intermediate’ linking basal to derived pterosaurs

These issues are resolved and settled
here and here when you add more taxa. It’s good for science to be critical. If nothing else this blog will hopefully show all readers that published scientific text and figures can sometimes include errors that can be exposed and corrected by colleagues.

It’s not okay
to disfigure the figures of other workers and then claim that’s the essence of their work (contra Fig. 1). We’ve seen this before with other PhDs.

References
Elgin RA, Hone DWE and Frey E 2011. The extent of the pterosaur flight membrane. Acta Palaeontologica Polonica 56 (1), 2011: 99-111. doi: 10.4202/app.2009.0145
Elgin RA 2014. Palaeobiology, Morphology, and Flight Characteristics of Pterodactyloid Pterosaurs. Innaugural Dissertation. Zur Erlangung der Doktorwürde Fakultät für Chemie und Geowissenschaften Institut für Geowissenschaften Ruprecht-Karls-Universität Heidelberg. Available online  here.
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 and Hone DWE 2010a. An external mandibular fenestra and other archosauriform character states in basal pterosaurs. Palaeodiversity 3: 225–233
Nesbitt SJ and Hone DWE 2010b. An external mandibular fenestra and other archosauriform character states in basal pterosaurs. Palaeodiversity 3: 225–233

https://pterosaurheresies.wordpress.com/2012/04/13/a-supertree-of-pterosaur-origins-hone-and-benton-2007-2009/

http://www.reptileevolution.com/pterosaur-wings.htm

https://pterosaurheresies.wordpress.com/2011/11/18/did-dimorphodon-have-an-external-mandibular-fenestra/

https://pterosaurheresies.wordpress.com/2013/01/16/a-closer-look-at-the-antorbital-fossa-in-two-pterosaurs-raeticodactylus-and-dimorphodon/

E. O. Wilson: Advice for young scientists

Readers of this blogpost will appreciate
what the ‘Ant Man’ E. O. Wilson has to say to budding scientists. Click the image to play.

Wilson’s principles:

  1. Find a field which interests you deeply and focus on that.
  2. A certain level of a subject (e.g. mathematics) is already enough to achieve excellence.
  3. March away from the sound of the guns. (don’t enter the fray, create your own fray)
  4. The more difficult the problem; the greater will be the importance of the solution

One of the responders wrote:
“One thing I would say to any scientist – including young scientists – is to avoid dogma. Scientists these days are guilty of things that they sometimes accuse religious people of, and that is making speculations and passing them as fact. If you have a hypothesis or claim, prove it! Write a paper detailing your methodology, describe your results and put forward your conclusion. Then let the reader come to his or her own conclusion whether your hypothesis has any merit.”

Once a children’s book, now an academic paper on PeerJ.

The children’s book,
GIANTS of Land, Sea & Air – Past & Present (Fig. 1 PDF) came out in 1986 and featured all of the largest animals to scale on dozens of pages alongside humans for scale.

Figure 1. The cover of Giants, the book that launched my adult interest in dinosaurs, pterosaurs and everything inbetween.

Figure 1. The cover of Giants, the book that launched my adult interest in dinosaurs, pterosaurs and everything inbetween.

The PeerJ online academic paper
(McClain et al. 2015) featured many of the same sea creatures and many more (Fig. 2) to scale with a human swimming alongside. Lacking are any of the terrestrial, aerial and prehistoric creatures you’ll find in GIANTS.

Figure 2. Poster turned on end illustrating the largest creatures in the sea to scale from McClain et al. 2015,

Figure 2. Poster turned on end illustrating the largest creatures in the sea to scale from McClain et al. 2015,

Sorry I didn’t see this online paper when it first came out a few years ago. 
It just came to my attention today. I suppose the inspiration was by convergence, but 1986 was long enough ago that a 10-year-old reader then would have been close to forty in 2015.

PS.
I just got a thumb’s down from the PeerJ voters for wondering if any of the authors were aware of the earlier children’s book. First bad review I’ve had! Or was I not supposed to mention it at PeerJ?

References
McClain et al. (15 co-authors) 2015. Sizing ocean giants: patterns of intraspecific size variation in marine megafauna. PeerJ 3:e715; DOI 10.7717/peerj.715

The soft underbelly of a phylogenetic analysis

Here’s another rejection letter
that sees things the way the editors want to see it, not the way things need to be seen. I post these reviews and replies because someday you may want to publish a paper yourself and you need to see what editors are willing to say and do to keep, in this case, the origin of pterosaurs a mystery, and to keep amateurs from embarrassing the academic community by reporting that all they need do is add a few more relevant taxa.

Associate Editor Comments:

The intro: “The manuscript argues for a hypothesis that places Longisquama, Sharovipteryx, Cosesaurus, and a small number of other taxa as being especially closely related to pterosaurs, with their respective morphologies informing the long sought-after origin of characteristic pterosaur traits. The manuscript quite correctly identifies its preferred hypothesis as a minority viewpoint, lamenting the fact that its previous versions continue to be widely ignored by other pterosaur and archosaur workers. The hypothesis is based on a phylogenetic analysis of 231 multistate characters and 1090 taxa — from which the tree topology of 24 taxa relevant to the arguments of the paper were figured and discussed. The results of the entire analysis are available only on the author’s website and to my knowledge have never been published in a peer-reviewed platform.” That will change when one editor and one reviewer let the work see publication, but apparently not on this editor’s watch. 

Where the teeth are bared: “It is an understatement to say that these results differ significantly from those of other studies, with every major reptile clade, as typically recognized, being extensively paraphyletic.” All clades presented in the LRT are monophyletic and fully resolved. This editor is working from an old textbook. Taxon exclusion led to errors in prior studies. This can be readily checked by simply adding taxa and checking that all taxa document a gradual accumulation of derived traits in competing cladograms. That’s why the large reptile tree is so large, to minimize taxon exclusion problems that plague smaller studies. 

There is only one way to get published: “The author states that his character matrix is not really drawn from existing studies but rather was “largely built from scratch.” One could interpret this as an admirable attempt to shed the existing assumptions that burden other studies, but ultimately this hypothesis will never overturn existing paradigms until it demonstrates that it better explains the totality of the existing data. This study certainly does not do that. Simply disregarding a large percentage of the characters that the larger community of workers has decided are important for resolving reptile phylogeny in favor of those the author deems relevant is never going to accomplish this goal.” See below.

Sidenote: “The criticisms of the author’s approach by Hone and Benton 2007 still appear to be relevant – at least they have never been directly addressed, nor are they addressed in this manuscript.” Yes, they are. Hone and Benton excluded the fenestrasaur taxa that overturn the pterosaur origin question in Peters 2000, after promising to test them. Why is every paleo colleague afraid of Cosesaurus (the subject of the submitted manuscript)?

Case closed: “Until the author explicitly demonstrates why the characters he omits should not be included or how adding taxa and characters to an existing matrix, such as that found in the Nesbitt (2011) study, produces the promoted tree topology, I cannot recommend publishing this work or sending it out for further review.”  Problem 1: Nesbitt’s 2011 paper was on archosauriforms. Pterosaurs were thrown into that study, but they are not archosauriforms, as documented 11 years earlier. Problem 2: Adding taxa or characters to an existing matrix assumes the existing matrix is faultless. It is not. Nesbitt 2011 suffers from some inappropriate taxon inclusion and a great deal of taxon exclusion, along with some bad scoring that we looked at in a nine-part series ending here. Problem 3: Peters 2000 added taxa to four prior phylogenetic analyses and recovered the same results each time. None of those four were built on prior analyses. Now let’s move forward 11 years. Why was Nesbitt 2011 published when it mentioned, but did not include relevant taxa reported by Peters 2000? Editors and referees let that pass. Why? Have the rules changed?

Evidently it matters who the author is, and how well they are connected in the academic community, not how well a project is researched.

Editors and referees are only human. They have an agenda and a world view, like everyone does. They see what they want to see, comment on what they want to comment on and maintain whatever status quo they currently follow. How do we know this in this case? Note how little was said in this review (not one sentence) about the new pterosaur traits found in Cosesaurus, which formed the subject of this paper.

My reply:

Dear [Editors]:

Thank you for your kind reply and review.

Ultimately the number of characters or their publication history means little, since one set of two hundred characters will result in the same tree topology as another set of two hundred characters. The character list is the soft underbelly of any analysis, the part editors and reviewers go to when they cannot argue against the demonstrated gradual accumulation of derived traits shown by the included taxa, universally excluded from other studies that include pterosaurs. 

Maintaining the majority view will only keep the origin of pterosaurs in the dark. 

Best regards,

References
Nesbitt SJ 2011. The early evolution of archosaurs: relationships and the origin of major clades. Bulletin of the American Museum of Natural History 352: 292 pp.
Peters D 2000b. A reexamination of four prolacertiforms with implications for pterosaur phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106: 293–336.

Happy Holidays, Everyone!

I wish you all the best!
Here at the David Peters Studio I have not kept up with my usual one-a-day posts (and feeling guilty about it). Having already covered just about every clade out there, I’m reduced to commenting about the paleo news as it comes out and rechecking all the links and data at ReptileEvolution.com, which this blog post supports.

I’ve also managed to squeeze out
a few papers. Digging deeper into various subjects always brings up some dirt and some gold. There’s no reward in publishing a paper, other than the personal satisfaction in knowing you’ve shed a little light on the dark corners of a subject.

It’s important for all of us to be life-long learners.

Thank you
for your readership.

Would you like to read a rejection notice, or two?

In the past week
I submitted a comment to Royal Society Proceeedings B on Foth and Joyce 2017. In it I suggested that the origin of turtles was diphyletic and that would affect the placement of the basalmost turtle in the work of Foth and Joyce.

Referee number 1 wrote:
“This paper is unsuitable for Proceedings B (or any scientific journal) and should be rejected. It is ostensibly a response to a recent paper by Foth & Joyce on the disparity of the turtle skull over time, but in reality it doesn’t address this study at all, but is a back-handed attempt by the author to publish an iconoclastic phylogenetic analysis based on an inadequate dataset riddled with errors and methodological flaws. Sorry, there is no way to be kind about this manuscript.”

Referee number 2 (Walter Joyce, one of the original authors) wrote:
“the attached manuscript by David Peters is a response to an article I published earlier this year with Christian Foth in Proceedings B regarding the evolution of cranial disparity in turtles (Foth and Joyce 2017). Although I welcome any scientific debate regarding this paper, I would like to suggest outright rejecting this contribution for one single reason: It is an open trade secret that David Peters has been developing an enormous phylogeny of reptiles that produces highly outlandish results. One such outlandish result is the polyphyletic origin of turtles. This undertaking has been submitted to many journals over the years and has been rejected every time, as basic tenants of sound cladistic analysis are not followed therein, mostly an adherence to the use of character observations that can be reproduced by people who are not David Peters. I am certain that countless scientists invested countless hours in providing sound arguments why this tree should be rejected and I will therefore save myself the work here. If anything, this phylogeny should receive full peer review in a standalone publication, and not be slipped into the sphere of published scientific literature as part of a not-quite appropriate criticism of Foth and Joyce (2017).”

And here is my reply to the editors:
“Critical thinking is a requirement in science and I’ve had a few hours now to critically think about the replies I received from the two referees. I hope these comments will help you in future endeavors.

1. You already know that referees should be unbiased when they approach a manuscript. Asking Dr. Joyce to be a referee runs counter to that ideal. After all, I was commenting on his paper. His comments should have been requested only after two unbiased referees had ok’d the manuscript for publication.

2. Some referees like to accept manuscripts knowing ahead of time they will reject them. Is there any method you use to prevent this?

3. Whenever I review a manuscript I review some of the details within the manuscript, pointing out errors, if any, congratulating insights, if any. This was not done by either referee. There is no indication that either referee actually read the manuscript, let alone tested the hypotheses that resulted with the matrix provided.

4. The paper was about taxon exclusion. Foth and Joyce excluded taxa pertinent to the origin of turtles, which affected their basalmost taxon and the rest of their phylogram. That point was ignored by both referees who described ‘an inadequate data set’ (did they actually see the dataset, or go by rumors?). No specifics were put forth. No testing of the analysis was described. That’s what I do in such cases. I run the matrix looking for mismatches. Anyone who has the same taxon list, no matter what their character list, will come to the same results as I did, unless they omit certain pertinent taxa, as Foth and Joyce did.

5. Joyce wrote: “It is an open trade secret that David Peters has been developing an enormous phylogeny of reptiles that produces highly outlandish results.”

To that point, many results of my studies follow traditional topologies: birds nest with birds, turtles with turtles, etc. When topologies shift it is virtually always because the large size of the cladogram allows taxa that have not been tested together to be tested together. That the results upset untested traditions and paradigms are THE reason why this work should be published. The origin of turtles could have been known for the last fifty years. I just included taxa that were previously excluded.

Joyce may be upset because i pointed out this oversight, after all the hours he put into his project. That’s never welcome news, especially when that correction comes from someone without a PhD. It is potentially embarassing. Nevertheless, even if the hypotheses comes from an obscure patent clerk, this is how we build our science. The present facts should be central to the case, not any disparaging rumors about the scientist.

The data presented has to be good. Otherwise there is no way for the cladogram to have high Bootstrap scores throughout. The software is unbiased with regard to output. Unfortunately, pride, shame and other emotions are involved here when it comes to the referees. Some don’t like change.

Thank you for reading this. I don’t ask for any revision to the status of my manuscript, only that you review your policies so bias does not influence the next few incoming manuscripts.

Best regards,”