Andrea Cau 2019 is critical of the LRT

Google translated from Theropoda.blogspot.com March 2019
This just came to my attention, two years after publication by Andrea Cau, PhD. Unfortunately I can’t give credit to the reader who sent me an email with this link because he or she operates under a pseudonym.

“The “The Pterosaur Heresies” site constitutes a sort of “permanent spam” for anyone who wants to search for information and images online relating to fossil amniotes. The author of the site, David Peters, has for years been proposing his own personal and idiosyncratic systematic of tetrapods, which he divulges online through his site, and which is illustrated with a large cladogram having over a thousand taxa included, but which, for today, it has never been published in the technical literature nor is it replicable in any way by third parties, since the author has never published a list of characters or a matrix.”

This is a false statement. Since this online experiment is an ongoing project, taxa and characters are often added on a daily to weekly basis. Scores are changed as experience with new taxa grows. Even so the MacClade matrix (which I have been working with for the past ten years) has always been available by request by clicking on the yellow .nex icon on the webpage that includes the large reptile tree (LRT). Many interested parties have done so over the years.

“Therefore, the phylogeny proposed by Peters is not testable and therefore it is not science, but pseudoscience.”

No. Anyone can test it at any time.

Added a day later: I requested Cau’s .nex file in order to test it. That request was denied this morning. Therefore, ironically, the phylogeny proposed by Cau “is not testable” and quoting Cau himself, “therefore it is not science.” I wouldn’t call it pseudoscience. That would be inappropriate.

“Instead of playing honestly like all of us paleontologists who submit our hypotheses to peer-reviewed scientific journals, Peters is all about rhetoric to self-confirm his own personal scenario of reptilian evolution.”

Not exactly. I have submitted manuscripts to several peer-reviewed academic journals. Nature, Science, Journal of Vertebrate Paleontology, Ichnos, Historical Biology and several other journals (list online here with abstracts) have published my manuscripts over the years.

Added a day later: I report results recovered from software that phylogenetically analyzes input taxa, characters and scores. There is no personal scenario here. I report results, hoping that someday others will duplicate taxon lists. Many have done so. Click here for that list.

“One of Peters’ rhetorical claims is that taxonomic sampling is sufficient to produce a “valid phylogeny”, that is, backing his rhetoric on all other authors, that his phylogeny is the best because it includes a thousand species, against those of other researchers who rarely exceed the hundreds of species analyzed.”

Not exactly. Due to the wide gamut of the taxa included in the LRT, I am often able to indicate a problem in smaller studies that pertinent taxa have been excluded, or irrelevant taxa have been included. Cau’s editorial is either not well researched, because it omits important facts, or it is colored by a rather common irritation that an amateur is pointing out errors of omission in the work of professionals and PhDs.

“The reason why Peters’ phylogeny contains thousands of species is that the list of traits he claims to analyze is very short, with a low number of items analyzed, less than 300. This makes the result of his analyzes extremely doubtful, given that it is extremely unlikely that with not even 300 characters spread over 1000 species, we can have a tree that is completely resolved and devoid of unstable areas.”

Not exactly. The character list is only 235. The fact that each character is multi-state (often up to 10 states) multiplies the efficacy by several magnitudes. The fact is the LRT continues to be able to lump and separate taxa. That’s a fact. The only weakness is my lack of experience with the data and taxa that are added and added and added. Heck, it even works with fish when their bones are provided with tetrapod homologs. Importantly I tend to avoid taxa represented by just a few bones.

“I say this from experience, given that in 15 years I have assembled a matrix of theropods that analyzes more than 1800 characters in over 500 species, and I have found (and like me, all those who carry out serious phylogenetic analyzes with fossils have observed) that all ‘to increase taxa, it is necessary to introduce new characters that describe potentially significant characteristics and which, before the addition of new species, could not be variable (and therefore not significant for identifying clades).”

If Cau is analyzing 500 theropods it is a good guess that some taxa are represented by just a few bones. When a skull taxon nests with a pelvis taxon, then there will inevitably be loss of resolution.

“Obviously, having a few hundred characters, it is quite easy and quick to add new species, since the encodings to be made are relatively few. This is how he gets such a matrix!”

True. When I need more characters, I add more, but I haven’t really needed that to any great extent. Cau is working from a false paradigm. He should test it!

“The situation changes when you have more than 1000 characters, and therefore it takes a lot of work to encode each new species included.”

In my experience, that represents overkill. The degree of precision increases with every new character, but it pretty much levels off with 150 multi-state characters. Thereafter the increase in precision is incremental to miniscule.

“Therefore, since a serious phylogenetic analysis must have a sampling of characters adequate to the number of species, whoever proposes a phylogeny based on not even 300 characters out of over 1000 species, is, in the best of options, lying to himself.”

Testing says otherwise. How can I lie to myself when the software determines relationships that greatly resemble one another? Dr. Cau has turned his ire from taxa and characters to an ad hominem attack. That’s not good science. The scientific method requires that you repeat the prescribed experiment, follow the prescribed methods and report results. Don’t run your own experiment and report that mine doesn’t work based on your results. Suggestions for Dr. Cau: 1) use only every third character to test results. 2) delete incomplete taxa to test results. 3) Examine the pertinent specimens first hand. 4) Provide tracings and reconstructions so readers know the basis for your scores.

“Peters declares that his hypothesis is testable by anyone: listening to him, it is enough to assemble a phylogeny of reptiles, without prejudice, without taxonomic omissions.”

Not exactly. There are always omissions. That’s why I keep adding taxa to the LRT.  What the LRT represents today is a pretty wide gamut of vertebrate taxa with few to no major clades omitted.

“Therefore, if I were to assemble a matrix of reptiles from scratch, including characters at an order of magnitude similar to his matrix, I would have to obtain a phylogeny similar to his.”

That is a guess. Now turn that ‘if” into a deed.

“The fact that no phylogeny produced in scientific literature produces a phylogeny remotely similar to its own (where the synapsids are internal to the diapsids, and where the pterosaurs result with the squamates, just to mention some of its unusual characteristics) may mean, alternatively that : – All other paleontologists are incompetent and unable to do phylogenetics or that – Peters is incompetent and unable to do phylogenetics.”

Not exactly. Due to the wide gamut of taxa employed by the LRT, wider than in any prior published study, whenever taxa that have never been tested together are now tested together certain hypothetical interrelationships may develop that have been overlooked due to taxon exclusion. Cau’s diphyletic conclusion omits the third possibility: that adding taxa will result in matching tree topologies.

“Who is right? We accept the challenge! Indeed, I accepted it a few years ago, and tried to construct a phylogeny of Reptilia that was assembled from scratch, based exclusively on the characteristics deducible in the literature from the anatomical descriptions of fossil taxa.

As I assembled this matrix, I realized that it was necessary to add characters that were absent in the first few iterations, because I noticed characters that were shared by the new taxa I added and by some of the taxa already present, characters that were not yet in the matrix.

In the end, I found that as I added taxa, the phylogeny tended to produce a small number of scenarios, but nevertheless these were the most frequent with each update of the matrix.

Characters in the LRT are generic, good for almost every situation. I did have to add “no skull” to the headless chordates when they were entered. But otherwise, the original 235 multi-state scores were good to go! And, yes, I am as surprised as you are with regard to their longevity and universality.

In the current version, the assembled matrix has 100 taxa and 355 characters. Although Peters’ rhetoric will complain that 100 taxa are too few, the sample nevertheless took one representative of each major Reptilia group, so it is already an exhaustive sampling of the reptilian anatomical disparity. The matrix also includes soft-part characters (such as integument or internal organs) as it also includes 4 living species representing the 4 main groups of reptiles: chelones, lepidosaurs, crocodiles and birds. It samples species from the Carboniferous to the present, focusing mainly on the Triassic, the period in which pterosaurs appear. The analysis is at the scale of the species (apart from a handful of taxa, however codified on the basis of a few very similar species). I analyzed the matrix both using parsimony and using Bayesian inference which combines morphology and stratigraphy.”

Here Cau is showing his own results from his own taxon list (see below). 100 taxa are likely cherry-picked based on his access to data, even though he doesn’t think so. Did Cau include amphibian-like reptiles? No. Did Cau include fenestrasaurs? Yes, but he did not examine them first-hand. Did Cau examine his results for faults? Clearly no.

“These are the results: 
Pterosauria is monophyletic, and is internal to:
crown-Reptilia (the clade comprising turtles, lepidosaurs and archosaurs)
Sauria (the clade comprising lepidosaurs and archosaurs)
Archosauromorpha (the clade including birds and crocodiles and all taxa closest to them than lepidosaurs)
Archosauria (the clade formed by birds and crocodiles)
pan-Aves (the clade including birds and all taxa closer to them than crocodiles).”

This is the traditional nesting for pterosaurs, but it depends on the omission or poor-scoring of pertinent taxa. Earlier I tested Nesbitt 2011 and found dozens of mistakes in the scores. When corrected Nesbitt’s tree more closely resembles the topology of the LRT.

Added a day later: As noted above, Cau wrote to tell me this morning he would not provide his data file, so I cannot report on scores Cau made to pertinent taxa that I have studied firsthand (Peters 2000) and he has not reported doing so.

“That is, my analysis, based on the anatomical data of 100 reptiles, supports Ornithodira, which is precisely the hypothesis supported by the vast majority of studies on fossil reptiles, and which therefore fully and unquestionably refutes the phylogeny proposed by Peters.”

Readers should know that this analysis comes as news to me. You might think that scientists would share results in cases like this, but they don’t.

“Therefore, returning to the original question of who is incompetent in carrying out phylogenetic analyzes, there are two options: – or I am incompetent in carrying out phylogenetic analyzes and by pure chance I have obtained the same evolutionary scenario resulting from dozens of other paleontologists (who, obviously, are just as incompetent as me) or – Dave Peters is incompetent in doing phylogenetic analysis. You decide which is the most logical explanation.”

Interesting editorial. It does not follow the scientific method, nor was Cau polite enough to send me a .nex file of his results before he launched into this tirade. That shows lack of respect, perhaps contempt, certainly no attempt at reconciliation or consensus. Did Cau realize that Peters 2000, which nested pterosaurs with tanystropheids, Macrocnemus, Langobardisaurus, Cosesaurus, Sharovipteryx and Longisquama came to that conclusion after simply adding these taxa to four previously published analyses? That would have been the first step.

“DISCLAIMER: Contrary to Peters, this post does not intend to revolutionize the phylogeny of reptiles or to propose a new standard hypothesis for pterosaurs (also because, as you have seen, the result coincides with the scenario shared by the majority of paleontologists). If you want to learn something about the evolution of reptiles you have to read the scientific literature published according to the criteria of peer review among serious paleontologists, and not follow the gurus of the net.”

Reading between the lines, Cau has just reported that he has not reviewed Peters 2000, which is in “the scientific literature, published according to the criteria of peer review among serious paleontologists.” The same goes for several other published papers, all of which were peer-reviewed. 

“Rather, here I simply wanted to test Peters’ rhetorical statements playing exactly in his field, to demonstrate that there is no “heretical science” as opposed to a “mainstream science”, but only “good science” which follows a repeatable method, as opposed to a “pseudo-science” that pretends to be scientific and instead is basically a dirty play with data and with the good faith of the readers.”

Cau just told us that he did not follow “a repeatable method”, but instead ran his own experiment with his own list of taxa and not following the literature. Remember when Hone and Benton 2007 said they were going to test Peters 2000 vs. Bennett 1996 in their supertree analysis of pterosaur origins, then in 2009 dropped all reference to Peters 2000 and gave credit to Bennet for both opposing views?

Whenever scientists like Cau claim to be testing using the scientific method in order to discredit someone, check to make sure they really are doing so transparently.

“PS: you may be wondering what is the point of wasting time and energy to deny a pseudo-scientific site that spreads similar ‘cialtronato’ online. Others have talked about it extensively before me, but I think that a scientist has a duty not only to spread scientific knowledge but also to dismantle and demolish mystification and pseudoscience.”

In doing so, make sure you follow every step of the scientific process. As revealed here, Cau did not repeat the experiment, was apparently unaware of the literature and did not communicate is displeasure personally prior to publishing his opinion. His lack of peer review, whether he considers me a peer or not, left him exposed to same criticism he proposed in 2019.

“The site “The Pterosaur Heresies” very subtly spreads a form of pseuso-palentology that harms non-professional readers who may come across that site and think it is a reliable source of paleontological information.”

Don’t trust any source for paleo information. Run the experiment yourself. Find out for yourself. That is good science. Don’t trust anyone who asks you to trust them, as every parent tells their children.

“This is not the case: as I have shown in this post, even trying to “do as he says”, and therefore producing a “ex novo” phylogeny, released from the “official paleontologists” and built independently, without prejudice of any kind in this regard. the evolution of reptiles, drawing directly from the anatomical descriptions of the reptiles, produces a result that not only denies Peters’ absurd phylogenies, but also confirms the robustness and validity of the scenario constructed by the international paleontological community.”

He says “without prejudice”, but did he employ the same taxon list? That’s all I ask. Now let’s look at the cladograms on his blogsite, illegible at their published size. Perhaps clicking on them will expand them to reveal the taxon list.

After clicking on the cladogram: I am disappointed. The legibility does not improve. Seymouriamorpha is the outgroup taxon. That’s not a good start. Eothyris, Paleothyris and Petrolacosaurus and Mesosaurus are the next few taxa. Those cherry-picked taxa are not basal amniotes/reptiles in the LRT, nor are they related to one another. Taxon exclusion by Cau hides the basal dichotomy that splits reptiles at their origin.

Figure 1. Scleromochlus, a basal crocodylomorph

Looking at taxa pertinent to pterosaurs, Cau nests Scleromochlus (Fig. 1) at the base of the Pterosauria. Evidently he does not care that Scleromochlus has vestigial hands and lacks a fifth toe. Cau is not using logic here.

Cau employs Cosesaurus and Sharovipteryx, but did he see these taxa firsthand? I did. Did he create reconstructions so he and we know he fully understands what he is seeing? I did. Did he show the prepubis and pteroid in Cosesaurus? He did not, but you can see them here.

Figure 2. 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.

Some other odd cousins arise in Cau’s cladogram:

1. Parasuchus, the phytosaur, nests with Alligator, the crocodylomorph.
2. The ‘rib’ glider Icarosaurus is in the turtle lineage.
3. Long-snouted aquatic Mesosaurus nests with short-snouted terrestrial Acleistorhinus.

Like Darren Naish,
Andrea Cau worked hard for his PhD in the hope of making discoveries in paleontology. When writing papers, the review process takes months that might result in a rejection.

By contrast, 
the LRT can add taxa and make comment within 24 hours, making discoveries without the cost of a PhD. Several times the LRT recovered hypothetical relationships years before they were published by PhDs. You can see that list here. Cau dismissed all of those discoveries as lucky. So…

1. Cau is not without prejudice.
2. Cau did not check the results of his cladogram for logic
3. Cau did not show his tracings or make reconstructions. Scores are suspect.
4. Cau did not employ taxa pertinent to the basal reptile dichotomy
5. Cau did not send me his manuscript for peer review, so this is the review he never asked for.

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.

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.

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 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.

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.

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.

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.

Unfavorable mention on a Joe Rogan podcast two years ago

About two years ago
paleontologist, Trevor Valle, appeared on a Joe Rogan podcast (link here and below) entitled “Paleontologist Trevor Valle Debunks ‘Dinosaurs Never Existed’ Conspiracy.” Between 4:30 and 6:30 minutes into the podcast Valle said several things about me and this webpage that are not true. See below.

The following is a copy of the email
I sent to Trevor Valle. Another copy went into the comments section of the Joe Rogan podcast about 8pm CDT, September 9, 2018. Evidently there’s a jungle of misunderstanding out there that needs to be trimmed back.

---

Hi Dr. Valle:

I just saw your YouTube video on the Joe Rogan podcast.

You said a few things about me (I am David Peters) that are not true.

1. “He’s a jackass.” We’ve never met.

2. “All reptiles are mammals.” Actually just the opposite. All mammals are reptiles (= amniotes, under the new tetrapod family tree that minimizes taxon exclusion, see below). I hope you just had a memory lapse and misspoke and that you did check the site out first and not just rely on hear-say.

3. “All of these clades should be in this…and all of this crap” The new tetrapod family tree has a magnitude more included taxa than any prior study. Some taxa not previously tested together now nest together. Since this is science, anyone can duplicate the study using a similar list of taxa/specimens and their own list of character traits. I encourage everyone interested to do so. Note: DNA studies are widely known not to duplicate trait studies, and the new tetrapod family tree is similar to other trait studies in that regard. Here, birds still nest with birds, snakes with snakes, etc. So there are broad areas of agreement with past studies. Importantly, every branch of the tree shows a gradual accumulation of traits that appears to mirror actual evolutionary pathways. Some do break paradigms and traditions. Also note, whenever taxa have been tested together later by other workers, as in Chilesaurus, Diandongosuchus, Lagerpeton and others, their results confirm the earlier results recovered here.

4. “He wholesale copied from a colleague of mine, posted it, which is a violation of copyright, because he’s attempting to supersede that work by importing his own ideas to it.” Not sure which blogpost is the focus of your interest here, but I commonly copy and criticize pertinent parts of publications in order to help spread the news and, whenever necessary, to show errors and omissions. In science this is the process for arguing a new hypothesis. Copyright laws are not violated when arguing scientific validity. Whether it’s ‘confirmation’ or ‘refutation’ this is all legal, standard and how could we ever do without it? All work is cited. Often links are made to the original sites.

5. “He will refuse any critical comments to be posted on his WordPress site.” Actually just the opposite. I rarely get feedback, but it’s all there to be viewed over the last 7 years. I do edit emotionally charged words (cussing) from reader replies and I edit out ad hominem attacks as they are inappropriate for a scientific discussion.

Moreover, I make changes all the time whenever new data comes in, because, like anybody, I make mistakes, too. Nearly every one of the 1284 included taxa was new to me when I first studied it. Any scientist would say the same thing.

Trevor, since the cladogram is the core of the study, I encourage you to look at the site and tell me which taxa should not nest together and where they should nest instead. I would hate to think that you simply listened to an opinion without checking out the facts.

Sometimes it takes an outsider to shed light on false paradigms. I have been published in Nature, Science, the Journal of Vertebrate Paleontology, Ichnos, Historical Biology and other peer-reviewed academic publications, so despite lacking a PhD, I have made contributions to the literature and continue to do so.

A large gamut analysis of the tetrapod family tree has been long sought by the paleo community. Now that it is available online, apparently that’s not what they really wanted all along.

Best regards, and let’s have lunch sometime.

David Peters
www.ReptileEvolution.com/reptile-tree.htm
www.PterosaurHeresies.Wordpress.com

 

Let’s open up an old can of worms…

Three and half years ago
ReptileEvolution.com got a sound thrashing from Dr. Darren Naish writing form his Scientific American blog, Tetrapod Zoology. Today with 350 more taxa added and the tree still fully resolved, let’s add some ‘post-its’ to ten images of Darren’s blogpost (Figs. 1-10) to see how things stand today. Both adversaries are still out there on the Internet. Neither has buckled under.

This will be a long post
So the gist of it is:

1. Naish paints me as an outsider, only part of the paleo background. True – for most workers
2. Naish uses art and hypotheses that are not in my website. Some perjorative art he uses are from other artists. He had permission to use all my artwork, so bringing in these oddities was not necessary given his headline. 
3. Naish spends many paragraphs talking about pre-ReptileEvolution errors that I made. One reason for starting a fresh website was to rid myself of old errors, but with this ‘history’ tainting all of my present work Naish provides no possibility for future redemption or honor.
4. Naish claims that I see certain things in fossil photos that are not there in fossils. None of these are present in ReptileEvolution.com. If so, let me know so I can remove them.
5. Naish claims that I see certain things in fossils that are not visible in fossil photos. So, what can one do? (see below)
6. Naish blackwashes the entire ReptileEvolution website, all of its data, all of its images, then and forever in the future. He leaves no stone unturned.
7. Naish supports traditional trees, even those that nest pterosaurs close to phytosaurs and erythrosuchids and those that refuse to include fenestrasaurs. These are problems that need to be resolved in academia.
8. Naish wants me to add hundreds of more characters. As we’ve seen earlier, that doesn’t statistically help much after 200 traits and can be a never ending request.
9. Several times Naish provides high praise before he buries the knife. I won’t do that.
10. Both of us are unmoved regarding our stances.

Bottom line:
No one is perfect. No matrix is perfect. No interpretation is perfect. Even so, superior provisional hypotheses can be advanced by increasing the number of taxa in a taxon list. The more data, the less any single error affects the rest of the matrix and the more unbiased opportunities are present for nesting. If, in the end, all sister taxa look like sisters, with gradual accumulations of traits for all derived taxa, and the tree is completely resolved with high Bootstrap scores, isn’t that what we’re all looking for? Doesn’t that more closely model actual evolutionary events?

On the other hand, if Naish is correct
If my cladogram is built on (hundreds of) thousands of errors, even after fixing tens of thousands of errors, how is a fully resolved tree demonstrating gradual accumulations of derived traits for every taxon even possible?

When Naish is writing on his blog
and as I am writing here, we lose our scientist mantles and become journalists. In that role we have the obligation to name sources, be specific, inform the reader, write about what the headline promises, and try to maintain a balanced unprejudiced view. Any variation from this becomes propaganda. To that end, if you have any questions regarding topics that arise here, look up the answers on previous blog posts or on ReptileEvolution.com or drop me a note.

All of these pages can be enlarged with a click.
Some Carl Sagan quotes break up the long page images here and give you time to digest.

Figure 1 of 10. Click to enlarge. Monitor shot of Tet Zoo blog with annotations in yellow.

Below (Fig. 2) you’ll see some bizarre Pterodactylus art
that Naish says was illustrated as if my hypotheses were correct. To be fair, I show you a Pterodactylus from ReptileEvolution.com (Fig. 1a). Why did Naish choose to show the bizarre artwork of another artist instead of using one from the website he was critical of?

Figure 1a. Pterodactylus scolopaciceps, BSP 1937 I 18, No. 21 in the Wellnhofer 1970 catalog.

 

Figure 2 of 10 from Tetrapod Zoology.

“For me, it is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring.”
— Carl Sagan —

Figure 3 of 10 from Tetrapod Zoology.

 

The truth may be puzzling.
It may take some work to grapple with.
It may be counterintuitive.
It may contradict deeply held prejudices.
It may not be consonant with what we desperately want to be true.
But our preferences do not determine what’s true.
— Carl Sagan —

Figure 4 of 10 from Tetrapod Zoology.

Here’s one Pteranodon from ReptileEvolution.com. 
(Fig. 4b) Why didn’t Naish use this one by hand instead of the Pteranodon from Hell? Did he venture into propaganda? Did he want to make my work look unworthy of respect?

Figure 4b. The UALVP specimen of Pteranodon. Note the lack of taper in the rostrum along with the small size of the orbit.

Figure 5 of 10 from Tetrapod Zoology.

The poor graduate student at his or her Ph.D. oral exam
is subjected to a withering crossfire of questions
that sometimes seem hostile or contemptuous;
this from the professors who have the candidate’s future in their grasp.
— Carl Sagan —

Figure 6 of 10 from Tetrapod Zoology.

Every kid starts out as a natural-born scientist,
and then we beat it out of them.
A few trickle through the system with their wonder and enthusiasm for science intact.

— Carl Sagan —

Figure 7 of 10 from Tetrapod Zoology.

I think people in power have a vested interest to oppose critical thinking.
— Carl Sagan —

Figure 8 of 10 from Tetrapod Zoology.

It is undesirable to believe a proposition
when there is no ground whatever for supposing it true.
— Carl Sagan —

Figure 9 of 10 from Tetrapod Zoology.

At the heart of science
is an essential balance between two seemingly contradictory attitudes –
an openness to new ideas, no matter how bizarre or counterintuitive,
and the most ruthlessly skeptical scrutiny of all ideas, old and new.
This is how deep truths are winnowed from deep nonsense.
— Carl Sagan —

Figure 10 of 10 from Tetrapod Zoology.

In the end
is it good to have an an adversary/nemesis? Does conflict help advance Science? I think of it as necessary and invigorating. An adversary can be like a cleaner fish, helping one get rid of errors. I think it is also important to recognize value where present and to discuss specifics and details whenever possible.

On the subject of outsiders and insiders
JL Powell 2014 writes: “Luiz Alvarez was another resented outsider, resented by author and geologist Charles Officer. 

Outsiders do not know the mores for a given field and would be unlikely to uphold them if they did. Outsiders can resurrect a question that insiders have long stopped asking, 

Insiders may find it almost impossible to change their mind publicly, which may be equivealent to renouncing their life’s work. Even if insiders do not cast aspersions on the character and training of an individual outsider, they may still resent the implication that their discipline is incapable of solfing its won problems using its own methods.” 

References
Powell JL 2014. Four Revolutions in the Earth Sciences: From Heresy to Truth. Columbia University Press.

 

Carroll 1988

Figure 1. Vertebrate Paleontology by RL Carroll 1988 is one of the starting points for this blog and ReptileEvolution.com

In 1988
Dr. Robert L. Carroll published a large work devoted to the study of fish and tetrapods: Vertebrate Paleontology and Evolution. Between its black covers and silver dust jacket there was – and is – an immense amount of data on just about every taxon known at the time… a time just before software driven phylogenetic analysis became de rigueur.

My copy
has been used so much it has a broken binder, which makes every section lighter, easier for scanning.

For its time, and for a few decades later
Vertebrate Paleontology and Evolution was the ‘go-to’ textbook for students and artists of this science. (See below).

A few quotes from the Amazon.com website:

1. “This book was my textbook for Vertebrate Paleontology and Evolution at the University of Rochester back in 1992.”
2. “the only easily available work that goes to any depth on this intensely interesting subject.”
3. “The book is very daunting to look at if you just flip through it. However, it does a nice job of introducing concepts and terms to the reader. Its organization is straightforward, starting with the simplest vertebrates and eventually finishing with mammals.:
4. “Just realize that some of the information may not reflect our current understanding since the book is over 10 years old and many new finds have come to light, new ideas have been introduced, and old ideas reexamined.”
5. “It’s an essential for anyone building a library of paleo textbooks.”
6. “I’m a working fossil preparator and this is the primary reference text used in paleontology labs at the American Museum of Natural History, Yale Peabody Museum and others I’m sure.”
7. “I had Romer’s Vertebrate Paleontology, which is an excellent book, until a paleontologist friend directed me to Carroll’s book. He acknowledges Romer’s work in the field but this is an updated version (for the time of publication).”
8. “If you want to chart the course of evolution up to the present – read this book!”

Carroll 1988 updated
Romer’s Vertebrate Paleontology  (1933, 1945, 1966) which was the ‘go-to’ textbook of its day.

ReptileEvolution.com
updates portions of Carroll 1988. Likewise and in due course, someone someday may want to update ReptileEvolution.com. I hope they do so.

Every so often
it’s good to give credit to one’s mentors and resources. Sometimes you learn by doing. Other times you learn by reading. I suppose everyone who writes such a large gamut book knows he/she is doing something to help future students and enthusiasts who they will never meet. I feel the same way, butI imagine both Carroll and Romer were additionally warmed by a healthy royalty check once or twice a year.

References
Carroll RL 1988. Vertebrate Paleontology and Evolution. W. H. Freeman and Co. New York.
Romer AS 1966. Vertebrate Paleontology. University of Chicago Press, Chicago; 3rd edition

wiki/Vertebrate_Paleontology_and_Evolution

2015 readership stats

Slow news day… 
so here is a summary look back to 2015, and a tentative look forward to 2016.

If you ever wondered…
Pterorsaurheresies.wordpress.com had 130,000 (not unique) visitors in 2015. If I was counted each time I accessed the blog to write or correct it, then you can probably halve that number.  :-)  There were about 300 unique readers a day, rising to 500+ on hot news and controversy.

ReptileEvolution.com had

1. 58,494 unique visitors
2. 1.64 visits per visitor (average)
3. 2.94 pages/visit (average)
4. 14.03 hits/visit average (1,351,877 hits in total) about the same as in other years.
5. Click here to add to the 2016 visitor totals at ReptileEvolution.com.

While I appreciate the readership,
for the most part both sites are forums for me to learn about various taxa and report what I find. Sometimes the results align with published work. Sometimes… not so much. The blog and website are my hobby and my pleasure. What other science offers the opportunity to make discoveries from your desktop? Data change, so the digital data change as necessary. You can’t do that in paper media. You have to live with your mistakes…forever!. Plus you can’t animate a pterosaur take-off in paper media.

Frankly,
with my recent venture into theropods, I think most of the reptile topics and clades have been covered by now. Not sure that 2016 could ever be as rich as 2015 was.

Bottom line:
A wide gamut cladogram of the Amniota/Reptilia is still needed in Academia. Now at 628 taxa the large reptile tree (+59 synapsids off to the side) is still fully resolved. Now at 221 taxa the large pterosaur tree is also in pretty good shape, demonstrating gradual accumulations of derived traits for all derived taxa. These studies are still far too large to get published in a paper medium. No one would want to check those 140,000 scores — especially if the results upset someone’s status quo.No one would want to be the referee on such a wide ranging analysis. No one is an expert on all those clades. It remains impossible for me or any one paleontologist to visit every taxon from the present inclusion set in one lifetime.  So, the study remains stuck in online limbo in its present shape — which is probably better than being tucked away on a college library bookshelf. No one has to approve my methods or results. But they can take advantage of the work for their own independent needs.

I still hope,
perhaps in vain, that some of the taxa and clades recovered here will someday inspire someone to at least consider adding a few taxa to their own more focused study beyond whatever traditional taxon list they feel compelled to use. Then I’ll report clade confirmation whenever that happens or rejection if that ever happens.

 

New ichthyosaur family tree by Ji et al. 2015

A recent paper on ichthyosaur systematics
(Ji et al. 2015, Fig. 1) adds newly discovered taxa and the tree is getting nice and big.

Unfortunately,
at the base of their cladogram Ji et al. place a distinctly different proximal outgroup for ichthyosaurs than what was recovered in the large reptile tree (subset shown in Fig. 1, click to enlarge). They appear to be guessing. Apparently they are not sure how ichthyosaurs are related to other reptiles.

Here 
proximal outgroup taxa for ichthyosaurs include Wumengosaurus, Thaisaurus and Xinminosaurus (in ascending order) not Thadeosaurus. These large reptile tree taxa demonstrate a gradual accumulation of basal ichthyosaur traits. The Ji et al taxa, Hovasaurus, Claudiosaurus and Thadeosaurus do not. In the large reptile tree these three are basal younginiformes, related, yes, but much more distantly related to ichthyosaurs.

Figure 1. Click to enlarge. Ichthyosaur family trees compared. Left: subset of the large reptile tree. Right: from Ji et al. 2015. Note the lack of correct outgroups in the Ji et al study. They have no idea which taxa are proximal ancestors. Yellow are taxa found in both trees.

Figure 1. Subset of the LRT focusing on the clade Ichthyosauria updated November 4, 2018 with a shift of the Hupehsuchidae closer to the base of the Ichthyosauria.

So, as an experiment, 
we’ll delete the large reptile tree proximal outgroup taxa in order to match more closely the Ji et al taxon list. What is recovered now?

1. Hovasaurus, Claudiosaurus and Thadeosaurus now nest together in an outgroup clade.
2. Hupehsuchus + Xinminosaurus, Grippia and (Utatsusaurus + (Shastasaurus  pacificus + Shastasaurus alexandrae) now form clades at the base of the Ichythyosauria.
3. Then Chaohusaurus nests at the base of the rest of the Ichthyosauria with the same topology as the subset of the large reptile tree.

A few differences between the two topologies without deletions…
Note the morphological mismatches in the Ji et al. topology not found in the large reptile tree.

1. In the large reptile tree Chaohusaurus nests between two similar taxa, Parvinatator and Besanosaurus. In the Ji et al. tree Chaohusaurus nests between the mismatched and odd Hupehsuchus and a clade of basal ichthyosaurs as the basalmost ichthyosaur, even though it has a derived ichthyosaur shape and traits.
2. In the large reptile tree the derived, but still Triassic, Cymbospondylus petrinus nests between its contemporary, Mixosaurus and several other giant serpentine ichthyosaurs. All have a depressed cranium with a central ridge. The unrelated flat-headed C. buchseri nests elsewhere with similar deep-bodied, high-crested Shonisaurus popularis. By contrast, in the Ji et al. tree C. piscosus (= petrinus) and C. buchseri nest together with the very primitive, very small, Xinminosaurus, which does not have such a depressed cranium with a central crest.
3. Ji et al. have a clade of Shastasauridae that includes only shastasaurs. In the large reptile tree, that clade also includes the odd little hupehsuchids and demonstrates how these little toothless enigmas evolved from larger forbearers. Ji et al. provided several skull reconstructions. Perhaps a few more would help to resolve the distinct topologies.

Those are the major issues.
The rest can be swept up later. I’d like to see the authors either expand their own taxon list or work off the large reptile tree to confidently establish a series of outgroup taxa for the Ichthyosauria that actually demonstrate a gradual accumulation of character traits, instead of doing what they did. Then we might have closer correspondence in tree topology. And we’re going to have to figure out Cymbospondylus… is it derived? or primitive?

References
Ji C, Jiang D-Y,  Motani R, Rieppel O, Hao -C & Sun Z-Y 2015. Phylogeny of the Ichthyopterygia incorporating recent discoveries from South China, Journal of Vertebrate Paleontology, DOI: 10.1080/02724634.2015.1025956

History of reptile Interrelationship hypotheses: Meckert’s PhD thesis

There is a long history
of workers creating hypotheses of reptile interrelationships going back to the mid 18th century (Carl von Linneaus 1758). That history, up until 1995 (Laurin and Resiz 1995 and Meckert 1995), was summarized by Dirk Meckert in his PhD thesis, which otherwise  concentrated on all available specimens of Barasaurus. You can download that thesis here online and read that short but fascinating history for yourself.

Some interesting notes arise from Meckert’s short history:

1. Some studies united pareiasaurs and turtles. Others did not.
2. Other studies united pareiasaurs, diadectids and procolophonids (which happened here just yesterday). Meckert wrote: “The Procolophoniformes contain Procolophonia and Testudinomorpha as sister-groups. Testudines are the sister-group of Pareiasauria within the Testudinomorpha.”
3. Mesosaurs are commonly considered of uncertain affinities. But not here.
4. Many prior studies had the synapsids branch off first. That is incorrect as shown here.
5. No prior studies recognized the original dichotomy of lepidosauromorphs and archosauromorphs.
6. No prior studies recognized Gephyrostegus bohemicus as a sister to the basalmost amniote.
7. Diadectomorpha have been nested in and out of the Amniota. They’re in here.

No studies prior to reptileevolution.com
have included as many as 571 individual species as taxa, not counting the therapsid tree (with 52 additional taxa) and pterosaur tree (with 228 additional taxa) for a total of 851 taxa.

Other studies more recent than 1995
(not included in Meckert’s history) include

1. http://www.palaeos.org/Reptilia and http://palaeos.com/vertebrates/amniota/reptiles.html
2. http://whozoo.org/herps/herpphylogeny.html
3. https://en.wikipedia.org/wiki/Amniote as determined by Benton, M.J. (2004). Vertebrate Paleontology. Blackwell Publishers. xii–452.
4. University of Maryland (John Merck)
5. online pdf, Amniote Origins and Nonavian Reptiles
6. YouTube video by Walter Jahn
7. Tree of Life
8. Hedges 2012
9. Gauthier, Kluge and Rowe 1988 online
10. Hill 2005
11. Mikko’s phylogeny archive
12. ReptileEvolution.com
13. Let me know if I missed any. I’ll add them here.

A while back
we looked at the differences between astronomy and paleontology. As noted earlier, time is never of the essence in paleontology — and that extends to idea acceptance. So many hypotheses of reptile interrelationships are still floating around out there. A definitive and all encompassing demonstration, like the large reptile tree, will probably just float forever with the other several dozen hypotheses out there, hashed, rehashed and rehashed again without end.

This is one of the frustrations of paleontology. And many think it is largely ego driven.

On that note
In astronomy the data, be it observation or spectral analysis, is immediate and widespread. You just have to look up with the right tool in the right direction. Or study the shared data (photos, etc.) Everyone can confirm the observation.

In paleontology the data comes out piecemeal, in low resolution, or imprecise tracings, not from every angle of view. Some key parts are lost and others are hidden beneath other bones or matrix. Sometimes you have to assemble dozens or hundreds of specimens for a proper study. No one is interested in confirming observations or analyses perhaps for years if ever. They’re all too busy with their own projects. Checking the characters and scores of an analysis can take weeks, months or years (as long as it took to build originally), and to do so requires the same amount of globe-hopping to see all the specimens in all the museums. No one is going to do that. They’d rather be making their own discoveries… and adding their taxa to established trees created by hungry PhD candidates, like Dirk Meckert in 1995, done at the nadir or advent of their experience.

The paleo-mantra remains: you must see the specimen!
And even that is no guarantee.

And if you want to break a paradigm or two,
like Ostrom did in the 1960s, you might have to wait for widespread (but never universal) acceptance. Paleontologists like their paradigms. They don’t like to give them up.

References
Benton MJ 2004. Vertebrate Paleontology. Blackwell Publishers. xii–452.
Carroll RL 1988. Vertebrate Paleontology and Evolution, WH Freeman & Co.
Laurin M and Reisz R 1995. A reevaluation of early amniote phylogeny. Zoological Journal of the Linnean Society, 113: 165–223.
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Meckert D 1995. The procolophonid Barasaurus and the phylogeny of early amniotes. PhD thesis McGill University. Online Barasaurus dissertation

 

 

 

Novel insights – part 5

Earlier here, here, here and here we looked at novel insights recovered from the large reptile tree. Today we’ll continue and finish with derived archosauromorphs in part 5.

New archosauromorpha

1. Euarchosauriforms (sans parasuchia and proterochampsidae) start with Euparkeria,  derived from the FMNH specimen of Youngoides, which has a small antorbital fenestra.
2. Vjushkovia is a basal rauisuchid.
3. Decuriasuchus is not a rauisuchid, but a pre-archosaur/pre-poposaur derived from basal rauisuchids like Vjushkovia.
4. Ticinosuchus has a sharp triangular premaxilla and is basal to the aetosaurs.
5. A menagerie of archosauriformes, Arizonasaurus, Yarasuchus, Qianosuchus, Ticinosuchus, Stagonolepis and Aetosaurus form a clade.
6. Lotosaurus is not related to Arizonasaurus, but to Silesaurus.
7. Poposaurs include Turfanosuchus at the base.
8. Gracilisuchus is a basal archosaur/crocodylomorph. Archosaurs include crocs and dinos and that’s all.
9. The calcaneal heel appeared and disappeared several times.
10. Protodinosaurs include PVL 4597, Lewisuchus, Pseudhesperosuchus and Trialestes, not pterosaurs, Lagerpeton or Marasuchus.
11. Marasuchus is a basal theropod.
12. Phytodinosauria is a clade including Eoraptor, Sauropodomorpha and Ornithischia.
13. Damonosaurus Jeholosaurus and Chilesaurus are basal ornithischians.
14. The pubis of Pisanosaurus was rotated during taphonomy. When repaired it looks like a standard ornithischian partial pelvis.

Novel insights – part 2

Earlier we looked at some of the novel paleontological insights brought to you by reptileevolution.com. Today we’ll continue with the higher (new) lepidosauromorphs.

New Lepidosauromorpha 2

1. Macroleter and Lanthanosuchus are sister taxa.
2. Nyctiphruretus, Sauropareion and owenettids are not procolophonids. They are pre-lepidosauriformes.
3. Coletta is not a procolophonid, but a basal lepidosauriform.
4. Saurosternon and Palaegama are basal to the erroneously-called ‘rib’ gliders.
5. Coelurosauravus and Mecistotrachelos are sisters to the kuehneosaurids with homologous dermal structures (not ribs).
6. Xianglong is a late surviving sister to the kuehneosaurids, not related to Draco, the living rib glider, which does indeed glide with its ribs, distinct from the others.
7. Basal lepidosaurs split between sphenodontids and tritosaurs + pre-squamates.
8. Basal sphenodontids include Megachirella, Pleurosaurus and Marmoretta.
9. Derived sphenodontids include Azendohsaurus, Trilophosaurus, rhynchosaurs and their kin with several taxa, like Eohyosaurus as transitional taxa.
10. Tritosauria is an overlooked clade of lepidosaurs. It contains Huehuecuetzpalli, Tijubina, Macrocnemus, Langobardisaurus, Tanystropheus and the fenestrasaurs, Cosesaurus, Sharovipteryx, Longisquama and pterosaurs.
11. Lacertulus, Hoyalacerta and others are proto-squamates, nesting outside of the Squamata.
12. Scandensia, Calanguban and Euposaurus are basal squamates.
13. Geckos are the sister group to the clade that produced snakes.
14. Ardeosaurus is a basal member of that proto-snake/snake clade that has aquatic members, like Pontosaurus, not related to mosasaurs.
15. Burrowing snakes, like Leptotyphlops, are derived, not basal snakes.
16. Amphisbaenids and Dibamus are derived skinks.
17. Jesairosaurus and the drepanosaurs nest with kuehneosaurs as basal lepidosauriforms.

More later. Celebrating four years online this month.