So, you want to be a paleontologist…

Summary for those in a hurry:
Becoming a paleontologist who can support a family is difficult and rare. Up-and-comers end up supporting powerful professors. Outsiders and insiders with new ideas are sometimes ridiculed and/or ignored to silence debate and prevent upsetting the status quo.

PS (added 24 hours later). If you’re serious about paleontology, see Dr. Chris Brochu’s well-considered and insightful comments (below). Dr. Brochu agrees, disagrees and adds more data to many of the points made here.

Once you get your PhD in paleontology…
sure it’s a happy day of celebration, a great achievement invested with time and treasure. But then reality sets in as you realize you are not automatically a ‘made man‘ as in the gangster movie, “Goodfellas.”

You still need to get that first good paying job in paleontology,
and those are hard to come by. Black 2010 reports, “it is extremely difficult for researchers to find jobs and secure funding for their research. Prior to the beginning of the 20th century most paleontologists were self-funded enthusiasts who either used their family fortunes (O.C. Marsh and E.D. Cope, for example) or sold fossils (the Sternberg family, for example) to underwrite their work. For most paleontologists most of the time, research funding comes in the form of grants.”

Through the grapevine
I hear that anywhere from 40 to 80% of grant money goes to the university or museum that provides office space for the paleontologist. (Is that correct?).

It comes as a disappointment to many PhDs
that they end up as preparators, docents, research assistants, artists and librarians, rather than highly-paid professors making decisions, doing field work in the summer and buzzing around the world doing book tours. That jarring dose of reality comes at a time when young, former students are starting from scratch, trying to buy a house, start a family, pay off loans and hoping to make a name for themselves by publishing discovery after discovery.

Evidently it is worse for female students and scientists…
Harassment and bullying were chronicled in a recent (April 14, 2021) PBS NOVA documentary you can access here.  Some notes follow:

PAULA JOHNSON, M.PH., M.D. (President, Wellesley College): “The best estimates are about 50 percent of women faculty and staff experience sexual harassment. And those numbers have not really shifted over time. If you think about science, right now, we have a system that is built on dependence, really, singular dependence of trainees—whether they are medical students, whether they are undergraduates, or if they’re graduate students—on faculty, for their funding, for their futures. And that really sets up a dynamic that is highly problematic. It really creates an environment in which harassment can occur.”

KATHRYN CLANCY, PH.D. (Biological Anthropologist): “Generally speaking, sexual forms of sexual harassment, like come-ons, unwanted sexual advances, those are actually the rarest forms of sexual harassment. They actually don’t happen very much; mostly you see putdowns.”

One woman noted, “an invitation to have a beer with someone important interested in your poster sometimes has little or nothing to do with your poster.” It is noteworthy that the dropout rate in STEM studies is higher in women, who suffer from unequal treatment according to this documentary.

Fossils are hard to come by.
If post-grads don’t find their own fossils in the field, the fossils that come in the door are going to be distributed by the professor as they please, like a mother bird feeding hungry nestlings. (BTW, I’m talking about paleontologists who like bones. Others in the petroleum industry with a Master’s Degree make better money than a PhD in dinosaur studies because they are in greater demand.)

In the typical bell-curve of success after a doctorate,
every year or so, some few do come to international attention for their discoveries and publications. Most do not. Many struggle just to keep up an association with a university, quite aware of the fact that year after year another clade of young, eager, intelligent, well-connected future paleontologists with scholarships are coming into the professors’ view with the exact same dream and goal.

When grad students and post-docs are trying to establish themselves,
they tend to maintain relationships with universities and ally themselves with groups that huddle around and support established professors. It’s the only game in town. These 20- and 30-somethings are known to professors as ‘cheap labor’ due to an over supply of young, eager and bright hopeful students.

Older, established professors decide
who of their underlings gets funding and who goes hungry. Well-known professors bring a lot of money into universities, so universities undervalue underlings based on this value system.

New hypotheses that upset those in textbooks are not welcome.
If those ideas come from outside the tribe, someone is sent out to dismiss and dismantle that radical. Discoveries and hypotheses are welcome only if the professor is made a co-author and it doesn’t depart from the paradigm (i.e.  supporting invalid clades like ‘Ornithodira‘, ‘Avemetatarsalia’, ‘Afrotheria‘, ‘Laurasiatheria’ and ‘Cetacea‘).

Peer review was not always part of the publication process,
but it is now. Dinerstein 2017 wrote, “The controversies that have plagued peer review from its earliest days, censorship, conflict of interest, the tension between early reporting and veracity, the need to fill space, the desire for prestige and income remain with us today. They may have assumed different forms, but at their core are flaws in a system designed by flawed humans. It may not be the best system, but it is the one we use.”

According to Kampourakis et al. 2015,
“The peer review process can be one of the most subjective endeavors in the scholarly world. It should not be, and it does not have to be subjective, but it can be. Each reviewer has his/her own conceptualizations, views, experiences, and biases, which can collectively impact the stance taken toward a manuscript.”

Established authors,
who are often established professors, who are well-known to established editors, have an advantage over independent researchers. Reviewers (= referees) are typically other professors hoping to get their work favorably reviewed when their time comes. If papers support the general narrative found in textbooks, they are more likely to be published. Departures that show textbooks are in error are at a disadvantage. No one wants to weaken the power of established professors, least of all other professors who understand how to play the game.

More on manuscripts from Kampourakis et al.
“Most manuscripts are not appropriate for publication when we initially receive them. They always have limitations, which authors themselves are unable to identify—we know this from our own publication experiences. Therefore, if the editors only relied on reviewers for a decision, this would most likely be a “reject” one in the first place. Reviewers are always experts in their domains, and when their review is constructive, it provides crucial feedback to authors.”

Actually reviewers/ professors are not experts in their domain if they are teaching untenable traditions as facts. You wouldn’t think that happens, but it does.

Actually reviewers/ professors can not be experts if the subject of the manuscript is a discovery, something new, something not seen or understood before by anyone.

The issue is: will reviewers and editors recognize ‘the new order’ or will they defend ‘the old order’, the one they teach, the one that creates their monthly paycheck coming from lectures and textbooks.

Discoveries should be a cause for celebration,
if followed by confirmation after testing using methods and materials.

Instead
discoveries by outsiders encourage young PhDs (e.g Naish, Cau, Witton) to start name-calling (e.g. ‘pseudoscientist‘, ‘crank)‘. Be aware that this sort of behavior has a long history in humankind, going back at least as far as the Romans, who called non-citizens ‘barbarians’. So, if you make a discovery don’t hold your breath waiting for accolades and citations (see John Ostrom link below).

Name-calling by teachers/ professors/ colleagues is inappropriate.
Better to help colleagues with suggestions or data if genuine errors are found.

Errors are everywhere.
I just spent the weekend correcting errors in the LRT. Finding new insightful data is its own reward.

The LRT is online day and night, world-wide,
available to anyone looking for taxon list suggestions and citations. In like manner, ReptileEvolution.com is a source for data. It would be great if someone else were to create a parallel study to confirm, refute and compare discoveries found here. In the last ten years, no one has yet ventured forth to do this, or threatened to do this. That may be because they are stuck in the present academic world and all of its restrictions.

You should do science
because you love science.

There are only so many discoveries to be made, and fewer every year.
No PhD wants to simply confirm what someone else has already discovered. That’s not why they spent their time and treasure getting their PhDs. They want their own discoveries. When someone else makes a discovery, that’s one less out there waiting to be discovered. That’s the sort of frustration that has led to name-calling when it should have led to unemotional scientific confirmation or refutation following scientific methods and materials.

And speaking of vague insults,
the latest I’ve heard is “Your methods are flawed.” Really? No more specific instruction? No actual testing of the methods? I keep hearing, “your character list needs to be expanded.” Daily testing shows this is a myth. Experts are not always correct, as you will sooner or later find out for yourself.

Once you’ve shown and labeled
all your taxonomic data, let the software recover a cladogram in which all sister taxa actually look alike. This simple method has led to several satisfying discoveries, like ancestors for pterosaurs, snakes, whales, and turtles back to Ediacaran worms.  Make all  your .nex files available to strangers. Have the balls to tell PhDs that genetic analyses deliver false positives in deep time studies, if that’s what your studies reveal.

IMHO
Your methods are flawed” comes off as a vague and baseless claim coming from an immature and insecure worker who has turned to projecting their own faults on others. Pressed for details, something real scientists are usually eager to fill an hour with, disgruntled post-grads usually retreat to social media. Funny that the ones who say, “your methods are flawed” do not repeat the same insult to their fellow PhDs when they make the same discoveries years later.

By design, the manuscript review process
usually takes months. It might take years. This is also a professional ‘brake’ on new ideas that keep the established professors behind their lecterns for as long as possible. Why would a professor return a favorable review on a paper that upsets his own hypotheses, lectures and textbooks? Professors rely on lectures and books for their salaries, royalties and status. Any manuscript that upsets the status quo is going to sit at the bottom of their growing IN pile for as long as possible, then begrudgingly returned with a ‘NO’. Cogent reasons are not required by editors.

In an ideal world
arguments should be published immediately, while the subject is still fresh in the public’s mind and before inaccurate myths get out there and spread into the world of general knowledge. Colleagues should treat each other more like co-pilots rather than saints vs. sinners.

Even if you become a tenured professor,
you are not always free to do what you want to do. “One way of getting rid of tenured professor, that’s known, is you ask the person to report on their research and you load them up with teaching and you give them a lousy office. And then eventually they’ll just quit.” Eric Weinstein on Joe Rogan #1626 3:15 https://www.youtube.com/watch?v=l1jTUhwWJYA
Even tenured professors are steered.

The red pill and blue pill.
This is a common meme from a scene in the 1999 film The Matrix. It refers to a choice between the willingness to learn a potentially unsettling or life-changing truth, by taking the red pill, or remaining in contented ignorance with the blue pill. Over the last ten years of building the LRT I’ve come to realize when a PhD has taken the blue pill. Keep working and soon you will, too.

That’s why this blogpost exists.
Blogposts sponsored by major publications like Scientific American, are less about science and more about journalism, reporting the untested results of published papers.

Textbooks are too often used as unchangeable bibles,
instead of jumping off points for the next set of discoveries.

American physicist, Richard Feynman once said,
“As a matter of fact, I can also define science another way: Science is the belief in the ignorance of experts.”

Historically
it has taken an outsider, someone not beholding to one professor or to the rest of the professors, to clean house. Yale paleontologist John Ostrom was an insider with an outsider idea and even he had a frustrating story to tell about how long his ideas took to come to consensus.

The video above
at 33:40 discusses the tiny (5%) number of those who train for jobs in academia actually get jobs in academia. It also discusses the large percentage (50%) of grant money that goes directly to the university. Under this system the university hires students, often foreign students, to do the teaching for low wages leaving the successful grant writers to keep writing expensive grant applications.

ResearchGate.net
reports readership for my papers and manuscripts on their site has surpassed 5000 with some papers exceeding 600 reads. That’s good to hear. Just getting the information out is why anyone writes a manuscript. Nowadays everything is downloaded. If you’re not a card-carrying student or faculty member at many universities, you’re not going to be allowed in their libraries to browse the increasingly old-fashioned book shelves.

Finally, it’s up to others to approve or dismiss,
and that’s out of our control no matter if we publish fact or fancy, online or in the literature. Good luck in your career. Don’t let anything restrict your studies.


References
Black R 2010. https://www.smithsonianmag.com/science-nature/who-pays-for-dino-research-66263095/
Dinerstein C 2017. The surprising history of peer review. American Council of Science and Health. online here.
Kampourakis K et al. (3 co-authors) 2015. Peer review and Darwinian selection. Science & Education 24:1055–1057.

collegescholarships.org/scholarships/science/paleontology.htm
palass.org/awards-grants/grants/list-external-grants
usnews.com/education/best-graduate-schools/articles/what-paleontology-is-and-how-to-become-a-paleontologist

john-ostrom-the-man-who-saved-dinosaurs/
indeed.com/how-much-does-a-paleontologist-make
work.chron.com/salary-palaeontologist

For more PhD shenanigans, click on these links:
Padian 1 –  Padian 2 
Naish
Witton
Hone and Benton  –
Benton 1
Ezcurra 1
Cau 1

Bears, bears and more bears

This post had its genesis
in a recent YouTube video all about bears by Moth Light Media. After phylogenetic analysis in the large reptile tree (LRT, 1834+ taxa, subset Fig. 1) ‘bears’ are no longer monophyletic. Instead the various extant ‘bears’ are better considered giant kinkajous, weasels, wolverines and bush dogs, all converging on similar ‘bear’-like morphologies.

Figure 1. Subset of the LRT focused on Carnivora, a placental mammal clade. Note the polyphyletic nesting of various 'bears' indicating that they are all just large kinkajous, weasels, wolverines and bush dogs converging on similar bear-like morphologies.

Figure 1. Subset of the LRT focused on Carnivora, a placental mammal clade. Note the polyphyletic nesting of various ‘bears’ indicating that they are all just large kinkajous, weasels, wolverines and bush dogs converging on similar bear-like morphologies. Note the separation of seals (dark yellow) from sea lions (peach).

Jiangzuo and Flynn 2020
discussed the earliest ursine bear and the origin of plant-dominated omnivory in Carnivora. Unfortunately they worked within an invalid phylogenetic context brought about by taxon exclusion. The wolf, Canis lupus, was their outgroup taxon. So their cladogram was upside-down compared to the LRT (Fig. 1). Basalmost members of Carnivora and their outgroups among basalmost Placentalia were all agile arboreal omnivores, not digitigrade cursors (runners), like Canis.

Jiangzuo and Flynn consider the spectacled bear,
Tremarctos, a member of the ursine bears. In the LRT Tremarctos arises from the bush dog, Speothos, far apart from ursines.

Jiangzuo and Flynn consider the wolverine,
Gulo, a member of the mustelids. In the LRT the short face bear, Arctodus, arises from the wolverine, Gulo, apart from ursines. 

Jiangzuo and Flynn consider the giant panda,
Airluropoda, a type of bear. In the LRT it arises from the herbivorous kinkajou (genus: Potos) before the appearance of the ancestor of the rest of the ‘bears’, Mustela, the weasel.

Jiangzuo and Flynn do not include
Speothos or Potos in their text. The authors separate Gulo in the clade Mustelida, apart from bears in their study. So taxon exclusion mars this otherwise detailed study of bear dentition and diet.

In like fashion,
McLellan and Reiner 1994 also excluded a long list of pertinent taxa in their review of bear evolution.

Sharp-eyed readers will note the addition of two taxa
to the Carnivora, the sea otter (Enhydra) and the basal walrus (Protodobenus).


References
Jiangzuo Q and Flynn JJ 2020. The earliest ursine bear and the origin of plant-dominated omnivory in Carnivora. iScience 23, 101235, June 26, 2020.
McLellan B and Reiner DC 1994. A review of bear evolution. Int. Conf. Bear Res. and Manage. 9(1):85-96

 

Short-faced, big-eyed taxa at the base of all bony fish

The origin of bony fish 
is a traditional enigma. Apparently no one before the LRT derived bony fish from specific hybodontid sharks. Perhaps this is so due to a lack of effort. Evidently no prior workers applied tetrapod homologs to all vertebrate skulls, including sharks and sturgeons. Applying those homologs was required here in the large reptile tree (LRT) in order to score all taxa using a common set of traits.

According to Arratia 2010,
“Traditionally, fossils have played little role in most studies of the phylogenetic relationships of teleosts. The usual approach is to study only recent fishes and when fossils are considered their position is assumed in the cladogram. During the last few years this approach has been challenged by the inclusion of both fossil and recent species in phylogenetic studies.”

Unfortunately Arratia did not include enough fossil species. No sharks, No placoderms. No spiny sharks. No placoderms. No Gregorius (Fig. 1).

According to Arratia 2010,
“When fossil and recent taxa are included in phylogenetic analyses, the elopomorphs stand as the most plesiomorphic group among extant teleosts.”

Elopomorphs are not basal bony fish in the LRT where more taxa are included. Prohalecites (Fig. 1) and spiny sharks like Homalacanthus (Fig. 1) are basal taxa to their respective bony fish clades following the first great dichotomy of bony fish. Gregorius (Fig. 1) is their last common ancestor (LCA). Note the shorter rostrum and large eyes close to the anterior margin are juvenile traits retained into adulthood, as we discussed earlier.

Figure 1. Gregorius descends from Hybodus, the shark and is ancestral to Prohalecites at the base of the ray-fin bony fish. Gregorius is also ancestral to Homalacanthus at the base of the spiny sharks leading to lobefins, placoderms, catfish and a variety of other taxa.

Figure 1. Gregorius descends from Hybodus, the shark and is ancestral to Prohalecites at the base of the ray-fin bony fish. Gregorius is also ancestral to Homalacanthus at the base of the spiny sharks leading to lobefins, placoderms, catfish and a variety of other taxa. See figure 2 for a to scale view.

Figure 2. Representatives from the Early Devonian radiation that gave us bony fish, including Prohalecites and Homalcanthus.

Figure 2. Representatives from the Early Devonian radiation that gave us bony fish, including Prohalecites and Homalcanthus. Harpagofututor is close to living moray eels.

A short face and large orbit
characterize both branches of basal bony fish in the LRT, derived from Gregorius, a late survivor ion  the Late Carboniferous of an Late Silurian radiation.

Figure 1. Taxa from the LRT on one branch of the bony fish. Doliodus is one of these.

Figure 3. Taxa from the LRT on one branch of the bony fish. Doliodus is one of these.

Figure 1. Click to enlarge. Acanthodians and their spiny and non-spiny relatives in the LRT (subset Fig. 2), not to scale.

Figure 4. Acanthodians and their spiny and non-spiny relatives in the LRT (subset Fig. 2), not to scale.

Due to taxon exclusion,
Arratia 2010 lists the moray eel, Gymnothorax, and the gulper eel, Eurypharynx (Fig. 5), as elopomorphs. By contrast, when more taxa are added, as in the LRT, both nest closer to Gregorius and hybodontid sharks, both basal to the bony fish first dichotomy.

Figure 6. Eurypharynx evolution. This clade split from Gregorius prior to the major split in bony fish.

Figure 5. Eurypharynx evolution. This clade split from Gregorius prior to the major split in bony fish.

Some taxa (e.g  spiny sharks) at basal nodes in the LRT
are not mentioned by Arratia 2010. Some elops relatives (e.g. the swordfish, Xiphias) are not mentioned by Arratia 2010. Osteoglossum (Fig. 6) nests in the other bony fish clade, the one that includes placoderms, catfish, lobe fins and spiny sharks, and not at the base.

Figure 1. The arowana, an Amazon River predator, nests with Late Jurassic Dapedium in the LRT.

Figure 6. The arowana, an Amazon River predator, nests with Late Jurassic Dapedium in the LRT.

After spending several months 
with ninety+ ray fin fish, trying to shuffle and reshuffle them into their evolutionary order in the LRT (correcting hundreds of mistakes along the way) only a relative few LRT characters turn out to be important for lumping and splitting bony fish. And many of these recur as reversals and convergent trait, making the task more difficult.

  1. Orbit close to the tip of the rostrum, in the middle of the skull vs. close to the rear margin. Sometimes a sword can lengthen the rostrum
  2. Sagittal crest or not
  3. Maxilla either with teeth and a butt joint with the premaxilla, or loosely overlapping the premaxilla without teeth, or other variations
  4. Circumorbital bones absent, or present as a gracile ring, or present as large plates extending toward the preopercular, or as a gracile ring extending to the preopercular
  5. Rostral profile convex or cornered or straight or concave
  6. Coracoid short or long or essentially absent
  7. Parietals meet medially or split by an intervening postparietal
  8. Naris separate from the orbit or confluent
  9. Etc., etc.

Earlier we looked at the various radiations of bony fish
from a variety of spiny sharks in their ancestry (Fig. 4). Since then more taxa have been added, especially on the ray-fin clade. Please see the LRT for the latest cladogram.


References
Arratia G 2010. Critical analysis of the impact of fossils on teleostean phylogenies, especially that of basal teleosts. In: Morphology, Phylogeny and Paleobiogeography of Fossil Fishes Elliott DK, Maisey JG, Yu X and Miao D (eds.): pp. 247-274, 15 figs., 6 tabs. Verlag Dr. Friedrich Pfeil, München, Germany – ISBN 978-3-89937-122-2

https://pterosaurheresies.wordpress.com/2020/05/08/an-unexpected-resolution-to-the-spiny-shark-problem/

Scapulocoracoid and humerus ‘assigned’ to Lagerpeton might belong to Procompsognathus

McCabe and Nesbitt 2021
assigned a disarticulated Late Triassic scapulocoracoid and humerus (MCZ 101542) to Lagerpeton (Fig. 1) in the absence of any pervious similar bones for the Lagerpeton holotype.

Gutsy.
Workers have been trying to rebuild a chimaera of Lagerpeton from disassociated parts for several years now, hoping it will somehow shed some insight into dinosaur and pterosaur origins.

This is all for naught because Lagerpeton is a bipedal chanaresuchid that ran on two toes, not an archosaur (dinosaurs + crocs) or fenestrasaur (pterosaurs and their ancestors).

Figure 1. Tropidosuchus and Lagerpeton compared to the new material (MCZ 101542).

Figure 1. Tropidosuchus and Lagerpeton compared to the new material (MCZ 101542).

How can McCabe and Nesbitt assign that pectoral girdle?
The holotype of Lagerpeton lacks any pectoral girdle material. So we can only imagine missing elements based on phylogenetic bracketing and comparative anatomy.

Figure 2. MCZ 101542 scapulocoracoid and humerus compared to Dromomeron humerus.

Figure 2. MCZ 101542 scapulocoracoid and humerus compared to Dromomeron humerus.

Given that,
does the MCZ 101542 material closely resemble comparable bones in closely related taxa? In the large reptile tree (LRT, 1810+ taxa) Lagosuchus nests with Tropidosuchus (Fig. 1), not with dinosaurs or pterosaurs.

A problem arises.
Tropidosuchus (Fig.1) has a larger, hourglass-shaped scapula with a short ‘waist’. By contrast the MCZ 101542 scapula (Fig. 1) has a smaller, straighter, narrower, more rectangular shape. So, maybe we should look for a better match… if there is one.

Figure 2. MCZ 101542 compared to Marasuchus and Lagosuchus.

Figure 2. MCZ 101542 compared to Marasuchus and Lagosuchus.

Is material from another taxon a little more similar?
Marasuchus (Fig. 2; PVL 3871) has a more robust, but otherwise similarly straight scapulocoracoid with a dinosaurian deltopectoral crest located about a third the way down the slender humerus, and more similar in scale. Lagosuchus (Fig. 2; UPLR 090) has a similarly gracile scapulocoracoid (at least what’s left of it). It’s all iffy.

McCabe and Nesbitt also make comparisons
when they note, “Compared to Lagosuchus talampayensis (PVL 3871), the scapular blade of MCZ 101542 is much more strap-like (near parallel anterior and posterior side) and the distal end expands more in Lagosuchus talampayensis.” 

Their table 2 lists ‘species’ Marasuchus‘ with specimen number PVL 3871. So their Marasuchus (PVL 3871) is not Lagosuchus (UPLR 090; Fig. 2).

McCabe and Nesbitt also write
“The glenoid of MCZ 101542 is directed posteroventrally like that of other avemetatarsalians (e.g., lagerpetids, Lagosuchus talampayensis, silesaurids, dinosaurs).”

In the LRT Avemetatarsalia is a junior synonym for Reptilia because it also include pterosaurs. Lagerpetids are proterochampsids, not dinosaur relatives. And, once again the authors’ Table 2 does not match their text with regard to nomenclature and specimen numbers.

Figure 3. Ixalerpeton compared to MCZ 101542.

Figure 3. Ixalerpeton compared to MCZ 101542.

The protorosaur, Ixalerpeton
(Fig. 3) is similar in size to MCZ 101542, but the shapes are slightly different.

The authors note,
“Within Lagerpetidae, the humerus of Ixalerpeton polesinensis (ULBRA-PVT059) is more robust than MCZ 1010541 (Fig. 4), with proportionally much larger proximal and distal expansions. The proportions of the humerus of Lagosuchus talampayensis (PVL 3871) matches that of MCZ 101541, with overall weakly expanded articular ends.”

Would you like to see a ‘Hail Mary’ pass based on taxon exclusion?
The authors report, “Overall, the gracile proportions of MCZ 101541 (= MCZ 101542 = the humerus) are unlike early archosaurs and their close relatives.”

When workers give up like this,
it’s usually due to taxon exclusion, whether intentional or not.

Figure 4. Procompsognathus has proportions that precisely fit the MCZ 101542 material.

Figure 4. Procompsognathus has proportions that precisely fit the MCZ 101542 material.

 

In this case there is a close match for the gracile proportions
of MCZ 101542 and it comes from a taxon that happens to be missing the scapulocoracoid and humerus, the Late Triassic theropod from Germany, Procompsognathus (Fig. 4), a taller relative of Marasuchus in the LRT. Like a lock and a key, a Yin and a Yang, the MCZ material is a perfect fit including the narrow, but deep anterior torso required to fit the narrow but deep scapula and coracoid. The authors did not mention Procompsognathus. So taxon exclusion continues to be a problem here. If inappropriate, at least it should have been considered and eliminated.

Still, this is only a gutsy guess.
See how reconstructions can help?

The LRT uses more complete taxa
whenever possible. To assign two bones to a specific genus is getting close to “Pulling a Larry Martin.” Be careful when you go there. It’s worth a shot (Fig. 4), but it’s easy to be wrong.


References
McCabe MB and Nesbitt SJ 2021. The first pectoral and forelimb material assigned to the lagerpetid Lagerpeton chanarensis (Archosauria: Dinosauromorpha) from the upper portion of the Chañares Formation, Late Triassic. Palaeodiversity, 14(1) : 121-131.

wiki/Procompsognathus

Tynskya and Messelastur enter the LRT with overlooked bird taxa

Today
two birds enter the LRT, nesting at nodes the experts overlooked. Both were considered closely related members of the clade Messelasturidae. “Initially interpreted as stem-owls, more recent studies have shown that they are actually closely related to modern parrots and are in the same order, Psittaciformes,” according to Wikipedia.

Not true in the LRT.

Backstory #1:
Didunculus, the tooth-billed pigeon (Fig. 1) does not nest in the large reptile tree (LRT, 1807+ taxa) with pigeons or dodos. Instead Didunculus nests with Falco, the falcon, far from pigeons, close to owls, owlets and swifts, something we learned a few years ago.

Figure 2. Figures of the Didunculus skeleton.

Figure 1. Figures of the Didunculus skeleton.

Today’s first bird is
Messelastur (Fig. 2) from the famous middle Eocene Messel pit.

Figure 2. Messelastur skull with colors added.

Figure 2. Messelastur skull with colors added. Note the displaced beak tip and another possible displaced premaxillary bone.

The literature on Messelastur includes:

Peters 1994 (not me) considered Messelastur a member of the Accipitridae (= hawks, eagles, Old World vultures and kin, but not owls). Note the sharp predaceous beak.

Mayr 2005 wrote: “They [Messelasturidae] provide a morphological link between Strigiformes and Falconiformes (diurnal birds of prey), and support the highly disputed falconiform affinities of owls in combining derived tibiotarsus and tarsometatarsus characters of owls with a more plesiomorphic, ‘falcon-’ or ‘hawk-like’, skull morphology.”

Wikipedia 2021 reports, “more recent studies have shown that they are actually closely related to modern parrots and are in the same order, Psittaciformes.” Psittaciformes = parrots (Fig. 3). The Wiki author was citing:

Mayr 2011, who wrote, “If future data strengthen their psittaciform affinities, they not only add a distinctive new taxon to the stem lineage of Psittaciformes, but also show that some stem group Psittaciformes were predatory birds.”

When added to the LRT
Messelastrus nests not with parrots (Fig. 3), but with Didunculus (Fig. 1). Parrots still nest with hoatzins, giant flightless parrots, sparrows and chickens far from hawks, owls and kin.

Figure 3. Skeleton of Ara macao, the scarlet macaw. Note the skeleton has pedal digits 3 and 4 switched.

Figure 3. Skeleton of Ara macao, the scarlet macaw. Note the skeleton has pedal digits 3 and 4 switched.

Backstory #2:
Apus,
the common swift, does not follow tradition and nest with hummingbirds in the LRT. Rather, as we learned several years ago the swift nests with Aegotheles, the owlet, close to owls and other predatory birds.

Figure 2. Apus the common swift is actually a close relative of the falcon and owl, not a hummingbird.

Figure 4. Apus the common swift is actually a close relative of the falcon and owl, not a hummingbird.


Mayr 2000 first described

Tynskya (Fig. 4) an early Eocene Green River bird he considered a link between falcons and owls. In the LRT Tynskya nests with Apus, the swift (Fig. 4), not far from falcons and owls. The skull of Tynskya had huge eyes and a tiny beak, just like Apus, along with hundreds of other aligning traits.

Figure 5. Tynskya in situ and with some parts pulled out for clarity. Apparently the pelvis and backbone are still buried in this ventral view of the torso, dorsal view of the skull after neck torsion.

Figure 5. Tynskya in situ and with some parts pulled out for clarity. Apparently the pelvis and backbone are still buried in this ventral view of the torso, dorsal view of the skull after neck torsion. The ‘x’ marks a broken humerus.The broken sternum is reassembled at lower left.

As you can see,
in both new taxa (above) more closely related taxa were excluded, something the LRT is designed to minimize. Minimizing taxon exclusion will help you nest taxa that display traits convergent with unrelated taxa, like hawks and parrots. Fewer enigmas result, if that’s okay with you. Enigmas and mysteries make paleontology more interesting and intriguing. Unfortunately, the LRT has removed many over the last ten years.


References
Mayr G 2000a. A new raptor-like bird from the Lower Eocene of North America and Europe. Senckenbergiana lethaea 80:59–65.
Mayr G 2005. The postcranial osteology and phylogenetic position of the Middle Eocene Messelastur gratulator Peters, 1994—a morphological link between owls (Strigiformes) and falconiform birds? Journal of Vertebrate Paleontology 25(3):635–645.
Mayr G 2011. Well-preserved new skeleton of the Middle Eocene Messelastur substantiates sister group relationship between Messelasturidae and Halcyornithidae (Aves, ? Pan-Psittaciformes). Journal of Systematic Palaeontology 9(1):159-171.
Peters DS 1994. Messelastur gratulator n. gen. n. spec., ein Greifvogel aus der Grube Messel (Aves: Accipitridae). Courier Forschungsinstitut Senckenberg 170:3–9.

wiki/Accipitridae
wiki/Didunculus
wiki/Tooth-billed_pigeon

Haya 2021: still suffering from taxon exclusion

Barta and Norell 2021
give us a detailed look at every bone in the basal ornithischian, Haya griva (Fig. 1). We looked at Haya earlier here and nested it close to Pisanosaurus in the large reptile tree (LRT, 1810+ taxa).

Figure 1. Haya in lateral view.

Figure 1. Haya in lateral view.

For reasons unknown
Barta and Norell did not include Chilesaurus and Daemonosaurus (Fig. 2) in their text or phylogenetic analysis.

Figure 1. Skulls of Daemonosaurus, Haya and Jeholosaurus to scale.

Figure 1. Skulls of Daemonosaurus, Haya and Jeholosaurus to scale.

The hypothesis of interrelationships 
that nested Chilesaurus and Daemonosaurus as phytodinosaurs basal to Ornithischia (Fig. 2) has been online since 2011.

Figure 2. Subset of the LRT focusing on the Phytodinosauria with Buriolestes at its base.

Figure 2. Subset of the LRT focusing on the Phytodinosauria with Buriolestes at its base.

No matter how much detail you put into your study of a taxon
it is all for naught if you decide to exclude pertinent taxa. You will not understand the phylogeny of that taxon, how it relates to others. Haya is a basalmost ornithischian in the LRT, an hypothesis of interrelationships not confirmed by Barta and Norell due to taxon exclusion. They had a chance to deliver big news and muffed it.

The Barta and Norell cladogram suffered from massive loss of resolution
at many nodes. Never a good sign. If you can tell two taxa apart generically, as fossils, you should be able to lump and separate them in a cladogram.

Perhaps too many incomplete taxa were tested.
Don’t include incomplete taxa until you have your tree topology all worked out first.


References
Barta DE and Norell MA 2021. The osteology of Haya griva (Dinosauria: Ornithischia) from the Late Cretaceous of Mongolia. Bulletin of the American Museum of Natural History 445: 1-111.

 

Brocklehurst and Field 2021: Tooth loss in birds

Brocklehurst and Field 2021 report,
“The origin of crown bird edentulism has been discussed in terms of a broad-scale selective pressure or trend toward toothlessness, although this has never been quantitatively tested. Here [Fig. 1], we find no evidence for models whereby iterative acquisitions of toothlessness among Mesozoic Avialae were driven by an overarching selective trend. Instead, our results support modularity among jaw regions underlying heterogeneous tooth loss patterns, and indicate a substantially later transition to complete crown bird edentulism than previously hypothesized (∼ 90 MYA). We show that patterns of avialan tooth loss adhere to Dollo’s law and suggest that the exclusive survival of toothless birds to the present represents lineage-specific selective pressures, irreversibility of tooth loss, and the filter of the K–Pg mass extinction.”

Never? Not true and more quantitively than in Brocklehurst and Field. According to the LRT a clade of Cretaceous toothed birds arose from a series of toothless taxa, including Megapodius (Figs. 2, 3). Brocklehurst and Field could have found this, too, but their taxon list is too small. Taxon exclusion is the #2 problem in paleontology.

Figure 1. Cladogram from Brocklehurst and Field 2021. Note the paucity of cherry-picked taxa compared to the LRT.

Figure 1. Cladogram from Brocklehurst and Field 2021. Colors added to clades. Note the paucity of cherry-picked taxa compared to the LRT. Entire clades of extinct birds are missing here due to taxon exclusion.

When you minimize taxon exclusion,
as in the LRT (subset Fig. 2) the actual patterns of evolution start to emerge. When you cherry-pick taxa (Fig. 1), you risk missing the important nodes and steps that Brocklehurst and Field missed.

Figure 4. Subset of the LRT focusing on birds. Chongmingia is highlighted in yellow in the Scansoriopterygidae.

Figure 4. Subset of the LRT focusing on birds. The amber box are the toothed Cretaceous birds, descendants of toothless taxa like Megapodius.

The Brocklehurst and Field 2021 study
depends on a valid phylogenetic context, but suffers from taxon exclusion. Only one ‘Archaeopteryx‘ taxon was used. A competing online cladogram (the LRT, subset Fig. 2) finds that nine of thirteen Solnhofen birds are needed to flesh out the origins of various succeeding bird clades, each with a few Solnhofen birds at their base.

Figure 1. Click to enlarge. Toothed birds of the Cretaceous to scale.

Figure 1. Click to enlarge. Toothed birds of the Cretaceous to scale.

Several toothless extant birds
that phylogenetically precede the Eogranivora to Ichthyornis and Yanornis clade (Figs. 2, 3) were excluded from this analysis. Missing taxa include Apteryx, Megapodius, and all members of the Palaeognathae, both living and extinct. Brocklehurst and Field missed a great opportunity due to taxon exclusion.


References
Brocklehurst N and Field DJ 2021. Macroevolutionary dynamics of dentition in Mesozoic birds reveal no long-term selection towards tooth loss, ISCIENCE (2021), doi: https://doi.org/10.1016/j.isci.2021.102243.

Purgatorius and Plesiadapis are still not primates contra Wilson et al. 2021

Short one today
on Purgatorius (Early Paleocene; Fig. 1), a mandible taxon considered by Wilson et al. 2021 to be a member of the Plesiadapiformes (Fig. x).

Figure 1. Purgatorius compared to other basal and often Paleocene mammals.

Figure 1. Purgatorius compared to other basal and often Paleocene mammals.

Wilson et all 2021 report
“Plesiadapiforms are crucial to understanding the evolutionary and ecological origins of primates and other euarchontans (treeshrews and colugos) as well as the traits that separate those groups from other mammals.”

No they are not.

Adding taxa
shifts plesiadapiformes deep into the clade Glires (Fig. x) where Plesiadapis joins Daubentonia as primate-like rodents close to Carpolestes and Ignacius.

Figure 1. Ignacius and Plesiadapis nest basal to Daubentonia in the LRT.

Figure 2. Ignacius and Plesiadapis nest basal to Daubentonia in the LRT.

Wilson et al. also reported
similarities in Purgatorius to Palaechthon, which nested in 2017 with the demopteran, Cynocelphalus in the large reptile tree (LRT, 1807+ taxa). Wilson et al. considered Palaechthon a member of the Plesiadapiformes.

Figure 1. Subset of the LRT focusing on basal placentals, including multituberculates.

Figure x. Subset of the LRT focusing on basal placentals, including multituberculates.

We looked at Purgatorius earlier
here in 2017.

Colleagues, expand your taxon lists.
If you don’t look in there, you won’t see what’s in there. So look. Add taxa. Sometimes traditions, professors and textbooks are not complete or incorrect. Find out for yourself.


References
Wilson MGP et al. , (9 co-aiuthors) 2021. Earliest Palaeocene purgatoriids and the initial radiation of stem primates Royal Society open science 8210050
http://doi.org/10.1098/rsos.210050

https://pterosaurheresies.wordpress.com/2019/03/07/tweaking-palaechthon-basal-volitantia/

Sea horse evolution back to large Cretaceous predators

Another series of taxa pulled from the LRT
focusing on phylogenetic miniaturization (PM) in the lineage of sea horses (Fig. 1). PM starts with 60cm-long Early Cretaceous Notelops and similar extant Scomberoides, the queenfish (Fig. 1), which is also (quite obviously) basal to mackerel and tuna.

Figure 1. Seahorse evolution back to Notelops (Early Cretaceous).

Figure 1. Seahorse evolution back to Notelops (Early Cretaceous).

Less obviously,
in the large reptile tree (LRT, 1806+ taxa) another descendant of Scomberoides is the 10x smaller zebra fish (Danio, Fig. 1).

Here’s where it gets interesting…
The sagittal crest present in Scomberoides (Fig. 1) is absent in Danio and the parietals return to meet each other medially, as in basal bony fish like Amia and Prohalecites. This phylogenetic reversal makes creating a cladogram more difficult, due to convergence, but all the more challenging. Danio descendants remains tiny and crestless. I have no data if Scomberoides hatchlings have crests or not. If so that would be a case of neotony leading to Danio.

Relative to Notelops
larger eyes are first seen, not in tiny Danio, but in big Scomberoides (Fig. 1), prior to PM. That increase in orbit size comes at the cost of a reduction in cheek plates that never comes back in descendant taxa. In Scomberoides the circumorbital ring actually overlaps the preopercular (light yellow) and hyomandibular (dark green). That’s a rare trait that makes it a bit difficult to score.

The jugal
(cyan color) in Danio (Fig. 1) is still large, though disconnected from the circumorbital ring where Gregory 1933 labels it the symplectic. According to Wikipedia, the symplectic is “an additional bone linking the jaw to the rest of the cranium.”  That also makes that bone difficult to score. Seeing this bone in a variety of taxa led to the conclusion that it was homologous to the jugal. Starks 1901 listed several synonymies used by various authors for bones of the fish skeleton. None synonymized the jugal and symplectic. That may have changed in the 120 years since. Let me know, if so.

Stickleback stickles
readily seen in Gasterosteus, are first seen in Scomberoides (Fig. 1), though lost in Danio.

Jaw joint migration from behind the orbit
to way out in front of the orbit in this series of taxa starts with Scomberoides, documents a mid-point in Danio, and reaches a conclusion in Gasterosteus (Fig.1).

Figure x. Rayfin fish cladogram. This one represents the latest subset of the LRT.

Figure x. Rayfin fish cladogram. This one represents the latest subset of the LRT.

That’s the utility of the LRT
and the ready-at-your-fingertips online data with all bones colorized using DGS.


References
Starks EC 1901. Synonymy of the fish skeleton. Proceedings of the Washington Academy of Sciences 3:507-539. PDF here.

Cawley et al. 2020 did not realize Mesozoic pycnodonts were derived from extant bonefish

Cawley et al. 2020
brought us an overview of a clade of Mesozoic fish, the Pycnodontiformes (Fig. 1).

From the abstract
“Two other neopterygian clades possessing similar ecological adaptations in both body morphology (†Dapediiformes) and dentition (Ginglymodi) also occurred in Mesozoic seas.”

Short note: Dapediformes includes Dapedium and kin (taxa related to gars, like Lepisosteus in the LRT). Ginglymodi includes Semionotiformes (Semionnotus) and Lepidotidae (Lepidotes and Lepisosteus (= gars)). These taxa nest basal to catfish + placoderms in the LRT. They are Silurian in origin, not related to Pycnodus (Fig. 2) and Albula (Figs. 1, 3) in the LRT.

From the introduction:
“The overarching goal of this study is to evaluate the success but also final demise of pycnodontiform fishes, which represented the major marine actinopterygian elements from the Late Triassic to Palaeogene.”

Figure 1. Color image from Cawley et al. 2020. Albula added. Taxa below the gray line are Semionotiformes unrelated to pycnodontiformes.

Figure 1. Color image from Cawley et al. 2020. Albula added. Taxa below the gray line are Semionotiformes unrelated to pycnodontiformes.

Unfortunately Cawley et al. fails to mention
the extant pycnodontiform, the bonefish, Albula, which nests with the pycnodontiforms, Flagellipinna and Pycnodus (Agassiz 1835), in the large reptile tree (LRT, 1804+ taxa).

Also unfortunately,
Cawley et al. inappropriately includes several members of the Dapediidae and Semionotiformes (Fig. 1). Due to taxon exclusion the authors don’t realize these taxa nest in the other major clade of bony fish, apart from most ray fins, closer to spiny sharks, placoderms and lobefins, far from Pycnodus and Albula.

Cawley et al. reports, 
“Pycnodontiforms represent a well-defined monophyletic group…”

then admits,
“but the intrarelationships of various taxa and groups remain debated.” The LRT tests virtually all other fish clades.

Figure 2. Pycnodus with bones colorized according to tetrapod homologies. Third frame shows maxilla and lacrimal returned to in vivo positions.

Figure 2. Pycnodus with bones colorized according to tetrapod homologies. Third frame shows maxilla and lacrimal returned to in vivo positions.

Wikipedia reports,
Pycnodontiformes is an extinct order of bony fish. The group evolved during the Late Triassic and disappeared during the Eocene. The group has been found in rock formations in Africa, Asia, Europe, North and South America. The pycnodontiforms were small to middle-sized fish, with laterally-compressed body and almost circular outline. Pycnodontiform fishes lived mostly in shallow-water seas. They had special jaws with round and flattened teeth, well adapted to crush food items. One study links the dentine tubules in pycnodont teeth to comparable structures in the dermal denticles of early Paleozoic fish. Some species lived in rivers and possibly fed on molluscs and crustaceans.”

Figure 1. Albula vulpes skull with highly derived facial bones reidentified here. Note the lateral premaxillary processes and 'floating' cheek bones. Green vertebrae are caudals.

Figure 3. Albula vulpes skull with highly derived facial bones reidentified here. Note the lateral premaxillary processes and ‘floating’ cheek bones. Green vertebrae are caudals.

Pycnodus according to Wikipedia
“The known whole fossils of Pycnodus are around 12 centimetres (5 in) long, and have a superficial resemblance to angelfish or butterflyfish. The animals, as typical of all other pycnodontids, had many knob-like teeth, forming pavements in the jaws with which to break and crush hard food substances, probably mollusks and echinoderms. These teeth are the most common form of fossil.”

According to Wikipedia
Bonefishes live in inshore tropical waters and moves onto shallow mudflats or sand flats to feed with the incoming tide. The bonefish feeds on benthic worms, fry, crustaceans, and mollusks. Ledges, drop-offs, and clean, healthy seagrass beds yield abundant small prey such as crabs and shrimp. It may follow stingrays to catch the small animals they root from the substrate.”

Apparently no one has reported
that pycnodontiformes is an extinct clade within the extant clade Albulidae. Likewise no one has reported that Semionotifomes are not related to Pycnodontiformes. If so, please send the citation so I can promote it here.


References
Agassiz JLR 1835.Recherches sur les Poissons fossiles, 5 volumes. Imprimerie de Petitpierre et Prince, Neuchaatel, 1420 pp.
Bleeker P 1859. xx
Cawley JJ et al. (5 co-authors) 2020.
Rise and fall of Pycnodontiformes: Diversity, competition and extinction of a successful fish clade. Ecology and evolution DOI: 10.1002/ece3.7168

wiki/Pycnodontiformes
wiki/Pycnodus
wiki/Bonefish

Pycnodontiformes Berg 1937
Albulidae Bleeer 1859