Brusatte 2022 reports, ‘How mammals conquered the world after the asteroid apocalypse’ – without saying ‘How’

According to SciAm.com
“Steve Brusatte is a professor at the University of Edinburgh and author of The Rise and Reign of the Mammals, a new narrative history of mammal evolution (Mariner Books, 2022).”

Brusatte is a good writer, full of superlatives, active verbs and exciting adjectives. He’s popular with the public and the media. Unfortunately, Brusatte keeps demonstrating his lack of understanding the subject matter. He’s young. He hasn’t done the necessary analyses. He repeats what he learned in school. Too often his own words have internal conflicts (see below).

Sometimes young scientists need to curb their impulses to write books and use that time to create their own wide gamut cladogram in order to confirm and establish interrelationships. Then, with that authority, is the time to write the book. You don’t want to spread misinformation in permanent media, especially if that includes the potential for decades of professional embarrassment due to printed errors.

Figure 1. Ectoconus is an Early Paleocene, sheep-sized terrestrial former tree shrew.

Brusatte begins with the discovery of a new Ectoconus fossil:
“This fossil mammal, Ectoconus, was a revolutionary. It lived a mere 380,000 years after the worst day in Earth history, when a six-mile-wide asteroid ended the Age of Dinosaurs in fire and fury, ushering in a new world.”

First time we’ve ever heard Ectoconus was “a revolutionary.” Brusatte doesn’t report how it was a revolutionary, other than it was a placental mammal, like us. It’s not a new taxon. Cope described a complete skeleton (Fig 1) in 1884.

Brusatte writes,
“We actually know very little about the mammals that endured the extinction and persevered during the next 10 million years, during the Paleocene epoch.”

We actually know quite a bit about “the mammals that endured the extinction”, according to Brusatte himself! After all he “actually” wrote an entire book about it (see above), and the rest of the SciAm article (see below). This is example #1 of internal conflict mentioned above. We’ve seen this many times before. Paleontologists like to set up imagined problems so they can come in as heroes with imagined solution, too often failing due to taxon exclusion.

“Dinosaurs became giants and excluded mammals from large-bodied niches. Mammals did the opposite: with their small body sizes, they could exploit ecological niches that the bigger dinosaurs couldn’t access.”

Readers: Is this correct? Giant vs small? Or is this over simplification? Were there no small to medium dinosaurs? No medium to large mammals, like… Ectoconus (Fig 1)? [Internal conflict #2]. Maybe the situation is more complex than “dinosaurs became giants”.

“A bounty of pint-sized mammals—none larger than a badger—lived underfoot of the dinosaurs.”

Underfoot? Or above the heads of dinosaurs? The LRT indicates many Mesozoic mammals were arboreal.

“One such group—the multituberculates—flourished in the Cretaceous underworld… Meanwhile, as multituberculates prospered, three other groups quietly branched off on their own. These trailblazers gave rise to the three mammal lineages that persist today.”

After analysis multituberculates are highly derived members of placental clde Glires, the gnawing clade. We have Jurassic porcupines (Maiopatagium). Brusatte doesn’t know this.

“These trailblazers“ (= multituberculates) did not give rise to the three mammal lineages that persist today. That’s a textbook myth Brusatte repeats without testing.

“The molecular clock—a technique that uses DNA differences among modern species and back calculates to estimate when they diverged—predicts that some placental lineages, including primates, lived alongside the dinosaurs. Although paleontologists are desperate to recover fossils of such early placentals, they have yet to be found.”

The LRT uses traits to determine the same conclusion. Look at Nasua, the coatimundi, and the very similar lemur, Lemur. Both are basal placentals, likely appearing in the Early Jurassic, and still living today! This phylogenetic information was overlooked by Brusatte. DNA (= genomic testing) is to be avoided in deep time analyses.

Figure 2. The coatimundi (Nasua) compared to the ring-tailed lemur (Lemur).

Brusatte wrote,
“Perhaps surprisingly, mammals were doing well in the latest Cretaceous. At least 30 species lived in Montana back then, filling many ecological roles at the base of the dinosaur-dominated food chain, including bone crunchers, flower eaters, insectivores and omnivores.”

Bone crunchers? Flower eaters? Could Brusatte be more specific? His readers are not children. Here I’m going to guess: Bone crunchers are triisodontids = archaic hippos crunching grasses and pond plants. Flower eaters are herbivores in general, from rabbits and squirrels to deer and pygmy opossums since ‘herbivores’ do not make Brusatte’s list even though his Ectoconus (Fig 1) was an herbivore.

“The vast majority of these creatures were metatherians (early members of the marsupial line) or multituberculates. Early cousins of placentals called eutherians were present, though rare.”

In the LRT, multituberculates are placentals. Brusatte should have known this if he had spent a little time to test them, rather than rely on outdated university textbooks.

Early cousins of placentals called eutherians? The LRT does not recover this distinction. Nor does Brusatte explain this distinction. Earlier he said there there were only three mammal lineages, which is correct. Brusatte makes it sound like there was one more.

“The earliest Paleocene scene is dire. There is a fossil locality in Montana dated to approximately 25,000 years after the asteroid hit, called the Z-Line Quarry. It reeks of death. Almost all the mammals that flourished in the region in the Cretaceous are gone; only seven species remain.”

Seven species? Which seven? How diverse or restricted?

“Several other fossil sites divulge what was happening over the next 100,000 to 200,000 years. If you pool together all mammals from this time, there are 23 species.”

Let’s take a moment to digest this. Brusatte is telling his readers how extremely rare fossils are in general. He tells us what all paleontologists know. There are only a few tiny windows of time within a few tiny windows of geography that preserve fossils. That means there are huge expanses of unaccounted, unsurveyed, undug time and geography that multiply those numbers by simple extrapolation.

Brusatte reports,
“A paltry 7 percent of mammals survived the carnage.”

Earlier Brusatte reported 7 of 30 species survived, then 23 of 30 species. Neither of those represent seven percent. Or is Brusatte talking raw numbers from two tiny windows in time and space. In any case, which ones? How? The word “How” is in the headline, so we’re looking for a payoff.

Brusatte provides only this clue,
“This bleak state of affairs raises a question: What allowed some mammals to endure? The answer became apparent when Wilson Mantilla looked at the victims and survivors. The survivors were smaller than most of the Cretaceous mammals, and their teeth indicate they had generalist, omnivorous diets. The victims, on the other hand, were larger, with more specialized carnivorous or herbivorous diets.”

Remember Brusatte’s parameters: “The survivors were smalller” and omnivores. The “victims… were larger” and herbivores. These parameters can be immediately tested by the larger herbivorous Early Paleocene survivor Ectoconus (Fig 1) featured by Brusatte in his introduction. This is internal conflict #3.

Brusatte writes:
“Around 100,000 years postasteroid a new eutherian appeared in Montana and swiftly became common. Purgatorius, with gentle molar cusps for eating fruits and highly mobile ankles for clinging and climbing in the trees, was an early member of the primate line.”

This is incorrect. Purgatorius (Fig 3) is a late survivor of a Jurassic radiation of shrinking colugos, like Palaechthon. Basalmost primates are rather larger lemurs, similar in size and shape to basalmost carnivores, like living coatimundis and raccoons, also Jurassic in origin.

Figure 3. Purgatorius compared to other basal and often Paleocene mammals.

Brusatte wrote,
“Ectoconus, whose skeleton we excavated in 2014, was one of these trailblazers. When it was bounding through swampy rain forests and snacking on leaves and beans 65.6 million years ago, it was the largest mammal that had ever lived there.”

Internal conflict #3 repeated. This is just the sort of placental Brusatte said did not make it through the asteroid hit (see above). Since this specimen was found in New Mexico, not far from the Yucatan impact, Brusatte needs to explain this anomaly. This is the ‘how’ we’re wondering about, but Brusatte never gets around to explaining.

Brusatte wrote,
“The Paleocene mammals were not so easily categorized, however. They were clearly much larger than any Cretaceous mammals”

Here Brusatte reports the survivors were “larger than any Cretaceous mammals”.
Earlier Brusatte reported, “The survivors were smaller than most of the Cretaceous mammals.“
Someone is not proofreading Brusatte’s text for internal conflict.

“and they lacked epipubis bones at the front of their pelvis, suggesting they had large placentas to nourish their young in utero. Thus, they were assuredly placentals. But their skeletons seemed peculiar—stocky and muscle-bound, with mashups of features seen in various groups of modern-day mammals.”

I realize Brusatte is writing for a popular audience, but epipubes are absent in some marsupials, present in some placentals. Putting all your phylogenetic faith in one or a few traits is called “Pulling a Larry Martin“. Only a last common ancestor determines which fossil taxa are in one clade or another.

Brusatte wrote,
“Tom and his crew have collected thousands of fossils, which paint a vivid picture of Paleocene life within the first million years of the asteroid.”

Notice: the picture has gone from ‘bleak‘ to ‘vivid‘, both describing only two small windows of fossil localities. Neither is close to a million years after the asteroid. Or is there a third locality?

Figure 4. A subset of the LRT representing the second half of placental evolution. Ectoconus nests with the pantodonts in the right column.

Bursatte continues:
“Among the roster of archaic placentals are animals like Ectoconus, which are shoehorned into a nebulous group called condylarths.”

Shoehorned? Does that mean it’s not a good fit? Why does Bursatte even mention ‘Condylarthra‘ when Wikipedia indicates this term has little to no academic standing and a traditional nebulous meaning?

“Members of this group were mainly plant eaters or omnivores with sturdy builds; many of them had hooves. They shared the herbivore niches with pantodonts—barrel-chested leaf gobblers with enormous hands and feet, which achieved sizes comparable to modern cows.”

In the LRT Ectoconus is precisely a pantodont, the clade basal to living edentates. That’s a phylogenetic story completely missed by Brusatte. And once again, were the survivors smaller or larger than their Cretaceous ancestors? This time they are comparable to modern cows.

Figure 5. Traditional Taeniodonta in a cladogram. With more taxa this clade splits up according to the colors shown here.

Brusatte continues:
“Another group, the taeniodonts, were gargoyle-esque diggers, which used their huge clawed forearms to tear through dirt and their massive jaws and enlarged canines to root out tubers.”

Traditional taeniodonts are paraphyletic (Fig 5). So this is not a clade. Mistakes like these keep undercutting Brusatte’s authority.

“All these mammals would have feared the triisodontids, the terrors of the Paleocene, which looked like wolves on steroids and smashed the bones of their prey with crushing molars.”

As explained yesterday, triisodontids were archaic hippos, herbivores with crushing molars, not ‘wolves on steroids’. Early carnivores were like coatimundis, raccoons and meerkats.

“We are building a vast data set of fossil and extant mammals, and their anatomical and genetic features, so that we can construct a master family tree.”

That’s a great concept! More taxa create a better “master family tree” (subset Fig 4).

“Our preliminary results are encouraging. Some of the archaic species, such as taeniodonts, might have stemmed from Cretaceous eutherian ancestors and thus would be among the most primitive placentals on the trunk of the family tree.”

Keep adding taxa, Dr. Brusatte until you find taeniodonts are not a natural group and ‘eutherians’ are placentals going back to the Jurassic.

“Others, including some of the condylarths, share features with today’s hoofed mammals and are probably proto-horses and proto-cattle.”

Probably? Yes, they are proto-cattle (Fig 4). That’s what you find after testing.

“Although the precise locations of condylarths and taeniodonts and their archaic ilk in the family tree remain to be worked out, we are already grasping what they were like as living, breathing animals.”

The precise locations have already been worked out in the LRT with full resolution. Next efforts from anywhere will either confirm, refute or correct the LRT.

Brusatte writes,
“Chief among these hallmarks of placental mammals is the capacity to birth well-developed young, which gestate for a prolonged period inside the mother before being born in an advanced state.”

Actually not so well developed in the first half of placental evolution, when many placental babies remained small, helpless and nest-bound, like humans, mice and dogs. In the second half (Fig 4) placentals are much better developed, able to walk behind, swim with or cling to their mothers almost immediately after birth.

Brusatte reports,
“Larger [placental] offspring could more easily grow into larger adults, which may have enabled the first placentals to rapidly balloon in stature within a few hundred thousand years of the dinosaurs’ demise, after 160 million years of being stuck at tiny sizes.”

This sounds like another Brusatte generalization with plenty of exceptions. For instance, wombats and kangaroos are big marsupials while bats and shrews are small placentals.

Figure 6. A large marsupial Diprotodon museum mount and dorsal views of the manus and pes.

Brusatte reports,
“The relative brain sizes of the archaic placentals were laughably small compared with not only those of today’s mammals but even those of the Cretaceous species living with the dinosaurs. The first placentals, it seems, got so big so fast that their brains couldn’t initially keep pace.”

This sounds like another Brusatte generalization with plenty of exceptions. Which Late Cretaceous placentals? Which Early Paleocene placentals? Were they related? If Brusatte could show this happening in a lineage, that would support his claim. Such a lineage is known (Fig 7), and it includes Ectoconus. Unfortunately lacking his own LRT, Brusatte is not aware of this natural clade. Again, do the work, THEN write the book and the article.

Figure 7. The origin of edentates includes the large, clawed herbivorous Paleocene Ectoconus, an asteroid survivor from New Mexico. How it survived is not explained by Brusatte 2022.

In summary,
Brusatte doesn’t tell his SciAm readers “how mammals conquered the world”. That would have been fascinating. The ‘how’ remains eagerly awaited. Instead Brusatte repeats old tropes and untested hypotheses, ignores internal inconsistencies and demonstrates a need to get up to speed phylogenetically. No doubt Dr. Brusatte has a full daily agenda at this stage in his young life: writing books, traveling to dig sites and conferences, his own scientific studies, working with students, perhaps raising a family. A busy day makes it difficult to put in as much time as needed (several years) to get up to speed phylogenetically.

References
Brusatte S 2022. How mammals conquered the world after the asteroid apocalypse. ScientificAmerican.com article
Cope ED 1884. The Amblypoda. The American Naturalist 18 (112):6=461-471.
Shelley SL, Williamson TE and Brusatte SL 2015. Resolving the higher-level phylogenetic relationships of “Triisodontidae” (‘Condylarthra’) within Placentalia, October 2015, Society of Vertebrate Paleontology (abstract)

http://reptileevolution.com/ectoconus.htm
S Brusatte mentions in the PterosaurHeresies

Triisodon quivirensis enters the LRT and pops a few myths reported by S Brusatte this week in Scientific American

According to Wikipedia,
“Triisodontidae is an extinct, probably paraphyletic, or possibly invalid family of mesonychian placental mammals.”

Triisodon quivirensis (Matthew 1901, 1937, Fig 1) does nest with mesyonychids and hippos in the large reptile tree (LRT, 2092 taxa). Paratriisodon is a good match to Andrewsarchus, as documented earlier here. Since Andrewsarchus is not a mesonychid, these two purported members are indeed paraphyletic (= unrelated to each other.) As far as I can tell other triisodontids are known from scraps, like teeth, so they can’t be tested in the LRT.

Figure 1. Triisodon skull somewhat restored. Frame 1 museum mount. Frame 2 colors added and teeth restored. Note the tiny orbit surrounded by dense bone. This is a basal mesonychid/hippo, so it is not ‘the terror of the Paleoene’, contra Brussatte 2022.

Wikipedia continues:
“Most triisodontid genera lived during the Paleocene in North America, but the genus Andrewsarchus (if it is a mesonychian, and not an artiodactyl) is known from the middle Eocene of Asia.”

Andrewsarchus is not a mesonychian nor an artiodactyl, but a leptictid angalid close to Rhynchocyon.

“Triisodontids were the first relatively large predatory mammals to appear in North America following the extinction of the non-bird dinosaurs.”

Triisodontids were not predatory. Like hippos and Mesonyx, they were herbivores with big canines and plant-crushing molars.

“They differ from other mesonychian families in having less highly modified teeth.^“

Actually, Triisodon doesn’t differ very much from mesonychids and hippos, taxa apparently omitted from consideration, unless the Wiki authors are considering hippos artiodactyls, which they are not.

In a 2016 conference paper, Williamson, Brusatte and Shelley wrote:
“Triisodontids are an archaic group of mammals that possess dental adaptations for carnivory, but are not members of the order Carnivora.”

This is an old myth that goes back to consider mesonychids as predators.

“They were probably apex mammalian predators for much of the early Paleocene.”

No, they were paleo-hippos. Herbivores. The skull above (Fig 1) is from the Middle Paleocene, according to the museum label.

“The wolf-sized species of Triisodon were the largest triisodontids and were also among the largest mammals of their time.”

This appears to be true. Late Paleocoene Coryphodon was 2.5m long, which is considerably larger than a wolf, but considerably later than the Middle Paleocene.

“A new specimen of the poorly known species Triisodon crassicuspis clarifies the diversity and evolutionary history of triisodontids and provides new morphological information that helps to untangle triisodontid interrelationships and aids in establishing the place of triisodontids on the mammalian tree of life.”

This sounds exciting. Unfortunately, this promise is followed by a history of Triisodon scrappy specimens (edited out here). Then the reappraisal reappears.

“A new specimen of T. crassicupsis allows a reappraisal of this enigmatic taxon. During the 2015 field season, a partial skull and skeleton (NMMNH P-72096) was recovered from basal Torrejonian age strata of the Nacimiento Formation in Kimbeto Wash.”

Perhaps this is the specimen in figure 1. The Torrejonian age is Middle Paleocene. In any case new specimens are always welcome, but reappraisals must include a wide gamut of related and unrelated taxa, not just the taxon in question. A panoramic view is needed, not a focused view.

Recently Brusatte 2022 wrote,
“All these mammals would have feared the triisodontids, the terrors of the Paleocene, which looked like wolves on steroids and smashed the bones of their prey with crushing molars.”

Triisdontids were not the terrors of the Paleocene. They were the hippos of the Paleocene. Those crushing molars were for grass and other pond plants.

“Untangling the genealogical relationships of these archaic placentals is challenging. My research group is currently working with Williamson, Carnegie Museum of Natural History mammalogist John Wible and other colleagues on this Gordian knot of phylogeny. We are building a vast data set of fossil and extant mammals, and their anatomical and genetic features, so that we can construct a master family tree.”

Excellent news! A competing analysis for the LRT! But, please, Dr. Brusatte discard, avoid and ignore all ‘genetic features‘. Too often genes recover false positives, too often based on geography (e.g. Afrotheria). Lingering question: Do genes have features?

According to SciAm.com
“Steve Brusatte is a professor at the University of Edinburgh and author of The Rise and Reign of the Mammals, a new narrative history of mammal evolution (Mariner Books, 2022).”

Matthew 1901 described
“The oldest known mammal skull (Triisodon heil/irinianus).”

Back then, this was. Here’s the skull (Fig 2).

“The skull compares most nearly with those of Arctocyon (Cernaysien), Mesonyx (Bridger and Uinta), and Periptychus (Torrejon).”

Back then, that’s how fossils were described, about a century before software assisted phylogenetic analysis and long before lots of other taxa were discovered and published.

Figure 2. Triisodon partial skull images from Matthew 1901, which he described as ‘the oldest mammal skulls known.” Note the plural. Evidently several skulls or partials were known then.

Funny thing…
The Triisodon heilprinianus skull (Fig 2) bears a closer resemblance to Mesonyx (Fig 3), other than the tooth wear. Note the large orbits, lacking in the figure 1 specimen. The figure 2 specimen also lacks the large circular glenoid joint found in Mesonyx (Fig 3) and Triisodon. The teeth are smaller. Scale bars were not published for these taxa. They appear to be related.

Figure 3. Skull of Mesonyx. Colors and animation added here. Note the similarities and differences compared to Triisodon in figure 2.

References
Brusatte S 2022. How mammals conquered the world after the asteroid apocalypse. ScientificAmerican.com article
Matthew WD 1901. Additional observations on the creodonta. Bulletin of the American Museum of Natural History 14:30–32.
Matthew WD 1937. Paleocene faunas of the San Juan Basin, New Mexico. Transactions of the American Philosophical Society. American Philosophical Society. 30 (3532): 1–510.
Shelley SL, Williamson TE and Brusatte SL 2015. Resolving the higher-level phylogenetic relationships of “Triisodontidae” (‘Condylarthra’) within Placentalia, October 2015, Society of Vertebrate Paleontology (abstract)

wiki/Triisodontidae
wiki/Triisodon

The big boa in a sauropod nest: Sanajeh restored

Wilson et al. 2010 described a Late Cretaceous 3.5m snake,
Sanajeh indicus (GSI/GC/2901–2906), curled around a nest of titanosaur sauropod dinosaur eggs, including one hatchling (Fig 1). Pretty spectacular.

Figure 1. Fossil from Wilson et al. 2010 showing Sanajeh and dinosaur eggs in situ. Diagram from Wilson et al. 2010 distorted for a closest match to the fossil. Not sure why the authors chose to create the diagram they way they did. Usually in situ diagrams are exact. Note: the dorsal view of the skull in the diagram is more complete than the in situ skull (Fig 2).

From the Wilson et al. abstract:
“Recent phylogenetic analyses differ in their interpretations of the origin and interrelationships of snakes, resulting in polarized views of snake ecology, habit and acquisition of features associated with wide-gaped feeding (macrostomy).

Many, many workers have attempted to understand the origin of snakes.
In every case they cherry-picked taxa, instead of letting their own wide-gamut cladogram tell them where snakes nest.

By contrast
in 2011 the large reptile tree (LRT, subset Fig 7) nested snakes with Eichstaettisaurus.
In 2013 the LRT nested snakes with Adriosaurus and Ardeosaurus.
In 2015 and ever since (Fig 7), snake ancestors, like Norellius, nested with gecko like Tchingisaurus.

“Here, we report a new specimen of the Late Cretaceous nest predator Sanajeh indicus that helps to resolve the origin of macrostomy”.

Macrostomy = ‘big mouth’ refers the ability of some fish and snakes to engulf and swallow very large prey, even if that takes a while to do.

“The new specimen preserves an ossified upper temporal bar and a posteriorly expanded otooccipital region that lacks a free-ending supratemporal bone and retains a lizard-like palatomaxillary arch that allows limited movements during swallowing.

I don’t see an ‘ossified upper temporal bar’ in the fossil, but restoration of an extended squamosal (magenta Fig 2) produces an upper temporal bar. The occipital region is laterally expanded. The skull lacks a ‘free-ending supratemporal bone’ due to a misidentifcation. The traditional supratemporal is bright green in figure 2. The heretical squamosal is magenta (= hot pink) here. This traditional mistake is taught in university textbooks and was rectified here in 2018 based on homologus elements in previously overlooked snake precursor taxa (Fig 7).

Figure 2. Sanajeh skull from Wilson et al. 2010. Colors and restoration added here. Of course, the restoration is speculative, which is why these traits cannot be scored in the LRT. The extended restored squamosal (not a supratemporal) forms an upper temporal arch.

Wilson et al. continue:
“Phylogenetic analyses of a large-scale total evidence dataset resolve Sanajeh near the base of Pan-Serpentes, as the sister group of Najash, Dinilysia and crown-group Serpentes.

Too little is known of the Sanajeh skull (Fig 2) to attempt a nesting in the LRT. However a restoration based on existing elements indicates it likely nests between Boa and Crotalus (the rattlesnake). Restoration is speculation, not evidence worth scoring.

Figure 3. Subset of the LRT from 2018 showing stem snakes, snakes and their sister group, the geckos. Cherry-picking is minimized here by taxon inclusion. The squamosal is in magenta.

Wilson et al. continue:
“The Cretaceous Tetrapodophis and Coniophis represent the earliest-diverging members of Pan-Serpentes.”

Tiny Coniophis is known from a maxilla and dentary, not enough to enter the LRT. The burrowing snakes are all tiny and so is Coniophis. Tiny Tetrapodophis is a snake because it nests at the node (Figs 3, 7) that is the last common ancestor of all living snakes.

“The Cretaceous hindlimbed pachyophiids and Cenozoic Australian ‘madtsoiids’ are inside crown Alethinophidia, whereas mosasaurs are recovered invariably within anguimorphs”.

This was in the era of Pythonomorpha, when it was popular to nest snakes with mosasaurs. The LRT does not recover these two clades together.

“Our results suggest that the wide-gape condition in mosasaurs and snakes might have evolved independently, as functionally distinct mechanisms of prey ingestion”.

The LRT also documents a separate and unrelated origin for mosasaurs and snakes.

“The intermediate morphology preserved in Sanajeh indicates that ingestion of large prey items (macrophagy) preceded wide-gaped, unilateral feeding (macrostomy), which appeared 35 Myr later, in the common ancestor of pachyophiids, Cenozoic Australian ‘madtsoiids’ and alethinophidians”.

The LRT documents a different origin for snakes than Wilson et al. envisioned with taxon exclusion in 2010 (Fig 4).

Figure 4. Cladogram from Wilson et al. 2010 nesting Sanajeh with several snake taxa. There are no outgroup taxa in this cladogram.

Wilson et al. cherry-picked outgroup taxa for their cladogram
(Fig. 4). “Consensus of the single most parsimonious trees derived from analyses employing Amphisbaenia and Varanoidea as outgroups.“

Those are not snake outgroups in the LRT. But then Wilson et al. published several years before snake ancestors were identified by the LRT. In any case, whenever someone cherry picks ingroup and outgroup taxa, the cladogram will inevitably suffer.

Figure 5. Xenopeltis. As in other tetrapods, the quadrate articulates with the squamosal, a bone missing in Sanajeh. Note the difference in teeth in Xenopeltis compared to Sanajeh.

Wilson et al. wrote,
“As in basal alethinophidian snakes such as Xenopeltis [Fig 5], the supratemporal has a wide articular surface for the quadrate on its lateral margin and a very short, free-ending posterior margin that does not extend posteriorly beyond the otic capsule. Importantly, the position of the quadrate articular facet, which is on the lateral surface of the supratemporal and located dorsal to the juxtastapedial recess, suggests that the jaw joint of Sanajeh was positioned lateral to the posterior margin of the braincase, as it is in basal snakes.”

As in other tetrapods, the supratemporal in Xenopeltis (Fig 5) does not articulate with the quadrate. The squamosal articulates with the quadrate. A restoration (Fig 2) might have helped Wilson et al. understand Sanajeh better. In the LRT a restored Sanajeh nests close to boa constrictors (appropriate for a baby sauropod killer).

Figure 6. Yurlunggur, an early boa from Australia. That transverse crack in the parietal made me misunderstand this area of the skull. Colors repaired here. The squamosal is hot pink/magenta. The supratemporal is bright green, distinct from most snake skull diagrams.

PS
While working on Sanajeh, another snake taxon, Yurlunggur (Fig 5, Scanlon 1992, Oligocene-Miocene, Australia, up to 6m long), became better understood, was rescored and now nests with Boa in the LRT.

Figure 7. Subset of the LRT from 2019 focusing on geckos and their sister snake ancestors. See the LRT for updates in the last three years.

Scanlon’s 1992 cladogram
(Fig 8) demonstrates the sort of problems snake workers experienced back in 1992 without a valid outgroup taxon or a series of valid outgroup taxa (Fig 7). Note the nesting of the extremely tiny and derived Leptotyphlops arising from a giant generalized terrestrial Dinilysia and then giving rise to decreasingly derived burrowing snakes ultimately giving rise to the same sort of terrestrial snakes represented by Pachyrhachis, Yurlunggar and Dinilysia. Essentially parts of Scanlon’s cladogram are upside-down. Try to guard against this.

Figure 8. Cladogram from Scanlon 1992. Colors added here. Always recheck your cladogram to make sure it is not deriving less derived taxa from more derived taxa, as in this cladogram. Compare to the snake subset of the LRT in figure 7.

References
Scanlon JD 1992. A new large madtsoiid snake from the Miocene of the Northern Territory. The Beagle, Records of the Northern Territory Museum of Arts and Sciences 9(1):49-60.
Wilson JA, Mohabey DM, Peters SE, Head JJ 2010. Benton MJ ed. Predation upon Hatchling Dinosaurs by a New Snake from the Late Cretaceous of India. PLoS Biology. 8 (3): e1000322. doi:10.1371/journal.pbio.1000322

Coniophis, the “Lucy” of Snakes?

A new view on snake origins: snake ancestors were gecko sisters

Gekkos and snakes: Not a novel hypothesis

The Origin of Snakes Goes Way, Way Back

Glareola, the pratincole, enters the LRT with owlets and nightjars, not plovers

According to Wikipedia,
Old World Glareola pratincola (Linneaus 1766, Figs. 1–3) is a member of the wading Charadriiformes. Thus it is supposed to be phylogenetically similar to plovers. Let’s test that.

Figure 1. The collared pratincole, Glareola pratincola, in vivo, in a typical plover environment.

Wikipedia also reports,
“Pratincoles are unusual among waders in that they typically hunt their insect prey on the wing like swallows, although they can also feed on the ground.”

“Unusual among waders”. That’s a potential clue.

Figure 2. Glareola skull in 3 views. 24-28cm long, 60º–70cm wingspan. Colors added here.

Here,
in the large reptile tree (LRT, 2091 taxa) Glareola nests between Tyto the owl and the owlet, Aegotheles + the nightjar, Lyncornis. Tynskya and the swifts are also related, not with the convergent swallows).

Glareola came to my attention
because the gene study Prum 2015 nested it basal to Uria, the flying bird that also swims with its wings. That’s four nodes apart from the plover, Charadrius in Prum 2015. So no one agrees with one another. Here’s an opportunity for you. Test this taxon and nest it. Let us know what you recover.

This appears to be a novel hypothesis of interrelationships.
If not, please provide a citation so I can promote it here.

References
Linneaus C von 1766. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio duodecima, reformata. pp. 1–532. Holmiæ. (Salvius)

wiki/Collared_pratincole

Ezcurra and Sues play the taxon exclusion gambit with Sphodrosaurus and fail several times

From the Ezcurra and Sues abstract:
“Most Triassic terrestrial diapsids belong to two clades, Lepidosauromorpha or (the more diverse) Archosauromorpha.”

The authors have it backwards. One clade of diapsids nests within Lepidosauromorpha in the large reptile tree (LRT, 2089 taxa). The other clade of convergent diapsids nests within Archosauromorpha. Taxon inclusion resolves all such issues.

“Nevertheless, the phylogenetic relationships of some Triassic diapsids have remained uncertain for decades because of the lack of preservation of phylogenetically relevant anatomical regions or because of unusual combinations of features.”

The authors are ten years too late. The phylogenetic relationships of all Triassic diapsid-grade taxa tested in the LRT are completely resolved.

Figure 1. Sphodrosaurus latex cast. Colors added here. Shown full scale @72dpi. Yellow area might be a precursor plastron, or not. Could just be mud.

Figure 2. Inner mandible of Sphodrosaurus from Ezcurra and Sues 2022. Their diagram (top) shows the splenial on the upper edge, the one with the coronoid. Derived turtle (snappping turtle – Chelydra) inner mandible (middle). Same colors applied to photo of Sphodrosaurus (bottom) from Ezcurra and Sues.

Ezcurra and Sues continue:
“One of these enigmatic forms is the small-sized Sphodrosaurus pennsylvanicus from the Upper Triassic Hammer Creek Formation of the Newark Supergroup in Pennsylvania (USA).”

Sphodrosaurus (Fig. 1) has nested between Sclerosaurus and Arganceras in the LRT since October 2018, derived from pareiasaurs like Bunostegos and basal to soft shell turtles including Odontochelys. These taxa are all omitted from Ezcurra and Sues.

“It was first identified as a procolophonid parareptile, later as a probable rhynchosaur archosauromorph, and more recently as an indeterminate neodiapsid.”

Co-author Sues in Sues and Reisz 2008 misidentified Sclerosaurus as a procolophonid due to taxon exclusion and there is no such thing as a parareptile due to taxon exclusion.

The authors don’t realize all rhynchosaurs are lepidosaur rhynchocephalians due to taxon exclusion. They are following the Benton myth.

There is no such thing as a neodiapsid due to taxon exclusion, but this clade is taught in college textbooks.

Let’s solve this problem together. Stop cherry-picking your taxon list. Include such a wide gamut of taxa that your software can tell you where new and enigmatic taxa nest.

“Here we revise the anatomy of Sphodrosaurus pennsylvanicus in order to include it for the first time in a quantitative phylogenetic analysis, which is focused on Permo–Triassic neodiapsids.”

Ironically if Ezcurra and Sues had focused on all the reptiles they omitted they would have solved the Sphodorosaurus problem.

Colleagues: don’t attempt to focus your studies when nesting enigmatic taxa. Instead keep a panoramic view. Add more taxa when trying to nest problems like Sphodrosaurus. Or go online to find candidate solutions to your phylogenetic problems.

Co-author Sues in Sues, Baird and Olsen 1993
reexamined Sphodrosaurus nearly 30 years ago and determined that the specimen was not a procolophonid, but some sort of diapsid or neodiapsid. They also noted “This combination of characters has not been found in any other known diapsid.”

That’s known as a red flag. Look elsewhere or add taxa.

Figure 3. Subset of the LRT focusing on turtles and their ancestors. Sphodrosaurus nests with softshell turtles here.

Ezcurra and Sues continue:
“Sphodrosaurus pennsylvanicus is recovered in this analysis as a doswelliid proterochampsian within Archosauromorpha. As a result, this taxon is added to the list of doswelliids known from the Carnian–Norian of the eastern and south-western USA.”

This is incorrect due to taxon exclusion. Long and narrow Doswellia is related to the SAMPKK 10603 specimen attributed to Proterosuchus. A few nodes apart, proterochampsids arise from Diandongosuchus and kin in the LRT.

Colleagues: Build your own LRT. Then mistakes like this won’t happen.

“Previous authors recognized that the most unusual feature of Sphodrosaurus pennsylvanicus is its proportionally very large skull.

Ezcurra and Sues are “Pulling a Larry Martin.” As you can see, this unscientific practice reaches the highest levels in this paper. Test more taxa to avoid this mistake.

“Phylogenetic generalized least squares regressions confirmed that Sphodrosaurus pennsylvanicus has a larger skull than the vast majority of Permo–Triassic diapsids. Optimization in the phylogeny of the skull width to presacral length ratio shows the most likely scenario is that the extremely broad skull of Sphodrosaurus pennsylvanicus is autapomorphic, but it is not unique among archosauromorphs, being paralleled by hyperodapedontine rhynchosaurs and the proterochampsian Proterochampsa barrionuevoi.”

“The most likely scenario…” When you find yourself typing those words into your manuscript realize that you have now left the realm of science and are entering the realm of speculation.

“Autapomorphic…” When you find yourself typing those words into your manuscript realize that you are looking at exactly the wrong taxa as candidate sisters. Look elsewhere. In evolution nothing is autapomorphic, except when excluding pertinent taxa.

Rhynchosaurs are not archosauromorphs in the LRT.

Lacking their own LRT, Ezcurra and Sues are stumbling around in a dark room, cherry-picking taxa to nest their favorite enigmas and failing again and again due to taxon exclusion.

3m long Proterochampsa does have an enormous skull. That skull is as long as the pre-sacral length. That’s not the case with 24cm long Sphodrosaurus (Fig 1) with a much smaller skull and shorter, wider torso, twice as wide as the skull, as in Sclerosaurus (Fig 4).

“Exploration of a morphospace of linear measurements shows that Sphodrosaurus pennsylvanicus shares strong similarities with the probably semi-aquatic Proterochampsa barrionuevoi, suggesting that the former species may have had a similar mode of life.

Compare Sphodrosaurus to its closest relatives in the LRT (Figs 3, 4). That makes tiny Sphodrosaurus a phylogenetically miniaturized taxon at the genesis of soft-shelled turtles, a late-surviving precursor to a coeval Late Triassic Odontochelys.

Figure 4. Sphodrosaurus to scale with Sclerosaurus and Odontochelys, taxa omitted from Ezcurra and Sues 2022.

Ezcurra and Sues continue:
“A linear discriminant analysis of ungual functional categories found that the only preserved ungual of Sphodrosaurus pennsylvanicus was suitable for digging or some other way of substrate processing.”

Morphospace studies are also a complete waste of time without a proper phylogenetic context, currently lacking in Ezcurra and Sues 2022 and prior studies of Sphodrosaurus.

Ezcurra and Sues report,
“The new data set is composed of 190 active terminals and 887 active characters.”
It would have been better the other way around. The LRT tests 2089 taxa (= active terminals). Only two included taxa in the Ezcurra and Sues study were lepidosauromorphs, Marmoretta and Huehuecuetzpalli. No turtles or pareiasaurs are mentioned in the text, either.

Ezcurra and Sues nest Sphodrosaurus
(their figure 10) at the base of a clade that includes Jaxtasuchus, then Doswellia + Rugarhynchos. These nested not far from Vancleava + Litorosuchus in their study.

By contrast in the LRT Jaxtasuchus and Litorosuchus nest together as elongate armored protorosaurs derived from elongate unarmored Malerisaurus, a taxon deactivated by Ezcurra and Sues. Vancleavea nests with thalattosaurs when thalattosaurs are included in the taxon list. Rugarhynchos is a former Doswellia sp., so someone thought they were congeneric at one time. Don’t exclude or deactivate taxa or you’ll end up with a similar mess.

Ezcurra and Sues report,
“We thank the reviewers Stephan Spiekman and Brenen Wynd and the editor Richard Butler for their suggestions and comments.”

These esteemed workers also share blame for letting this study reach publication without requiring the inclusion of competing candidate taxa known since 2018 and suspected since Rice et al. 2016.

Ezcurra and Sues 2022 mentioned other reptile enigmas,
“their phylogenetic positions have been controversial in recent decades (e.g. Pachystropheus rhaeticus: Huene 1935; Elachistosuchus huenei: Janensch 1949; Sphodrosaurus pennsylvanicus: Colbert 1960; Colobops noviportensis: Pritchard et al. 2018). These species are generally represented by specimens with limited anatomical information, which is the main reason for their uncertain phylogenetic position.”

The LRT nested Sphodrosaurus in 2018, Elachistosuchus in 2015, and Colobops in 2018 with Marmoretta, moving both to the Rhynchocephalia in 2020. Pachystropheus, known from scattered bones, is not going to be attempted.

References
Colbert EH 1960. A new Triassic procolophonid from Pennsylvania. American Museum Novitates 2022:1–19.
Ezcurra MD and Sues H-D 2022. A re-assessment of the osteology and phylogenetic relationships of the enigmatic, large-headed reptile Sphodrosaurus pennsylvanicus (Late Triassic, Pennsylvania, USA) indicates archosauriform affinities. Journal of Systematic Palaeontology. 0 (0): 1–35. doi:10.1080/14772019.2022.2057820
Meyer H von 1859. Sclerosaurus armatus aus dem bunten Sandestein von Rheinfelsen. Palaeontographica 7:35-40.
Rice R, Kallonen A, Cebra-Thomas J and Gilbert SF 2016. Development of the turtle plastron, the order-defining skeletal structure. PNAS 113 (19):5317–5322.
Sues H-D, Baird D and Olsen PE 1993. Redescription of Sphodrosaurus pennsylvanicus Colbert, 1960 (Reptilia) and a Reassessment of its Affinities. Annals of Carnegie Museum 62(3):245-253.
Sues H-D and Reisz RR 2008. Anatomy and Phylogenetic Relationships of Sclerosaurus armatus (Amniota: Parareptilia) from the Buntsandstein (Triassic) of Europe. Journal of Vertebrate Paleontology 28(4):1031-1042. doi: 10.1671/0272-4634-28.4.1031 online

wiki/Arganaceras
wiki/Sclerosaurus
wiki/Sphodrosaurus
reptileevolution.com/arganaceras.htm

Parapengornis enters the LRT close to Pengornis, but closer to Gretcheniao

Hu et al. 2015 described
a virtually complete, but crushed enantiornithine bird, Parapengornis (Figs 1, 2).

Figure 1. Parapengornis in situ and diagram from Hu et al. 2015. Displayed at full scale on 72dpi monitors. Colors and 2x foot recon added here.

Parapengornis eurycaudatus
(Hu, O’Connor, Zhou and Farke 2015, IVPP V18687; Early Cretaceous) is close to Pengornis, but closer to Gretcheniao (Fig 3, Chiappe et al. 2019), so could not be mentioned by Hu et al. 2015.

Figure 2. Parapengornis skull in situ and reconstructed in lateral view. Colors added here. Upper diagram from Hu et al. 2015. Compare to DGS color tracing (middle).

According to Wikipedia,
“Parapengornis was a large pengornithid, distinguished from its relatives by a combination of features such as the many slender, constricted teeth with pointed and recurved apices, with short cervical (neck) vertebrae at the front, but those further back elongated, a broad pygostyle, and a Y-shaped furcula (wishbone).”

Figure 3. Gretcheniao skull in situ and recnstructed.

We looked at
Gretcheniao (Fig 3) earlier here.

Figure 4. Bohaiornis guoi skull insitu and reconstructed using DGS methods. Note the extremely gracile jugal, maxilla and other bones, framing a large orbit and antorbital fenestra.

A related taxon, Bohairornis,
Hu et al. 2011; Early Cretaceous; LPM B00167; IVPP V17963, Fig 4) also enters the LRT today. It is notable for its extremely gracile skull bones.

Figure 5. Shenqiornis now nests with the IVPP V 12707 hatchling. It’s a strong match. Shenqiornis diagram traces the plate and counterplate elements.

PS
The IVPP V 12707 hatchling (w/o wings,, Fig 5) now nests with Shenqiornis (also Fig 5). Once again, phylogenetic analysis matches a juvenile to an adult.

References
Chiappe LM, Meng QJ, Serrano F, Sigurdsen T, Min W, Bell A and Liu D 2019. New Bohaiornis-like bird from the Early Cretaceous of China: enantiornithine interrelationships and flight performance. PeerJ 7:e7846 DOI 10.7717/peerj.7846
Hu D, Li L, Hou L and Xu X 2011. A new enantiornithine bird from the Lower Cretaceous of western Liaoning, China. Journal of Vertebrate Paleontology. 31 (1): 154–161.
Hu H, O’Connor J, Zhou Z and Farke AA. 2015. A New Species of Pengornithidae (Aves: Enantiornithes) from the Lower Cretaceous of China Suggests a Specialized Scansorial Habitat Previously Unknown in Early Birds”. PLOS ONE. 10 (6): e0126791.

wki/Pengornis
wki/Chiappeavis
wiki/Gretcheniao
wiki/Parapengornis
wiki/Bohaiornis
wiki/Shenqiornis

Taxon exclusion mars Oxford early reptile study

Brocklehurst, Ford and Benson 2022 omitted dozens of pertinent taxa
(Figs 1, 3, 4) as they reported, “The origin of amniotes 320 million years ago signaled independence from water in vertebrates and was closely followed by divergences within the mammal and reptile stem lineages (Synapsida and Reptilia).”

The three Oxford authors were too late. Twice. In 2011 the large reptile tree (LRT, 2088 taxa) split basal Reptilia (= Amniota) into Lepidosauromorpha (including turtles) and Archosauromorpha (including Synapsida). That amniote split was already radiating in the Viséan, 345–331 mya. So the authors undershot the origin of reptiles by at least 25 million years — and a decade, both due to taxon exclusion

Don’t let taxon exclusion be the downfall of your paper.
Don’t cherry-pick taxa. Brocklehurst, Ford and Benson thought the basalmost reptile/ amniote, Silvanerpeton, and other amphibian-like amniotes (Fig 1) were not worth testing. As a result the authors considered three basal amniotes,Tseajaia, Limnoscelis and Gephyrostegus, as non-amniote outgroups. That’s been wrong/ misguided/ old-fashioned for far too long. Adding taxa (the list is online) is so simple. Why don’t workers do it? It doesn’t take a PhD to figure this out.

Figure 1. Click to enlarge. Gephyrostegus moves to the base of the Archosauromorpha with its long-legged, hump-backed relatives.

Without a valid phylogenetic context (due to taxon exclusion)
the Brocklehurst, Ford and Benson cladogram (Fig 2) supports current myths taught in vertebrate paleontology textbooks. The authors did not have the scientific curiosity, or were not brave enough, to add pertinent taxa identified a decade ago by the LRT. All three authors are from Oxford University. If that is what they are teaching there, you might think about getting your paleo education elsewhere.

Brocklehurst, Ford and Benson report,
“thus far there has been no study of macroevolutionary patterns during the origin and early radiation of amniotes including a broad selection of all clades, allowing direct comparison of the evolutionary patterns within the major lineages, and across many anatomical regions.”

The LRT is exactly that study the authors say does not exist. What does that make them? Because Brocklehurst, Ford and Benson kept their blinders on, and omitted pertinent taxa, these three PhDs fell far short of their goal and created a phylogenetic mess (Fig 1). They cherry-picked their taxon list from past cherry-picked lists instead of expanding their list to let their software tell them which taxa were outgroup and ingroup taxa and how they were all interrelated, like the LRT (subsets Figs 3, 4).

Figure 2. Cladogram from Brocklehurst, Ford and Benson 2022, Colors added here.

Taxon exclusion problems
Outgroup taxa in the Brocklehurst, Ford and Benson amniote study include Seymouria (which is good) and three reptiles: Gephyrostegus, Tseajaia and Limnoscelis (which is not good).

Missing reptilomorph outgroup taxa include Utegenia, Tulerpeton, Eucritta (Fig 4).

Missing ingroup taxa include the last common ancestor of all amniotes: Silvanerpeton (Fig 1).

Missing basal lepidosauromorpha include, Urumqia (Figs 1, 4), Bruktererpeton, Cephalerpeton, Procolophon, Diadectes, Tetraceratops, Orobates, Stephanospondylus, Kudnu, Carbanodraco, and others.

Missing basal archosauromorpha include Eldeceeon, Diplovertebron, Romeriscus, Bystrowiella, Solenodonsaurus, Chroniosuchids, Westlothiana, Casineria, Brouffia, Coelostegus and Anarosaurus (basal to mesosaurs) among others (Fig 3).

As a result the following errors appear in Brocklehurst, Ford and Benson:
“Synapsida” should not include Caseasauria.

‘Reptilia” should split captorhinids (Lepidosauromorpha) from Hylonomus and kin (Archosauromorpha). Taxon exclusion is the problem here, too.

Amniota should not split “Reptilia” from “Synapsida”.

Strange nestings include:
The diapsids Petrolacosaurus and Araeoscelis (with dual temporal openings) improperly nesting basal to protodiapsids (with a single temporal opening). When things go wrong phylogenetically like this, the order sometimes appears upside-down. When this happens it should raise a red flag. Don’t ignore red flags like this. Inspect them and add taxa.

Varanodon, Varanops and kin nest outside the Synapsida, far apart from Varanosaurus nesting correctly within the Synapsida.

Only taxon exclusion, and probably a slew of bad scores,
recovers this traditional shuffled topology (Fig 2).

The authors do not show reconstructions of included taxa,
so they hope their readers trust their ability to score traits. By contrast the LRT shows reconstructions of every included taxa (e.g. Fig. 1) for complete transparency.

Figure 3. Subset of the LRT from 2019 focusing on basal Archosauromorpha including Vaughnictis and Cabarzia nesting at the base of the Protodiapsid-Synapsid split. Note all the large varanopids nest together here in the Synapsida, separate from small varanopids in the Protodiapsida.

I could go on,
but if you are interested in all the details, you can compare the LRT (subsets Figs 3, 4) with the Brocklehurst, Ford and Benson cladogram (Fig 2).

Figure 4. Subset of the LRT from 2021 focusing on basal Lepidosauromorpha and Reptilomorpha.

Simply adding correctly scored taxa resolves all phylogenetic issues.
Be brave. Be curious. Be scientific. Add taxa. Simple as that.

Workers:
don’t keep your blinders on. Show some curiosity. Show some integrity. Show some independence. Remember, you are supposed to be scientists, always testing for confirmation, refutation or correction. You can teach from the standard textbook when it is correct and depart from it when it needs to be updated. Your students will appreciate your efforts.

References
Brocklehurst N, Ford DP and Benson RBJ 2022. Early origins of divergent patterns of morphological evolution on the mammal and reptile stem-lineages. Sytematic Biology 0(0):1–15. https://doi.org/10.1093/sysbio/syac020

Early Silurian Loganellia and a whale shark to scale. Well, sort of…

Just had to do something with this photo
(Fig 1) of a young Philippine man holding a baby whale shark (Rhincodon), which can grow to become the largest fish in the world. That it happened to be portrayed at the same angle as an Early Silurian Loganellia fossil (Fig 1) was a plus. Here the two are presented together for the first time, to the same scale, separated by a mere 440 million years.

Figure 1. Baby whale shark (Rhincodon) found in the Philippines compared to scale with Early Silurian Loganellia.

Loganellia scotica
(Traquair 1898; Early Silurian) is an advanced thelodont with pectoral fins, a heterocercal tail, a mandible and other traits otherwise found in the extant whale shark, Rhincodon. This open water feeder with a carpet of teeth, none on the margin of the jaws, gave rise to sharks, like Ginglymostoma and Rhincodon. The skin had a shark-like sandpaper appearance and texture. The mouth was terminal and transverse.

Figure 2. Another Loganellia fossil. Colors added here.

Loganellia entered the LRT
with Rhincodon in November 2019 (link below). Since then I haven’t seen any competing analyses. If you know of one, please send it in so I can promote it here.

According to the National History Museum in London, “Shark-like scales from the Late Ordovician have been found, but no teeth. If these were from sharks it would suggest that the earliest forms could have been toothless. Scientists are still debating if these were true sharks or shark-like animals.”

References
St. John OH and Worthen AH 1883. Description of fossil fishes: a partial revision of the Cochliodonts and Pasmmodonts. Geological Survey of Illiniois 7:55–264.
Traquair RH 1898. Report on fossils fishes. Summary of Progress of the Geological Survey of the United Kingdom for 1897: 72-76.
Žigaite Ž and Goujet D 2012. New observations on the squamation patterns of articulated specimens of Loganellia scotica (Traquair, 1898) (Vertebrata: Thelodonti) from the Lower Silurian of Scotland. Geodiversitas 34 (2): 253-270.

wiki/Rhincodon
wiki/Longaniella
nhm.ac.uk/discover/shark-evolution-a-450-million-year-timeline.html

washingtonpost.com/science/2022/05/14/whale-sharks-deaths-ships/

Loganellia scotica: even more like a tiny whale shark

Penguin origins from terns and murres/guillemots illustrated and on YouTube

The origin of penguins in the LRT
(subset Fig 3) was established and updated several years ago. Presently the complete LRT documents a comprehensive lineage of penguin ancestors back to pre-Cambrian worms.

Today
we’ll review the present taxonomic situation close to penguins. A few graphics (Figs 2, 3 should remove any last bits of mystery. After seeing this evidence you may wonder why this low-hanging fruit is not more widely known and understood. Apparently few workers want take the deep dive into penguines. If you doubt the present evidence (Figs 2,3), run your own analysis and let us know your results.

Bonaparte 1831
placed penguins into the family Spheniscidae. Sharpe 1891 placed penguins into the order Sphenisciformes.

Neither of these classifications shed much light on penguin origins from other birds.

According to Wikipedia,
“The oldest known fossil penguin species is Waimanu manneringi, which lived in the early Paleocene epoch of New Zealand, or about 62 mya.”

The Wiki authors chose not to consider the origin of penguins from other birds.

Gene studes by Prum et al. 2015
(Fig 1) nested penguins between loons (Gavia) and the North Pacific albatross (Phoebastria).

Neither of these genomic recoveries are correct according to the trait-based LRT (Fig 3). Nor do they reveal the origin of underwater flying in penguins. For instance, loons paddle with their feet underwater while keeping their wings tucked in. The albatross is a specialist in soaring, which is rather distinct from penguin locomotion.

Now do you understand why ‘deep time studies in genomics are no better than alchemy’?

Figure 1. Subset from the genomic study of Prum et al. 2015, focusing on penguins and their genomic kin. This is the study that nested flamingos with grebes (Phoenicopterus and Rollandia at top). This study separates Uria (pink) from Spheniscus (blue).

From Penguins-World.com
“In general, three groups of birds share many similarities with the modern penguins, suggesting that these groups could have some ancestor in common. These groups are:
A) Petrels and Albatrosses.
B) Loons.
C) Frigatebirds.”

None of these guesses are correct according to the LRT (subset Fig 3).

Figure 2. The origin of penguins. like Spheniscus, from terns, like Thalasseus, and guillemots (= murres), like Uria. Note the giant sternum on Uria for strong flying with rapid wing beats, as in hummingbirds. Note the more robust skeleton of flightless Spheniscus, especially the scapula, clavicle and wing bones.

According to
the large reptile tree (LRT, 2085 taxa, subset Fig 2) underwater flying penguins like Aptenodytes and Spheniscus are derived from underwater + above water flying guillemots (= murres) like Uria (Figs 2, 3). These, in turn, evolved from flying and only shallow diving terns like Thalasseus.

Figure 3. Subset of the LRT focusing on penguins and their relatives. Murres are guillemots. Note the penguin-like stance and coloration. These birds can fly both underwater and above the water. One is not related to the other, demonstrating sufficient convergence to confuse ornithologists.

The LRT continues to offer
the only trait-based study of birds and chordates. The LRT nests some guillemots with penguins. Other guillemots, nearly identical by convergence (Fig 3), give rise to extinct flightless auks (Pinguinus) and razorbills (Alca) with similar short wings which flap rapidly in the air and underwater. As we learned earlier here, the razorbill-related thick-billed murres/guillemots were named first, so the penguin-related, thin-billed murres/guillemots need a new generic name. And probably a new popular name, too.

I realize this is confusing. Convergence always is, especially when it goes unrecognized.

It is a credit to the LRT that traits never designed to separate some Uria species from other so-called ‘Uria‘ species were able to separate one from another with complete resolution (Fig 3). This is why I encourage everyone to build their own LRT for the authority that will give them. Perhaps then we can avoid the myth-making of genomic studies like Prum et al. 2015 (Fig 1) and the vague guesses of others.

YouTube video of terns flying and diving. This is step one in the evolution of penguins.

YouTube video of guillemots flying with rapid wing beats.

Youtube video of guillemot flying underwater with slower, stronger wing beats. This is step two in the evolution of penguins.

YouTube video of penguins flying underwater with shorter wing feathers (not shorter wings) and no longer able to fly in the air. This is the final step in the evolution of penguins.

Still not convinced?
If you have a better solution that explains and documents the origin of penguins, work it up and let us know.

References
Bonaparte CL 1831. Giornale Arcadico di Scienze, Lettere ed Arti 49: 62.
Prum et al. (6 co-authors) 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526:569–573. online
Sharpe RB 1891. A Review of Recent Attempts to Classify Birds: an address delivered before the Second International Ornithological Congress on the 18th of May, 1891. Budapest: Office of the Congress.
wiki/Penguin

A tale of two murres: Uria lomvia is not related to Uria aalge

Murres and the origin of penguins

Publicity
npr.org/the-evolutionary-history-of-penguins-is-far-from-black-and-white

https://www.penguins-world.com/penguin-evolution/

Sharks are neotonous sturgeons

According to Wikipedia:
“The customary view is that jaws are homologous to the gill arches.

This view is based on the appearance of basal sharks like Cladoselache in which the large jaws parallel and resemble the smaller gill arches behind them (Fig 1). This is such a reasonable and teachable view that it has become ‘the customary view’.

Even so, this view also needs to be run through phylogenetic analysis.

Figure 1. Classic reconstruction of Cladoselache, a shark taxon with jaws resembling gill arches.

According to Wikipedia:
‘It is now accepted that the precursors of the jawed vertebrates are the long extinct bony (armoured) jawless fish, the so-called ostracoderms.”

That turns out to be correct. Hemicyclaspis is an ostracoderm. Semi-jawed tube-feeders and fully-jawed (but toothless) taxa follow ostracoderms (Fig 2).

Figure 2. Origin of toothless jaws from the ostracoderm, Hemicyclaspis, to Thelodus, Acipenser (sturgeon) and Chondrosteus.

According to Wikipedia:
“The earliest known fish with jaws are the now extinct placoderms and spiny sharks.”

According to the large reptile tree (LRT, 2085 taxa) pre-jaws also first appeared in Early Silurian Thelodus (Fig 2). Real jaws without teeth are also present in Early Silurian Loganellia, a basal whale shark. These two are coeval with the earliest placoderms and spiny sharks, both nesting as much more derived bony fish in the LRT. So that means there are many more Late Ordovician and Early Silurian fish fossils just waiting to be discovered.

Tube-feeding, toothless, bottom-dwelling sturgeons
and biting, toothless, open-water dwelling, Chondrosteus (Fig. 2) are transitional taxa between ostracoderms and sharks in the LRT (Fig 4).

The kicker is:
tiny larval sturgeons have a few tiny teeth (Fig 2). These appear on an angled precocial premaxilla, looking like a fused set of first gill arches. The premaxilla is supported by a similarly angled lacrimal, looking like a larger set of unfused second gill arches artculating with a toothed dentary + articular. These, in turn, are supported by an angled hyomandibular, articulating with a mobile quadrate and posterior jaw elements. So, the origin of jaws story turns out to be a little more complicated than the current paradigm involving basal sharks like Cladoselache (Fig 1).

DGS (digital graphic segregation) and comparative anatomy (Fig 3) can shed light on this natural history conundrum.

Figure 3. Acipenser (sturgeon) embryo compared to Isurus (shark) adult. Only embryo sturgeons have teeth, when they are free-swimming copepod eaters. Adult sturgeons are bottom dwellers. We have no hatchling and juvenile ostracoderms at present, only the bottom-dwelling adults.

Even a cursory look
at embryo sturgeons and and adult sharks (Fig 3) reveals a long list of similarities, including teeth. That brings up the hypothesis that basal sharks, like Isurus, are neotonous sturgeons, retaining an open water predatory lifestyle, like embryo sturgeons, rather than descending to the sea floor to become bottom feeders, like adult sturgeons.

This hypothesis is further cemented
by bottom-dwelling sharks, like sawfish, skates and rays, that develop sturgeon-like small ventral mouth parts that extend in a sturgeon-like fashion.

Figure 4. Fish evolution from Birkenia to Amia documenting the sturgeon to shark to bony fish transition.

Reversals and neotony are as common as
convergence in vertebrate phylogeny. Don’t victimize your studies by focusing on one or a few traits (that’s called “Pulling a Larry Martin“). Instead run your wide gamut analysis with hundreds of traits. Will that work? The LRT is fully resolved and all sister taxa look similar, have similar niches and are often similar in size (if chronologically nearly coeval). So this method does recover reasonable results regardless of reversals, neotony and convergence.

This appears to be a novel hypothesis of interrelationships.
If not, please send a citation so I can promote it here.

References
wiki/Fish_jaw

What do larval sturgeons eat (when they have teeth)?