High-crested mahi-mahi (Coryphaena) enters the LRT

Updated February 7, 2020
with the addition of the pupfish, Pseudorestias, a closer sister to the wolffish, Anarhichas.

The speedy maui-mahi
(genus: Coryphaena, Fig. 1) nests in the large reptile tree (LRT, 1556 taxa) with the cave-swelling wolffish, Anarhichas (Fig. 2), basal to the barracuda (see update above) and several other clades.

FIgure 1. Mahi-mahi (Coryphaena) mounted as if in vivo.

Figure 2. Anarhichas in vivo. Note the basic similarities between this cave dweller and its open seas cousin, Coryphaena (Fig. 1).

Coryphaena hippurus (Linneaus 1758; 1.5m length) is the extant open seas predator mahi-mahi or dolphinfish, here related to the similar, but slower cave-dwelling, Anarhichas (below). The dorsal fin starts at the skull. The caudal fin is deeply forked. The teeth are small. Males have a tall forehead.

Figure 2. This is where the high forehead of the male mahi-mahi (Corphaena) comes from, one of the very few fish with a frontal crest. 

Anarhichas vomerinus (Linneaus 1758; 1.5m length) is the extant Atlantic wolffish. It nests between the perch clade an the barracuda, Sphyraena (see update above). The marginal and vomer teeth are robust. The conjoined temporal fenestra meet dorsally along a thin ridge. Pelvic fins are absent.

Figure 1. Skull of the wolffish, Anarhichas. Compare to the pupfish in figure 3.

References
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.

wiki/Atlantic_wolffish
wiki/Mahi-mahi

Hughes et al. 2018 ray-fin fish cladogram: genes vs. traits

Zoologists are increasingly relying on genomics (genes)
to reconstruct nature’s family trees, to their peril. We’ve already seen how genes fail to match phenomic (trait-based) tests, the only kind that can include and incorporate fossil taxa.

Hughes et al.  2018 report,
“Ray-finned fishes form the largest and most diverse group of vertebrates. Establishing their phylogenetic relationships is a critical step to explaining their diversity. We compiled the largest comparative genomic database of fishes that provides genome-scale support for previous phylogenetic results and used it to resolve further some contentious relationships in fish phylogeny. Our time-calibrated analysis suggests that most lineages of living fishes were already established in the Mesozoic Period, more than 65 million years ago.”

Hughes et al. employed no fossil taxa
and failed to confirm the tree topology recovered by the large reptile tree (LRT, 1553 taxa) which tests physical traits as well as large clades omitted or overlooked by Hetal.

Let’s compare trees.

1. Hughes et al. do not separate lungfish from other lobefins, but lump them all in the monophyletic outgroup Sarcopterygii. The LRT starts earlier, with jawless theolodonts. Some traditional ray-fins are lobefins. Some lobefins give rise to tetrapods. Others give rise to ray-fins (Fig. 1). 
2. Hughes et al. do not test members of the shark + ratfish clade.
3. Hughes et al. nest sturgeons (Pseudoscaphirhynchus, Acipenseriformes) between dissimilar bichirs (Polypterus) and bowfins (Amia). The LRT nests sturgeons with more similar ratfish.
4. Hughes et al. do not test members of the placoderm clade.
5. Hughes et al. nest catfish (Clarias, Siluriformes) with dissimilar knife fish (Gymnotus). (Gymnotiformes).  The LRT nests catfish as placoderm sisters, not far from the morphologically similar basal shark with similar tooth pads, Rhincodon. Thus the radiation of convergent ray fin fish was established in the Silurian, not the late Cretaceous.
6. Hughes et al. nest the bichir, Polypterus, as the basalmost ray fin fish. The LRT nests air breathing Polypterus with similar lungfish, and Polypterus is not the basalmost ray fin fish in the LRT (see 1–5 above). 
7. Hughes et al. nest garfish (Lepisosteiformes) with dissimilar Amiiformes. The LRT nests garfish with sticklebacks while Amiiformes (Amia) nest between tuna (Thunnus) and arowana (Osteoglossum) among living taxa. 
8. Hughes et al. nest dissimilar tarpons and eels together (clade: Elopomorpha). The LRT nests more similar carp (Cyprinus) with tarpons (Megalops) and eels nest in many places, but European eels (Anguilla) nest with similar cusk eels (Dicrolene), derived from fast-swimming rudder fish (Seriola zonata). 
9. Hughes et al. nest dissimilar goosefish (Lophius, Lophiformes) with pufferfish (Diodon) and triggerfish (Balistes, Tetraodontiformes). The LRT nests goosefish with more similar (when you look at their skulls) knife fish (Gymnotus) + electric eels (Electrophorus) 
10. …and so it continues with little consensus.

Figure 2. Subset of the LRT focusing on basal vertebrates. Colors indicate various naris configurations. Some palates are not known.

As we’ve seen before with birds, mammals and reptiles in general,
deep time genomic (gene) studies fail time and again to provide a tree topology in which sister taxa demonstrate a gradual accumulation of derived traits — which is the ultimate validation test of any cladogram. Gene studies, like Hughes et al., that a priori exclude taxa based on traits (= ‘pulling a Larry Martin’): assuming that no ray fin fish are convergent, or that all eels are related to one another, are also doomed to fail.

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References
Hughes L et al. (20 co-authors) 2018. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. PNAS 115(24):6249–6254.

pnas.org/cgi/doi/10.1073/pnas.1719358115

New ‘rodents and rabbits’ cladogram

Asher et al. 2019
bring us a new phylogenetic + genomic cladogram of rabbits + rodents (clade = Glires) that fails to include taxa recovered by the large reptile tree (LRT, 1552 taxa, subset Fig. 1).

From their abstract:
“Our results support the widely held but poorly tested intuition that fossils resemble the common ancestors shared by living species, and that fossilizable hard tissues (i.e. bones and teeth) help to reconstruct the evolutionary tree of life.”

From their results:
“Our analysis supports Glires and three major clades within crown Rodentia: Sciuromorpha (squirrels and kin), Myomorpha ((beavers + gophers) + mice and kin), and Ctenohystrica (porcupines, chinchillas and kin).”

Figure 1. Subset of the LRT focusing on Glires and subclades within. This is an older image not updated yet with the dormouse, Eliomys.

The LRT
also supports these divisions. It also supports the basal nesting of ‘Tupaiidae’ relative to Glires. It does not support the inclusion of Primates within Glires, but the two are sister clades within a single clade. The LRT supports the basal nesting of Didelphis relative to Metatheria and Eutheria.

Some oddities in the results of Asher et al. 2019.

1. Papio, the baboon, nests between Dermoptera (flying lemurs/colugos) and Plesiadapis + lemurs. That’s way too primitive for such a derived monkey.
2. Rodent-toothed Pleisadapis nests with baboons and lemurs. This is a traditional nesting not recovered by the wider gamut LRT where Plesiadapis nests closer to multituberculates and the aye-aye, Daubentonia.

Asher et al. 2019 included dormice
(Eliomys and kin; Fig. 2), and found them to be rather primitive, closer to squirrels. So Eliomys was added to the LRT and it nested with Mus, the mouse.

Figure 2. Eliomys, the dormouse.

How to tell a mouse from a dormouse.
The skulls are similar, but different. The dormouse tail is furry, not scaly. Dormice are more arboreal. The dormouse hibernates rather than seeking warm spots. Fossil dormice are found in the Eocene, but their genesis must go back to the Early Jurassic, where multituberculates are found, according to the LRT.

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References
Asher RJ, Smith MR, Rankin A and Emry RJ 2019. Congruence, fossil and the evolutionary tree of rodents and lagomorphs. Royal Society Open Science 6:190387. http://dx.doi.org/10.1098/rsos.190387

Pseudictops: what little we know is unique

There are not many mammals with crenulated/serrated teeth.
Pseudictops lophiodon (Matthews, Granger and Simpson 1929, Sulimski 1968, Late Paleocene, 57 mya; Fig. 1; AMNH 21727) is one such mammal. From the start Pseudictops was compared to anagalids like Leptictis (Fig. 2), a basal elephant shrew and ancestor to tenrecs, pakicetids and odontocete whales.

Figure 1. Pseudictops lophiodon compared to the slightly larger Siamotherium. The mandible is extremely robust and appears to nearly lack a coronoid process, distinct from most mammals.Note the crenulations and and/or robust serrations on the anterior teeth.

Figure 1a. Pseudictops anterior teeth.

The dentary incisors
are deeply rooted in a deep dentary. Not sure why the two dentaries (Fig. 1) have distinct shapes. Perhaps they are not actually related to one another or perhaps some parts are missing from the smaller one and plasterered over.

Figure 2. Leptictis, an early Oligocene elephant shrew.

Now that you’ve met Pseudictops, a quick look at Ictops
reveals a cranium with a double parasagittal crest, as in sister taxon, Leptictis. 

Figure 3. Rhynchocyon (above) and Macroscelides (below) compared. Though both are considered elephant shrews, they nest in separate major mammal clades in the LRT.

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References
Matthew WD, Granger W and Simpson GG 1929. Additiions to the fauna of the Gashato Formatin of Mongolia. American Museum Novitates 376:1–12.
Sulimski A 1968. Paleocene genus Pseudictops Matthew, Granger and Simpson 1929 (Mammalia) and its revision. www.palaeontologia.pan.pl/Archive/1968-19–1011-129–10-14.pdf

 

The genesis of external and internal nostrils

The origin of choanae
(internal nostrils) from the primitive dual external naris of basal vertebrates was ‘settled’ over a decade ago with the observation that Kennichthys (Fig. 1; Zhu and Ahlberg 2004; Janvier 2004) had a naris/choana at the rim of its jaws. At the time, Kennichthys was thought to be an osteolepiform and basal to tetrapods. In other words, that was the phylogenetic context at the time.

Figure 1. From Janvier 2004, evolution of the internal naris (choana) from primitive dual external nares. No bony ray fin fish, sharks and placoderms are shown here, distinct from the LRT in figure 2.

However, a novel phylogenetic context
arises by greater taxon inclusion in the large reptile tree (LRT, 1548 taxa; Fig. 2).

Figure 2. Subset of the LRT focusing on basal vertebrates. Colors indicate various naris configurations. Some palates are not known.

The LRT indicates
that Kennichthys was a terminal taxon, not leading to higher taxa. Polypterus and Powichthys have/had a single external and internal naris. This pattern leads by homology to tetrapods and osteolepiforms. A reversal took place with a traditional osteolpiform, Onychodus (Fig. 3), which has dual external nares, like ray fin fish, AND an internal naris. Thereafter the internal naris disappears and dual external nares are retained.

FIgure3. Several views of the Onychodus skull. Note the twin external nares AND the internal naris. 

Lungfish have/had two internal nares.
Some higher, predatory placoderms have a single external naris (not sure about the palate). A clade including living lizardfish (Trachinocephalus), Cheirolepis, and spiny sharks by convergence seem to have one external naris (not sure about the palate).

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References
Chang M and Zhu M 1993. A new Middle Devonian osteolepidid from Qujing, Yunnan. Mem. Assoc. Australas. Palaeontol. 15 183-198.
Janvier P 2004. Wandering nostrils. Nature 432:23–24.
Zhu M and Ahlberg P 2004. The origin of the internal nostril of tetrapods. Nature 432:94-97.

wki/Stensioella
wiki/Kenichthys

The origin of marine crocs re-revised

Revised August 09, 2019
with the addition of the Dyoplax skull (Fig. 7b) recently downloaded from Maisch et al. 2013. 

Also revised March 31, 2019, 
with a repaired nesting for Fruitachampsa (Figs. 4,5) a sister to Protosuchus in the LRT (subset Fig. 3), not a sister to marine crocs.

Figure 1. Several Jurassic sea crocs, apparently derived from Late Triassic Dyoplax.

Dr. Andrea Cau 2019
recently revised the affinities of the extinct marine crocs (Figs. 1,2). Here (Fig. 3), with more outgroup taxa, the affinities of the outgroups are more refined by adding taxa omitted by Cau. The in-group marine croc clade of Cau 2019 continue as is untested.

Figure 2. Reduced from Cau 2019 showing Fruitachampsa as the proximal outgroup for marine and river crocs. The outgroup Postosuchus is not related to Crocodylomorpha in the LRT.

As we learned earlier
choosing outgroup taxa is not as scientific as letting a wide gamut phylogenetic analysis, like the large reptile tree (LRT, 1549 taxa, subset Fig. 3), choose outgroup taxa for you. 

Figure 3. Subset of the LRT with the addition of Lagosuchus next to Saltopus among the basal bipedal Crocodylomorpha. The nesting of skull-only Yonghesuchus near the skull-less taxa provides clues to the morphology of the skulls in the headless taxa.

Strangely,
the proximal outgroup taxon for marine crocs recovered by Dr. Cau (Fig. 2) was tiny Fruitachampsa (Figs. 3, 4), a small, gracile Late Jurassic biped sprinter that nests with other bipedal crocodylomorphs in LRT and Cau’s cladogram. Fruitachampsa would seem to have few traits in common with river and marine crocs. Dyoplax has more.

Figure 4. Fruitachampsa reconstructed. Note the many homologies with Scleromochlus and the few with marine crocs.

Cau did not include Dyoplax
in his cladogram.

Figure 5. Fruitachampsa skull. The vomers are missing. The chonae are conjoined medially, contra Clark 2011.

While we’re on the subject of Fruitachampsa,
it had an enormous notch for a mandibular fang, much larger than necessary. The medial choana is similar to sister taxa.

Despite appearances
Dyoplax (Fig. 7) is not considered a crocodylomorph, let alone an outgroup to marine crocs, as we learned earlier here.

Figure 7. Dyoplax arenaceus Fraas 1867 is a mold fossil recently considered to be a sphenosuchian crocodylomorph. Here it nests as a basal metriorhynchid (sea crocodile) in the Late Triassic.

Figure 7b. Added 08/09/19 from Maisch et al. 2013. DGS sutures do not match sutures found by Maisch et al. Hypothetical missing parts based on phylogenetic bracketing ghosted on.

In the LRT
(subset Fig. 3) Dyopolax (Figs. 7, 7b) is the outgroup taxon to marine crocs while Dibrothosuchus (Fig. 8) is basal to this clade + river crocs.  

Figure 8. Dibothrosuchus nests basal to all later quadrupedal crocs, including marine crocs, in the LRT. The hind limbs are not known. Phylogenetic bracketing suggests shorter legs are more likely.

Once again,
a wide gamut phylogenetic analysis is key to recovering interrelationships.

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References
Cau A 2019. A revision of the diagnosis and affinities of the metriorhynchoids (Crocodylomorpha, Thalattosuchia) from the Rosso Ammonitico Veronese Formation (Jurassic of Italy) using specimen-level analyses. PeerJ, DOI 10.7717/peerj.7364
Clark JM 2011. A new shartegosuchid crocodyliform from the Upper Jurassic Morrison Formation of western Colorado. Zoological Journal of the Linnean Society, 2011, 163, S152–S172. doi: 10.1111/j.1096-3642.2011.00719.x

Meet Seazzadactylus, the newest Late Triassic pterosaur

Dalla Vecchia 2019 introduces us to
Seazzadactylus venieri (Figs. 1–3; MFSN 21545), a small Late Triassic pterosaur known from a nearly complete, disarticulated skeleton (Fig. 2). The tail is supposed to be absent, but enough is there to show it was very gracile. The gracile feet are supposed to be absent, but they were overlooked. The rostrum was artificially elongated, but a new reconstruction (Fig. 3) takes care of that. A jumble of tiny bones in the throat (Fig. 4) were misidentified as a theropod-like curvy ectopterygoid, but the real ectopterygoid fused to the palatine as an L-shaped ectopalatine was identified (Figs. 3,4). 

Figure 1. Seazzadactylus (at far right) nests between the two Austriadactylus specimens in the LPT.

Seazzadactylus is a wonderful find,
and DGS methodology (Fig. 1) pulled additional data out of it than firsthand observation, which was otherwise quite thorough (with certain exceptions).

Figure 2. Seazzadactylus in situ and tracing from Dalla Vecchia 2019. Colors added here.

Dalla Vecchia reports

1. The premaxillary teeth are limited to the front half of the bone. Dalla Vecchia did not realize that is so because, like other Triassic pterosaurs, the premaxilla forms the ventral margin of the naris, dorsal to the maxilla (Fig. 3).
2. A misidentified theropod-like ectopterygoid and pterygoid. Dalla Vecchia should have known no pterosaur has an ectopterygoid shaped like this. Rather the curvy shape represents a jumble of bones (Fig. 4). The real ectopalatine in Seazzadactylus has the typical L-shape (Figs. 3, 4) found in other pterosaurs.
3. The scapula is indeed a distinctively wide fan-shape.
4. The proximal caudal vertebrae are present, as are several more distal causals. All are tiny.

Figure 3. Seazzadactylus reconstructed using DGS methods. No such reconstruction was produced by Dalla Vecchia. This is a primitive taxon precocially and by convergence displaying several traits found in more derived taxa.

Figure 4. Seazzadactylus bone jumble, including the L-shaped ectopalatine (orange + tan). No pterosaur has a theropod-like ectopterygoid. That’s a loose jumble of bone spurs and shards.

It is easy to see how mistakes were made.
Colors, rather than lines tracing the bones, would have helped. Using a cladogram with validated outgroup taxa and more taxa otherwise were avoided by Dalla Vecchia for reason only he understands.

Figure 5. Seazzadactylus pectoral girdle.

Phylogenetically Dalla Vecchia reports,
“Macrocnemus bassanii, Postosuchus kirkpatricki and Herrerasaurus ischigualastensis were chosen as outgroup taxa.” (Fig. 6)

Funny thing…
none of these taxa are closely related to each other or to pterosaurs (Macrocnemus the possible distant exception) in the large reptile tree (LRT, 1549 taxa) where no one chooses outgroup taxa for pterosaurs. PAUP makes that choice from 1500+ candidates.

Figure 6. Cladogram by Dalla Vecchia 2019 showing where Seazzadactylus nests. Their is little to no congruence between this cladogram and the LPT (subset Fig. 7), exception in the anurognathids. This cladogram needs about 200 more taxa to approach the number in the LPT.

Within the Pterosauria,
Dalla Vecchia nests his new Seazzadactylus between Austriadraco and Carniadactylus within a larger clade of Triassic pterosaurs that does not include Preondactylus, Austriadactylus or Peteinosaurus. Dalla Vecchia’s cladogram includes 27 taxa (not including the above mentioned outgroup taxa). In the large pterosaur tree (LPT, 239 taxa) Austriadraco (BSp 1994, Fig. 8) is a eudimorphodontid basal to all but two members of this clade. Carniadactylus (Fig. 8) is a dimorphodontid closer to Peteinosaurus. So there is little to no consensus between the two cladograms.

Figure 7. Subset of the LPT focusing on Triassic pterosaurs and their many LRT validated outgroups.

Publishing in PeerJ may cost authors $1400-$1700 (or so I understand).
Dalla Vecchia asked his Facebook friends for monetary help to get this paper published. I offered $900, but only on the proviso that the traditional outgroup taxa (listed above and unknown to me at the time) not be employed. You can understand why I cannot support those invalidated (Peters 2000) outgroups. Dr. Dalla Vecchia’s rejected my offer with a humorless invective of chastisement that likened my offer to one traditionally made by the Mafia. A more polite, ‘no thank-you,’ would have sufficed. Just today I learned of Dalla Vecchia’s ‘chosen’ outgroups (see list above). Kids, that’s not good science.

Figure 8. Seazzadactylus sister taxa in the Dalla Vechhia 2019 cladogram to scale.

Bottom line:
A great new Triassic pterosaur! We’ll hash out the details as time goes by.

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References
Dalla Vecchia FM 2019. Seazzadactylus venieri gen. et sp. nov., a new pterosaur (Diapsida: Pterosauria) from the Upper Triassic (Norian) of northeastern Italy. PeerJ 7:e7363 DOI 10.7717/peerj.7363
Peters D 2000a. Description and Interpretation of Interphalangeal Lines in Tetrapods.  Ichnos 7:11-41.
Peters D 2000b. A Redescription of Four Prolacertiform Genera and Implications for Pterosaur Phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106 (3): 293–336.

Putting a speedometer on a fish cladogram

If you think about it
fish swim in about three basic speeds: fast (like swordfish), slow (like sea horses) or they are bottom dwellers, sit-and-wait predators (like frogfish). We know some bottom dwellers eventually grew legs and became tetrapods. I hope you find this interesting as I apply colors according to fish speeds in this subset of the large reptile tree (LRT, 1548 taxa, Fig. 1), seeking phylogenetic patterns, if they exist.

Figure 1. Subset of the LRT focusing on basal vertebrates (fish) colorized according to speed/metabolism.

Not sure what else can be said here.
Evolution can take a bottom dweller and turn it into an open water speedster, but usually not the other way. The genus Seriola is an exception giving rise to mudskippers and frogfish. We are descendants of bottom dwellers. So are birds, bats and pterosaurs.

If any of the above generic names don’t ring a bell,
type them into the keyword search box.

 

Robustichthys: another nail in the coffin of the traditional clade ‘Holostei’

Updated May 3, 2020 with a new nesting for Robustichthys
with the armored catfish, Hoplosternum (Fig. 1).

Figure 1. Hoplosternum in vivo. You can see the armor/bone beneath its shiny skin. A sister to Robustichthys in the LRT.

We looked at the breakup of the traditional clade ‘Holostei’
earlier here. Today’s new taxon (Fig. 1) does not repair that breakup.

Figure 1. Robustichthys in situ.

Described as “the largest holostean of the Middle Triassic,”
Robustichthys luopingensis (Xu et al. 2014, Xu 2019; Figs. 1, 2) does not nest with other traditional holosteans in the large reptile tree (LRT, 1548/1680 taxa). Rather it nests with Pholidophorus (Fig. 3), a tuna-like fish from the Late Triassic. The skulls are nearly identical (Figs. 2, 3), more so that the two skulls attributed to Pholidophorus (Fig. 3). Adding colors to match tetrapod patterns (Fig. 2) is a practice I have encouraged all paleoichthyologists to adopt.

Figure y. Hoplosternum skull with bones identified as homologs to those in Robustichthys.

Figure z. Skull of Robustichthys and reconstruction of same. Note resemblance to Hoplosternum (Fig. y), distinct from diagram in Xu 2019.

Earlier the LRT nested
three traditional extant ‘holosteans’, Amia, the bowfin, the distinctly different Lepisosteus, the gar, and Pholidophorus (Fig. 3), from the Late Triassic, several nodes apart from one another (Fig. 4), creating a polyphyletic clade ‘Holostei’. Robustichthys nests with Pholidophorus. So traditional traits that describe members of the traditional clade ‘Holostei’ are convergent among ray-fin fish in the LRT, which tests skull and skeleton traits.

Xu 2019 only mentions Pholidophorus (while pulling a Larry Martin),
“Recently, Arratia (2013) described that the symplectic also articulates with the lower jaw in the pholidophorid Pholidophorus gervasutti, but this condition, unknown in other early teleosts, probably represents another convergent evolution.” Xu did not include the LRT sisters and cousins, Pholidophorus, Strunius, and Thunnus, among several other taxa that split gars from bowfins in the LRT. Neither did any of the prior workers who produced cladograms included in Xu 2019. So, taxon exclusion is once again the problem here. The only way to test convergence in evolution is to test it, not dismiss it, as Xu did.

What is a Symplectic?
“relating to or being a bone between the hyomandibular and the quadrate in the mandibular suspensorium of many fishes that unites the other bones of the suspensorium.”

Figure 4. Pholidophorus holotype from Arratia 2013, overlay drawing from Agassiz 1845.

Robustichthys luopingensis (Xu et al. 2014; Xu 2019; Middle Triassic) was described as the largest holstean fish of the Middle Triassic, but here the clade Holostei is polyphyletic and Robustichthys nests alongside the armored catfish, Hoplosternum. The long frontal extends posterior to the orbit. The expanded jugal is split up. The maxilla is absent, as in all catfish.

Figure 2. Subset of the LRT focusing on basal vertebrate (fish).

You may wonder
how the LRT is able to recover so many novel solutions that fall outside mainstream hypotheses. Evidently students and professors follow textbooks, the textbooks the professors write and update. The LRT confirms and/or refutes textbooks as it tests every possible combination of the 1548 taxa now employed. It does not matter that the multi-state character count is only a fraction of the taxon count. It does not matter if I do not see the specimen in person and use a professionally rendered drawing (Fig. 3).

What matters is taxon inclusion.
You can’t tell who is related to who else unless you invite them all to participate. That is the number one issue separating this growing online hypothesis of interrelationships and all others.

What matters is lumping and separating all tested taxa
to get a completely resolved tree and making sure that all sister taxa document a gradual accumulation of derived traits (which could include losses of certain bones or bone processes.

Reporting results that differ from the mainstream is not a crime
and does not injure reputations, in the long run. The competition is fierce for discoveries and those who invest heavily into their PhDs and the papers they write fear they have the most to lose. Contra this hypothesis, I’ve never seen a PhD pilloried for making a mistake (unless it was in a tent out in the field with a female student). So all you PhDs out there… relax. If you don’t want to fix the problems in our field of study by including a wider gamut of taxa, let the LRT do it.

As you’ll find out someday, some traditions and paradigms are wrong.
Don’t trust authority. Don’t trust the LRT. Find out for yourself which hypotheses are wrong and right by running your own tests. Let me know if you find a different tree topology than the LRT.

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References
Xu G-H 2019. Osteology and phylogeny of Robustichthys luopingensis, the largest holostean fish in the Middle Triassic. PeerJ 7:e7184 DOI 10.7717/peerj.7184
Xu G-H, Zhao L-J and Coates MI 2014. The oldest ionoscopiform from China sheds new light on the early evolution of halecomorph fishes. Biology Letters 10(5):20140204
DOI 10.1098/rsbl.2014.0204.

‘When whales walked: Journeys in Deep Time’ from PBS

PBS produced a nearly two hour dive into
various ‘new’ paleo-insights featuring many of paleontology’s rising stars and taxa. They called it, “When whales walked: Journey in Deep Time.” The photography and special effects were excellent. Trailer here.

The first chapter (crocs)
starts in Madagascar caves where Voay, the so-called ‘horned’ crocodile fossils are found (Fig. 1). Dr. Evon Hekkala uses DNA to chart croc evolution. Today only it’s cousin, the Nile crocodile, still lives in Madagascar.  (Surprised that Dr. Chris Brochu (U of Iowa) was not interviewed, since he has done so much work with these crocs.)

Figure 1. Dr. Evon Hekkala shows off a horned crocodile skull found in a Madagascar cave.

Chapter two (pre-crocs)
Dr. Bhart-Anjan Bhullar (Yale) takes us back to the Triassic, “in many ways the Age of Crocodiles”, as he assembles the bones of Poposaurus (Fig. 2). Preview here. Bhullar says, “These animals show us what crocodiles were like at the beginning of their evolution.” That’s close, but not true. Actually Poposaurus was basal to poposaurs and archosaurs (crocs + dinos), so it nests just outside of the croc clade. Junggarsuchus or Pseudhesperosuchus would have made his statement true, but he had Poposaurus in his cabinets at Yale. He also had another specimen, a real Triassic croc.

Figure 2. Revised skull reconstruction for the PEFO specimen. Here the anterior is considered a premaxilla. Those teeth are shaped like triangles, but they are very deeply rooted and exposed very little, which casts doubts on its hypercarnivory.

Continuing….
Bhullar next showed us a tiny ‘sphenosuchian’, nearly complete and nicknamed ‘little foot’ and cf. Dromicosuchus: YPM VP 57103). Originally it was discovered atop Popoposaurus.

Figure 3. The so-called ‘little foot’ specimen found with Poposaurus in Utah. YPM-VP-57103

Then Bhullar pulled a Larry Martin,
describing unique shared characters, rather than deciding what a croc is after phylogenetic analysis. We looked at YPM-VP-57103 earlier here.

Unfortunately,
Bhullar next held up a Euparkeria fossil and told viewers this specimen does not belong in the ancestry of crocs. That may be correct or incorrect depending on how you read it. According to the large reptile tree (LRT, 1546 taxa) Euparkeria nests so far back in the ancestry of crocs, it is too early to be a crocodylomorph.

Figure 4. YPM VP 057 103 reconstructed using color tracings from figures 1 and 2 in two scales. The smaller one shows the tail attached.

Chapter three (another croc)
Dr. Diego Pol (AMNH) presented a Jurassic notosuchid with a short snout and  large eyes on the side (not on the top). Pol discussed the variety of crocodylomorphs, but showed very few.

Chapter four (birds)
Dr. Julia Clarke (U of Texas) discussed birds and mentioned, “They can dive so deep into waters that light cannot reach.” Hmmm. Never heard that before. Clarke repeated the tradition based on genomic studies that half the total number of birds are passerines (song birds). By contrast, in the LRT sparrows (genus: Passer) give rise only to hoatzins, parrots and moas.

The PBS narrator noted that birds evolved from dinosaurs, then asked the silly question, “How could something so huge and heavy evolve into something so light?” According to the LRT, dinosaur taxa in the bird lineage were never huge, never heavy. Rather many basal small taxa gave rise to larger taxa—including moas and elephant birds, which are huge and heavy birds, as everyone knows. I just pulled a Larry Martin.

Chapter five (more birds)
Dr. Jacques Gauthier (Yale) said “Deinonychus altered everything we know about dinosaurs and birds” and that’s one of the major embarrassments according to Dr. John Ostrom, Gauthier’s mentor.  Gauthier mentions the first feathers were for warmth. Actually that was secondary. Warmth only happens when lots of feathers spread into a thick coat around the body. Gauthier describes the flight stroke of birds as they lift their forelimbs over the back, which is “very weird for tetrapods.” Gauthier makes no mention of Ken Dial‘s work or the elongation and locking down of the coracoids that enable a flight stroke in pterosaurs and birds.

Chapter six (more birds)
Dr. Jingmai O’Connor (USC, IVPP) describes dinosaurs buried in volcanic ash. Specimens document every stage of the dino–bird transition as they once lived side-by-side. She shows and discusses Caudipteryx, Jeholornis and Confuciusornis. O’Connor said an abbreviated tail evolved many times in dinosaurs and birds. You heard that here first, following a paper on pygostyles by O’Connor.

Chapter seven (more birds)
Dr. Erich Jarvis (The Rockefeller U) studies bird brains, learned behavior, and bird song evolution. The PBS narrator asks, “We all want to know is the bird family tree correct?” Jarvis says, he trusts genes to infer relatedness, and “most people trust DNA.” The LRT shows that “most people” are wrong. Jarvis thinks that “just a handful survived the (Cretaceous) mass extinction: shorebirds. ducks, geese, ostriches, emus.” This quietly omits one of the most highly derived bird clades, penguins in the Paleocene.

Chapter eight (whales)
Dr. Mark Uhen (George Mason U) mentioned that Charles Darwin suggested something like a bear could become a mysticete, then described a history of fossil whale discovery beginning with Basilosaurus, first thought to be a giant sea serpent.

Dr. Philip Gingerich (U Michigan) was highlighted for his discoveries in 1975, but even he made the mistake of assuming whale monophyly and descent from artiodactyls (a primitive deer). The LRT recovers at least two origins for extant whales where tenrecs nest basal to odontocetes and desmostylians nest basal to mysticetes. Gingerich discovered Pakicetus in Pakistan, which was once close to Madagascar, where tenrecs are found today.

Figure 5. At the Museum of Natural History in Paris, Dr. Christian De Muizon shows off the complete reconstruction of the Pakicetus skeleton, surprisingly an ancient relative of modern day whales.

Chapter nine (more whales)
Dr. Christian De Muizon (Muséum National d’Histoire Naturelle, Paris, Fig. 5) shows off a complete skeleton of Pakicetus, saying, “It looks like a dog with a long snout and webbed feet,” ignoring the fact that it looks more like a big tenrec and tenrecs echolocate.

Dr. Carlos Peredo (George Mason U) says baleen whales and toothed whales had their split early within cetacea (30 mya), in the descendants of Dorudon. By contrast, in the LRT the odontocete/mysticete split was much earlier, in the Jurassic. when tree shrews diversified.

Chapter ten (elephants)
Something about elephant tracks and extinction. Interesting to watch, but not much to comment about.