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.

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.

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.


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.

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.

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.

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

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


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 2015, evolution of the internal naris (choana) from primitive dual external nares.

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.

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.

FIgure 1. Several views of the Onychodus skull.

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).


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. 

Figure 2. Several Jurassic sea crocs, apparently derived from Late Triassic Dyoplax.

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 1. Reduced from Cau 2019 showing Fruitachampsa as the proximal outgroup for marine and river crocs.

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 focusing on Crocodylomorpha. Here, with more outgroup taxa, Fruitachampsa nests far from marine and river crocs.

Figure 3. Subset of the LRT focusing on Crocodylomorpha. Here, with more outgroup taxa, Fruitachampsa nests far from marine and river crocs. Why is the Fruitachampsa score <50? It was scored without post-crania. Saltopus has no crania. So when post-cranial traits are added to Fruitachampsa (soon) expect that score to increase. Update: Fruitachampsa nests closer to Scleromochlus than to Saltopus by 3 steps.

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 the small, gracile, Late Triassic biped sprinter Scleromochlus (Figs. 4, 5) in LRT. Fruitachampsa would seem to have few traits in common with river and marine crocs.

Figure 1. Fruitachampsa reconstructed. Note the homologies with Scleromochlus.

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

Cau did not include Scleromochlus
in his cladogram (Fig. 1), nor did he include Dyoplax.

Figure 2. Fruitachampsa skull to scale with Scleromochlus skull.

Figure 5. Fruitachampsa skull to scale with Scleromochlus skull. No antorbital fenestra is present according to Clark 2011, but phylogenetic braceting with Scleromochlus indicates otherwise. Apparently the jawline has phylogenetically eroded. The vomers are missing. The chonae are conjoined medially, contra Clark 2011.

While we’re on the subject of Fruitachampsa,
it appears to have an antorbital fenestra conjoined with the jawline rather than a very deeply emarginated jawline when put into a phylogenetic context. For similar reasons, the central fenestra in the palate is likely the conjoined choanae of primitive crocodylomorphs like Scleromochlus, rather than the posteriorly shifted choanae of derived eucrocs.

Faxinalipterus matched to Scleromochlus. The former is more primitive, like Gracilisuchus, in having shorter hind limbs and more robust fore limbs. The maxilla with fenestra and fossa, plus the teeth, are a good match.

Figure 6. Faxinalipterus matched to Scleromochlus. The former is more primitive, like Gracilisuchus, in having shorter hind limbs and more robust fore limbs. The maxilla with fenestra and fossa, plus the teeth, are a good match.

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 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.

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.

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.


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 venirei (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 nests between the two Austriadactylus specimens in the LPT.

Figure 1. Seazzadactylus 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.

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.

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).

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.

Figure 5. Seazzadactylus pectoral girdle.

Phylogenetically Dalla Vecchia reports,
Macrocnemus bassaniiPostosuchus 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 5. Cladogram by Dalla Vecchia 2019 showing where Seazzadactylus nests

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.

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. Kids, that’s not good science.

Figure 6. Seazzadactylus sister taxa in the Dalla Vechhia 2019 cladogram to scale.

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.


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.

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’

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.

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 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 2. Skull of Robustichthys. Compare to Pholidophorus in figure 3.

Figure 2. Skull of Robustichthys from Xu 2019, colors added to match tetrapods. Compare to Pholidophorus in figure 3.

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, Thunnus and Saurichthys, 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 3. Pholidophorus in situ and two skulls attributed to this genus. Compare the one on the left to figure 2. No tested fish in the LRT is closer to Robustichthys than Pholidophorus.

Figure 3. Pholidophorus in situ and two skulls attributed to this genus. Compare the one on the left to figure 2. No tested fish in the LRT is closer to Robustichthys than Pholidophorus.

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 Pholidophorus. The long frontal extends posterior to the orbit. The expanded jugal is further split up. Postparietals are absent. In their place the supratemporals rise to the midline. The mandible has a tall coronoid process.

Figure 4. Subset of the LRT focusing on fish. Note the traditional members of the Holostei do not nest together here largely because they don't look alike, but more like other, more attractive taxa.

Figure 4. Subset of the LRT focusing on fish. Note the traditional members of the Holostei do not nest together here largely because they don’t look alike, but more like other, more attractive taxa. Please see the LRT for all updates to this cladogram. Robustichthys nests with Pholidophorus, but strangely has not been tested with it in any prior holostean cladogram.

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.


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.