July 2011-July 2018: Marking 7 years of paleo-heresies.

On July 12, 2011
a new blogpost entitled, “Welcome to The Pterosaur Heresies” first appeared online. It was (and is) meant to be the newsletter for taxon additions to the large reptile tree (LRT, 1255 taxa) at ReptileEvolution.com. More complete explanations and documentation can be provided here than at ReptileEvolution.com.

Starting two days later (July 14, 2011) and for the next three days,
the several hypotheses of pterosaur origins were compared one with another.

About a week later (July 22, 2011)
a completely resolved family of pterosaurs was presented. This was the first one to include several specimens from all well-known genera and the first to include tiny Solnhofen pterosaurs, first listed by Peters 2007. Previously tiny pterosaurs had been ignored based on the false premise that they were juveniles of larger specimens. That is a disproved hypothesis that continues to make the rounds. And we said goodbye to the clade, “Pterodactyloidea” because now 4 clades are recovered that share all of the pterodactyloid-grade traits, while two others share some, but not all of those traits. Have other workers started to include tiny Solnhofen pterosaurs in their analyses? No.

On the last day of that first month (July 31, 2011)
a  phylogenetic analysis of just 235 taxa was presented that recovered a completely resolved and diphyletic Reptilia (= Amniota), with one branch, the new Lepidosauromorpha, containing turtles, pterosaurs and lepidosaurs and their many relatives. The other branch, the new Archosauromorpha, contained mammals, enaliosaurs, archosaurs and their many relatives. An amphibian-like reptile, Gephyrostegus was their last common ancestor.  Today, with more than 1000 additional taxa, the original topology from seven years ago remains unchanged. Have other workers started to include basal amphibian-like reptiles in their analyses? No.

In the seven years since July 2011
hundreds of exciting and heretical discoveries have been recovered. Some of these resolve long-standing problems by simply adding taxa. Others shed new light on topics that were not thought to be problems at all by simply adding taxa. Ironically, several other workers gained worldwide acclaim for ‘discovering’ relationships that were recovered in the LRT and promoted here years earlier. Still other workers continue to criticize the LRT, claiming it should have failed some time ago, but the LRT continues to grow.

Unfortunately,
a propagandistic pall was cast on the LRT, so most workers have ignored the taxon inclusion/exclusion suggestions offered here, leaving their work open to criticism from the ever-growing authority of the LRT.

Whatever the faults of the LRT,
the specimens included here need only be included in more focused analyses using independent character lists to test them. In other words, the faults don’t have to be employed, only the suggested taxa. When that happens, confirmation of the LRT has been the typical result. Why? Because the wide gamut and sheer number of taxa minimize the possibility of taxon exclusion, the number one problem in prior, less inclusive analyses. If you have a tetrapod of unknown affinity, test it here at the LRT.

One unexpected and disappointing discovery:
DNA analysis, the standard for crime-fighting and paternity questions, has not been able to replicate the results of wider trait studies. Rather, DNA studies lose their efficacy over large phylogenetic distances when compared to the trait-oriented LRT. Worse yet for paleontology, DNA cannot be used with most fossils. Unfortunately, many paleontologists still believe in the validity of DNA studies.

Figure 2. Dr. Sean Carroll and Dr. Antonis Rokas

Figure 1. Dr. Sean Carroll and Dr. Antonis Rokas

On that note…
Quoted from EvolutionNews.org, “Finally, a study published in Science in 2005 (Rokas and Carroll 2006) tried to use genes to reconstruct the relationships of the animal phyla, but concluded that “despite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” The following year, the same authors published a scientific paper titled, “Bushes in the Tree of Life,” which offered striking conclusions. The authors acknowledge that “a large fraction of single genes produce phylogenies of poor quality,” observing that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.” The paper suggests that “certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.” The paper even contends that “the recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.”

I was not aware of that 2005 paper
before a few days ago. It needs to be more widely considered.

While other blogs journalistically report on the works of others,
the Pterosaur Heresies scientifically tests the work of others. That’s what sets it apart. That’s what makes it fun, interesting and rewarding. That’s what makes it controversial. Hopefully, that’s why you’re a subscriber. If, instead, you keep waiting for the LRT to crash and burn, well, that should have happened by now, don’t you think?

This July 2018,
seven years after it was started in 2011 with 235 taxa, there are 1000+ more taxa, all gradually blended in a tree topology that has been growing organically and with virtual complete resolution (some taxa known only from mandibles and other scraps are less resolved). Still, critics keep harping on the same perceived shortcomings (too many taxa, too few traits, not enough firsthand observation, lack of expertise)—while not harping on the shortcomings of traditional studies (principally taxon exclusion) that fail to produce gradually blended (= similar) sister taxa. There has always been a double standard at play, not only here, but for new hypotheses in geology, astronomy, physics, and paleontology. It’s universal and has been at work for centuries. It used to be that religious leaders led the charge against new ideas. Now we have PhDs trying to do the same.

Even scientists are not immune from this thing we call ‘human nature.’
Dr. J Ostrom complained about it, too. It’s human nature to follow authority, to go with the majority, and to suppress contra-indicators. Facts sometimes take decades to be widely accepted, and that’s just the way it is. It’s not acceptable, but that’s the way it is.

The beauty of science is
you, yes you can perform your own analysis to confirm or refute any analysis you read about here or anywhere. If I can do it… you can do it.

Thank you for your readership.
If there are subjects/taxa you want me to cover, or issues that need resolution, let me know. I look forward each day to corresponding with each and every one of you.

References
Peters D 2007. The origin and radiation of the Pterosauria. Flugsaurier. The Wellnhofer Pterosaur Meeting, Munich 27
Rokas A and Carroll SB 2006. Bushes in the Tree of Life. PLoS Biology, 4(11): 1899-1904.

refined-fine-tuned-placental-mammal-family-tree/

 

Advertisements

What is Periptychus carinidens?

Figure 1. Subset of the LRT focusing on the nesting of Periptychus.

Figure 1. Subset of the LRT focusing on the nesting of Periptychus.

Short answer:
In the large reptile tree (LRT, 1253 taxa, subset Fig. 1) Periptychus (Figs, 2–4) nests between basal phenacodonts like Phenacodus, Thomashuxleya and Pleuraspidotherium, and derived phenacodonts, like Gobiatherium + Arsinoitherium and Coryphodon + Uintatherium. These are all extinct herbivores from a clade that was recovered here first. Some derived taxa had ornate skull bumps/horns.

Previously known
as a condylarth from less complete materials (Cope 1881), the latest academic paper on Periptychus (Shelley, Williamson and Brusatte 2018) was still unable to determine closest relatives based on new data. No cladogram was presented. Sisters listed above were not listed in the text. Rather, the authors called it, “A robust, ungulate-like placental mammal.” 

Figure 2. Periptychus skull in 3 views.

Figure 2. Periptychus skull in 3 views ftom Shelley, Williamson and Brusatte 2018, colors added.

Think of Periptychus as a placental herbivore with very primitive feet…

Figure 3. Periptychus skeleton restored.

Figure 3. Periptychus skeleton restored from Shelley, Williamson and Brusatte 2018.

… and hands (no reduced digits). This mammal is remarkable for its long list of unremarkable traits.

Of course,
this was only the ‘warm-up act’ for the big, bizarre uintatheres to follow.

Figure 4. Manus and pes of Periptychus with some bones restored.

Figure 4. Manus and pes of Periptychus with some bones restored.

 

References
Cope ED 1881. The Condylarthra (Continued). American Naturalist 84;18: 892–906.
Shelley SL, Williamson TE and Brusatte SL 2018. The osteology of Periptychus carinidens: A robust, ungulate-like placental mammal (Mammalia: Periptychidae) from the Paleocene of North America. PLoS ONE 13(7): e0200132.

https://doi.org/10.1371/journal.pone.0200132

The origin of pterosaurs delayed…

In Peters 2000
pterosaurs were found to be indisputably derived from the fenestrasaurs, Longisquama, Sharovipteryx and Cosesaurus in order of increasing distance.

In Peters 2007
pterosaurs (and other fenestrasaurs) were found to be indisputably derived from a new clade of lepidosaurs, including Huehuecuetzpalli.

In Peters 2011–2018
more taxa (up to 1253 at last count) cemented those relationships. Other works, cited below, further cement those relationships.

Switek 2018 reported,
“We’ve cataloged plenty of species, with more named every year, but understanding how they [pterosaurs] fit into the Mesozoic world has eluded us.”

This, dear readers,
is called suppression. Perhaps Dr. SC Bennett (personal communication) said it best, “You won’t get published and if you do get published, you won’t be cited.” What other science is like this?

Dr. J. Ostrom, famous for his bird origin work, lamented the same problem. 
According to the Hartford Courant (2000), “In 1973, Ostrom broke from the scientific mainstream by reviving a Victorian-era hypothesis (see above) that his colleagues considered far-fetched: Birds, he said, evolved from dinosaurs. And he spent the rest of his career trying to prove it.” With the announcement of the first dinosaurs with feathers from China, Ostrom (then age 73) was in no mood to celebrate. He is quoted as saying, ““I’ve been saying the same damn thing since 1973, `I said, `Look at Archaeopteryx!’” Ostrom was the first scientist to collect physical evidence for the theory. Ostrom provoked a debate that raged for decades. “At first they said, `Oh John, you’re crazy,”’ Ostrom said in 1999.”

So, it’s not just me. It’s paleontology.
For readers thinking about getting into this field, here’s fair warning. And I’m going to call it out every time I see it, just like John Ostrom did.

References
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.
Peters D 2002. A New Model for the Evolution of the Pterosaur Wing – with a twist 
Historical Biology 15: 277-301
Peters D. 2007. The origin and radiation of the Pterosauria. Flugsaurier. The Wellnhofer Pterosaur Meeting, Munich 27
Peters D 2009. A reinterpretation of pteroid articulation in pterosaurs. Journal of Vertebrate Paleontology 29: 1327-1330
Peters D 2011. A Catalog of Pterosaur Pedes for Trackmaker Identification
Ichnos 18(2):114-141.http://dx.doi.org/10.1080/10420940.2011.573605
Peters D 2011–2018. ReptileEvolution.com and PterosaurHeresies.Wordpress.com
Switek B. 2018. https://blogs.scientificamerican.com/laelaps/digging-into-pterosaur-diets/

Hartford Courant (2000)

Think of aardvarks and sloths as naked and hairy glyptodonts respectively

Because
that’s what they really are… aardvarks are naked and sloths are hairy glyptodonts. And, yes, that comes as a surprise, it breaks a paradigm, it spins your head around, it’s heretical… and it’s exactly where the data takes us.

The Edentata is an odd clade
in which the basalmost taxa, like Barylambda, Glyptodon and Holmesina are very large. On the other hand, terminal extant and derived taxa, like Peltephilus and Cyclopesare much smaller, just the opposite of most mammal clades (in which smaller usually lead to larger, following Cope’s Rule.)

Figure 1. Subset of the LRT focusing on edentates and their outgroup, Barylambda. Here two glypotodonts nest at the bases of the two major clades.

Figure 1. Subset of the LRT focusing on edentates and their outgroup, Barylambda. Here two glypotodonts nest at the bases of the two major clades.

According to Wikipedia,
“Glyptodontinae (glyptodonts or glyptodontines) are an extinct subfamily of large, heavily armored armadillos which developed in South America and spread to North America.”

In the large reptile tree (LRT, 1252, edentate subset Fig. 1) the glyptodont, Glyptodon, nests between the massive Barylambda and giant sloths, followed by smaller tree sloths and small extinct horned armadillos, like Peltephilus and Fruitafossor. On another branch (Fig. 1) another large glyptodont, Holmesina, nests between the massive Barylambda and the much smaller aardvark, Orycteropus, the armadillo, Dasypus, and the anteaters, Tamandua and Cyclopes.

Such a big-to-small phylogenetic pattern,
is known as phylogenetic miniaturization or the Lilliput Effect and is often the product of neotony (adults retaining juvenile traits, including juvenile size).

Figure 2. Holmesina, the glyptodont ancestor to aardvarks, anteaters and armadillos.

Figure 2. Holmesina, the glyptodont ancestor to aardvarks, anteaters and armadillos. Those are aardvark hands (Fig. 3), glyptodont feet.

Holmesina (Fig. 2) is added to the LRT today.
Basically it is a longer-snouted glyptodont, basal to the longer snouted above-mentioned aardvarks, armadillos and anteaters.

Following a reader comment,
(suggesting ‘taxon exclusion’ was the issue that did not unite glyptodonts with armadillos) I was looking for a transitional taxon to more closely nest glyptodonts with armadillos, rather than sloths. I did so and the tree topology did not change when Holmesina was added. Armadillos are still one taxon removed from glyptodonts, but at least now we have a glyptodont on the long-nosed clade of aardvarks, etc.. As before, aardvarks nest between glyptodonts and armadillos. Looking at all the edentate taxa in detail and overall. I think this nesting and this tree topology seem very reasonable (= it produces a gradual accumulation of derived traits at all nodes and between all taxa).

Figure 3. Orycterpus, the extant aardvark, is a living sister to Barylambda from the Paleocene.

Figure 3. Orycterpus, the extant aardvark, is a living sister to Barylambda from the Paleocene. Aardvarks traditionally nest alone, but in the LRT they are edentates without armor… or hair.

Other workers, like Fernicola, Vizcaíno and Fariña 2008,
described the phylogeny of glyptodonts by putting taxa like Holmesina at the base while omitting Barylambda. Thus such studies do not present the full picture due to taxon exclusion. Everyone seems to omit Barylambda and all the other edentate outgroups back to Devonian tetrapods… but not the LRT.

Goodbye ‘Xenarthra’. Goodbye ‘Pilosa’. Goodbye ‘Cingulata’.
According to Wikipedia, “The order Pilosa is a group of placental mammals, extant today only in the Americas. It includes the anteaters and sloths, including the extinct ground sloths, which became extinct about 10,000 years ago.” According to Wikipedia, Cingulata, part of the superorder Xenarthra, is an order of armored New World placental mammals.” In the LRT ‘Xenarthra’ (Cope 1889) is a junior synonym for ‘Pilosa’ (Flower 1883) and that is a junior synonym for Edentata (Darwin 1859).

References
Darwin C 1859. On the origin of species.
Fernicola JC, Vizcaíno SF and Fariña RA 2008.
The evolution of armored xenarthrans and a phylogeny of the glyptodonts. Chapter 7 in: The Biology of the Xenarthra, Eds: Vizcaíno SF and Loughry WJ. University Press of Florida.
Gaudin TJ and Croft DA 2015. Paleogene Xenarthra and the evolution of South American mammals. Journal of Mammalogy 96 (4): 622–634. https://doi.org/10.1093/jmammal/gyv073

http://www.finedictionary.com/Edentata.html

 

 

 

 

Marmosa, Caluromys and Chironectes: the living, breathing origin of the Eutheria

These are the mouse, wooly and water opossums:
Marmosa (Fig. 1), Caluromys (Fig. 4) and Chironectes (Figs. 8, 9). As traditional didelphids, they’ve received too little attention. In a world in love with DNA phylogenetic analysis, they’ve received too little attention. In the large reptile tree (LRT, 1252 taxa, subset Fig. 3) these are the much sought after transitional taxa between Metatheria (marsupials) and Eutheria (placentals).

As simple and logical as this sounds
the present hypothesis of interrelationships (Fig. 3) is heretical. From Novacek 1989, 1992 to Tarver et al. 2016 other workers have placed armadillos, pangolins and elephants at the base of the Eutheria using gene analyses. As mentioned earlier, it is discouraging to see serious paleontologists (references below, including a certain science blogger) among the ‘believers’ as they embrace and put their faith in a method (gene analysis) that fails to deliver a gradual accumulation of derived traits at every node in large phylogenetic analyses, hoping for eventual redemption. They just accept the results without questioning. And that is surprising, because as a professor, you can’t really explain to students how these results gradually evolve. Rather these studies mix up and confuse the placental clades as others have mixed up the bird clades using DNA. We’ll take a look at these influential placental DNA papers and list their problems in detail in a few days. It’ll be horrible, untenable and illogical, so prepare yourself.

FIgure 1. Marmosa murina in vivo.

FIgure 1. Marmosa murina in vivo. Yes, this pouch less marsupial is carrying babies in front of its thigh. This is what basal placentals, like bats and flying lemurs do.

 

Marmosa murina
(Gray 1821, Voss and Jansa 2009) 
is one of 19 species of ‘mouse opossums’ native from Mexico to Argentina. In the large reptile tree (LRT, 1252 taxa, Fig. 3) Marmosa nests at the base of the last metatherian clade prior to the origin of eutherians (placentals), the clade that includes MonodelphisChironectes (a swimmer) and Volaticotherium (a glider). Like other mouse opossums (Fig. 5) Marmosa lacks a marsupium (= pouch) like its sisters (Fig. 5).

Marmosa waterhousi (Gray 1821) skull is shown below (Fig. 2).

Figure. 2. Marmosa waterhousi skull.

Figure. 2. Marmosa waterhousi skull.

 

Caluromys derbianus
(Allen 1904; Fonseca and Astúa 2018; Fig. 4) is the living ‘wooly opossum’, native to Central America. Sometimes it feeds inverted as seen in bats and hypothesized for pre-bats. It is an omnivore, like related placental carnivore, Nandinia.

Caluromys nests just inside of the first placental clade, Carnivora, alongside Vulpavus (Fig. 6), a taxon omitted from all prior papers on didelphids. Basal Carnivora are larger than other basal shrew- and mouse-sized placentals. In like fashion, Caluromys is the largest of these opossums, similar in size and shape to Vulpavus.

Figure 4. Subset of the LRT focusing on the Metatheria (=Marsupials). Here the diprotodont dentition evolved twice.

Figure 3. Subset of the LRT focusing on the Metatheria (=Marsupials). Here the diprotodont dentition evolved twice.

As we discussed earlier
here regarding Mondelphis (a genus including 22 species of short-tailed opossum) and the origin of bats and dermopterans, the transition from metatherians to eutherians was a gradual one that took place at this phylogenetic transition. So there is no great revelation here, just more evidence piling on.

Figure 1. Caluromys skull and mandible (sized to fit).

Figure 4 Caluromys skull and mandible (sized to fit).



Voss and Jansa found a ‘pouch’ in Caluromys,
but no pouch in the slightly more primitive and perhaps more plesiomorphic, Marmosa and Monodelphis. They report, “The marsupium of Caluromys philander uniquely consists of deep lateral skin folds that enclose the nursing young and open in the midline.” 

But wait!
In this regard the marsupium of Caluromys more closely resembles that of placental dermopterans and bats, taxa that expand these deep lateral skin folds to create newborn nurseries and ultimately, gliding membranes. Volaticotherium also has extensive lateral skin, so many transitional taxa were experimenting with this trait. Voss and Jansa do not mention the term ‘Eutheria’ and do not mention placentals as descendants of mouse opossums in their paper. This was an opportunity missed, but resolved here.

Didelphids
Take a look at the nesting of Didelphis in the LRT (subset in Fig. 3) and you’ll see that this is the primitive clade from which all other metatherians evolved. Most large carnivores and herbivores split off on a separate clade, leaving the mouse-sized didelphids (the Proeutherians) a more direct route to the Eutherian grade. This hypothesis of interrelationships has not been noticed or published before.

Pouch-less marsupials?
Why not just call them what they are? Transitional taxa. This is exactly how the Eutheria evolved from the Metatheria. Is this a heretical hypothesis? Or is it just another overlooked hypothesis that should have been proposed a century ago.

Figure 6. Mammary glands in pouchless marsupials. These taxa have not been tested in the LRT.

Figure 5. Mammary glands in pouch-less marsupials (mouse opossums). Pouch-less marsupials? Why not just call them what they are? Transitional taxa.

Other hypotheses
In the pre-cladistic era, Lillegraven et al. 1987 described the origin of Eutherian mammals “with high intensity food habits, small body masses and adaptations to very cold climates.” The authors focused on soft tissue traits the involve reproduction and metabolismn and put forth a hypotheses as to how nonspecific eutherians could have arisen from nonspecific metatherians… when they could have just studied mouse, wooly and water opossums and removed the guesswork. As mentioned above, modern authors delved far astray in their search for taxa at this transition.

In a very real sense
when you look at these images of mouse, wooly and water opossums you’re looking at an excellent example of the last common ancestors of all placental mammals, probably originating in the Early Jurassic (based on the first appearance of placental multituberculate Megaconus in the Middle Jurassic, in the LRT). These small didelphids are not terminal taxa. They are living breathing late-surviving representatives of an Early Jurassic split between pouch-less metatherians and pouch-less eutherians.

Figure 8. Caluromys, the largest of the mouse opossums, to scale with its LRT sister, Vulpavus, a basal member of Carnivora.

Figure 6. Caluromys, the wooly opossum, to scale with its LRT sister, Vulpavus, a basal member of Carnivora.

Here’s an unexpected finding:
Caluromys, the woolly opossum, nests as the basalmost member of the Carnivora (Fig. 3), but it retains a pouch. Time in the pouch is not particularly short. Size at birth is not particularly large. Sister taxa, including Vulpavus and Deltatherium, are both extinct, so we don’t know whether they had a pouch, but we know that on the main branch of carnivores, starting with Nandinia, the pouch was gone, convergent with mouse opossums (Fig. 5). Caluromys also has more molars than other carnivores and a longer nasal bone.

But remember,
in phylogeny it’s not the particular cherry-picked traits that determine what clade a taxon is a member of, its the nesting within a clade based on a suite of traits that is paramount.

So, similar to mammal-like reptiles,
amphibian-like reptiles, walking whales and dinosaur-like birds, Caluromys was a very basal metathere-like carnivore. And that’s how evolution really works in trait analysis.

Figure 8. Chironectes minimus skull.

Figure 8. Chironectes minimus, the water opossum, skull.

We didn’t spend much time with the water opossum, Chironectes.
It’s important to note that it, too, has a pouch. This sole aquatic marsupial has a water-proof pouch with a unique sphincter for access. And it nests in the LRT as the proximal outgroup taxa to the Eutheria, although the aquatic niche and webbed feet are autapomorphies not retained in descendant taxa among the placental mammals. These traits have had the entire Cretaceous and Cenozoic to develop after that phylogenetic split.

When you’re looking for transitional taxa,
keep looking for the little, plain, brown taxa and you will often find them.

Figure 9. Chironectes minimus, the water opossum, in vivo.

Figure 9. Chironectes minimus, the water opossum, in vivo. This sole aquatic marsupial has a water-proof pouch with a unique sphincter for access.

References
Allen JA 1904. Mammals from southern Mexico and Central and South America. Bulletin American Museum of Natural History 20(4): 29-80.
Burnett GT 1830. Illustrations of the Quadrupeda, or Quadrupeds, being the arrangement of the true four-footed Beasts indicated in outline. Quarterly Journal of Science, Literature and Art, July to December, 1829, 336–353.
Cifelli RL 1993. Theria of metatherian-eutherian grade and the origin of marsupials. In FS Szalay, MJ Novacek, and MC McKenna (editors), Mammal phylogeny: Mesozoic differentiation, multituberculates, monotremes, early therians, and marsupials, 205–215. New York: Springer.
Gray JE 1821. On the natural arrangement of vertebrose animals. London Medical Repository 15(1):296–310.
Hallstrom BM, Kullberg M, Nilsson MA and Janke A 2007. Phylogenomic data analyses provide evidence that Xenarthra and Afrotheria are sister groups. Molecular Biology and Evolution 24, 2059–2068.
Lillegraven JA, Thompson SD, McNab BK and Patton JL 1987. The origin of eutherian mammals. Biological Journal of the Linnean Society 32:281–336.
Murphy WJ, et al. 2001. Molecular phylogenetics and the origins of placental mammals. Nature 409, 614-618.
Naish D 2015. The Refined, Fine-Tuned Placental Mammal Family Tree. scientificamerican.com/tetrapod-zoology/
Novacek MJ 1989. Higher mammal phylogeny: the morphological-molecular synthesis. In Fernholm, B., Bremer. K. & Jornvall, H. (eds) The Hierarchy of Life. Elsevier, Amsterdam, pp. 421-435.
Novacek MJ 1992a. Fossils, topologies, missing data, and the higher level phylogeny of eutherian mammals. Systematic Biology 41, 58-73.
Novacek MJ 1992b. Mammalian phylogeny: shaking the tree. Nature 356, 121-125.
Pine RH, Flores DA and Bauer K 2013. The second known specimen of Monodelphs unistriata (Wagner) (Mammalia: Didelphimorphia), with redescription of the species and phylogenetic analysis. Zootaxa3640 (3):425-441.
Tarver JE et al. 2016. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biol. Evol. 8(2):330–344. doi:10.1093/gbe/evv261
Voss RS and Jansa SA 2009. Phylogenetic relationships and classification of didelphid marsupials, an extant radiation of New World metatherian mammals. Bulletin of the American Museum of Natural History, no. 322. PDF
Wildman et al. 2007. Genomics, biogeography, and the diversification of placental mammals. Proceedings of the National Academy of Sciences of the United States of America 104, 14395-14400 PDF.

wiki/Monodelphis
wiki/Marmosa
wiki/Caluromys derbianus
https://animaldiversity.org/accounts/Chironectes_minimus/
wiki/Water_opossum

Origin of pterosaurs and origin of archosauriforms abstracts

Part 2 
The following manuscripts are independently published online without peer-review at the DavidPetersStudio.com website. http://www.davidpetersstudio.com/papers.htm

Better to put them out there this way
than to let these works remain suppressed. Hope this helps clarify issues.


Peters D 2018c.
Cosesaurus avicepsSharovipteryx mirabilis and Longisquama insignis reinterpreted
PDF of manuscript and figures

Currently the majority of pterosaur and archosaur workers maintain the traditional paradigms that pterosaurs appeared suddenly in the fossil record without obvious antecedent and that pterosaurs were most closely related to archosaurs because they shared an antorbital fenestra and a simple hinge ankle. Oddly, these hypotheses continue despite the widely accepted acknowledgement that no archosauriformes document a gradual accumulation of pterosaurian traits. The minority view provided four phylogenetic analyses that documented a gradual accumulation of pterosaurian traits in three fenestrasaurs, Cosesaurus aviceps, Sharovipteryx mirabilis, and Longisquama insignis and their ancestors. These three also had an antorbital fenestra and a simple hinge ankle by convergence. Unfortunately the minority view descriptions also included several misinterpretations. Those are corrected here. The revised descriptions add further support to the nesting of pterosaurs with fenestrasaurs, a clade that now nests within a new clade of lepidosaurs between Sphenodontia and Squamata. The new data sheds light on the genesis of active flapping fight in the nonvolant ancestors of pterosaurs.


Peters, D. 2018d
Youngoides romeri and the origin of the Archosauriformes

Prior workers reported that all specimens attributed to Youngopsis and Youngoides could not be distinguished from the holotype of Youngina capensis. Others considered all specimens attributed to ProterosuchusChasmatosaurus and Elaphrosuchus conspecific. In both cases distinct skull shapes were attributed to taphonomic variations due to distortion pressure or allometric growth. Here a large phylogenetic analysis of the Amniota (1248 taxa) tests those hypotheses. The resulting tree recovers a den of small Youngina specimens preceding the Protorosauria. Another specimen nests at the base of the Protorosauria. Six others nest between the Protorosauria and the Archosauriformes. The most derived of these bears a nascent antorbital fenestra. Two other putative Youngina specimens nest at unrelated nodes. In like fashion, the various specimens assigned to Proterosuchus are recovered in distinct clades. One leads to the Proterochampsidae, Parasuchia and Choristodera. The latter lost the antorbital fenestra. Another clade leads to all higher archosauriforms. The present analysis reveals an evolutionary sequence shedding new light on the origin and radiation of early archosauriforms. Taphonomic distortion pressure and allometry during ontogeny were less of a factor than previously assumed. The splitting of several specimens currently considered Youngina and Proterosuchus into distinct genera and species is supported here.


These manuscripts benefit from
ongoing studies at the large reptile tree (LRT, 1251 taxa) in which taxon exclusion possibilities are minimized and all included taxa can trace their ancestry back to Devonian tetrapods.

The diet of Thylacoleo, the giant sugar glider

The diet of Thylacoleo, the so-called ‘marsupial lion,’
has been a puzzle for decades. The jaws and teeth look dangerous and carnivorous, but Thylacoleo nests in the middle of an herbivorous clade of wombat-like marsupials.

That’s the problem.
Morphology and phylogeny provide the problem… and the answer to the diet of Thylacoleo. This answer could have been known decades earlier, but alas… the same taxon exclusion issue that pervades paleo was also present here.

Morphology
One look at the palate of Thylacoleo documents a very different sort of mammal palate:

  1. The jawline curves laterally near the premolars
  2. Several molars seem to have fused to become one giant tooth
  3. There is an asymmetry in the lineup of the posterior teeth
Figure 1. The palate of Thylacoleo is unusual in several respects. See text for details.

Figure 1. The palate of Thylacoleo is unusual in several respects. See text for details. Vertical arrows point to asymmetries. Horizontal arrow lines up with parasagittal plane.

 

Phylogeny
In the large reptile tree (LRT, 1250 taxa) the closest living sisters to Thylacoleo, the sugar gliders, like Petaurus, should provide some sort of natural guidance as to what the giant sugar glider ate. And they do.

Sugar glider diet
From the Wikipedia page on sugar gliders: Sugar gliders are seasonally adaptive omnivores with a wide variety of foods in their diet… In summer they are primarily insectivorous, and in the winter when insects (and other arthropods) are scarce, they are mostly exudativorous (feeding on acacia gum, eucalyptus sap, manna, honeydew or lerp). Sugar gliders have an enlarged caecum to assist in digestion of complex carbohydrates obtained from gum and sap.

To obtain sap and nectar from plants, sugar gliders will strip the bark off trees or open bore holes with their teeth to access stored liquid gum. Little time is spent foraging for insects, as it is an energetically expensive process, and sugar gliders will wait until insects fly into their habitat, or stop to feed on flowers. They are opportunistic feeders and can be carnivorous, preying mostly on lizards and small birds. They eat many other foods when available, such as nectar, acacia seeds, bird eggs, pollen, fungi and native fruits. Pollen can make up a large portion of their diet, therefore sugar gliders are likely to be important pollinators of Banksia species.”

Well, there you have it. 
Little sugar gliders can be carnivorous. They can also strip bark off trees to get at the gum inside. That’s a rare diet. As sister taxa, giant sugar gliders, like Thylacoleo, were therefore likely also carnivorous and/or stripped bark off trees to get at the gum. For the latter odd reason the odd skull of Thylacoleo was likely adapted, and predation, if you insist, but predators don’t have the odd palate and teeth that Thylacoleo has.

We don’t have to provide a narrow dietary answer for Thylacoleo
because the diet of living sugar gliders is diverse. AND sugar gliders provide the long-sought carnivorous exception to this herbivorous clade.

Petaurus breviceps (Waterhouse 1839; Early Miocene to present; up to 30cm) is the extant sugar glider, a nocturnal squirrel-like marsupial able to climb trees and glide with furry membranes between the fore and hind limbs. An opposable toe is present on each hind foot. Sharp claws tip every digit.

Thylacoleo carnifex (Owen 1859; Pliocene-Pleistocene; 1.14 m long) was a giant sugar glider like Petaurus. Thylacoleo had the strongest bite of any mammal with the largest, sharpest molars of any mammal. It had fewer but larger teeth than Petaurus. The manus included retractable claws. The pes had a very large heel bone (calcaneum). This supposedly carnivorous ‘marsupial lion’ nests with herbivores. Pedal digit 1 likely had a phalanx and claw, but it has not been shown. Sugar gliders strip bark off of trees and the very odd teeth of Thylacoleo could have done the same on a larger scale.

References
Owen R 1859. On the fossil mammals of Australia. Part II. Description of a mutilated skull of the large marsupial carnivore (Thylacoleo carnifex Owen), from a calcareous conglomerate stratum, eighty miles S. W. of Melbourne, Victoria. Philosophical Transactions of the Royal Society 149, 309-322.
Waterhouse GR 1838. Observations on certain modifications observed in the dentition of the Flying Opossums (the genus Petaurus of authors). Proceedings of the Zoological Society of London. 4: 149–153.

wiki/Petaurus
wiki/Thylacoleo
NOVA | Bone Diggers | Anatomy of Thylacoleo | PBS
https://en.wikipedia.org/wiki/Sugar_glider
https://www.wired.com/2009/06/thylacoleo-herbivore-or-carnivore/