When pre-primates split from pre-rodents

A quick look at two closely related taxa today.
Hapalodectes (IVPP V5235, Fig. 1; Paleocene. China) nests at the base of the clade of primates (lemurs through humans, Fig. 3). Notice the narrow, transverse premaxilla and large canine.

Figure 1. The IVPP V5235 specimen of Haplodectes. Note the large canine and small, transverse premaxilla, traits shared with higher primates.

Figure 1. The IVPP V5235 specimen of Hapalodectes. Note the large canine and small, transverse premaxilla, traits shared with higher primates.

On the other hand
Ptilocercus
(Fig. 2; extant, Thailand, the pen-tailed tree shrew) nests at the base of the clade of rodents and rabbits and kin. Notice the large premaxilla (yellow) and small canine (orange). This represents the genesis of gnawing teeth in this clade.

Figure 2. The skull of Ptilocercus, nesting at the base of the rodent/rabbit clade. Note the large premaxilla (yellow) and small canine (orange).

Figure 2. The skull of Ptilocercus, nesting at the base of the rodent/rabbit clade. Note the large premaxilla (yellow) and small canine (orange).

These mouse-sized arboreal taxa
are late survivors of an earlier Middle Jurassic radiation. Both have a complete circumorbital ring, atypical for most mammals.

Figure 3. Subset of the LRT focused on Primates and basal Glires.

Figure 3. Subset of the LRT focused on Primates and basal Glires.

 

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Toxodon: now closer to kangaroos than to wombats

Figure 1. The skulls of Toxodon, Procoptodon and Interatherium resemble one another more than their post-crania might suggest. Now they nest together in the LRT (subset in figure 2).

Figure 1. The skulls of Toxodon, Procoptodon and Interatherium resemble one another more than their post-crania might suggest. Now they nest together in the LRT (subset in figure 2).

Another short one today
just to dash off a progress report as I wrestle with metatherian data. Like everyone else, I’m learning as I go. Toxodon and Eurygenium (Fig. 1) were always close to Interatherium, which was recently nested at the base of all kangaroos with the addition of the short-faced kangaroo, Procoptodon to the large reptile tree (LRT, 1258 taxa). Bulky, quadrupedal Toxodon and Eurgenium previously nested with quadrupedal wombats. 

The loss of pedal digit 1
found in kangaroos, interatheres and
Toxodon + Eurygenium turns out to be not a convergence, but a homoplasy as the Toxodon + Eurygenium node shifts over to the Interatherium node. All three are quadrupeds.

Now basal wombats with five pedal digits,
like the koala, no longer have four-toed taxa, like Eurygenium and Toxodon, separating them from their five-toed ancestors. 

Interatheres are getting to be more interesting. 

Figure 2. Subset of the large reptile tree focusing on the Metatheria. The tree is fully resolved, but many bootstrap scores under 50 indicate that only one or two characters separate those nodes with low scores. Scores higher than 50 are separated by three or more traits.

Figure 2. Subset of the large reptile tree focusing on the Metatheria. The tree is fully resolved, but many bootstrap scores under 50 indicate that only one or two characters separate those nodes with low scores. Scores higher than 50 are separated by three or more traits.

BTW
loss of pedal digit 1 also occurs alone in the wolf-like marsupial carnivore, the Tasmanian wolf, Thylacinus, by convergence.  By convergence, pedal digit 1 also shrinks in the bandicoot (Perameles) clade.

Geologically
western Gondwana (Africa + South America) separated from eastern Gondwana (Madagascar, India, Australia, Antartica) about 180 mya (Jurassic). That’s when the ancestors of South American Interatherium and Toxodon separated from the Australian ancestors of kangaroos. This is one way to estimate the antiquity of mammal clades.

Final thought for paleontologists and soon-to-be-paleontologists:
Reexamining data, like this, is good science. Making mistakes. like this, goes with the territory. Naiveté and enthusiasm go hand-in-hand. Apologies often follow. Gaining experience is a slog, but worthwhile when the puzzle pieces fit better in the end. More work often brings new insight. 

 

 

Dryolestes, a tiny mammal mandible with many molars

Figure 1. Having 7 or 8 molars is very unusual for mammals. So finding a close match for Dryolestes is easy, once you have Docodon and Amphitherium. Dryolestes is the most derived of these three.

Figure 1. Having 7 or 8 molars is very unusual for mammals. So finding a close match for Dryolestes is easy, once you have Docodon and Amphitherium. Late Jurassic Dryolestes is the most derived of these three based on the anterior lean of the coronoid process and the shamrock-shaped molars, reduced from their Middle and Late Jurassic relatives. 

With only the mandible + teeth to work with
(Fig. 1) the data on Dryolestes is too sparse to enter into the LRT, but having 8 molars in the Late Jurassic is atypical enough to make finding a close relative relatively easy—if you have Docodon and Amphitherium (Fig. 1) in your list. The best place to look for tiny Jurassic mammals with so many molars is within the Prototheria (Monotremata), which now includes extant toothless taxa.

Wikipedia offers
a cladogram that nests Dryolestes close to Amphitherium, but the next taxon at the next node is Vincelelestes, which has very few molars and large saber teeth and therefore is in no way related. Docodon does not appear on that cladogram. The plasticity of the tooth shapes is quite apparent here. Dryolestes looks like to was more interesting in sieving than in cracking beetle shells. But who knows?

All these taxa have been known for over 150 years. Wikipedia reports, “It has been suggested that this group [Dryolestoidea] is closely related to modern therian mammals.  Dryolestid dentition is thought to resemble the primitive mammalian dentition before the marsupial-eutherian differentiation and dryolestids are candidates to be the last common ancestor of the two mammalian subclasses.”

The burrowing placental, Necrolestes, is listed as a dryolestoid in Wikipedia.

References

wiki/Dryolestes
wiki/Dryolestidae
wiki/Dryolestoidea

 

Naked, horned and pocket gophers

Figure 1. Subset of the LRT focusing on the rabbit/rodent and kin clade where gophers nest with hedgehogs.

Figure 1. Subset of the LRT focusing on the rabbit/rodent and kin clade where gophers nest with hedgehogs.

In the large reptile tree (LRT, 1258 taxa, Fig. 1) the naked mole rat (genus: Heterocephalus, Fig. 2) nests with the hedgehog clade, one node off from the mouse/rat/clade. So the naked mole rat should be the  naked mole gopher.

Figure 1. The naked mole rat, Heterocephalus is closer to hedgehogs than to rats.

Figure 2. The naked mole rat, Heterocephalus is closer to hedgehogs than to rats.

Heterocephalus glaber (Rüppell 1842-5; 8-10cm) is the extant naked mole rat. It has a cold-blooded metabolism, lives underground, and can move backwards as fast as forward. Not the claws, but the teeth (protruding outside the lips) are used for digging. Heterocephalus is essentially hairless, lives in a colony dominated by a queen and may live up to 32 years in a low oxygen environment, or several times longer than related taxa.

Figure 2. Naked mole rat (Heterocephalus) skull in several view. The mandibles are disarticulated here, but the glenoid appears to be reduced to absent, providing great mobility to the jaws.

Figure 2. Naked mole rat (Heterocephalus) skull in several view. The mandibles are disarticulated here, but the glenoid appears to be reduced to absent, providing great mobility to the jaws.

Ceratogaulus hatcheri is the extinct horned gopher (Fig. 3). It nests with the naked mole rat in the LRT (Fig. 1).

Figure 3. Ceratogaulus, the extinct horned gopher

Figure 3. Ceratogaulus, the extinct horned gopher

Thomomys bottae (Figs. 4, 5) is the extant pocket gopher, another rodent nesting with hedgehogs.

Figure 4. Skull of Thomomys, the extant pocket gopher.

Figure 4. Skull of Thomomys, the extant pocket gopher. No large retroarticular process here.

These taxa look like rodents
but they nest with hedgehogs. So do we expand our concept of rodents (lumping)? Or make new clades (splitting)?

Figure 5. Skeleton of Thomomys, the pocket gopher.

Figure 5. Skeleton of Thomomys, the pocket gopher.

 

Rodentia is characterized by a single pair of continuously growing incisors in each of the jaws, as opposed to rabbits, which have two incisors.

Glires (Latin glīrēsdormice) is a clade consisting of rodents and lagomorphs (rabbits, hares, and pikas). In the LRT many more clades of small mammals nest with rabbits and rodents.

Euarchontoglires (synonymous with Supraprimates) is a clade of mammals, the living members of which belong to one of the five following groups: rodentslagomorphstreeshrewscolugos and primates. In the LRT rodents nest with primates, but not colugos.

References
Rüppell E 1842-5. Säugethiere aus der Ordnung der Nager, beobachtet im nordöstlichen Africa. Museum Senckenbergianum: Abhandlungen aus dem Gebiete der beschreibenden Naturgeschichte. 3: 99–101.

wiki/Hedgehogs
wiki/Erinaceus
wiki/Echinops
wiki/Naked_mole-rat

https://blogs.scientificamerican.com/tetrapod-zoology/african-mole-rats-so-much-more-than-just-the-naked-mole-rat/

Molecules vs morphology in mammals: Beck and Baillie 2018

Some published thoughts
on traits vs. molecules just out in the last week.

Beck and Baillie 2018 titled their paper: 
“Improvements in the fossil record may largely resolve the conflict between morphological and molecular estimates of mammal phylogeny.” No. Just the opposite. But you can see exactly where they put their faith… not in what they can see and measure.

From the abstract (annotated):
“Morphological phylogenies of mammals continue to show major conflicts with the robust molecular consensus view of their relationships.” True.

“This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships, particularly for fossil taxa for which, in most cases, molecular data is unlikely to ever become available.” Just the opposite. Doubts should have been raised about molecular data, which can be influenced by local viruses. Only physical traits, i. e. the expression of activated molecules, resolves relationships, as the large reptile tree (LRT, 1255 taxa) attests. 

“We tested this under a hypothetical ‘best case scenario’ by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive molecular phylogeny of mammals, and then seeing what effect inclusion of these predicted ancestors had on unconstrained analyses of morphological data. We found that this resulted in topologies that are highly congruent with the molecular consensus, even when simulating the effect of incomplete fossilisation. Most strikingly, several analyses recovered monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria.” In other words, we used our imaginations to make molecule phylogenies work, rather than considering the possibility that molecular phylogenies did not work. 

“Our results suggest that, at least in principle, improvements in the fossil record may be sufficient to largely reconcile morphological and molecular phylogenies of mammals, even with current morphological character sets.” They used far too few taxa. And they used suprageneric taxa. They avoided fossil taxa. This is omitting available data. 

This is not the way science is supposed to work.
So why was this published?

References
Beck RMD and Baillie C 2018. Improvements in the fossil record may largely resolve the conflict between morphological and molecular estimates of mammal phylogeny. bioRxiv doi:10.1101/373191. First posted online July 20, 2018.
http://www.biorxiv.org/content/biorxiv/early/2018/07/20/373191.full.pdf

The pink fairy armadillo joins the LRT as a glyptodont…

…not an armadillo.
The pink daily ‘armadillo’ (genus: Chlamyphorus) nests with the much larger glyptodont, Holmesina in the large reptile tree (LRT, 1255 taxa, subset Fig. 4), not with Dasypus novemcinctus, the extant llong-nosed armadillo nesting on the other side of the aardvark Orycteropus. Another fairy armadillo (genus: Calyptophractos) is also described here.

The pink fairy armadillos
(genus: Chlamyphorus trunca) and the greater fairy armadillo (genus: Calyptophractos retusus) are little glyptodonts. This is not heretical news (Fig. 1).

Figure 3. When glyptodonts were nested with armadillos, the fairy armadillos nested with extinct glyptodonts. Cladogram from xx

Figure 1. When glyptodonts were nested with armadillos, the fairy armadillos nested with extinct glyptodonts. Cladogram from Delsuc et al. 2016, a DNA analysis. No aardvarks were tested here.

Using DNA
(both ancient and modern) Delsuc et al. 2016 nested the fairy armadillo with the extinct glyptodont, Doedicurus (Fig. 1). We already know not to trust DNA evidence in paleontology, but in this case trait analysis supports something like this arrangement of taxa. The distance is not great either way.

Figure 2. DNA analysis by Möller-Krull et al. 2007 omits fossil taxa and aardvarks and arrives at this tree topology of extant edentates.

Figure 2. DNA analysis by Möller-Krull et al. 2007 omits fossil taxa and aardvarks and arrives at this tree topology of extant edentates.

Delsuc et al. 2016 nested fairy armadillos with glyptodonts
when they attempted to nest glyptodonts within the armadillo clade using DNA, omitting other fossil taxa.  I did not see LRT outgroups in their cladogram, nor did I see the aardvark.

Figure 3. Skulls of Holmesina and Calyptophractus compared.

Figure 3. Skulls of Holmesina and Calyptophractus compared. When they are together, the similarities are obvious.

Here in the LRT Calyptophractus is a phylogenetic miniature of Holmesina, with a shorter rostrum and expanded cranium (Fig. 3), along with its much smaller size and thinner scales. In lateral view the skulls are quite alike and distinct from all other edentates.

We know that aardvarks (genus: Orycteropus) nest with edentates because all the other possibilities were offered and found to be not as parsimonious (similar). Earlier we looked at the nesting of Holmesina and the phylogenetic fact that all aardvarks, armadillos and anteaters are derived from various types of glyptodonts.

Figure 2. Subset of the LRT focusing on the Edentata. Armored taxa are color tinted and their branches are thicker.

Figure 4. Subset of the LRT focusing on the Edentata. Armored taxa are color tinted and their branches are thicker.

References
Delsuc F et al. 2016. The phylogenetic affinities of the extinct glyptodonts. Current Biology 26(4):R155–R156.
Harlan R 1825. Annals of the Lyceum of Natural History of New York 1:235.
Möller-Krull M et al. 2007. Retroposed Elements and Their Flanking Regions Resolve the Evolutionary History of Xenarthran Mammals (Armadillos, Anteaters, and Sloths). Mol. Biol. Evol. 24 (11): 2573–2582. PDF
Yarrell W 1828. On the osteology of the Chlamyphorus truncatus of Dr. Harlan microform; in a letter to N.A. Vigors. Zoological Journal 3:544–554.

AKA
Pink Fairy Armadillo, Lesser Fairy Armadillo, Lesser Pichi Ciego, Pichiciego
http://www.iucnredlist.org/details/4704/0

Greater Fairy Armadillo, Burmeister’s Armadillo, Chacoan Fairy Armadillo, Greater Pichi Ciego: http://www.iucnredlist.org/details/4703/0

wiki/Pink_fairy_armadillo

https://www.amnh.org/explore/news-blogs/research-posts/study-finds-relationship-between-glyptodonts-modern-armadillos/

https://www.forbes.com/sites/shaenamontanari/2016/02/23/ancient-dna-from-extinct-glyptodont-reveals-it-was-a-really-big-armadillo/#2cb057ae287d

Juvenile Rhamphorhynchus and flightless pterosaur abstracts

Part 4
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 2018g. First flightless pterosaur
PDF of manuscript and figures

Pterosaur fossils have been discovered all over the world, but so far no flightless pterosaurs have been reported. Here an old and rarely studied pterosaur fossil (Sos 2428) in the collection of the Jura Museum in Eichstätt, Germany, was re-examined and found to have a reduced pectoral girdle, small proximal wing elements (humerus, radius and ulna), three vestigial distal wing elements, the relatively longest pelvis of any pterosaur and the widest gastralia, or belly ribs. This discovery represents a unique morphology for pterosaurs. The Jura specimen lacked the wing size, forelimb muscularity and aerodynamic balance necessary to sustain flapping flight. It was a likely herbivore.


Peters D 2018h. First juvenile Rhamphorhynchus recovered by phylogenetic analysis
PDF of manuscript and figures
Standing seven to 44 centimeters in height, a growing list of 120+ specimens assigned to the pterosaur genus Rhamphorhynchus are known chiefly from the Solnhofen Limestone (Late Jurassic, southern Germany). An early study recognized five species and only one juvenile. A later study recognized only one species and more than 100 immature specimens. Phylogenetic analyses were not employed in either study. Workers have avoided adding small Solnhofen pterosaurs to phylogenetic analyses concerned that these morphologically distinct specimens were juveniles that would confound results. Here a large phylogenetic analysis that includes tiny Solnhofen pterosaurs tests that concern and seeks an understanding of relationships and ontogeny within the Pterosauria with a focus on Rhamphorhynchus. 195 pterosaurs were compiled with 185 traits in phylogenetic analysis. Campylognathoides + Nesodactylus were recovered as the proximal outgroups to the 25 Rhamphorhynchus specimens. The ten smallest of these nested at the clade base demonstrating phylogenetic miniaturization. Two Rhamphorhynchus had identical phylogenetic scores, the mid-sized NHMW 1998z0077/0001, and the much larger, BMNH 37002. These scores document a juvenile/adult relationship and demonstrate isometry during pterosaur ontogeny, as in the azhdarchid, Zhejiangopterus, and other pterosaurs. Rather than confounding results, tiny Solnhofen pterosaurs illuminate relationships. All descended from larger long-tailed forms and nested as transitional taxa at the bases of the four clades that produced all of the larger Late Jurassic and Cretaceous pterodactyloids. No long-tailed pterosaurs survived into the Cretaceous, so miniaturization was the key to pterosaur survival beyond the Jurassic.

These manuscripts benefit from
ongoing studies at the large reptile tree (LRT, 1256 taxa) in which taxon exclusion possibilities are minimized and all included taxa can trace their ancestry back to Devonian tetrapods.