Asioryctes: Re-restoring a pes, re-nesting a taxon

I should have noticed this pairing earlier.
Evidently it escaped everyone else’s notice, too. Asioryctes nemegetensis (Kielan-Jaworowska 1975, 1984; Figs. 1,2; middle Late Cretaceous, Djadokhta Formation, ~85 mya) is a good match for the living bandicoot, Perameles. Maga and Beck 2017 nested Asioryctes with the coeval Ukhaatherium, and the extant Perameles with another bandicoot, Echymipera.

FIgure 1. Skulls of Asioryctes, Perameles and Macrotis compared.

FIgure 1. Skulls of Asioryctes, Perameles and Macrotis compared. The overall shapes are similar, and so are the teeth, and other details. Historically the feet have been different, and that’s our starting point. 

Figure 2. Left: original restoration of Asioryctes pes. Colors added. Right: New restoration based on phylogenetic proximity to Perameles and other marsupial taxa with vestigial digit 1 and gracile digits 2 and 3 (grooming claws).

Figure 2. Left: original restoration of Asioryctes pes. Colors added. Right: New restoration based on phylogenetic proximity to Perameles and other marsupial taxa with vestigial digit 1 and gracile digits 2 and 3 (grooming claws). 

The first three taxa
are members of the large reptile tree (LRT, 1272 taxa), but the first two don’t nest together. The LRT now nests Asioryctes with Perameles and Macrotis, two extant bandicoots. Ukhaatherium nests with the basalmost members of Theria several nodes earlier.

One of the problems with this
is the original restoration of the Asioryctes pes, based on disarticulated parts (Kielan-Jaworowska 1975; Fig. 2). The REAL problem is no other mammal has gracile lateral metatarsals. Sans the pes, the skull nests with Perameles and Macrotis (Fig. 1), taxa with only a vestige pedal digit 1 and reduced digits 2 and 3.

Hmmm.
That opens up a possibility not foreseen by Kielan-Jaworowska.

A new restoration
of the illustrated elements (Fig. 2) identifies the slender metatarsals as 2 and 3. The tarsal elements are all present (contra Kielan-Jaworowska 1975) just reidentified here in accord with a standard bandicoot foot.

And… so… for the first time
we can see a predecessor taxon demonstrating a transitional morphology to the reduced pedal digits 1–3 seen in bandicoots and kangaroos.

References
Geoffrey Saint-Hilaire E 1803. Note sur les genres Phascolomis et Perameles, nouveaux genres d’animaux à bourse. Bulletin des Sciences par la Société Philomathique de Paris 80, 49–150.
Kielan-Jaworowska Z 1975. 
Preliminary description of two new eutherian genera from the Late Cretaceous of Mongolia. Palaeontologia Polonica 33:5-15.
Kielan-Jaworowska, Z 1984. Evolution of the therian mammals in the Late Cretaceous of Asia. Part VII. Synopsis. Palaeontologia Polonica 4:173-183. online pdf
Maga AM and Beck RMD 2017. Skeleton of an unusual, cat-sized marsupial relative (Metatheria: Marsupialiformes) from the middle Eocene (Lutetian: 44-43 million years ago) of Turkey. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0181712

wiki/Asioryctes
wiki/Perameles
wiki/Macrotis

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Mammal taxa: size categories

A few days ago, we looked at a revised and expanded cladogram of the Mammalia based on skeletal traits (distinct from and contra to a cladogram based on DNA). Yesterday we looked at the deep time chronology of mammals. Today we add size categories to the cladogram to indicate Cope’s Rule (size increase over time) and phylogenetic miniaturization (size decrease over time, Fig. 1).

Looking at various mammal taxa size categories:

Figure 2. Subset of the LRT focusing on mammals. Color bars indicate size categories.

Figure 2. Subset of the LRT focusing on mammals. Color bars indicate size categories. The general trend is toward larger taxa with only a few phylogenetic miniaturization reversals.

Some notes:

  1. Mouse-sized taxa are typical at the origin of the Mammalia and the Metatheria (Marsupialia) with a few taxa growing to cat-sized. The few human-sized taxa are wolf-like or kangaroos. The two cow-sized metatherians are giant wombats.
  2. Cat-sized taxa are typical at the origin of the Eutheria (placentals). Larger taxa do not appear until after the large dinosaurs became extinct. Note: during the Mesozoic some large pre-mammals, like Repenomamus, remained.
  3. There are no elephant-sized prototheres or metatheres.
  4. There are no mouse-sized taxa more derived than Maelestes and close kin.
  5. Phylogenetic miniaturization attends the origin of mammals, the origin of the Hadrocodium clade, and after the glyptodonts. Little to no evidence of miniaturization appears at the origin of metatherians and eutherians. Slight evidence of miniaturization also appears at Ocepeia (pre mysticetes), Cainotherium (pre-artiodactyls) and Ectocion (pre-hyrax/elephant/siren).

Much earlier we looked at birth types (helpless vs. able) in a previous cladogram of the Mammalia that is as up-to-date as this one, but the point is made. We also briefly looked at the flexible spinal column of basal mammals vs. the less flexible spine of derived mammals.

Cladogram of the Mammalia (subset of the LRT)

A summary today…
featuring a long cladogram (Fig. 1), a subset from the large reptile tree (LRT, 1259 taxa) focusing on the Mammalia. This is how this LRT subset stands at present. Not much has changed other than the few node changes from the past week.

The transition from Prototheria to Theria (Metatheria)
includes long-snouted taxa, like Ukhaatherium. Nearly all Prototheria are also long-snouted (Cifelliodon is the current sole exception).

The transition from Metatheria to Eutheria (simplified)
includes small omnivorous didelphids arising from the carnivorous/herbivorous split among larger metatherians. Basal Carnivora, the most basal eutherian clade, are also omnivores. Caluromys, the extant wooly opossum, has a pouch, but nests at the base of all placental taxa (the LRT tests only skeletal traits), so it represents the size and shape of the earliest placentals (contra O’Leary et al. 2013)… basically didelphids without pouches, and fewer teeth, generally (but not always).

Basal members of most placental clades
are all Caluromys-like taxa, with a rapid radiation in the Late Triassic/Early Jurassic generating most of the major placental clades in the LRT (Fig. 1). Larger members of each of these placental clades appeared in the fossil record only after the K-T extinction event. So hardy where these basal taxa, that many still live to this day.

As shown earlier, higher eutheria are born able to able to walk or swim. They are no longer helpless with arboreal parents (tree-climbing goats the exception). Basal eutherians reproduce more like their metatherian ancestors, with helpless infants.

Figure 1. Subset of the LRT focusing on mammals.

Figure 1. Subset of the LRT focusing on mammals. Extant taxa are colored. Thylacinus is recently extinct.

The latest competing study
(O’Leary et al. 2013, Fig. 2) recovers the highly specialized edentates, aardvarks, elephants and elephant shrews as the most primitive placentals. Carnivora + bats are quite derived in the O’Leary team cladogram, somehow giving rise to ungulates and whales. This is an untenable hypothesis. It doesn’t make sense. Evidently the O’Leary team had faith that smaller didelphid-like ancestors would fill in the enormous phylogenetic gaps in their cladogram. By contrast the LRT has all the operational taxonomic units (OTUs) it needs to produce a series of gradually accumulating derived traits between every taxon in its chart (Fig. 1). The LRT makes sense.

Figure 5. Simplified version of the O'Leary et al 2013 cladogram showing placental relations exploded after the K-T boundary.

Figure 5. Simplified version of the O’Leary et al 2013 cladogram showing placental relations exploded after the K-T boundary.

References
O’Leary, MA et al. 2013. The placental mammal ancestor and the post-K-Pg radiation of  placentals. Science 339:662-667. abstract
Wible JR, Rougier GW, Novacek MJ, Asher RJ 2007. Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary Nature 447: 1003-1006

https://pterosaurheresies.wordpress.com/2016/08/31/another-look-at-the-oleary-et-al-hypothetical-ancestor-of-placentals/

https://pterosaurheresies.wordpress.com/2013/02/15/post-k-t-explosion-of-placentals-oleary-et-al-2013/

ArchibaldEtAl.pdf
protungulatum-donnae website

Apatemys revisited with DGS

Another short one today
in which the skull elements of Apatemys chardini (Marsh 1872, Eocene, Figs. 1, 2) are restored to their in vivo positions as determined by molar occlusion and jaw glenoid insertion.

Figure 1. Apatemys skull traced and reconstructed using color overlays (DGS).

Figure 1. Apatemys skull traced and reconstructed using color overlays (DGS). Yes, quite a bit of the mandible appears to be hidden beneath the broken coronoid process. 

Apatemys chardini (Marsh 1872, Eocene, 50-33 mya) was a squirrel-lke arboreal herbivore with a massive skull. Here it nests between the much larger Trogosus and the more plesiomorphic, Tupaia, a tree shrew. Apatemys had long slender fingers, a long flexible lumbar region, and a long gracile tail.

This taxon also gives rise to the shrew Scutisorex (check out the similar teeth, for instance), and the former tenrecs, Limnogale and Potamogale. All three are extant.

Figure 1. Apatemys, only complete fossil skeleton of an apatemyid, turns out to be a basal shrew. So this clade is not extinct.

Figure 2. Apatemys, only complete fossil skeleton of an apatemyid, turns out to be a squirrel-like  basal shrew. So this clade is not extinct. 

References
Marsh OC 1872. Preliminary description of new Tertiary mammals. Part II. American Journal of Science 4(21):202-224.

wiki/Apatemyidae

 

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