Macrauchenia: the good and bad of genomic studies

From the Wesbury et al. 2021 abstract
“The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia (Fig. 1). Our dated phylogenetic tree (Fig. 2) places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of B66Ma.”

Note they don’t ask us to pay as much attention to the proximal outgroup for Macrauchenia: the clade Carnivora (Fig. 2).

Figure 1. Macrauchenia museum mount.

Figure 1. Macrauchenia museum mount.

According to Wikipedia
Laurasiatheria is a gene-based clade “that includes that includes hedgehogs, even-toed ungulates, whales, bats, odd-toed ungulates, pangolins, and carnivorans, among others.”

Isn’t that an odd assemblage? 
Think about it. According to Wesley et al. (Fig. 2), sabertooth cats are closer to horses, rhinos and Macrauchenia than other long-legged, placental herbivores. By the way, in gene studies elephants appear in an unrelated major clade, Afrotheria.

Figure 1. Gene-based cladogram from Westbury et al. 2021 (slightly compressed to fit). Note the close relationship between Carnivora and Macrauchenia here. That is not replicated in a trait-based study (Fig. 2).

Figure 2. Gene-based cladogram from Westbury et al. 2021 (slightly compressed to fit). Note the close relationship between Carnivora and Macrauchenia here. That is not replicated in a trait-based study (Fig. 2).

A more reasonable, trait-based, phylogenetic analysis
(the large reptile tree, LRT, 1794+ taxa, subset Fig. 3) also nests the Macrauchenia clade basal to tapirs, rhinos and horses. The outgroup is the hyrax + elephant + manatee clade, then the artiodactyls, then the mesonychids + hippos + desmostylians + mysticetes. Off this chart (Fig. 3), the clade Carnivora is the basalmost placental clade, not the proximal outgroup to Macrauchenia.

Figure 2. Subset of the LRT focusing on derived placentals. Yellow highlights the Macrauchenia clade.

Figure 3. Subset of the LRT focusing on derived placentals. Yellow highlights the Macrauchenia clade.

Perhaps taxon exclusion is at fault here.
On the other hand, gene studies too often produce such odd interrelationships (Carnivora nesting closer to Macrauchenia than other herbivore clades). Gene studies too often deliver false positives in deep time studies. That’s a fact, not a hypothesis.

If your professor is asking you to help out on a deep time genomic study,
run.


References
Westbury M et al. (21 co-authors) 2021. A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica. Nature Communications | 8:15951 | DOI: 10.1038/ncomms15951 |www.nature.com/naturecommunications

https://en.wikipedia.org/wiki/Laurasiatheria
reptileevolution.com/macrauchenia.htm

Priacodon: How to tell a crown mammal from a mammal mimic

Jäger et al. 2020 discuss ‘molar’ occlusion
in a tiny taxon, Priacodon fruitaensis (LACM 120451, Fig. 1), they said was a crown mammal (a clade with living relatives). Priacodon is principally represented by a mandible with teeth and a maxilla with teeth. Triconodont ‘molar’ cusps are three in number and aligned like a row of three knives distinct from basal cynodonts and basal mammals.

Figure 1. Priacodon µCT scans from Jäger et al. 2020. Colors and restoration added. This looks like a mammal jaw. The LRT nests it with mammal mimics. That's an odd sort of canine with more than one cusp.

Figure 1. Priacodon µCT scans from Jäger et al. 2020. Colors and restoration added. This looks like a mammal jaw. The LRT nests it with mammal mimics. That’s an odd sort of canine with more than one cusp.

The authors wrote: 
“Triconodontids are a clade of the eutriconodontans which is a clade of early crown mammals with a fossil record from the Late Jurassic through the Late Cretaceous.”

So this clade had plenty of time to develop their unique teeth and convergent jaw joints alongside crown mammals (= monotremes + marsupials + placentals).

By contrast 
the large reptile tree (LRT, 1786+ taxa, subset Fig. 4) nested Priacodon and kin like Sinocodon (Fig. 2), within a clade of mammal mimics arising from the cynodont,  Pachygenelus, and preceding the Last Common Ancestor of all living mammals, Megazostrodon (Fig. 5). That LCA status makes Megazostrodon the most primitive of crown mammals. Any taxa preceding Megazostrodon are excluded from crown mammals. A valid cladogram is needed to place taxa within a crown clade or outside it. Jäger et al. did not provide a cladogram.

Wang et al. 2001 provided a traditional cladogram of mammals and pre-mammals. That was invalidated in 2016 by the addition of taxa to the LRT.

The single replacement of milk teeth with adult teeth
also marks Megazostrodon as a mammal because toothless hatchlings are initially feeding on their mother’s mammary glands, but that’s beside the point. That’s a trait, not a phylogenetic nesting  node.

Figure 1. Sinoconodon growth series including jaws and teeth, here colorized from Zhang et al. 1992.

Figure 2. Sinoconodon growth series including jaws and teeth, here colorized from Zhang et al. 1992. Note the lack of tiny post-dentary bones in this mammal-mimic.

Unfortunately,
this is a continuing problem in mammal paleontology going back before Repenomamus (Fig. 3), an Early Cretaceous mammal-mimic, typically considered the largest mammal in the Cretaceous. According to Wikipedia, “Repenomamus is a genus of triconodonts, a group of early mammals with no modern relatives.” According to the LRT, they have no living relatives because they are pre-mammals or mammal-mimic cynodonts.

Tiny post-dentary bones
This is a classic case of “Pulling a Larry Martin” because both Repenomamus and Priacodon have a certain trait shared with mammals by convergence. They lack the small post-dentary bones thought to be lost only in mammals. As a result they also have a dentary-squamosal jaw joint. The authors put all their money on this single trait and did not recognize the possibility of convergence. They didn’t provide a phylogenetic analysis that included all pertinent taxa.

In counterpoint, 
Megazostrodon (Fig. 5) retains tiny post-dentary bones. These ultimately migrate to help form the middle ear bones of higher mammals.

A few years ago
I had a chat with co-author R Cifelli in Oklahoma with regard to the nesting of multituberculates in Glires in the LRT. Multis redevelop tiny post-dentary bones by reversal according to the LRT, which tests a suite of 235 traits from head to tail. Cifelli wasn’t ready to consider non-traditional solutions based on an expanded taxon list and the possibility of a reversal.

Figure 4. Repenomamus reconstructed using DGS methods. The manus and feet are loose figments at present. Despite its predatory nature, note the reduction in canines, a clade trait.

Figure 3. Repenomamus reconstructed using DGS methods. The manus and feet are loose figments at present. Despite its predatory nature, note the reduction in canines, a clade trait.

Relatives of Sinoconodon replace their teeth multiple times,
(Fig. 2) as in cynodonts and reptiles in general. But even if they had single tooth replacement, their nesting on the LRT apart from crown mammals indicates they are not crown mammals, but mammal-mimics. Like Repenomamus (Fig. 3) and Priacodon (Fig. 1), Sinoconodon also lacked tiny post-dentary bones and had a dentary-squamosal jaw joint.

In their conclusion, the Jäger et al. note:
“Triconodontidae exhibit a molar series that is unique among mammals and is not directly comparable to any extant counterpart.” That’s because triconodonts are not related to extant counterparts, aka: crown mammals. These esteemed authors “Pulled a Larry Martin” by putting a few traits ahead of a suite of hundreds of traits in a phylogenetic analysis.

Convergence runs rampant in the LRT.
The LRT weeds out convergence. That’s why you need to run your own analysis and expand your own taxon list. Don’t rely on a few traditional traits.

Figure 2. Subset of the LRT highlighting the anomodontia and dicynodontia closer to the origin of the Therapsida.

Figure 4. Subset of the LRT from 2019 focusing on the Therapsida. Red taxa were tested separately due to too few characters known for a permanent place in the LRT.

Whatever Jäger et al. discovered
by closely examining the occlusal pattern in Priacodon, their study was hobbled by their invalid assignment of Priacodon to the clade crown Mammalia. Despite years in this profession, they had no idea that triconodonts were mammal mimics. To avoid problems like this, get a wide-angle view before setting up your microscopic views.

Figure 1. Megazostrodon skull in several views. Drawings from Gow 1986. Colors applied here.

Figure 5. Megazostrodon skull in several views. Drawings from Gow 1986. Colors applied here.

Taxon exclusion continues to be the number one problem in paleontology,
as you can see dozens of times if you click here: keyword: taxon+exclusion.


References
Jäger KRK, Cifelli RC and Martin T 2020. Molar occlusion and jaw roll in early
crown mammals. Scientific Reports (2020) 10:22378 https://doi.org/10.1038/s41598-020-79159-4
Wang Y-Q, Hu Y-M, Meng J and Li C-K 2001. An ossified Meckel’s cartilage in two Cretaceous mammals and origin of the mammalian middle ear. Science 294:357–361.

wiki/Crown_group
wiki/Repenomamus
wiki/Priacodon

The spectacled bear (Tremarctos) is not a ‘bear’ in the LRT

Summary of today’s post:
Convergence is rampant in the clade Carnivora, and elsewhere, too, as longtime readers already know only too well. Even so, the LRT (Fig. 3) lumps and splits them all.

Figure 1. Tremarctos ornatus, the spectacled bear of South America, nests with the South American bush dog (Fig. 2) in the LRT (figure 3).

Figure 1. Tremarctos ornatus, the spectacled bear of South America, nests with the South American bush dog (Fig. 2) in the LRT (figure 3).

Most mammal workers consider the spectacled bear,
South America’s only ‘bear’ (genus: Tremarctos ornatus; Fig. 1), a singular bear, genetically and phylogenetically distinct from all other bears. That’s why I added it to the LRT (Fig. 3), where no taxon stands alone.

Figure 2. The South American bush dog, Speothos, nests with the South American spectacled bear, Tremactos, in the LRT.

Figure 2. The South American bush dog, Speothos, nests with the South American spectacled bear, Tremactos, in the LRT.

Surprisingly,
or perhaps not surprisingly, given their geographic proximity, the South American spectacled bear, Tremarctos (Fig. 1), did not nest with the other bears, like Ursus and Arctodus (Fig.3). Instead it nested with the South American bush dog, Speothos (Fig. 2). One is big, the other not so big.

Figure 2. Tremarctos skull in 3 views.

Figure 2. Tremarctos skull in 3 views.

Both the spectacled bear and bush dog are primitive
to the clade of cats + dogs + hyaenas in the LRT (Fig. 3). So, if you’re counting, that makes three origins for carnivores we call ‘bears’. In that regard ‘bears’ are similar to ‘turtles‘ (2 origins),  ‘whales‘ (2 to 3 origins), ‘diapsids‘ (2 origins) and ‘synapsids‘ (2 origins).

Figure 3. Tremarctos nest with Speothos in this subset of the LRT.

Figure 3. Tremarctos nest with Speothos in this subset of the LRT.

Distinct from prior cladograms,
in the large reptile tree (LRT, 1734+ taxa; subset Fig. 3) the South American ‘bear’ (Tremarctos) nests with the South American bush dog (Spetheos). Both nest at the base of the dog + cat + hyaena clade, several nodes apart from extant bears, like Ursus, and the extinct short-face bear, Arctodus, which arises from the wolverine (Gulo).

Figure 2. Speothos, the South American bush dog, skeleton and in vivo.

Figure 2. Speothos, the South American bush dog, skeleton and in vivo.

Speothos veanticus 
(Lund 1842; up to 75cm in length) is the extant South American bush dog, traditionally considered a basal dog. Here Speothos nests at the base of cats + hyaenas + dogs. Miacis is a similar sister basal to sea lions, both derived from another short-legged carnivore, MustelaSpeothos was first identified as a fossil, then as a living taxon. Webbed toes allow this genus to swim more effectively.

Tremarctos ornatus
(Cuvier 1825) is the extant spectacled bear. Not related to other bears, here it nests with another South American member of Carnivora, Speothos, at the base of cats + dogs + hyaenas + aardwolves.

Figure 6. The South American bush dog, Speothos, nests with Tremarctos, at the base of the cat-dog-hyaena clade in the LRT.

Figure 6. The South American bush dog, Speothos, nests with Tremarctos, at the base of the cat-dog-hyaena clade in the LRT.

This may be a novel hypothesis of interrelationships.
If not please provide the prior citation so I can promote it here. Testing taxa that have never been tested together before is what the LRT does.


References
Cuvier F 1825.  In: Geoffroy Saint-Hilaire E.; Cuvier F. (eds.) Histoire naturelle des mammifères, avec des figures originales, coloriées, dessinées d’après des animaux vivans: publié sous l’autorité de l’administration du Muséum d’Histoire naturelle (50). A. Belin, Pari
Lund PW 1842. Fortsatte bernaerkninger over Brasiliens uddöde dirskabning. Lagoa Santa d. 27 de Marts 1840. Kongelige Danske Videnskabernes Selskab Afhandlinger 9:1-16.
wiki/Bush_dog
wiki/Spectacled_bear

Middle Jurassic moonrat: Asfaltomylos patagonicus

Ever since the LRT nested multiberculates within Glires,
we’ve been looking for non-multituberculate members of Glires (rats, rabbits, tree shrews, etc.) from the Jurassic to support that novel hypothesis. Here’s one.

Martin and Rauhut 2005
redescribed the mandible and teeth belonging to Asfaltomylos (Rauhut et al. 2002; Fig. 1) famous for being the first Jurassic mammal from South America and for apparently lacking a canine and incisors.

The question:
Is this an egg-laying monotreme (clade: Prototheria)? That’s what both Rauhut et al. 2002 and Martin and Rauhut 2005 thought based on tooth shape and a post-dentary groove in the medial dentary. They also excluded taxa listed below (and shown in figure 1). Such bias is a too common fault in traditional paleontology, as long time readers are well aware.

Figure 1. Asfaltomylos (MPEF-PV 1671) is a tiny mandible with teeth from in Jurassic strata in South America. Note the shape of the posterior premolar and how it relates to the giant posterior premolar in Carpolestes. The canine is tall. Not sure if Asfaltomylos had large incisors. Either way it does not matter, based on comparisons to Echinosorex and Erinaceus, the living moonrat and hedgehog.

Figure 1. Asfaltomylos (MPEF-PV 1671) is a tiny mandible with teeth from in Jurassic strata in South America. Note the shape of the posterior premolar and how it relates to the giant posterior premolar in Carpolestes. The canine is tall. Not sure if Asfaltomylos had large incisors. Either way it does not matter, based on comparisons to Echinosorex and Erinaceus, the living moonrat and hedgehog. Only the posterior molar in Erinaceus looks like the two molars in Asfaltomylos, separated in time by 166 million years.

Based primarily on tooth morphology,
Rauhut et al. 2002 considered Asfaltomylos a member of the Australosphenida, a clade of southern Jurassic mammals that is said to convergently evolve tribosphenic molars with northern mammals and probably gave rise to monotremes. Their taxon restricted cladogram nested Asfaltomylos between Shuotherium (Fig. 2) and several untested taxa leading to several platypus-like  taxa (including genus: Ornithorhynchus; Fig. 3.)

Question for you, dear readers:
Do the mandibles of Asfaltomylos (Fig. 1) and Shuotherium (Fig. 2) resemble one another? They should, given their proximity in the Rauhut et al. and Martin and Rauhut cladograms. If you think they don’t look similar, perhaps we need to expand the taxon list.

Figure 2. Medial view of Shuotherium. The last premolar is similar to the first molar, the coronoid process is tiny and the retroarticular process is absent, all distinct from Asfaltomylos (Fig. 1).

Figure 2. Medial view of Shuotherium. The last premolar is similar to the first molar, the coronoid process is tiny and the retroarticular process is absent, all distinct from Asfaltomylos (Fig. 1).

As a test, let’s add all the mammals in the LRT.
When we do, and based on very few mandible characters, Asfaltomylos foregoes the Prototheria and nests with derived members of Glires, derived from moonrats, the only members of Glires that sometimes do not have large gnawing incisors (yet another reversal).

Only the posterior molar
in the hedgehog, Erinaceus (Fig. 1), looks like the two molars in Asfaltomylos, separated in time by 166 million years. The premolar is nearly identical.

Moonrats
(Fig. 4) have an appropriately primitive appearance, and are different from other members of Glires in being chiefly carnivorous.

Rougier et al. 2007
considered Henosferus another member of the clade ‘Australosphenida’. With its  complete dental formula on a low profile mandible, Henosferous (Fig. x) nests with other basalmost therians, like Morganucodon (Fig. 3) in the LRT, not close to Asfaltomylos. So members of the invalidated clade ‘Australosphenida’ are polyphyletic in the LRT.

Figure 1. Henosferus mandible restored by Rougier et al. 2005 from several broken specimens.

Figure x. Henosferus mandible restored by Rougier et al. 2005 from several broken specimens.

Phylogenetic miniaturization and neotony
answer the problems posed by the low number of molars and the retention of the postdentary trough in Asfaltomylos. As you may recall, mammals recapitulate their phylogeny during ontogeny and Asfaltomylos matured at an earlier stage of development due to its small size.

Tooth morphology is something else to be ware of in phylogenetic analyses.
As an example, whale teeth devolved from multi-cusped in a square in their four-limbed terrestrial ancestors, to multi-cusped in a row in archaeocetes with flukes, to simple cones and toothlessness in derived odontocetes.

Figure 1. Brasilodon compared to Kuehneotherium, Akidolestes and Ornithorhynchus, the living platypus.

Figure 3. Brasilodon compared to Kuehneotherium, Akidolestes and Ornithorhynchus, the living platypus, and Monodelphis, a living tree opossum.

The problem is,
the high coronoid process and retroarticular (angular) process of Asfaltomylos are not found in Ornithorhynchus (Fig. 3) nor in other Prototheres in the large reptile tree (LRT, 1631+ taxa, Fig. 2). Prototheria are notable for their long rostra, lots of teeth and low coronoid process, traits that don’t match the  Asfaltomylos mandible. The medial surface of Asfaltomylos does include a dentary trough in which tiny posterior jaws bones would soon evolve to become ear bones… except that happens by convergence in highly derived arboreal mammals, like multituberculates, that experience that reversal in the auditory region, to the chagrin of Jurassic mammal workers worldwide.

Figure 3. Echinosorex, the extant moonrat, looks like an opossum, but nests with Deinogalerix in the large reptile tree.

Figure 4. Echinosorex, the extant moonrat, looks like an opossum, but nests with Deinogalerix in the large reptile tree.

In the LRT
Asfaltomylos nests with the moonrat Echinosorex, not far from Carpolestes (Fig. 1), a plesiadapiform in the LRT. 

Here’s a thought:
Take a look at that tall, narrow, posterior premolar in Asfaltomylos. That’s what turns into a similar posterior premolar in moonrats and hedgehogs. That’s what turns into a large cutting premolar in Carpolestes and multituberculates. 

Figure 1. Subset of the LRT focusing on Glires and subclades within.

Figure 5. Subset of the LRT focusing on Glires and subclades within. Moonrats and hedgehogs are not too far from Carpolestes and arboreal taxa like aye-aye.

Once again, the LRT shows why it is so important
to test all enigma taxa against a wide gamut of taxa, like the LRT. The LRT minimizes bias in the choice of the inclusion set of taxa. The number of characters for the mandible in the LRT comes down to less than dozen. Tooth cusp characters are largely omitted. So character count is, once again, shown to be not nearly as important, contra the opinions of workers who ask for more characters to no advantage.


References
Martin T and Rauhut OWM 2005. Mandible and dentition of Asfaltomylos patagonicus (Australosphenida, Mammalia) and the evolution of tribosphenic teeth. Journal of Vertebrate Paleontology 25(2):414–425.
Rauhut OWM, Martin T Ortiz-Jaureguizar E and Puerta P 2002. A Jurassic mammal from South America. Nature 416:165–168.
Rougier, GW, Martinelli AG, Forasiepi AM and Novacek M J 2007. New Jurassic mammals from Patagonia, Argentina : a reappraisal of australosphenidan morphology and interrelationships. American Museum novitates, no. 3566. online here.

wiki/Asfaltomylos

https://pterosaurheresies.wordpress.com-henosferus/

Earliest Paleocene mammals recovered from concretions

Lyson et al. 2019 bring us a peek
into a selection of mammal skulls (Fig. 1) preserved in concretions buried in the first few hundreds of thousands of years (up to 1million years) of sediment following the K-T extinction event (= KPgE) 66mya.

Figure 1. From Lyson et al. 2019 showing skulls of increasing size following the KPgE.

Figure 1. From Lyson et al. 2019 showing skulls of increasing size following the KPgE. These come from a variety of clades, not a single one. Tiny taxa were omitted from every stratum.

 

The illustration of skull through time from Lyson et al. 2019
from one locality (Fig.1 ) suggests that mammals were small immediately following the KPgE and thereafter increased and diversified over time. No doubt that happened in a general sense. However…

Placed into a phylogenetic context
(using the large reptile tree (LRT, 1590 taxa) indicates the skulls are from a wide variety of mammals, not a single clade. Lyson et al. omitted tiny taxa from every stratum, evidently to make them tell this tale.

  1. Didelphodon is a highly derived creodont marsupial in the LRT (Fig. 2).
  2. Baioconodon is a related marsupial not yet in the LRT
  3. Loxolophus A is a third creodont in the LRT
  4. Loxolophus B is a fourth creodont in the LRT
  5. Ectoconus is a basal terrestrial herbivorous placental (= basal condylarth) in the LRT
  6. Carsioptychus (originally Plagioptychus) nests with Sinonyx in the Anagale / tenrec / odontocete clade in the LRT. It was a mesonychid mimic.
  7. Taeniolabis is a highly derived multituberculate member of Glires
  8. Eoconodon nests with Mesonyx or Sinonyx, a mesonychid mimic (Fig. 3). I need more data than just a mandible.

In other words,
these taxa come from a variety of marsupial and placental clades, all with origins deep in the Mesozoic. The increases in skull size in the graphic (Fig. 1) following the extinction event was done by cherry-picking these skulls and omitting small taxa. We know that tiny rodents, primates and tree shrews were present in the earliest Paleocene because we have them today and we have them in the Jurassic. The authors told the story they wanted to tell and my hat is off to them. The publicity rush (see links below) and PBS NOVA special (see YouTube video below) that attend the publication of their paper attests to the industry they tapped into that exists to promote stories that otherwise would not have risen to this level of interest. After all, other fossils found in concretions don’t get this sort of press. 

Even so,
it’s always good to see paleontology told so well on the screen. And discoveries are always worthwhile. Some of these taxa (see list above) had to be added to the LRT to figure out just what they were in a phylogenetic sense, and that’s always interesting as well. 

Figure 6. Didelphodon from Wilson et al. 2016 had a 12 cm long skull.

Figure 2. Didelphodon from Wilson et al. 2016 had a 9 cm long skull.

Figure 3. Eoconodon was either a mesonychid like Mesonyx, or a pre-tenrec mesonychid-mimic like Sinonyx. You can see how similar the mandibles are to each other. Even the teeth are similar.

Figure 3. Eoconodon was either a mesonychid like Mesonyx, or a pre-tenrec mesonychid-mimic like Sinonyx. You can see how similar the mandibles are to each other. Even the teeth are similar.

References
Lyson TR et al. (15 co-authors) 2019. Exceptional continental record of biotic recovery after the CretaceousâPaleogene mass extinction. Science: eaay2268 (advance online publication) DOI: 10.1126/science.aay2268
Wilson GP, Eddale EG, Hoganson JW, Calede JJ and Vander Linden A 2016. A large carnivorous mammal from the Late Cretaceous and the North American origin of marsupials. Nature Communications 7:13734  PDF

https://science.sciencemag.org/content/early/2019/10/23/science.aay2268

https://www.sciencemag.org/news/2019/10/how-life-blossomed-after-dinosaurs-died

https://www.pbs.org/wgbh/nova/article/fossils-million-years-after-dinosaurs-died/

https://phys.org/news/2019-10-fossil-trove-life-fast-recovery.html

https://www.nationalgeographic.com/science/2019/10/new-fossils-show-mammals-growth-spurt-after-dinosaurs-died-corral-bluffs/

https://www.sciencealert.com/stunning-fossil-trove-shows-how-mammals-flourished-after-the-dinosaurs-died

The bush dog, first known as a fossil, enters the LRT

Figure 1. Speothos is the living bush dog from South America.

Figure 1. Speothos is the living bush dog from South America. This taxon is basal to cats + dogs + hyaenas.

The South American bush dog
Speothos veanticus (Lund 1842; up to 75cm in length; Figs. 1, 2) is traditionally considered a basal dog (family: Canidae). Here Speothos nests at the base of cats + hyaenas + aardwolves + dogs. Miacis is a similar sister basal to sea lions and both are derived from another short-legged carnivore, the European mink, Mustela. Speothos was first identified as a fossil, then as a living taxon. Webbed toes allow this genus to swim more effectively.

Figure 2. Speothos, the South American bush dog, skeleton and in vivo.

Figure 2. Speothos, the South American bush dog, skeleton and in vivo.


References
Lund PW 1842. Fortsatte bernaerkninger over Brasiliens uddöde dirskabning.Lagoa Santa d. 27 de Marts 1840. Kongelige Danske Videnskabernes Selskab Afhandlinger 9:1-16.

wiki/Bush_dog

 

Simbakubwa: Not a giant carnivore. More like a hippo.

Borths and Stevens 2019 might have been confused by the giant canines
and giant molars of Simbakubwa (Fig. 1). The authors thought they were dealing with a giant carnivore related to hyaenodonts and creodonts (hence the title of their paper).

The large reptile tree (LRT, 1546 taxa) makes no assumptions. The LRT minimizes confusion by testing a wider gamut of taxa, including mesonychids (Fig. 2) and hippos. It turns out the great size of Simbakubwa is actually no big deal because it’s closer to hippos than lions. Most hippos are much bigger than most carnivores.

Figure 1. Simbakubwa from Broths and Stevens 2019, colors added, and compared to a lion mandible. Note the two medial views of the mandible with different shapes. Dorsal view of indented mandible and palate is similar to hippos.

Figure 1. Simbakubwa from Broths and Stevens 2019, colors added, and compared to a lion mandible. Note the two medial views of the mandible with different shapes. Dorsal view of indented mandible and palate is similar to hippos.

Simbakubwa kutokaafrika (Borths and Stevens 2019; Miocene, 23mya; size; Fig. 1) was originally considered a gigantic carnivore, a member of the Hyaeondonta and Creodonta. Here it nests with Ocepeia (Fig. 3) as an offshoot of basal hippos with anteriorly placed eyes, convergent with carnivores, derived from mesonychids (Fig. 2).

Strangely
in dorsal view the mandible (dentary) was originally presented with an unnatural lateral kink/bend, creating a large open space where the teeth do not occlude. The authors report, (dentary is reconstructed with the distal portion medially oriented out of natural position) and “the coronoid should be interpreted cautiously because it is reconstructed.”

Not sure why they published that mandible without fixing it. 
The authors note: “the tooth crowns are unworn”. Relative to the skull size, all the teeth were enormous and they extended far back in the skull. I note the shearing canines of extant hippos are already present here. It is also worthwhile to compare the only dentary premolar of Simbakubwa (Fig. 1) with the identical tooth found in the earlier mesonychid, Harpagolestes (Fig. 4). In any case, the suite to traits preserved nest Simbakubwa with mesonychid hippos, rather than hyaenodont creodonts (which are marsupials, not carnivores).

Hippos are not related to artiodactyls
in the LRT, contra the traditional myth. Hippo ancestors are basal to taxa leading to baleen whales. 

Figure 1. Mesonyx, the first known mesonychid was a sister to Hippopotamus in the large reptile tree. So maybe it was a plant eater.

Figure 2. Mesonyx, the first known mesonychid was a sister to Hippopotamus in the large reptile tree. So maybe it was a plant eater, even though, like Simbakubwa, it looks like a predator with large lower canines.

Wikipedia reports,
Simbakubwa, like other hyainailourids, probably was a specialist hunter and scavenger that preyed on creatures such as rhinoceroses and early proboscideans. It may have been somewhat less specialized in crushing bone than its later relatives such as Hyainailouros. However, like HyainailourosSimbakubwa possessed lingually rotating carnassial blades, ensuring a constant shearing edge throughout its life.” Hippos are also killers, but usually only for defense. They and all their sister taxa prefer plants.

Figure 1. Ocepeia: before and after. The original reconstruction is here compared to a tracing of CT scan, duplicated left to right.

Figure 3. Ocepeia: before and after. The original reconstruction is here compared to a tracing of CT scan, duplicated left to right.

Ocepeia daouiensis (Gheerbrant et al 2001, 2014; Paleocene, 60 mya; 9 cm skull length; Fig. 3) is a Hippopotamus ancestor derived from a sister to Merycoidodon. The original reconstruction was not an accurate representation of the fossil CT scan. The pneumatized skull contains many air spaces. The larger skulls have larger canines and so are considered male. The jugal deepens below the orbit, hiding the posterior molars in lateral view. The premaxilla is transverse. The upper canine rubs against the lower large incsior creating a facet, as in hippos and Harpagolestes (Fig. 4). Ocepeia was found with aquatic taxa and was probably amphibious.

Figure 5. Robust Harpagolestes nests between the hippos and Mesonyx.

Figure 4. Robust Harpagolestes nests between the hippos and Mesonyx. Note the identical lower premolar as in Simbakubwa (Fig. 1).

Several news organizations picked up on the sensational aspects
of this ‘gigantic carnivore’ discovery. Unfortunately, this may become embarrassing for the authors when confirmed.

The good news is:
we have more hippo and mysticete ancestors to study!


References
Borths MR and Stevens NJ 2019. Simbakubwa ￿kutokaafrika, gen. et sp. nov. (Hyainailourinae, Hyaenodonta, ‘Creodonta,’ Mammalia), a gigantic carnivore from the earliest Miocene of Kenya. Journal of Vertebrate Paleontology e1570222 (20 pages) https://doi.org/10.1080/02724634.2019.1570222

wiki/Simbakubwa

https://www.ranker.com/list/killer-hippos-are-dangerous/mariel-loveland

https://www.washingtonpost.com/news/senegals-killer-hippo-problem/

http://blogs.discovermagazine.com/deadthings/2019/04/18/simbakubwa/#.XTX-IRTT63A

https://www.cbsnews.com/news/giant-lion-fossil-found-inside-drawer-at-kenyan-museum-2019-04-19/

Allactaga and Pedetes enter the LRT

Those leaping rodents from Africa,
jerboas (genus: Allactaga) and jumping hares (genus: Pedetes, Fig. 1), are more closely related to chinchillas and guinea pigs (Cavia), than to the marsupial kangaroos (Macropus) they converge with.

Allactaga major (Cuvier 1836; Late Miocene to present; snout-vent length 5–15cm; Fig. 1) is the extant jerboa, a nocturnal bipedal rodent that burrows into sand during the day. The long hind limbs help it hop, like a kangaroo, zig-zagging over long distances, and avoid attacking owls. They can hurdle several feet in a single bounce. Some have short ears, others have giant ears for cooling. Closest relatives in the LRT include Pedetes and Chinchilla, not the traditional Mus.

Figure 1. Skeletons of Pedetes and Allactaga to scale.

Figure 1. Skeletons of Pedetes and Allactaga to scale. Not sure yet if the jerboa is a miniature spring hare, or if the spring hare is a giant jerboa.

Figure 3. The spring hare (Pedetes) nests with the jerboa (Allactaga) in the LRT.

Figure 2. The spring hare (Pedetes) nests with the jerboa (Allactaga) in the LRT.

Pedetes capensis (Illiger 1811; snout-vent length: 35-45cm; Figs. 1, 2) is the extant South African springhare, a diurnal burrower and a nocturnal hopper native to South Africa. Pedal digit 1 is absent. Young are born with fur and are active within days.


References
Cuvier F 1836. Proceedings of the Zoololgical Society of London 1836:141.
Illiger 1811. Prodromus systematis mammalium et avium additis terminis zoographicis utriusque classis, eorumque versione germanica. Sumptibus C. Salfeld, Berolini [Berlin]: [I]-XVIII, [1]-301.

wiki/Allactaga
wiki/Pedetes

Pholidocercus: a long tailed armadillo-mimic hedgehog

Reversals in this taxon make it interesting.
Pholidocercus hassiacus (Fig. 1; von Koenigswald & Storch 1983; HLMD Me 7577; Middle Eocene) is a member of the rabbit/rodent/multituberculate clade Glires, but without the large anterior incisors that are found in most other members. This is a reversal hearkening back to basal placentals.

Figure 1. Only one of the several Messel Pit Pholidocercus specimens. This one has a truncated tail and a halo of soft tissue (pre-spines).

Figure 1. Only one of the several Messel Pit Pholidocercus specimens. This one has a truncated tail and a halo of soft tissue (pre-spines).

Three upper molars are present,
as in primates, and basal members of Glires, like Ptilocercus, the tree shrew. Other hedgehogs have only two upper molars.

Four upper premolars are present,
one more than in basal placentals and other hedgehogs.

Other hedgehogs have a stub for a tail.
Yet another reversal, Pholidocercus has a long, tail. It is bony and armored,  analogous to that of an armadillo (genus: Dasypus). Sister hedgehogs have just a stub for a tail. The curling of all hedgehogs for defense also recalls the spinal flexion of armadillos for defense. This is a trait basal therian mothers originally used to help guide their newborns from birth canal to teat.

Figure 2. Pholidocercus skull with DGS colors added. Distinct from most members of the Glires, the canine becomes more robust in the hedgehog clade. Note the posterior jaw joint, the opposite of mouse-like rodents.

Figure 2. Pholidocercus skull with DGS colors added. Distinct from most members of the Glires, the canine becomes more robust in the hedgehog clade. Note the posterior jaw joint, the opposite of mouse-like rodents. The short jugal is typical of this clade. No elongate dentary incisors here, yet another reversal to a basal placental condition.

Those sacral neural spines
(Fig. 1) are taller than in sister taxa. Armadillos also have tall sacral spines.

The clade Lipotyphyla, according to Wikipedia
“is a formerly used order of mammals, including the members of the order Eulipotyphla as well as two other families of the former order Insectivora, Chrysochloridae and Tenrecidae. However, molecular studies found the golden moles and tenrecs to be unrelated to the others.” 

The clade Eulipotyphyla, according to Wikipedia
“comprises the hedgehogs and gymnures (family Erinaceidae, formerly also the order Erinaceomorpha), solenodons (family Solenodontidae), the desmansmoles, and shrew-like moles (family Talpidae) and true shrews (family Soricidae).”

The clade Erinaceidae, according to Wikipedia
“Erinaceidae contains the well-known hedgehogs (subfamily Erinaceinae) of Eurasia and Africa and the gymnures or moonrats (subfamily Galericinae) of South-east Asia.”

The LRT largely confirms this clade,
but moles (genus: Talpa) nest separately in the clade Carnivora with the mongoose, Herpestes.

When you come across a taxon like Pholidocercus
first you eyeball it and declare it a… a… well, there are so many reversals here that it is best to avoid pulling a Larry Martin and just add it to a wide gamut phylogenetic analysis to let a large suite of traits decide for themselves based on maximum parsimony. Luckily the LRT had enough taxa to nest Pholidocercus with confidence with the hedgehogs, despite the several distinguishing traits and reversals.

Just added to the LRT:
Echinosorex, the extant moonrat. It also has a long tail and nests with Pholidocercus.

References
von Koenigswald W and Storch Gh 1983. Pholidocercus hassiacus, ein Amphilermuride aus dem Eozan der “Grube Messel” bei Darmstadt (Mammalia: Lipotyphla). Senchenberg Lethaia 64:447–459.

wiki/Hedgehogs
wiki/Erinaceus
wiki/Echinops
wiki/Pholidocercus

Evolution of multituberculates illustrated

Updated the next day, January 5, 2019 with new interpretations of the post-dentary bones in figure 3, detailed here.

With the addition of four taxa
to the large reptile tree (LRT, 1370 taxa), a review of the Bremer scores helped cement relationships in the Primates + Glires clade (Figs. 1, 2). Yesterday we looked at plesiadapiform taxa (within Glires, Fig. 2) leading to the aye-aye, Daubentonia. Today we’ll look at a sister clade within Glires, one that produced the clade Multituberculata.

The traditional, but invalid outgroup taxon,
Haramiyavia, is a pre-mammal trithelodontid not related to the rodent-and plesiadapiform- related members of the Multituberculata in the LRT. More on that hypothesis below.

In Figure 1
look for the gradual accumulation of traits in derived taxa. Carpolestes (Late Paleocene) is a late survivor from a Jurassic radiation. Paulchoffatia is Latest Jurassic. Megaconus is Middle Jurassic. Vilevolodon, Xianshou and Rugosodon are Late Jurassic. Kryptobaatar is Late Cretaceous. Ptilodus is Paleocene. So this radiation had its genesis in the Early Jurassic and some clades, like Carpolestes, had late survivors.

Figure 1. LRT taxa in the lineage of multituberculates arising from Carpolestes and Paulchoffatia.

Figure 1. LRT taxa in the lineage of multituberculates arising from Carpolestes and Paulchoffatia. Carpolestes is a sister to Ignacius. The new taxon, Arboroharamiya, nests with Xianshou in the Han et al. cladogram.

It’s worth noting
that the one key trait that highlights many multituberculates, the oddly enlarged last premolar of the dentary, is also a trait found in the basal taxon, Carpolestes, but not in Paulchoffatia, (Fig. 1). Paulchoffatia has the odd mandible (dentary) without a distinct retroarticular process common to multituberculates, convergent with Daubentonia. That there is also no distinct glenoid process (jaw joint) in clade members made these jaw bones even harder to understand. Then I realized the jaw joints were mobile, slung in place by muscles, as in rodents and primates, rather than a cylindrical dentary/squamosal joint, as in Carnivorans.

There is one more elephant in the room
that needs to be discussed. Earlier we looked at the splints of bone at the back of the jaws in multituberculates identified as posterior jaw bones (Fig. 3), a traditional pre-mammal trait. Multis move the squamosal to the back of the skull and reduce the ear bone coverings (ectotympanics) that nearly all other placentals use to cover the middle ear bones. This reversal to the pre-mammal condition is key to the traditional hypothesis shared by all mammal experts that multis are pre-mammals. Embryo primitive therians have posterior jaw bones, but these turn into tiny middle ear bones during ontogeny. In multis their retention in adults is yet another example of neotony.

Why lose/reverse those excellent placental middle ear bones?
‘Why’ questions get into the realm of speculation. With that proviso, here we go.

Figure 2. Jaw muscles of the Late Cretaceous multituberculate, Catopsbaatar.

Figure 2. Jaw muscles of the Late Cretaceous multituberculate, Catopsbaatar.

The over-development of the lower last premolar
indicates some sort of preference or adaptation for food requiring such a tooth. The coincident and neotonous migration of the squamosals to the back of the skull (the pre-mammal Sinoconodon condition) enlarged the temporal chewing muscles (Fig. 2). The neotonous lack of development of tiny middle ear bones was tied in to that posterior migration. Evidently Jurassic and Cretaceous arboreal multis did not need the hearing capabilities provided by the tiny middle ear bones of most therians, but they needed larger jaw muscles. Evidently they were safe in the trees because there were few to no arboreal predators of mammals back then. Multis and rodents had the trees to themselves. Evidently that changed in the Tertiary, when multis became extinct, perhaps because birds of prey (hawks and owls) became widespread and only rodents could hear them coming. That’s a lot of guesswork. Confirmation or refutation should follow.

Figure 3. Images from Han et al. Color and white labels added. Here the malleus, incus and stapes have reverted to their pre-mammal states and configurations. Note the quadrate is in contact with the articular, as in pre-mammals as the dentary and squamosal become a sliding joint, carried by larger jaw muscles. Also note the various ectotympanic bones (yellow) also present, typical of Theria.

Figure 3. Images from Han et al. Color and white labels added. Here the malleus, incus and stapes have reverted to their pre-mammal states and configurations. Note the quadrate is in contact with the articular, as in pre-mammals as the dentary and squamosal become a sliding joint, carried by larger jaw muscles. Also note the various ectotympanic bones (yellow) also present, typical of Theria.

A recent paper by Han et al. 2017
on the Late Jurassic pre-mulltituberculate euharamiyidan, Arboroharamiya (Fig. 3), documents precisely the status of the middle ear/posteror jaw bones along with the phylogenetic reduction of the ectotympanic that frames the ear drum and forms a thin shell around the middle ear bones in more primitive members of the clade Glires (Fig. 4, evidently there is more variation in this, and I will take a look at that in the future). Han et al. report for Arboroharamiya, “The lower jaws are in an occlusal position and the auditory bones are fully separated from the dentary.” That is the mammal condition.

The Han et al cladograms
include a rabbit and a rodent, but suffer from massive taxon exclusion. As a result they mix up prototherians, metatherians and eutherians as if shuffling a deck of cards, as compared to the LRT. My first impression is that they use too many taxa known only form dental traits when they should have deleted those until a robust tree topology was created and established with a large suite of traits from more complete taxa, as in the LRT.  I will add Arboroharamiya to the LRT shortly.

Figure 2b. Subset of the LRT focusing on Primates + Glires.

Figure 4. Subset of the LRT focusing on Primates + Glires.

Unfortunately,
and I hate to report this, mammal experts have been guilty of depending on a short or long list of traits (which can and often do converge and reverse) to identify taxa and clades. As readers know, paleontologists should only depend on a phenomic phylogenetic analysis that tests a large suite of bone characters and a wide gamut of taxa. Analysis proves time and again to be the only way to confidently identify taxa and lump’n’split clades. Cladograms, when done correctly, weed out convergence. Otherwise, reversals, like the neotonous reappearance of post-dentary bones and the reotonous disappearance of ectotympanics, can be troublesome to deal with, causing massive confusion. A phylogenetic analysis quickly and confidently identifies reversals because all possible candidates are tested at one time. 

Unfortunately,
d
iscovering this little insight is yet another reason why other workers have dismissed the LRT, have attempted to discredit the LRT, and is causing confusion in yet another upcoming class of future paleontologists. Paleo students have to choose between relying on a short list of traits or performing a phenomic phylogenetic analysis. Only the latter actually works (see below) and avoids mixing in convergent traits.

If you don’t remember
‘amphibian-like reptiles,’ those are taxa, like Gephyrostegus, Eldeceeon and Silvanerpeton, that nest at the base of all reptiles in the LRT, but have no traditional reptile traits. Everyone else considers them anamniotes. In the LRT, based solely on their last common ancestor status/nesting, these taxa are known to have evolved the amniotic membrane, the one trait, by definition, that unites all reptiles (including birds and mammals) and labels the above basal taxa, ‘amphibian-lke reptiles.’

References
Han G, Mao F-Y, Bi-SD, Wang Y-Q and Meng J 2017. A Jurassic gliding euharamiyidan mammal with an ear of five auditory bones. Nature 551:451–457.
Urban et al. (6 co-authors) 2017. A new developmental mechanism for the separation of the mammalian middle ear ossicles from the jaw. Proceedings of the Royal Society B: Biological Sciences https://doi.org/10.1098/rspb.2016.2416