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/

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

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

Mesozoic mammals: Two views

Smith 2011 reported,
at the beginning of the Eocene, 55mya, “the diversity of certain mammal groups exploded.” These modern mammals”, according to Smith, ‘ consist of rodents, lagomorphs, perissodactyls, artiodactyls, cetaceans, primates, carnivorans and bats. Although these eight groups represent 83% of the extant mammal species diversity, their ancestors are still unknown. A short overview of the knowledge and recent progress on this research is here presented on the basis of Belgian studies and expeditions, especially in India and China.’

Contra the claims of Smith 2011
in the large reptile tree (LRT, 1354 taxa, subsets Figs. 2–4) prototherians are known from the late Triassic (Fig. 1). Both metatherians and eutherians are known from the Middle Jurassic. Many non-mammal cynodonts survived throughout the Mesozoic. In addition, the ancestors of every included taxon are known back to Devonian tetrapods.

Noteworthy facts after an LRT review (Fig. 1):

  1. All known and tested Mesozoic mammals (Fig. 1) are either small arboreal taxa or small burrowing taxa (out of sight of marauding theropods).
  2. All Mesozoic monotremes are more primitive than Ornithorhynchus and Tachyglossus (both extant).
  3. All Mesozoic marsupials are more primitive than or include Vintana (Late Cretaceous).
  4. All Mesozoic placentals are more primitive than Onychodectes (Paleocene).
Figure 1. Select basal cynodonts and mammals set chronologically. The divergence times for placentals (Eutheria), marsupials (Metatheria) and monotremes (Mammalia) are estimated here.

Figure 1. Select basal cynodonts and mammals set chronologically. The divergence times for placentals (Eutheria), marsupials (Metatheria) and monotremes (Mammalia) are estimated here.

Given those parameters
we are able to rethink which mammals were coeval with dinosaurs back on phylogenetic bracketing (= if derived taxa are present, primitive taxa must have been present, too).

Smith reports, “The earliest known mammals are about as old as the earliest dinosaurs and appeared in the fossil record during the late Trias around two hundred and twenty million years ago with genera such as Sinoconodon (pre-mammal in the LRT), Morganucodon (basal therian in the LRT) and Hadrocodium (basal therian in the LRT). However, the earliest placental mammals (Eutheria) were not known before the Early Cretaceous. Eomaia scansoria (not eutherian in the LRT) from the Barremian of Liaoning Province, China is the oldest definite placental and is dated from a hundred and thirty million years ago.”

Mesozoic Prototherians

  1. All included fossil taxa are Mesozoic. Two others are extant (Fig. 2).
Figure 2. Mesozoic prototherians + Megazostrodon, the last common ancestor of all mammals. Only two taxa (gray) are post-Cretaceous.

Figure 2. Mesozoic prototherians + Megazostrodon, the last common ancestor of all mammals. Only two taxa (gray) are post-Cretaceous.

Mesozoic Metatherians (Marsupials)

  1. Derived Vincelestes is Early Cretaceous, which means Monodelphis and Chironectes were present in the Jurassic.
  2. Derived Didelphodon is Late Cretaceous, which means sisters to Thylacinus through Borhyaena were also present in the Mesozoic.
  3. Derived Vintana is Late Cretaceous, which means sisters to herbivorous marsupials were also present in the Mesozoic.
Figure 3. Mesozoic metatherians (in black), later taxa in gray. Whenever derived taxa are present in the Mesozoic (up to the Late Cretaceous) then ancestral taxa, or their sisters, were also present in the Mesozoic. Didelphis is extant, but probably unchanged since the Late Jurassic/Early Cretaceous.

Figure 3. Mesozoic metatherians (in black), later taxa in gray. Whenever derived taxa are present in the Mesozoic (up to the Late Cretaceous) then ancestral taxa, or their sisters, were also present in the Mesozoic. Didelphis is extant, but probably unchanged since the Late Jurassic/Early Cretaceous.

Mesozoic Eutherians (= Placentals)

  1. Rarely are placental mammals identified from the Mesozoic, because many are not considered placentals.
  2. Placentals (in the LRT) are remarkably rare in the Mesozoic, but sprinkled throughout the cladogram, such that all taxa more primitive than the most derived Mesozoic taxon (Anagale and derived members of the clade Glires, Fig. 4, at present a number of multituberculates) must have had Mesozoic sisters (Carnivora, Volitantia, basal Glires). 
Figure 4. Mesozoic euthrerians (placentals, in black). Later taxa in light gray. All taxa more primitive than Mesozoic taxa were likely also present in the Jurassic and Cretaceous. None appear after Onychodectes. Madagascar separated from Africa 165-135 mya, deep into the Cretaceous with a population of tenrecs attached. No rafting was necessary. 

Figure 4. Mesozoic euthrerians (placentals, in black). Later taxa in light gray. All taxa more primitive than Mesozoic taxa were likely also present in the Jurassic and Cretaceous. None appear after Onychodectes. Madagascar separated from Africa 165-135 mya, deep into the Cretaceous with a population of tenrecs attached. No rafting was necessary.

The above represents what a robust cladogram is capable of,
helping workers determine the likelihood of certain clades appearing in certain strata, before their discovery therein, based on their genesis, not their widest radiation or eventual reduction and extinction. In other words, we might expect sisters to basal primates, like adapids and lemurs, to be present in the Mesozoic, but not sisters to apes and hominids. We should expect sisters to all tree shrews and rodents to be recovered in Mesozoic strata. We should expect to see sisters to Caluromys, Vulpavus and other small arboreal therians/carnivorans in Mesozoic strata, but not cat, dog and bear sisters.

References
Smith T 2011. Contribution of Asia to the evolution and paleobiogeography of the earliest modern mammals. Bulletin des séances- Académie royale des sciences d’outre-mer. Meded. Zitt. K. Acad. Overzeese Wet.57: 293-305

The extant pika has a Late Jurassic sister: Henkelotherium

We’ve known
since 2016 that the tiny Late Jurassic mammal, Henkelotherium is a basal rabbit (contra traditional studies that exclude rabbits). Today the extant pika (genus: Ochotona, Figs. 1, 2) enters the large reptile tree (LRT, 1348 taxa).

Figure 1. Pika skull (genus: Ochotona) in three views.

Figure 1. Pika skull (genus: Ochotona) in three views. It’s cuter with a coat of fur (Fig. 2).

Figure 2. Pika is a basal rabbit that prefers mountainous terrain. A sister, Henkelotherium, goes back to the Late Jurassic.

Figure 2. Pika is a basal rabbit that prefers mountainous terrain. A sister, Henkelotherium, goes back to the Late Jurassic.

Ochotona princeps (originally Lepus dauuricus Pallas, 1776; Link 1795; Richardson 1828) is the extant pika, a rock-dwelling herbivore nesting between Henkelotherium and rabbits. Pikas live in mountainous areas in Asia and North America. Distinct from Henkelotherium, Ochotona is larger, with a near complete loss of the tail. Both have spreading metatarsals and four upper molars. In pikas the second incisors are posteromedial to the first incisors, creating a larger cheek area. A medial pedal digit 1 is present in both.

Fossil pikas are known from the Miocene, 16mya, to the recent, but Henkelotherium goes back to the Late Jurassic.

Figure 2. Henkelotherium reconstructed from DGS tracings in figure 1. Note the tiny manus and large pes, traits that continue into extant rabbits.

Figure 3. Henkelotherium reconstructed from DGS tracings in figure 1. Note the tiny manus and large pes, traits that continue into extant rabbits. The image is 75% larger than life size.

Figure 4. Subset of the LRT featuring Ochotona and the rabbits.

Figure 4. Subset of the LRT featuring Ochotona and the rabbits.

Henkelotherium guimarotae (Krebs 1991; Late Jurassic 150 mya, Fig. 3) was traditionally considered eupantothere. Henkelotherium nests within the rabbit clade as a very early member of the tree shrew/ shrew/ rodent/ rabbit clade: Glires. Like its sisters, the manus was small and the pes had long digits with sharp claws. The lumbar region was long and flexible, ideal for hopping and galloping. Note the long robust tail.

This new nesting further confirms
the hypothesis that rodents (including multituberculates) and rabbits (including Henkeleotherium) had a deep Mesozoic origin (Fig. 5).

Figure 1. Select basal cynodonts and mammals set chronologically. The divergence times for placentals (Eutheria), marsupials (Metatheria) and monotremes (Mammalia) are estimated here.

Figure 5. Select basal cynodonts and mammals set chronologically. The divergence times for placentals (Eutheria), marsupials (Metatheria) and monotremes (Mammalia) are estimated here.

References
Link HF 1795.  Über die Lebenskräfte in naturhistorischer Rücksicht und die Classification der Säugthiere. – Beyträge zur Naturgeschichte (Rostock, Leipzig) 2: 1-41.
Kear BP, Cooke BN, Archer M and Flannery TF 2007. Implications of a new species of the Oligo-Miocene kangaroo (Marsupialia: Macropodoidea) Nambaroo, from the Riversleigh World Heritage Area, Queensland, Australia, in Journal of Paleontology 81:1147-1167.
Krebs B 1991. Skelett von Henkelotherium guimarotae gen. et sp. nov. (Eupantotheria, Mammalia) aus dem Oberen Jura von Portugal. Berl Geowiss Abh A.: 133:1–110.

wiki/Pika
wiki/Henkelotherium

 

False positives in an LRT subset lacking fossil taxa

I think you’ll find this phylogenetic experiment both
gut-wrenching and extremely illuminating. While reading this, keep in mind the importance of having/recovering the correct outgroup for every clade and every node. That can only be ascertained by including a wide gamut of taxa—including fossils. Adding taxa brings you closer and closer to echoing actual events in deep time while minimizing the negative effects of not including relevant/pertinent taxa.

Today you’ll see
what excluding fossil taxa (Fig. 1) will do to an established nearly fully resolved cladogram, the large reptile tree (LRT, 1318 taxa). Earlier we’ve subdivided the LRT before, when there were fewer taxa in total. Here we delete all fossil taxa (except Gephyrostegus, a basal amniote used to anchor the cladogram because PAUP designates the first taxon the outgroup).

PAUP recovers 250+ trees
on 264 (~20%) undeleted extant taxa.

  1. Overall lepidosaurs, turtles, birds and mammals nest within their respective clades.
  2. Overall lepidosaurs nest with archosaurs and turtles with mammals, contra the LRT, which splits turtles + lepidosaurs and mammals + archosaurs as a basal amniote dichotomy.
  3. Overall mammals are not the first clade to split from the others, contra traditional studies. All pre-mammal amniotes in the LRT are extinct.
  4. Within lepidosaurs, the highly derived horned lizards and chameleons are basal taxa, contra the LRT, which nests Iguana as a basal squamate.
  5. Within lepidosaurs, geckos no longer nest with snakes, contra the LRT.
  6. Crocodiles nest with kiwis, as in the LRT, but it is still amazing that PAUP recovered this over such a large phylogenetic distance.
  7. Within aves, so few taxa are fossils in the LRT that the tree topology is very close to the original.
  8. Within mammals marsupials no longer nest between monotremes and placentals
  9. …and because of this carnivores split off next.
  10. Contra the LRT, hippos are derived from the cat and dog clade, all derived from weasels.
  11. Within mammals odontocetes no longer nest with tenrecs.
  12. Within mammals mysticetes nest with odontocetes, no longer nest with hippos.
  13. Contra the LRT, whales are derived from manatees and elephants.
Figure 1. Subset of the LRT focusing on Amniota (=Reptilia) with all fossil taxa deleted. Gephyrostegus, a Westphalian fossil is included as the outgroup.

Figure 1. Subset of the LRT focusing on Amniota (=Reptilia) with all fossil taxa deleted. Gephyrostegus, a Westphalian fossil is included as the outgroup.

BTW,
here are the results based on using the basal fish, Cheirolepis, as an outgroup:

    1. The caecilian, Dermophis, nests as the basalmost tetrapod.
    2. Followed by the frog and salamander.
    3. Squamates branch off next with legless lizards and burrowing snakes at a basalmost node. Terrestrial snakes are derived from burrowing snakes. Gekkos split next followed by varanids and skinks. Another clade begins with the tegu and Lacerta, followed by iguanids. Sphenodon nests between the horned lizards, Moloch and Phyrnosoma + the chameleon.
    4. Turtles split off next with the soft-shell turtle, Trionyx, at the base.
    5. One clade of mammals split off next with echidnas first, then elephant shrews and tenrecs, followed by a clade including the pangolin, seals and other basal carnivores. Cats and dogs split off next followed by hippos, then artiodactyls, perissodactyls, the hyrax, elephants, manatees, mysticetes and odontocetes.
    6. Another clade of mammals include edentates, followed by tree shrews and glires, followed by (colugos + bats) + primates, followed by another clade of basal carnivores, followed by marsupials.
    7. The final clade is Crocodylus + extant birds, which are not well resolved and split apart into two major clades with some subclades maintaining their topology while other clades split apart. So the archosaurs nest together.

This test emphasizes the need for the inclusion of fossil taxa in order to recover a gradual accumulation of traits at all nodes, which takes us closer to actual evolutionary patterns in deep time.

The short-faced bear (Arctodus) is a giant wolverine in the LRT.

Yesterday we looked at three bears, Ursus, Arctodus (Fig. 1) and Ailuropoda (the polar bear, the short-faced bear and the panda bear). They do not form a single bear clade in the large reptile tree (LRT, 1299 taxa), but each is more closely related to small weasels and grew to bear-size by convergence.

For instance,
Arctodus is most closely related to today’s wolverine (Gulo gulo, Figs. 1, 2) among tested taxa, and the similarities are immediately apparent. Have they ever been tested together before? Let me know if this is so.

Figure 1. Arctodus (shor-faced bear) skeleton compared to the smaller Gulo (wolverine) skeleton. Both have similar proportions. Arctodus is larger than 3m, while Gulo is about 1m in length.

Figure 1. Arctodus (shor-faced bear) skeleton compared to the smaller Gulo (wolverine) skeleton. Both have similar proportions. Arctodus is larger than 3m, while Gulo is about 1m in length.

Arctodus simus (Leidy 1854; Cope 1874; up to 3 to 3.7m tall) is the extinct short-faced bear, one of the largest terrestrial mammalian carnivores of all time. Long limbs made it a fast predator. Being related to the wolverine made it short-tempered and dangerous.

Figure 2. Long-legged Gulo, the wolverine, is most similar to Arctodus, the short-faced bear in the LRT.

Figure 2. Long-legged Gulo, the wolverine, is most similar to Arctodus, the short-faced bear in the LRT. That’s a penile bone, not a prepubis.

Gulo gulo (Linneaus 1758; up to 110 cm in length) is the extant wolverine, a ferocious predator resembling a small bear. Note the tail length is midway between the long tail of weasels and the short tail of birds.

Figure 1. Subset of the LRT focusing on the Carnivora with tan tones on the bears newly added.

Figure 3. Subset of the LRT focusing on the Carnivora with tan tones on the bears newly added.

The red panda
(Ailurus) was also added to the LRT (Fig. 3) and, to no one’s surprise, nests with the raccoon, Procyon apart from the giant panda.

Figure 4. Gulo skull in lateral and dorsal views. Compare to Arctodus in figure 5.

Figure 4. Gulo skull in lateral and dorsal views. Compare to Arctodus in figure 5. The male skull has the larger and longer parasagittal crest.

The skulls of Gulo and Arctodus
(Figs. 4, 5) despite their size differences, are quite similar. Both display sexual dimorphism.

Figure 5. Arctodus (short-faced bear) skull in lateral view. Compare to figure 4.

Figure 5. Arctodus (short-faced bear) skull in lateral view. Compare to figure 4.

Taxon inclusion
sheds light on phylogenetic interrelationships.

If you have an interest in wolverine evolution,
I suggest you use the keyword “Gulo” or you’ll end up learning about Marvel’s superhero, also named Wolverine.

References
Cope ED 1879. The cave bear of California. American Naturalist 13:791.
Leidy 1854. Remarks on Sus americanus or Harlanus americanus, and on other extinct mammals. Proceedings of the Academy of Natural Sciences of Philadelphia 7:90.
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.

wiki/Gulo
wiki/Short-faced_bear

The most basal mammal in the LRT: Megazostrodon

I thought for many years
that Megazostrodon was known from only a fragment of skull, lacking both the anterior and posterior parts.

Then somehow this paper popped up on the Internet
Gow 1986 illustrated the skull of Megazostrodon (Fig. 1; BPI/1/4983; Crompton & Jenkins, 1968; Latest Triassic; 200 mya). Even without this skull data the large reptile tree (LRT, 1293 taxa) nested Megazostrodon at the base of the Mammalia. There is little  argument among paleontologists that this taxon is a close sister to the last common ancestor of all living mammals.

Often wrongly associated
with Morganucodon, the two are phylogenetically separated from one another by tiny Hadrocodium in the LRT. In Megazostrodon the zygomatic arch is straight (without the ascending arch). The skull lacks a sagittal crest.  As in modern marsupials, carnivores, primates and tree shrews the teeth have a standard incisor, canine, premolar and molar appearance. The permanent molars occlude precisely. Uniquely (as far as I know), the dentary has a coronoid boss and a coronoid process.

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

Figure 1. Megazostrodon skull in several views. Drawings from Gow 1986. Colors applied here. The upper molars are worn down.

The large reptile tree
(Fig. 2) presents a simple, validated topology of mammals and their ancestors based on hundreds of traits, very few of them dental. It differs in nearly every regard from the Close et al. 2015 study, which employs many dental taxa.

Figure 1. Subset of the LRT focusing on the Kynodontia and Mammalia. Non-eutherian taxa in red were tested in the LRT but not included because they reduce resolution. Eutherian taxa in red include a basal pangolin and derived xenarthran, clades that extend beyond the bottom of this graphic. The pink clade proximal to mammals was considered mammalian by Lautenschlager et al. due to a convergent mammalian-type jaw joint.

Figure 3. Subset of the LRT focusing on the Kynodontia and Mammalia. Non-eutherian taxa in red were tested in the LRT but not included because they reduce resolution. Eutherian taxa in red include a basal pangolin and derived xenarthran, clades that extend beyond the bottom of this graphic. The pink clade proximal to mammals was considered mammalian by Lautenschlager et al. due to a convergent mammalian-type jaw joint.

The first time I reconstructed Megazostrodon
(Fig. 4) the skull looked legit, and was approved by cynodont expert Jim Hopson, but it had some problems. I’m glad to finally get better data on this, that resolves scoring problems around this node.

Figure 1. Megazostrodon, an early mammal, along with Hadrocodium, a Jurassic tiny mammal.

Figure 4. Megazostrodon, an a Jurassic mammal, along with Hadrocodium, a Jurassic tiny mammal. The Megazostrodon skull shown here is not correct.

On a side note:
Wikipedia reports,Tinodon (Marsh 1887; YMP11843) is an extinct genus of Late Jurassic mammal from the Morrison Formation. It is of uncertain affinities, being most recently recovered as closer to therians than eutriconodonts but less so than allotherians.” 

Figure 1. Tinodon is best represented by an incomplete mandible with affinities to basal mammals.

Figure 5. Tinodon is best represented by an incomplete mandible with affinities to basal mammals and basal metatherians. Image from Morphobank.

 

Too few characters are present here
to add it to the large reptile tree, but if I have restored the missing parts correctly, then it is close to the base of the Mammalia and Theria near Megazostrodon.

References
Close RA, Friedman M. Lloyd GT and Benson RBJ 2015. Evidence for a mid-Jurassic adaptive radiation in mammals. Current Biology. 25 (16): 2137–2142. doi:10.1016/j.cub.2015.06.047PMID 26190074.
Crompton AW and Jenkins FA Jr 1968. Molar occlusion in late Triassic mammals, Biological Review, 43 1968:427-458.
Gow CE 1986. A new skull of Megazostrodon ( Mammalia, Triconodonta) from the Elliot Formation (Lower Jurassic) of Southern Africa. Palaeontologia Africana 26(2):13–22.
Marsh OC 1887. American Jurassic mammals. The American Journal of Science, series 3 33(196):327-348

wiki/Megazostrodon

 

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

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