Bears, bears and more bears

This post had its genesis
in a recent YouTube video all about bears by Moth Light Media. After phylogenetic analysis in the large reptile tree (LRT, 1834+ taxa, subset Fig. 1) ‘bears’ are no longer monophyletic. Instead the various extant ‘bears’ are better considered giant kinkajous, weasels, wolverines and bush dogs, all converging on similar ‘bear’-like morphologies.

Figure 1. Subset of the LRT focused on Carnivora, a placental mammal clade. Note the polyphyletic nesting of various 'bears' indicating that they are all just large kinkajous, weasels, wolverines and bush dogs converging on similar bear-like morphologies.

Figure 1. Subset of the LRT focused on Carnivora, a placental mammal clade. Note the polyphyletic nesting of various ‘bears’ indicating that they are all just large kinkajous, weasels, wolverines and bush dogs converging on similar bear-like morphologies. Note the separation of seals (dark yellow) from sea lions (peach).

Jiangzuo and Flynn 2020
discussed the earliest ursine bear and the origin of plant-dominated omnivory in Carnivora. Unfortunately they worked within an invalid phylogenetic context brought about by taxon exclusion. The wolf, Canis lupus, was their outgroup taxon. So their cladogram was upside-down compared to the LRT (Fig. 1). Basalmost members of Carnivora and their outgroups among basalmost Placentalia were all agile arboreal omnivores, not digitigrade cursors (runners), like Canis.

Jiangzuo and Flynn consider the spectacled bear,
Tremarctos, a member of the ursine bears. In the LRT Tremarctos arises from the bush dog, Speothos, far apart from ursines.

Jiangzuo and Flynn consider the wolverine,
Gulo, a member of the mustelids. In the LRT the short face bear, Arctodus, arises from the wolverine, Gulo, apart from ursines. 

Jiangzuo and Flynn consider the giant panda,
Airluropoda, a type of bear. In the LRT it arises from the herbivorous kinkajou (genus: Potos) before the appearance of the ancestor of the rest of the ‘bears’, Mustela, the weasel.

Jiangzuo and Flynn do not include
Speothos or Potos in their text. The authors separate Gulo in the clade Mustelida, apart from bears in their study. So taxon exclusion mars this otherwise detailed study of bear dentition and diet.

In like fashion,
McLellan and Reiner 1994 also excluded a long list of pertinent taxa in their review of bear evolution.

Sharp-eyed readers will note the addition of two taxa
to the Carnivora, the sea otter (Enhydra) and the basal walrus (Protodobenus).


References
Jiangzuo Q and Flynn JJ 2020. The earliest ursine bear and the origin of plant-dominated omnivory in Carnivora. iScience 23, 101235, June 26, 2020.
McLellan B and Reiner DC 1994. A review of bear evolution. Int. Conf. Bear Res. and Manage. 9(1):85-96

 

The coatimundi (Nasua) enters the LRT basal to almost all placentals

Traditionally
the coatimundi (Nasua nasua (Figs. 1, 3, 4; originally Viverra nasua Linneaus 1766) is considered a close relative of the raccoon (Procyon), a member of the Carnivora. So it has not gotten the spotlight it deserves.

Figure 1. The coatimundi (Nasua) compared to the ring-tailed lemur (Lemur).

Figure 1. The coatimundi (Nasua) compared to the ring-tailed lemur (Lemur).

By contrast, 
here in the large reptile tree (LRT, 1804+ taxa, Fig. x) Nasua nests outside the Carnivora, alongside Protictis, a Middle Paleocene taxon, and former enigma.

This nesting in the LRT
means the resemblance between coatimumndis and primitive carnivores, like Procyon, primitive primates, like Lemur (Fig. 1), and primitive tree shrews like Tupaia and Ptilocercus, is not mere convergence, but homology.

Overlooked until now,
coatimundis are basal to virtually all placental mammals, including primates and humans. That’s why they look like lemurs. That’s why they look like big tree shrews. That’s why they look like the LRT ancestor of bats, Chriacus, already with those large claws and feet able to rotate 180º enabling head-down descent from trees.

And that’s not all.
Coatimundis also dig with those big claws. So it is no coincidence that Talpa, the mole, is only a few nodes deep in the base of the Carnivora.

It is also worthwhile to compare
Nasua to an outgroup taxon, Caluromys (Fig. 4), an arboreal marsupial close to the base of the Placentalia.

Figure x. Subset of the LRT focusing on Carnivora and basal Placentalia after the addition of Nasua.

Figure x. Subset of the LRT focusing on Carnivora and basal Placentalia after the addition of Nasua. This phenomic cladogram is very different from genomic cladograms you may have seen, some that employ tapirs for outgroups.

Distinct from all members of the Carnivora
in the LRT, Nasua retains three large molars and a vestigial fourth along with a long list of other more subtle traits. Members of the Carnivora have only two molars typically with a large carnassial tooth preceding the upper molars.

Figure 2. Skull of Nasua compared to mid-Paleocene Protictis. The two are a close match and nest together in the LRT.

Figure 2. Skull of Nasua compared to mid-Paleocene Protictis. The two are a close match and nest together in the LRT. Shown about three-fifths life size.

According to Wikipedia
“Adult coatis measure 33 to 69 cm (13 to 27 in) from head to the base of the tail, which can be as long as their bodies. Males can become almost twice as large as females and have large, sharp canine teeth.Coatis have non retractable claws for climbing and digging. They prefer to sleep or rest in elevated places and niches, like the rainforest canopy, in crudely built sleeping nests. Coatis are active day and night but are not nocturnal animals. In the wild, coatis live for about seven years, while in captivity they can live for up to 15 or 16 years. Coatis communicate their intentions or moods with chirping, snorting, or grunting sounds. The pregnant females separate from the group, build a nest on a tree or in a rocky niche and, after a gestation period of about 11 weeks, give birth to litters of three to seven kits. About six weeks after birth, the females and their young will rejoin the band. Females become sexually mature at two years of age, while males will acquire sexual maturity at three years of age.”

The tail is not prehensile, but is used for balance.
Coatis able to rotate their ankles beyond 180°; they are therefore able to descend trees head first.

Figure 3. Skeleton of the coatimundi (Nasua) along with images of the hands, feet, antebrachium and humerus.

Figure 3. Skeleton of the coatimundi (Nasua) along with images of the hands, feet, antebrachium and humerus.

Although Middle Paleocene Protictis
(Fig. 2). nests alongside Nasua, they both had their origin deep in the Jurassic based on Jurassic remains of more derived taxa among the multituberculates. So the coatimundi was a friend, a meal, or at least an observer, of dinosaurs. This genus is a previously overlooked living relative of human ancestors, much more than the agricultural pest some people think.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Figure 4. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

This appears to be a novel hypothesis of interrelationships.
If not, please provide a citation and I will promote it here.


References
Linneaus C 1766. Systema naturae : per regna tria natura, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. 1 (12 ed.). Holmiae: L. Salvii.
wiki/Coati
wiki/South_American_coati

 

 

 

Carnivora genomic testing: Hassanin et al. 2021

From the abstract:
“The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora.”

Genomic tests too often do not and can not test fossil taxa leading to a problem with taxon exclusion. Moreover, genomic testing in deep time too often delivers false positives relative to phenomic (trait-based) traits that are designed to produce tree topologies in which all sister taxa greatly resemble one another, modeling micro-evolutionary events. Why this is so remains an unsolved problem. A phenomic cladogram (the LRT, subset Fig. x) that includes fossil taxa is found online here: http://reptileevolution.com/reptile-tree.htm

Figure 2. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Figure 1. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Talpa, the mole (Fig. 1), was excluded here, but nests within Carnivora in the phenomic analysis, the large reptile tree (LRT, 1803+ taxa, subset Fig. x).

Figure 1. Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Figure 2 Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Nandinia, the palm civet sure looks like it, but is not a basal member of Carnivora in the LRT, but a basal placental outgroup taxon to the clade Carnivora.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Figure 3. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Carnivora is the first major clade to split off
from basal Placentalia (Fig. x). Therefore, the proximal outgroup taxon, the woolly oppossum, Caluromys (Fig. 3) , should be included as the outgroup next time.

Figure 2. Subset of the LRT focusing on the Carnivora.

Figure x. Subset of the LRT focusing on the Carnivora.

By chilling contrast,
in the Hassanin et al. 2021 genomic analysis, a hoofed placental, the tapir (Tapirus), was used as the outgroup taxon. Given all other placentals for their choice of outgroup for Carnivora, why did they choose a relative of horses and rhinos? We’ve seen this sort of confused mayhem before and recently in genomic studies. Let’s all pray that the ghost of Alfred Sherwood Romer will come visit Hassanin et al. and all others who think this is a good idea.


References
Hassanin A, Veron G, Ropiquet A, Jansen van Vuuren B, Le´cu A, Goodman SM, et al. 2021. Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes. PLoS ONE 16(2): e0240770. https://doi.
org/10.1371/journal.pone.0240770

SVP abstracts 2: Barrett and Hopkins mishandle hyaena taxonomy

Cherry-picking taxa
(leading to both taxon exclusion and inappropriate taxon inclusion mars this otherwise earnest study.

From the Barrett and Hopkins abstract:
“The family Hyaenidae today is represented by only four living species, but this constitutes only a small fraction of known taxa from the fossil record. Results from both molecular and morphological analyses have shown disagreement in relationships, while certain hypothesized stem hyaenids and viverroids have received little to no phylogenetic assessment.”

First red flag: In the large reptile tree (LRT, 1749+ taxa; subset Fig. 3) viverroids (= civets), like Nandinia (Fig. 2) nest outside the clade Carnivora. Hyaenas, like Crocuta (Fig. 1), are highly derived carinvorans. Barrett and Hopkins think these two are related to one another based on Gray 1821 and gene studies. In the LRT civets are closer to their marsupial ancestors than to hyaenas, nesting with cats and dogs.

This taxonomic problem goes back to Gray 1821
who created the following clades of unrelated taxa. 

Viverridae (Gray 1821) defined as consisting of the genera Viverra (= large Indian civet), Genetta (= genet), Herpestes (= mongoose), and Suricata (= meerkat).

Viverroidea (Gray 1821, civets, mongooses, hyenas and aardwolves) is not supported by the LRT. Adding taxa lumps and separates these taxa.

Essentially viverroids were neither cat-like (= Felliformes) nor dog-like (Caniformes) carnivorans, a split still accepted by many mammal workers due to genomic results. The LRT (subset Fig. 3) does not agree with these lumps and splits.

Figure 3. Crocuta (hyena) skeleton. Note similarities to Canis (figure 2)

Figure 1. Crocuta (hyena) skeleton. Note similarities to Canis (figure 2)

Continuing from the Barrett and Hopkins abstract:
“These taxa include the percrocutids (bone-crushing, hyena-like viverroids), lophocyonids (extremely hypocarnivorous feliforms), and additional well-preserved, yet unassessed Miocene viverroids.”

Second red flag: Nandina, the palm civet (Fig. 2), and other vivveroids are small, mink-like arboreal taxa with short legs and a long tail. Percrocutids and hyaenas are terrestrial gallopers with a distinctly different morphology from head to toe.

Figure 1. Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Figure 2. Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Continuing from the Barrett and Hopkins abstract:
“Thus, to combine all available datasets, we performed a total-evidence Bayesian phylogenetic analysis inclusive of a sample of stem-to-derived hyaenids, herpestids, viverrids and other unassessed viverroid taxa.”

This is a classic case of taxon exclusion based on genomic studies. In other words, this study was doomed from the start.

Figure 2. Subset of the LRT focusing on the Carnivora.

Figure 3. Subset of the LRT focusing on the Carnivora.

Continuing from the Barrett and Hopkins abstract:
“The analyzed dataset includes stratigraphic occurrences, 257 morphological characters and mitochondrial genes of all living taxa in the analysis and ancient DNA from the cave hyena (Crocuta crocuta spelaea).”

“All living taxa in the analysis” = which living taxa? Hyaenas and palm civets? The genomic taxon list makes Gray 1821 quite a prognosticator, but neither study is supported when fossil taxa and traits are tested.  Let’s get back to trait (= phenomic) analysis. Genomes yield false positives too often and exclude too many extinct taxa.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

The transition from marsupial to placental was documented 
here (Figs. 3, 4) where viverrids, like Genetta nested at the base of the Placentalia, far from highly derived hyaenas and separated by ALL OTHER carnivorans.


References
Barrett PZ and Hopkins SS 2020. First total-evidence phylogeny of the hyaenidae and enigmatic viverroids reveals novel relationships. SVP abstracts 2020.
Gray JE 1821. On the natural arrangement of vertebrose animals. The London Medical Repository Monthly Journal and Review 15:296-310

A new genomic study of the Carnivora

Beware colleagues.
We learned long ago that genomic studies produce false positives in deep time studies. Genomic studies recover clades named for continents like Afrotheria and Laurasiatheria. So why are workers still dabbling in the dark art of deep time genomics?

From the Hassanin et al. 2020 abstract:
“The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversifications are still a matter of debate.”

Not true. The large reptile tree (LRT, 1747+ taxa) confidently nests Carnivora at the base of the Placentalia with outgroups extending to headless Cambrian chordates. The proximal outgroups and sisters to basal Carnivora look quite similar (Fig. 1) inside and out, even allowing for 200 million years of evolution since their radiation.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Continuing from the Hassanin et al. 2020 abstract:
“Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora.”

Hold on to your hats. Here comes a load of genomic misdirection.

“According to our divergence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloidea/Pinnipedia) diverged from each other during the Eocene,”

Phenomic studies, like the LRT, do not recover this clade.

“while all major groups of Feliformia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial divergences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene.”

 Phenomic studies, like the LRT, do not recover this clade. In the LRT, dogs and cats are highly derived sister taxa, along with hyenas and aardwolves. Seals and sea lions arise from separate terrestrial ancestors. Not all bears are related to Ursus. Weasels are basal to all of the above, including a long list of fossil taxa ignored by genomics. Potos flavus is the extant kinkajou, which was just added to the LRT, nesting between Procyon and the pandas, as expected.

Figure 2. Subset of the LRT focusing on the Carnivora.

Figure 2. Subset of the LRT focusing on the Carnivora. Genetta was just added to the LRT, nesting with Paleocenee Protictis.

In the LRT
Vulpavus, Protictis + Genetta and Nandinia are basalmost Placentalia, and the only tested placental outgroups to the Carnivora. Talpa, the mole, is an overlooked extant member of the Carnivora. Ursus arises apart from dogs + cats, which find last common ancestors in Tremarctos, Speothos and Borophagus. The short-faced bear, Arctodus, is a giant wolverine (Gulo). Seals and sea lions have separate terrestrial ancestors and became aquatic by convergence. The rest of the online LRT is here: reptileevolution.com/reptile-tree.htm


References
Hassanin A, et al. (7 co-authors) 2020. Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes. bioRxiv 2020.10.05.326090 (preprint)
doi: https://doi.org/10.1101/2020.10.05.326090
https://www.biorxiv.org/content/10.1101/2020.10.05.326090v1

Genomic studies:
Flynn JJ, et al. 2005. Molecular phylogeny of the Carnivora (Mammalia): assessing the impact of increased sampling on resolving enigmatic relationships. Syst Biol 54:317–37.

Borophagus enters the LRT, but not with Canis

The apex predator of North America
for tens of millions of years, Borophagus (Cope 1892; Fig. 1; 80 cm in length), the bone-crushing traditional ‘dog’ of the Middle Miocene to the Late Pliocene entered the large reptile tree (LRT, 1742+ taxa; subset Fig. 2), but not with Canis, the wolf. Rather Borophagus nested at the base of the clade containing two South American members of Carnivora, Speothos, the South American bush dog, and Tremarctos, the South American spectacled bear.

So Borophagus is not a canid in the LRT (contra tradtion).

Figure 1. Borophagus skull with colors added.

Figure 1. Borophagus skull with colors added.

In Borophagus secudus
the premaxilla extends to mid-canine and contacts the frontals, as in other clade members.

Figure 2. Subset of the LRT focusing on the Carnivora.

Figure 2. Subset of the LRT focusing on the Carnivora.

According to Wikipedia
“Borophagus, like other borophagines, are loosely known as “bone-crushing” or “hyena-like” dogs.”

“Typical features of this genus are a bulging forehead and powerful jaws. 

“Borophagus has been considered to be probably a scavenger by paleontologists in the past.[Its crushing premolar teeth and strong jaw muscles would have been used to crack open bone, much like the hyena of the Old World. However, Borophagus fossils are so abundant and geographically widespread that some paleontologists now argue that Borophagus must have been both the dominant carnivore of its time, and thus an active predator because carrion feeding alone could not have sustained such a large population.”


References
Cope ED 1892. A hyena and other Carnivora from Texas. American Naturalist 26:1028–1029.

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

Mellivora enters the LRT in a clade of giant honey badgers

Finally we know more about an extinct placental clade
that no one else recognized as an extinct placental clade. Clade members in the LRT included Patriofelis, Sarkastodon and Kerberos (Fig. 1). Now a living member, the honey badger, Mellivora capensis (also Fig. 1), enters the LRT within this clade.

Marsupials or placentals?
The problem is: these three extinct hyper-carnivores have been traditionally considered creodonts and within that clade: hyaenodonts and oxyaenids.
In the large reptile tree (LRT, 1730+ taxa) creodonts are marsupials. Distinct from them, but convergent in many ways, Mellivora, Patriofelis, Sarkastodon and Kerberos nest as clade members within the placental clade, Carnivora. This newly recognized honey badger clade nests between hyper-carnirorous wolverines + short face bears and the stylinodontid + earless seal clade

The placental honey badger clade
dentally converges with the marsupial creodont clade. Don’t put your trust in teeth, as we learned earlier.

According to BioWeb.uwlax.edu
honey badgers are members of the weasel clade, Mustelidae, apart from other mustelids. In the LRT, all derived members of Carnivora, including cats, dogs, bears, seals and sea lions are all derived from the mink/weasel (genus Mustela).

Figure 1. The honey badger clade, Kerboros, Patriolfelis and Sarkastodon. The only living representative is Mellivora to scale.

Figure 1. The honey badger clade, Kerberos, Patriolfelis and Sarkastodon. The only living representative is Mellivora to scale.

Mellivora capensis (originally Viverra capensis Scherber 1777; Fig. 2) is the extant honey badger or ratel, traditionally considered close to weasels. This carnivore has few natural predators because of its thick skin and ferocious defensive abilities.

Figure 1. The honey badger (Mellivora capensis) skull.

Figure 2. The honey badger (Mellivora capensis) skull.

Imagine the unreasonable viciousness of a honey badger
expanded to the size of Sarkastodon (Fig. 1).

Figure 2. The honey badger (Mellivora capensis) skeleton.

Figure 3. The honey badger (Mellivora capensis) skeleton.

This 3:20 minute honey badger video on YouTube
went viral (95.5 million views) awhile back. Quite the character, now finally understood phylogenetically.

The LRT solves problems
others don’t even think about. Adding taxa is the solution to many phylogenetic problems.


References
Schreber, JCDv 1777. “Das Stinkbinksen”. Die Säugethiere in Abbildungen nach der Natur mit Beschreibungen. Erlangen: Wolfgang Walther. pp. 450–451.

wiki/Honey_badger
wiki/Oxyaenidae

New study on Thylacosmilus atrox: “not a marsupial saber-tooth predator”??

Janis et al. 2020
bring us some heretical views regarding Thylacosmilus, the famous saber-toothed marsupial (Fig. 1).

Figure 2. Thylacosmilus skull. Note the deep maxillae in dorsal contact containing giant canine roots. These are not present in Patagosmilus.

Figure 1. Thylacosmilus skull. Note the deep maxillae in dorsal contact containing giant canine roots. These are not present in Patagosmilus.

For those in a hurry:
The Janis et al. study includes a phylogenetic analysis of placental sabertooth cats that nests the saber-toothed marsupial, Thylacosmilus (Fig. 1), at the base of the clade (Fig. 2). In a way, that is true, but this is missing so many transitional taxa that we’re left with apples and oranges. So, that’s not going to work because Janis et al. are testing analogy and convergence, rather than homology. It’s better to test apples and apples, even when dealing with stress tests, etc.

Figure 1. Cladogram from Janis et al. 2020. Note the lack of marsupial taxa, other than Thylacosmilus at the base.

Figure 2. Cladogram from Janis et al. 2020. Note the lack of marsupial taxa, other than Thylacosmilus at the base. Be wary whenever the taxon under review nests at the base of the cladogram.

Lacking here
is a phylogenetic analysis that includes the closest marsupial relatives of Thylacosmilus: 1. Schowalteria (Fig. 3), 2. Vincelestes + Conorytes, 3. Huerfanodon 4. Monodelphis + Chironectes. That’s how they line up in the large reptile tree (LRT, 1698+ taxa). You need related taxa to decipher the phylogenetic bracketing of Thylacosmilus based on homology, not analogy. The last two taxa are extant. One is an omnivore, the other an aquatic carnivore. Among the extinct taxa, Schowalteria, Vincelestes, Conoryctes and Huefanodon all appear to have been marsupial saber-toothed predators, contra the Janis et al. headline. Vincelestes goes back to the Early Cretaceous.

Figure 1. Showalteria. Not much there. Adding more rounds out the skull, a likely marsupial relative of Vincelestes.

Figure 3. Showalteria. Not much there, but enough to nest it with Thylacosmilus. Is this a predator? According to Wikipeia,.. no.

Janis et all. 2020 wrote:
“While the superficial appearance of Thylacosmilus atrox resembles that of placental saber- tooths, its detailed anatomy makes this animal an ecomorphological puzzle, and the analyses performed here show it to be unlike other carnivores, saber-toothed or otherwise”

That’s because they omitted related taxa…where are the comparable marsupials?

“While we can demonstrate that T. atrox could not have been a predator in the mode proposed for the saber-toothed feliform carnivorans, it is challenging to propose an alternative mode of life.”

That’s because they omitted related taxa…where are the comparable marsupials?

“We note that, while there is often the temptation to shoehorn an extinct animal into the ecomorphological role of an extant one (see Figueirido, Martín-Serra & Janis, 2016)—or even, as in this case, the proposed ecomorphological role another extinct animal—T. atrox may well have had no analogs in the extant or extinct fauna.

That’s because they omitted related taxa…where are the comparable marsupials?

“We extend this discussion of extinct animals without living analogs in the conclusions. Here we present some ecomorphological hypotheses for T. atrox that align with the peculiarities of its anatomy.”

  1. We note that the unusual subtriangular shape of these canines makes them appear more like a claw than a blade; and, like a claw, they appear well-adapted for pulling back.
  2. Our biomechanical study shows that both the skull and the canines of T. atrox are better in resisting pull back stresses than those of S. fatalis.
  3. The small infraorbital foramen of T. atrox supports the hypothesis that its canines were not used for killing prey, as it would not require such careful and precise positioning of the canines.
  4. The postcanine teeth of T. atrox exhibit blunted tip wear, unlike the shearing wear on the teeth of carnivores that specialize on flesh
  5. T. atrox was clearly not a bone-crusher: this type of diet is contraindicated by the DMTA analysis and the lack of cranial specializations (including evidence for powerful jaw adductors) seen in extant bone-crushers
  6. T. atrox had less powerful jaw adductor and head depressor muscles than placental saber-tooths. The cervical and caudal cranial anatomy are not indicative of the ability for extreme head elevation and forceful head depression, as observed in the anatomy of placental saber-tooths, implicated in those carnivores for a predatory head strike.
  7. The virtual absence of incisors (certainly the absence of a stout incisor battery) in T. atrox is challenging for the hypothesis of a cat-like mode of feeding, as it would have been unable to strip flesh from a carcass or transport its prey.

Janis et al. wonder:
“Could [soft internal organs] have been the preferred diet of the marsupial saber-tooth?”

Janis et al. propose:
“Incisor loss or reduction in mammals is correlated with the use of a protrusible tongue in feeding, as seen in myrmecophageous mammals.”

Janis et al. propose:
“T. atrox has been ‘‘shoehorned’’ (see Figueirido, Martín-Serra & Janis, 2016) into the saber-tooth ecological role: much less attention has been paid to the way in which this animal differs in its morphology from placental saber-toothed predators, making a similar type of predatory behavior unlikely.

“We advance the suggestion that it was not an active predator, but rather relied on the use of existing carcasses, deploying its large canines for carcass opening rather than for killing, a hypothesis supported by our biomechanical analyses that show superior performance in a ‘‘pull-back’’ scenario.”

“Thylcosmilus atrox was a very different type of carnivorous mammal than the placental saber-tooths: the oft-cited convergence with placentals such as Smilodon fatalis deserves a rethink, and the ‘‘marsupial saber-tooth’’ may have had an ecology unlike any other known carnivorous mammal.”

Figure 3. Maximum gape of Thylacosmilus.

Figure 4. Maximum gape of Thylacosmilus. At upper left is the placental, Smilodon, for comparison.

Geology = Environment
Thylacosmilus was found in a vast Miocene tidal flat environment with a wide variety of terrestrial and shalllow aquatic taxa. So that doesn’t help much.

Saving the best for last: getting back to Late Cretaceaous Schowalteria
Wikipeda report, “It is notable for its large size, being among the largest of Mesozoic mammals,[ as well as its specialization towards herbivory, which in some respects exceeds that of its later relatives.” This is based on tooth wear, with nearly all crowns gone (Fig. 3) in the only specimen known. Traditionally Schowalteria has been allied with styinodonts (Carnivora close to seals, but not to sea lions) and to taeinodonts (which the LRT found to be poylphyletic). Certainly, what little is known of Schowalteria is similar to these taxa. Others have omitted these LRT sisters in their analyses. Janis et al. omit the word ‘sister’ from their text.

Figure 1. Patagosmilus to scale alongside Hadrocodium. These sabetooth taxa are not directly related to Thylacosmilus in the LRT.

Figure 5. Patagosmilus to scale alongside Hadrocodium. These sabetooth taxa are not directly related to Thylacosmilus in the LRT.

Patagosmilus has been called a sister to Thylacosmilus,
but the LRT nested Patagosmilus (Fig. 5) with the tiny basal therian, Hadrocodium (Fig. 5) as we learned earlier here. Taxon inclusion produces surprises like this.

At times like this it’s good to test.
Deletion of Thylacosmilus changes nothing in the LRT. Deletion of Schowalteria changes nothing in the LRT.

In my opinion
it was great that Janis et al. 2020 tested Thylacosmilus with its placental analogs, but they should also have tested Thylacosmilus with its marsupial homologs.


References
Janis CM, Figueirido B, DeSantis L, Lautenschlager S. 2020. An eye for a tooth: Thylacosmilus was not a marsupial ‘‘saber-tooth predator’’. PeerJ 8:e9346 http://doi.org/10.7717/peerj.9346

https://en.wikipedia.org/wiki/Ituzaing%C3%B3_Formation

https://pterosaurheresies.wordpress.com/2018/12/20/marsupial-sabertooth-taxa-are-polyphyletic/

Recalibrating clade origins, part 4

Earlier
we looked at the first part and second part and third part of Marjanovic’s 2019 chronological recalibration of vertebrate nodes. Today we continue in part 4 of 5.

Mammalia (Prototheria + Theria)
Based on the literature, Marjanovic 2019 considers morganucodontans and tiny Hadrocodium to be mammalomorphs, not mammals. He is unsure about haramiyidans. With regard to the first dichotomy of mammals, he reported, “I recommend a hard minimum age of 179 Ma for this calibration.”

By contrast the large reptile tree (LRT, 1630+ taxa) nests Morganucodon (Late Triassic, 205 mya), Hadrocodium (Early Jurassic) and Henosferus (Middle Jurassic) together in the most basal subclass within Theria, part of the first dichotomy within Mammalia. Marjanovic considered Henosferus one of the oldest uncontroversial mammals at 179 mya. Megazostrodon is a late surviving (early Jurassic) last common ancestor taxon of all mammals in the LRT. It must have appeared prior to Morganucodon in the Late Triassic.

Theria (Metatheria + Eutheria)
Marjanovic reports, “The oldest securely dated eutherian is Ambolestes at 126 Ma.” Then he reports, “Accepting that Juramaia is not from the Lanqi Fm, I propose 160 Ma as the soft maximum age of this calibration.”

By contrast, Morganucodon (Late Triassic, 210mya) nests as the oldest therian. Ambolestes nests with Didelphis, the opossum, within the Theria, not Eutheria.  Thereafter the traditional Metatheria splits in three clades in the LRT, a largely herbivorous branch with Glironia and Marmosops at its base, and a largely carnivorous branch with Monodelphis and Chironectes at the base of one branch and Caluromys + Placentalia at yet another. So, while Caluromys (Fig. 3) retains a pouch, it is also the last common ancestor of all placentals.

Figure 1. Pteropus and Caluromys compared in vivo and three views of their skulls. Caluromys is in the ancestry of bats and shows where they inherited their inverted posture.

Figure 1. Pteropus and Caluromys compared in vivo and three views of their skulls. Caluromys is in the ancestry of bats and shows where they inherited their inverted posture.

Marjanovic often errors by not including extant taxa that are more primitive than extinct taxa that are older. This comes back to bite him several times, especially so when he relies on a single fossil tooth rather than a living animal he can hold. The LRT tests both living and extinct taxa to minimize taxon exclusion.

Marjanovic discusses the possibility that Sinodelphys is the oldest known metatherian, but Sinodelphys nests as one of the most primitive prototherians in the LRT, as we learned earlier here.

Placentalia (Atlantogenata + Boreo(eu)theria)
In the world of gene studies, Atlantogenata include the highly derived elephants and anteaters. The Boreoeutheria include the highly derived whales, humans and hooved mammals. Genomic studies deliver false positives, and these are among the most blatant, so ignore these. They don’t deliver a gradual accumulation of derived traits.

By contrast, in the LRT the first dichotomy in the placentalia splits arboreal Vulpavus from arboreal Nandinia and thereafter arboreal Carnivora (mongooses and raccoons) from arboreal Volantia (bats and colugos) + arboreal Primates and the rest of the Placentalia. All of these civet-like and tree opossum-like taxa look like Caluromys (Fig. 1), as you can see. Elephants and anteaters come later. Adding living taxa to Marjanovic’s search for primitive placentals would have helped clarify his research and conclusions, preventing him form perpetuating old myths.

Carnivora (Feliformia + Caniformia)
Marjanovic errs by reporting the basal dichotomy within Carnivora splits cats from dogs.

By contrast in the LRT cats and dogs are closely related and derived taxa, not basal. As mentioned above, civets, mongooses and raccoons are basal Carnivora.

Euarchontoglires/Supraprimates (Gliriformes + Primatomorpha)
Marjanovic discusses several poorly preserved, sometimes one tooth only, fossil taxa from the early Paleocene (65mya). Some of these are anagalids, which nest at the base of yet another clade in the LRT, the one with tenrecs and odontocetes (toothed whales).

By contrast in the LRT lemur-like adapids appear at the base of the Primates. Tree-shrews appear at the base of the Glires.

Marsupialia (Didelphimorphia – Paucituberculata + Australidelphia)

  • Didelphimorphia = opossums from North America
  • Paucituberculata = South American marsupials, sans Dromiciops
  • Australidelphia = Australian and Asian marsupials, plus Dromiciops

Marjanovic reports, “I therefore propose 55 Ma as a probably overly strict hard minimum age for this calibration.” He later reports, “Rather than the beginning of the Maastrichtian, I propose the beginning of deposition of the Lance and Hell Creek formations, where Glasbius has been found, as the hard maximum age for this calibration, which I estimate as 68 Ma.”

See Figure 1 for a different three-part marsupial split from the LRT. Dromiciops is only one of many similar herbivorous marsupials. Middle Late Cretaceous Asioryctes is a basal member of the largely herbivorous clade. Early Cretaceous Vincelestes is a basal member of the largely carnivorous clade. So Middle to Late Jurassic (175mya) is a better estimate for the genesis of marsupial diversity. That means marsupials dispersed during the Pangean era without the need of an oceanic dispersal.

Marjanovic mistakenly reports, “Marsupials, other metatherians and indeed other therians are wholly absent from the Late Cretaceous mammaliform record of South America, which consists instead of gondwanatherian haramiyidans and a very wide variety of meridiolestidan stem-theriiforms.”

  • Meridiolestida = non-therian mammals (= Prototheria, Montremata) seems to be based on tooth traits. Cronopio and Necrolestes are among the only tested taxa also  found in the LRT. Cronopio is an omnivorous member of the pre-metatherian Theria in the LRT. Necrolestes is a basal member of the placental clade, Glires, derived from the treeshrew Tupaia in the LRT. So, again, we have a mismatch due to not testing all the mammals against all the mammals. That is what makes the LRT such a powerful tool that should be more widely used to avoid such old school mythology.

More tomorrow as we conclude part 5 of 5.


References
Marjanovic D 2019. Recalibrating the transcriptomic timetree of jawed vertebrates.
bioRxiv 2019.12.19.882829 (preprint)
doi: https://doi.org/10.1101/2019.12.19.882829
https://www.biorxiv.org/content/10.1101/2019.12.19.882829v1