Purgatorius and Plesiadapis are still not primates contra Wilson et al. 2021

Short one today
on Purgatorius (Early Paleocene; Fig. 1), a mandible taxon considered by Wilson et al. 2021 to be a member of the Plesiadapiformes (Fig. x).

Figure 1. Purgatorius compared to other basal and often Paleocene mammals.

Figure 1. Purgatorius compared to other basal and often Paleocene mammals.

Wilson et all 2021 report
“Plesiadapiforms are crucial to understanding the evolutionary and ecological origins of primates and other euarchontans (treeshrews and colugos) as well as the traits that separate those groups from other mammals.”

No they are not.

Adding taxa
shifts plesiadapiformes deep into the clade Glires (Fig. x) where Plesiadapis joins Daubentonia as primate-like rodents close to Carpolestes and Ignacius.

Figure 1. Ignacius and Plesiadapis nest basal to Daubentonia in the LRT.

Figure 2. Ignacius and Plesiadapis nest basal to Daubentonia in the LRT.

Wilson et al. also reported
similarities in Purgatorius to Palaechthon, which nested in 2017 with the demopteran, Cynocelphalus in the large reptile tree (LRT, 1807+ taxa). Wilson et al. considered Palaechthon a member of the Plesiadapiformes.

Figure 1. Subset of the LRT focusing on basal placentals, including multituberculates.

Figure x. Subset of the LRT focusing on basal placentals, including multituberculates.

We looked at Purgatorius earlier
here in 2017.

Colleagues, expand your taxon lists.
If you don’t look in there, you won’t see what’s in there. So look. Add taxa. Sometimes traditions, professors and textbooks are not complete or incorrect. Find out for yourself.


References
Wilson MGP et al. , (9 co-aiuthors) 2021. Earliest Palaeocene purgatoriids and the initial radiation of stem primates Royal Society open science 8210050
http://doi.org/10.1098/rsos.210050

https://pterosaurheresies.wordpress.com/2019/03/07/tweaking-palaechthon-basal-volitantia/

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

 

 

 

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

Variation within the genus Tupaia (tree shrew)

Another tree shrew post today.
Following yesterday’s post on a partial Oligocene tree shrew fossil.

Figure 1. Skulls of Tupaia to scale, plus a list from Wikipedia and others shown here not on that list.

Figure 1. Skulls of Tupaia to scale, plus a list from Wikipedia and others shown here not on that list.

Tree shrews
in the large reptile tree (LRT, 1787+ taxa) are basal to several basal placental clades.

Figure 3. Subset of the LRT focusing on the clade Scandentia (tree shrews) and the three arboreal clades that arise from it.

Figure 2. Subset of the LRT focusing on the clade Scandentia (tree shrews) and the three arboreal clades that arise from it.

I didn’t realize the species variation
in the extant genus Tupaia (Fig. 1) was so wide. And that is only the part I was able to find (red species). These species are all variations on a Jurassic radiation, so they had a long time to evolve, chiefly in equatorial arboreal jungle environs. Some of these may enter the LRT. Can you tell which ones?

Tupaia chinensis (skull) Tupaia tana (the large tree shrew, Raffles 1821) extant, was derived from a sister to Ptilocercus and was basal to Macroscelides and Chrysochloris. The tree shrew acts like a squirrel, but instead of eating nuts, it eats insects. Tupaia probably originated deep in the Mesozoic (Late Jurassic), but their fossils go back only 3 million years. Note the dorsal expansion of the ear bones, which continues in Macroscelides and Chrysochloris. The incisors and canines are similar. The dentary incisors extend anteriorly, as in shrews like Scutisorex.


References
Raffles TS 1821. Descriptive Catalogue of a Zoological Collection made on account of the Honourable East India Company, in the Island of Sumatra and its Vicinity, under the Direction of Sir Thomas Stamford Raffles, Lieutenant-Governor of Fort Marlborough; with additional Notices illustrative of the Natural History of those Countries. The Transactions of the Linnean Society of London (Linnean Society of London) XIII: 239–340.

wiki/Tupaia

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.

Asiatherium enters the LRT: mammal nomenclature issues follow

Everyone agrees
that Asiatherium (Figs, 1,2) nests close to Monodelphis, Caluromys and placentals. Trofimov and Szalay 1994 agreed. So did Denyer, Regnault and Hutchinson 2020. So did the large reptile tree (LRT, 1729+ taxa, subset Fig. 3).

Figure 1. Asiatherium in situ from Szalay and Trofimov 1996.

Figure 1. Asiatherium in situ from Szalay and Trofimov 1996.

Asiatherium reshetovi (Trofimov and Szalay 1994, Szalay and Trofimov 1996; PIN 3907; Late Cretaceous; 80mya; Figs. 1, 2) is a key Mongolian metathere ancestral to monodelphids and Caluromys, which is ancestral to placentals. It is derived from Triassic sisters to extant late survivors, DidelphisGilronia and Marmosops.

Figure 2. Asiatherium skull slightly modified from Szalay and Trofimov 1996. Colors added here.

Figure 2. Asiatherium skull slightly modified (longer lateral view premaxilla to match dorsal and ventral views) from Szalay and Trofimov 1996. Colors added here.

The problem is,
according to results recovered by the LRT, mammal clade nomenclature needs to go back to basics. Several modern mammalian clade names are found to be junior synonyms of traditional clades in the LRT.

Prototheria (Gill 1872) is a junior synonym
for Monotremata (Bonaparte 1837) in the LRT.

According to Wikipedia, “Prototheria is a paraphyletic subclass to which the orders MonotremataMorganucodontaDocodontaTriconodonta and Multituberculata have been assigned, although the validity of the subclass has been questioned.”

In the LRT Morganucodon is a a marsupial (see below). Docodon is a taxon within Monotremata. Triconodon is a taxon within Monotremata. Multituberculata is a clade within the placental clade Glires (Fig. 4). So, the clade Monotremata is monophyletic and has precedence.

Theria (Parker and Haswell 1897) is a junior synonym
of Marsupialia (Illiger 1811). Metatatheria (Thomas Henry Huxley 1880) is also a junior synonym of Marsupialia.

The late-surviving basalmost marsupial in the LRT (Fig. 4), Ukhaatherium (Fig. 3), has epipubic (marsupial) bones. That long rostrum indicates this taxon is close to monotremes.

Figure 3. Ukhaatherium in situ.

Figure 3. Ukhaatherium in situ.

Unlike the monophyletic clade Monotremata,
a series of nested marsupial clades are present. The last of these gives rise to Placentalia, only one of several that lose the pouch (Fig. 4). New names are proposed here where appropriate:

  1. Marsupialia = Ukhaatherium and kin + all descendants (including placentals)
  2. Paleometatheria = Morganucodon and kin + all descendants.
  3. Didelphimetatheria = Eomaia and kin + all descendants
  4. Phytometatheria = Marmosops and kin + all descendants
  5. Carnimetatheria = Asiatherium and kin + all descendants
  6. Transmetatheria = Caluromys and kin + all descendants
  7. Placentalia = Vulpavus and kin + all descendants
Figure 4. Subset of the LRT cladogram of basal Mammalia. Note the traditional clade Metatheria is a grade with new names proposed here.

Figure 4. Subset of the LRT cladogram of basal Mammalia. Note the new names proposed here.

Basal marsupial taxa are omnivores. 
Derived phytometatheres are herbivores. Derived carnimetatheres are carnivores to hyper-carnivores. Transmetatheres (Carluromys) and basal Placentalia remain omnivores.

In the LRT Eutheria (Gill 1872) is a junior synonym
of Placentalia (Owen 1837). Omnivorous civets like Nandinia are basal placentals. Carnivora is a basal placental clade following basal placental civets.

Competing cladograms
Denyer, Regnault and Hutchinson 2020 recently looked at the marsupial patella, or more specifically the widespread absence or reduction of the kneecap. The authors concluded, “metatherians independently ossified their patellae at least three times in their evolution.”

Unfortunately, Denyer et al. tested Caenolestes, the ‘shrew opossum’. Not surprisingly it nested close to placentals in their cladogram. Caenolestes was earlier nested in the LRT within the placental clade, Glires, closer to shrews than to opossums. It has no pouch, but converges with marsupials in several aspects. Inappropriate taxon inclusion, like Caenolestes, occurs due to taxon exclusion. Excluded taxa would have attracted and removed the inappropriate taxon. Taxon exclusion plagues Denyer et al.

Historically, you may remember,
Bi et al. 2018, while presenting Early Cretaceous Ambolestes, suffered from massive taxon exclusion and traditional bias in attempting to produce a cladogram of mammals. Bi et al. recovered Sinodelphys (Early Cretaceous) and Juramaia (Late Jurassic) as ‘eutherians’. In the LRT both are monotremes.

Other basal mammal cladograms
depend too much on tooth traits. Convergence in tooth traits creates problems, as documented earlier. We’ll look at this problem in more detail soon.

The above subset of the LRT appears to be a novel hypothesis
of interrelationships. If not, please provide a citation so I can promote it.


References
Bi S, Zheng X, Wang X, Cignetti NE, Yang S, Wible JR. 2018. An Early Cretaceous eutherian and the placental marsupial dichotomy. Nature 558(7710):390395 DOI 10.1038/s41586-018-0210-3.
Denyer AL, Regnault S and Hutchinson JR 2020. Evolution of the patella and patelloid in marsupial mammals. PeerJ 8:e9760 http://doi.org/10.7717/peerj.9760
Szalay FS and Trofimov BA 1996. The Mongolian Late Cretaceous Asiatherium, and the early phylogeny and paleogeography of Metatheria. Journal of Vertebrate Paleontology 16(3):474–509.
Trofimov BA and Szalay FS 1994. New Cretaceous marsupial from Mongolia and the early radiation of Metatheria. Proceedings of the National Academy of Sciences 91:12569-12573

Chimento and Agnolin 2020: Litopterna interrelations suffers from taxon exclusion

Chimento and Agnolin 2020
discuss interrelationships within and outside the clade Litopterna, famous for including Macrauchenia (Fig. 1), the odd South American ungulate. Strangely the chalicotheres were excluded. In the large reptile tree (LRT, 1721+ taxa, subset Fig. 2), litopterns and chalicotheres nest in the same clade. Phylogenetically, Macrauchenia IS a chalicothere in the LRT.

Figure 1. Macrauchenia museum mount.

Figure 1. Macrauchenia museum mount.

From the abstract
“The Litopterna is an extinct clade of endemic South American ungulates that range from Paleocene up to late Pleistocene times. Because of their unique anatomy, litopterns are of uncertain phylogenetic affinities”

Not so. The LRT (Fig. 2) nests litopterns with high Bootstrap scores between paenungulates and perissodactyls and following chalicotheres. Omitting chalicotheres may be the cause of prior problems.

Figure 1. Subset of the LRT focusing on hoofed mammals.

Figure 1. Subset of the LRT focusing on hoofed mammals.

From the abstract
“However, some nineteenth century authors, considered litopterns as related to perissodactyl ungulates, a hypothesis recently sustained by molecular data. The aim of the present contribution is to include litopterns and other South American related taxa in a comprehensive phylogenetic analysis together with several extant and extinct basal perissodactyl ungulates.”

The Chimento and Agnolin taxon list is far from comprehensive. Many extant taxa were excluded.

Figure 3. From Chimento and Agnolin 2020, colors added. Grayed out taxa are not tested in the LRT. Many of these are based on teeth only.

Figure 3. From Chimento and Agnolin 2020, colors added. Grayed out taxa are not tested in the LRT. Many of these are based on teeth only.

“The analysis resulted in the nesting of litopterns and kin as successive stem-clades of crown Perissodactyla. Further, litopterns are not phylogenetically grouped with any North American basal ungulate, in agreement with some previous proposals”

Notably the authors excluded chalicotheres (Fig. 2) from their taxon list. Some of these are known from North America. Europe, Africa and Asia and they nest with Macrauchenia in the LRT. Phylogenetically, Macrauchenia IS a chalicothere in the LRT. Theosodon is a taxon employed by both cladograms. Macrauchenia is not found in the Chimento and Agnolin cladogram.

Figure. 2. Chalicothere skulls to scale. Lophiodon is an outgroup closer to tapirs.

Figure. 4. Chalicothere skulls to scale. Lophiodon is an outgroup closer to tapirs.

“Presence of pan-perissodactyls in South America and India indicates that southern continents probably played an important role in the early evolution of hoofed mammals.”

Or not. These continents might have been more of a backwater or refuge for highly derived taxa with earlier, pre-continental-separation origins.


References
Chimento NR and Agnolin FL 2020. Phylogenetic tree of Litopterna and Perissodactyla indicates a complex early history of hoofed mammals. Nature.com/scientific reports.

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

Ever hear of Palaeothentes?

Currently there is no Wikipedia page for this taxon.
Even so, I found it to be far more important at filling gaps and shaking up paradigms than it seemed at first. The small, dull-looking taxa tend to be like that, as readers now know.

You could find this rat-sized Miocene taxon
(Fig. 1) in Carroll’s 1988 book, Vertebrate Paleontology, now well-worn and in pieces due to constant page flipping and scanning. Today’s research has revealed several more precise and more recent resources.

Figure 1. Not a marsupial, and not a shrew opossum, Palaeothentes nests in the LRT at the base of the Apatemys + Trogosus clade nest to the clade of living shrew opossums within Glires.

Figure 1. Not a marsupial, and not a shrew opossum, Palaeothentes nests in the LRT at the base of the Apatemys + Trogosus clade next to the clade of living shrew opossums within Glires.

According to Abello and Candella 2010,
Palaeothentes minutes (Ameghino 1887) is a paucituberculatan (details below) from the Santa Cruz Formation The results indicate that Palaeothentes would have been an agile cursorial dweller, with leaping ability, similar to the extant paucituberculatan Caenolestes fuliginosus and the didelphid Metachirus nudicaudatus.”

Okay, so now we have a problem.
In the large reptile tree (LRT, 1445 taxa) Caenolestes is not a marsupial. It nests with Rhyncholestes and more distantly Apatemys and more distantly, the extant tree shrew, Tupaia and the extant shrew, Scutisorex. As noted earlier, shrew opossums are placental shrews, not marsupial opossums in the LRT.

Wikipedia reports,
“Like several other marsupials, they do not have a pouch, and it appears that females do not carry the young constantly, possibly leaving them in the burrow.”
That’s describes most rodent/rabbit/tree shrew mothers and their young.

Wikipedia reports,
“Paucituberculata is an order of South American marsupials. Although currently represented only by the eight living species of shrew opossums, this order was formerly much more diverse, with more than 60 extinct species named from the fossil record, particularly from the late Oligocene to early Miocene epochs.”

Let’s solve that problem
by adding Palaeothentes to the LRT. Doing so recovers this taxon at the base of the Apatemys + Trogosus clade, next to the clade that includes Caenolestes, within Glires, far from Marupialia.

I suspect taxon exclusion
is the cause for the present lack of confirmation for traditional consensus. Many PhDs over several decades have followed tradition in nesting and testing shrew opossums with marsupials without testing them against apatemyids apparently. That’s why the LRT is here, to test taxa that have never been tested together before.

But wait! There’s a novel twist here~~~~~~!
Carroll 1988 reports, “Caenolestids have long been recognized as being very distinct from other South American marsupials, but they share with them a highly distinctive pattern of the spermatozoa, which become paired within the epididymis. Paired sperm are not known in any placental groups or among the Australian marsupials.” 

Sorry.
Physical traits have to trump genes and sperm. It just has to be that way because the LRT includes fossil taxa, which never preserve sperm. There have to be rules that all participants abide by. Interesting that the gene for paired spermatozoa is localized to one continent, just as genes separate other placentals into afrotheres and laurasiatheres. By the way, “The data show that paired spermatozoa exhibit a significant motility advantage over single spermatozoa in a viscous medium” according to Moore and Taggart 1995, who tested Monodelphis, a South American opossum.

Finally
we have a last common ancestor for arboreal Apatemys (Eocene, North America) and terrestrial Trogosus (Eocene, North America), two former enigma taxa with little to no relationship with other better known mammal clades. All members of Glires had their genesis sometime in the Jurassic, based on the presence of highly derived multituberculates (clade: Glires) in the Jurassic.

Wikipedia considers
apatemyids and trogosinae (Tillodontia) to be members of the Cimolesta, “an extinct order of non-placental eutherian mammals.” This bungling of the mammal family tree is due to taxon exclusion and the lack of a phenomic (trait-based) wide gamut cladogram that includes all the taxa present in the LRT. Paleontology needs to toss off a wide range of useless tradition with a reptile revolution led by someone out there confirming (or refuting) the widest gamut cladogram presently available: the LRT.


Palaeothentes lemoinei (Ameghino 1887, MPM-PV 3566; Miocene) was considered a prehistoric shrew opossoum (clade: Paucituberculata) but here nests next to shrew opossums, at the base of the Apatemys + Trogosus clade within Glires. The skull is 2x wider than tall, the canines are still large, the last premolar is large with a flat occlusal surface and the nasals split to form a zigzag suture with the frontals.


References
Abello MA and Candela AM 2010. Postcranial skeleton of the Miocene Marsupial Palaeothentes(Paucituberculata, Palaeothentidae): Paleobiology and Phylogeny. Journal of Vertebrate Paleontology 30(5):1515-1527.
Ameghino F 1887. Enumeracions sistematicad e las especies de mamiferos
fosiles coleccionados por Carlos Ameghino en los terranos eocenos de la Patagonia austral y depositados en el Museo La Plata. Boletin Museo de La Plata, 1:1-26.
Carroll RL 1988. Vertebrate Paleontology and Evolution. W. H. Freeman and Co. New York.
Forasiepi AMSánchez-Villagra MR, Schmelzle T,  Ladevèze S and Kay RF 2014. An exceptionally well-preserved skeleton of Palaeothentes from the Early Miocene of Patagonia, Argentina: new insights into the anatomy of extinct paucituberculatan marsupials. Swiss Journal of Palaeontology, 133(1):1-21.
Moore HD and Taggart DA 1995. Sperm pairing in the opossum increases the efficiency of sperm movement in a viscous environment. Biol. Reprod. 52(4):947-53.
Osgood WH 1921. A monographic study of the American marsupial, Caenolestes. Field Museum of Natural History, Zoological series 14:1–156.

wiki/Apatemyidae
wiki/Paucituberculata
https://en.wikipedia.org/wiki/Shrew_opossum
wiki/Vertebrate_Paleontology_and_Evolution

Paucituberculata -Trouessart 1898, Ameghino 1894


There was some news
about Palaeothentes recently (see below). Note, the experts consulted here consider this genus a marsupial.

New Bolivian Marsupials from the Middle Miocene

Two new Royal Society papers suffer from taxon exclusion

Gutarra et al. 2019
tested the effects of several body plans on the hydrodynamic drag of simplified 3D digital ichthyosaurs. They reported, “Our results show that morphology did not have a major effect on the drag coefficient or the energy cost of steady swimming through geological time.”

Unfortunately
the Gutarra team included the basal sauropterygian ichthyosaur-mimic Cartorhynchus as their basal taxon, ignoring the following four valid ichthyosaur basal taxa.

  1. Wumengosaurus
  2. any hupehsuchid
  3. Thaisaurus
  4. Xinminosaurus

Given the Gutarra et al. similar results
for all included digitally generated taxa, it would have been instructive to test at least one of these basal taxa or perhaps outgroup taxa from the Mesosauria and/or Thalattosauria in order to set a baseline. Co-author professor MJ Benton has been reprimanded for excluding taxa several times before, and doggone it, he did it again.


Halliday et al. 2019
“supports a Late Cretaceous origin of crown placentals with an ordinal-level adaptive radiation in the early Paleocene, with the high relative rate permitting rapid anatomical change without requiring unreasonably fast molecular evolutionary rates.” 

By contrast
the large reptile tree (LRT, 1413 taxa) nests several placental taxa (like multituberculates) in the Jurassic with placental origins likely in the Late Triassic very soon after the origin of Mammalia.

Halliday’s team differentiates extant placentals from several extinct eutherians,
while the LRT finds only one extant taxa, the arboreal didelphid Caluromys, in the Eutheria outside of the Placentalia.

Halliday’s team cites the Luo et al. 2011 report
of “a Jurassic eutherian mammal” (= Juramaia) with reservations. In the LRT Juramaia nests with basal prototherians, not eutherians.

None of Halliday’s published work
matches the topology of the LRT. The Halliday team nests highly derived hedgehogs, elephants and armadillos as a closely related clade at the base of their cladogram of extant placentals.

By contrast and employing more taxa
the LRT documents the evolution of three clades of basal placentals, like arboreal civets, bats, dermopterans, pangolins and tree shrews (Primates + Glires), from arboreal marsupials, like Caluromys. 

Evolution: small changes over time.
The editors and referees approved Halliday’s ‘traditional’ topology. Someone should have checked results for relationships that minimize differences between recovered sisters. More taxa and avoiding genetic scoring would have helped.

Halliday’s study supports several invalidated genetic clades,
including Atlantogenata (anteaters + elephants and kin), Boreotheria (mice + whales + humans and kin), and Afrotheria (elephant shrews + elephants and kin). Even so, editors, paleoworkers and referees approved these untenable and refuted relationships.

That’s why the LRT is here,
to lift the covers and show you untenable traditional relationships, then to offer a tree topology in which all included taxa document a gradual accumulation of derived traits.


References
Gutarra S, Moon BC, Rahman IA, Palmer C, Lautenschlager S, Brimacombe AJ, and Benton MJ 2019. Effects of body plan evolution on the hydrodynamic drag and energy requirements of swimming in ichthyosaurs. Proc. R. Soc. B 286: 20182786. http://dx.doi.org/10.1098/rspb.2018.2786
Halliday TJD, dos Reis M, Tamuri AU, Ferguson-Gow H, Yang Z and Goswami A 2019. Rapid morphological evolution in placental mammals post-dates the origin of the crown group. Proc. R. Soc. B 286: 20182418. http://dx.doi.org/10.1098/rspb.2018.2418