Australopithecus enters the LRT with apes, not with humans

Lucy, the celebrated australopithecine, is an icon of evolution.
The bipedal ape, Australopithecus (Dart 1925, Late Pliocene to Early Pleistocene, 4.5 mya) Figs 1, 4), traditionally nests between chimps and humans as a primitive hominin. Bones and footprints are assigned to this genus and trackmaker.

Figure 1a. Bipedal Australopithecus traditionally nests between Ardipithecus and Homo sapiens, but not in the LRT. Now Australopithechus is bipedal by convergence with gibbons + humans.

Figure 1b. A more complete Australopithecus, nicknamed “Little Foot” on the left compared to “Lucy” on the right. Neither preserves a complete foot.

Here
Australopithecus (Figs 1, 4) nests between Proconsul + Pongo (the orangutan) and Pan (the chimp) + Gorilla (the gorilla) in the large reptile tree (LRT, 2074 taxa, subset Fig 2). That’s a novel nesting.

Homo erectus
(Fig 4), the Java Man, also enters the LRT alongside Homo sapiens (Fig 3). That’s not novel.

The LRT nesting of
Australopithecus with apes, rather than humans, breaks a traditional paradigm. If the LRT is valid, Australopithecus represents a dead-end bipedal genus arising in parallel to humans, not basal to humans. That’s an interesting story itself. According to the LRT (subset Fig 2), humans have new ancestors, some of which are still running around bipedally today (Fig 2).

Figure 2. Subset of the LRT focusing on primates after the addition of Australopithecus and Pongo.

Traditional clades
Hominini: Homo + Pan exclusive of Gorilla. No support from the LRT (Fig 2).
Homininae: Includes Gorilla exclusive of Pongo. No support from the LRT.
Homininidae: Includes Pongo exclusive of Hylobates. No support from the LRT.
Hominioidea: Includies Hylobates exclusive of Macaca. Support from the LRT.

Figure 3. Hominoid skeletons left to right: Hylobates, Homo, Pan, Gorilla, Pongo. Can you see the overall differences in these two clades? See figure 2.

The gibbon, Hylobates, entered the LRT
a few weeks ago (March 25, 2022). That post marked the start of today’s primate heresy supported here with the addition of pertinent taxa that further cement novel interrelationships.

Figure 4. Skulls of primates in the LRT in phylogenetic order in the LRT (subset Fig 2). The flat face of humans owes more to the flat face of gibbons, not chimps and auastralopithecines. Humans don’t have long-faced taxa in their ancestry.

Dart 1925 was confident enough
in his original description of Australopithecus africanus (Fig 4) that he called it a ‘man-ape‘. Subsequent papers (Johanson, White and Coppens 1978; Johanson and Taieb 1976; Johanson and White 1980) supported that phylogenetic assessment. Strait, Grive and Moniz 1997 ran a supportive cladistic analysis, but omitted Hylobates and Homo erectus. Likewise, Prang et al. 2021 reported, “Here, we use morphometric and phylogenetic comparative methods to show that Ardipithecus retains suspensory adapted hand morphologies shared with chimpanzees and bonobos.”

Funny, they don’t mention Hylobates, the gibbon (Fig 2), the taxon most known for brachiation (= suspensory adaptations)… and bipedal running.

The LRT does not support the nesting of Australopithecus close to Homo.
Gibbons (= Hylobates) are traditionally acknowledged as the basalmost ape, a basal hominoid, the lesser ape, then ignored in most human origin studies in favor of hominids and greater apes. Taxon exclusion rides again.

Gene analyses
support the isolation of Hylobates, a taxon likewise isolated geographically from chimps and gorillas. Endemic viruses affect deep time genetic studies (e.g. Afrotheria). A continent away Homo erectus was discovered and described by Dubois (1893, 1935, 1938) where Hylobates, the gibbon, runs wild today.

According to CosmosMagazine.com, “Eugène Dubois unearthed the very first fossils of Homo erectus – then dubbed Java Man – in 1891. At the time, Java Man was proclaimed as a “missing link” between apes and humans. Since then, Homo erectus has emerged as the most widespread of our ancient relatives. Remains throughout Africa, in Georgia in the Caucasus, in eastern China and on the Indonesian archipelago as far east as Java are all now considered to have come from the same long-surviving species.”

Gibbons ancestral to humans is NOT a novel hypothesis of interrelationships.
Dubois 1935 wrote: “Pithecanthropus [= Homo erectus] was not a man, but a gigantic genus allied to the gibbons, however superior to the gibbons on account of its exceedingly large brain volume and distinguished at the same time by its faculty of assuming an erect attitude and gait. It had the double cephalization of the anthropoid apes in general and half that of man.”

Ardipithecus (Fig 5) is the transitional taxon in the LRT between Hylobates and Homo.

Figure 5. Skeleton of Ardipithecus from Jay Matternes. Note the gibbon-like proportions and feet.

After catching hell from academics,
Dubois 1938 wrote: “I never imagined Pithecanthropus as a ‘giant Hylobates’, only as a giant descendant from a ‘generalized’ form, which had inherited from its ancestor, the ‘gibbonlike appearance’, but had … doubled [its] cephalization.”

Let me know if anyone else has supported Dubois’ hypothesis
of human-gibbon interrelationships with any citations between 1938 and 2022. Various authors indicate Dubois’ hypothesis has been universally rejected and mocked. Some authors accused Dubois of making a chimaera of a gibbon skull and a human femur. Before 1900 Dubois defended his hypotheses on Pithecanthropus in 19 papers, while colleagues published 95, often attacking Dubois’ findings.

References
Dart RA 1925. Australopithecus africanus the man-ape of South Africa. Nature 115:195–199.
Dubois E 1935. On the gibbon-like appearance of Pithecanthropus erectus. Proceedings Acad Sci Amsterdam 38: 578-585.
Dubois E 1938. The mandible recently described and attributed to the Pithecanthropus by G. H. R. von Koenigswald, compared with the mandible of Pithecanthropus erectus described in 1924 by Eug. Dubois. Proc Koninklijke Akad Wetenschappe Vol. 41, pt. 2:139–147.
Dubois E 1938. On the fossil human skull recently described and attributed to Pithecanthropus erectus by G. H. R. von Koenigswald. Proc Koninklijke Akad Wetenschappe Vol 41, pt. 4:380–386.
Johanson DC, White TD and Coppens Y 1978. A new species of the genus Australopithecus (Primates:Hominidae)from the Pliocene of Eastern Africa. Kirtlandia 28:l-14.
Johanson DC and Taieb M 1976.: Plio-Pleistocene hominid discoveries in Hadar, Ethiopia. Nature, 260:293-297.
Johanson DC and White TD 1980. On the status of Australopithecus afarensis. Nature, 207:1104-5.
Prang TC, Ramirez K, Grabowski M and Williams SA 2021. Ardipithecus hand provides evidence that humans and chimpanzees evolved from an ancestor with suspensory adaptations. Science Advances 7(9):eabf2474. doi: 10.1126/sciadv.abf2474
Strat DS, Grine FE and Moniz MA 1997. A reappraisal of early hominid phylogeny. Journal of Human Evolution 32(1):17–82.

wiki/Australopithecus
cosmosmagazine.com/history/palaeontology/java-mans-last-stand-2/
historyofinformation.com/detail.php?id=3603
YouTube: Australopithecus lectures and documentaries

The marsupial bear-dog has an overlooked sister

Several years ago,
the large reptile tree (LRT, 2070 taxa) separated one bear-dog taxon from several others. The one bear-dog, tentatively labeled ‘not Amphicyon‘ (Fig 1) nested with marsupial carnivores, far from the placental bear-dogs (genus: Amphicyon) close to extant hyenas in the clade Carnivora. The resemblance by convergence is notable, but the LRT separated them.

Figure 1. The skull here labeled ‘not Amphicyon’ is a marsupial bear-dog in the LRT. Compare to Megistotherium in figure 2. Does this taxon have a backstory, a scale bar and a museum number?

Today a previously mis-nested taxon,
Megistotherium (Fig 2) joins ‘not Amphicyon‘ (Fig 1) as housekeeping continues in the Mammalia clade of the LRT. Earlier I made the mistake of nesting Megistotherium within the Carnivora close to seals. Today it seems an odd fit given the narrow cranial area distinct from most, but not all placentals (see Andrewsarchus, figure 3, Stylinodon, Titanoides, Mesonyx). The unnamed taxon, “not Amphicyon” (Fig. 1) is a closer match for Megistotherium, a hypothetical relationship I overlooked previously. Considering the resemblance of the above-named taxa to each other and their disparate phylogenetic origins, this story may not be completely written yet. Let’s just call this ‘step two’, the sophomore level of understanding.

Figure 2. Megistotherium is another marsupial bear dog in the LRT. Note the anteriorly oriented orbits and the laterally expanded zygomatic arches (= jugal + squamosal).

These taxa are sisters to the clade
that includes sabertoothed Thylacosmilus.

Megistotherium osteothlastes (Savage 1973; Miocene, 23mya; 66cm skull length) was originally considered a giant hyaenodontid creodont. Here it nests with the marsupial bear-dog ‘not Amphicyon’ (Fig 1). The jaw muscles were enormous. The large diameter canines were housed in large, laterally expanded maxillae. The braincase was narrow. In overall size and general features, Megistotherium is similar, by convergence, to the giant leptictid, Andrewsarchus (Fig 3) and placental bear dogs, like Amphicyon.

The growth of the LRT
has been random and organic with 150,000+ corrections made over the last eleven years. The above corrections could have been made years earlier, but other taxa filled the past hundred+ weeks. Convergence has to be first suspected, then tested, then acknowledged as it is here.

Traditionally, and with little to no confidence,
creodonts are still considered to be placentals close to the clade Carnivora. Let’s put some effort into this with other cladograms using a similar taxon list and whatever character sets happen to also grow randomly and organically.

References
Savage RJ 1973. Megistotherium, gigantic hyaeonodont from Miocene of Gebel Zelten, Libya. Bulletin of the British Museum (Natural History) Geology 22(7):483–511.

wiiki/Megistotherium

Dr. Kevin Padian: ‘Why tyrannosaurid forelimbs were so short’

Padian 2022 adds his thoughts
to one of the perennial questions in paleontology, one often lampooned in cartoons.

Figure 1. Tyrannosaurus forelimb compared to Gorgosaurus. Everything is smaller in Gorgosaurus. Note the vestige of digit 3 in both taxa.

From the Padian abstract:
“The unusually shortened limbs of giant theropods, including abelisaurids, carcharodontosaurids, and derived tyrannosauroids such as Tyrannosaurus rex have long been an object of wonder, speculation, and even derision on the part of both paleontologists and the public. Two questions commonly asked are “Why did the forelimbs become so short?” and “What did the animals use such short forelimbs for, if for anything?” Because basal tyrannosauroids and their outgroups, as well as the outgroups of other giant theropods, had longer forelimbs, the foreshortening of these elements in derived taxa was secondary, and it ostensibly involved a shift in developmental timing of the forelimb elements.”

‘Why’ questions in evolution are interesting, but hard to argue in academic papers. Consider Padian’s paper a cautionary tale for this sort of ambition.

Figure 2. Tyrannosaurus (without feathers) to scale and directly compared to Zhenyuanlong (with feathers). As reported here in July 2017, Essentially, T-rex is just a giant, flightless Zhenyuanlong. No longer small enough to fly, the feathered flapping organs of T-rex became smaller due to lack of use.

From the Padian abstract:
“Factors proposed to have influenced the evolutionary foreshortening include natural selection, sexual selection, energetic compensation, ontogenetic vagaries, and rudimentation due to disuse. Hypotheses of use have varied from a supporting anchor that allows the hindlimbs a purchase to stand from a reclining position to a pectoral version of pelvic claspers during intercourse to a sort of waving display during sexual or social selection. None of these hypotheses explain selective regimes for reduction; at best, they might argue for maintenance of the limb, but in all cases a larger limb would have suited the function better.”

Forelimbs also become smaller in many omitted theropod clades, including flightless birds (Figs 2, 4, 6). This fact is conspicuous by its absence in this abstract. By the headline Padian seems to be treating tyrannosaurs as if they were somehow unique, ignoring the implication that whatever lessons Padian’s tyrannosaurs teach us, must be considered for all theropods with similarly small forelimbs, feathered or not.

Figure 3. Subset of the LRT focusing on Tyrannosaurus and kin. Note the nesting of Zhenyuanlong.

From the Padian abstract:
“It is likely that we have been looking the wrong way through the telescope, and that no specific function of the forelimbs was being selected; instead, another crucial adaptation of the animal profited from forelimb reduction.”

Or Padian might be keeping his blinders on. Consider this: Sometimes it is better to look through a fish-eye lens (to see more at once), rather than either end of a telescope, both of which restrict the view.

“Here I propose, in the context of phylogenetic, ontogenetic, taphonomic, and social lines of evidence, that the forelimbs became shorter in the context of behavioral ecology: the great skull and jaws provided all the necessary predatory mechanisms, and during group-feeding on carcasses, limb reduction was selected to keep the forelimbs out of the way of the jaws of large conspecific predators, avoiding injury, loss of blood, amputation, infection, and death. A variety of lines of evidence can test this hypothesis.”

Interesting. Possibly true. However, comparisons to similar phorusrhachids (Fig 4) are essential, but missing here. So is a valid phylogenetic context (Fig 3) including ancestral Zhenyuanlong (Fig 2), which also had large forelimbs provided with primary flight feathers lost in larger tyrannosaur descendants.

Figure 4. Llallawavis skeleton, one of the most complete phorusrhacids known. These birds are not mentioned in the Padian 2022 text. Neither is the word, ‘flightless’.

The Padian introduction does not starts off well.
“The oldest known tyrannosauroids, such as Dilong, were relatively small, the size of average coelurosaurians, only a meter or two long; Guanlong was somewhat larger, at about 3 m, and some such as Yutyrannus and Sinotyrannus were larger still, a size increase likely independent from those of later tyrannosaurids (Delcourt and Grillo 2018).”

None of those taxa nest with tyrannosaurs in the large reptile tree (LRT, 2070 taxa, subset Fig 2). Those taxa are all closer to basal theropods, spinosaurs and allosaurs. Zhenyuanlong (Fig. 3) is not mentioned in the text. Padian is borrowing a phylogeny without testing it or building one himself. This is why borrowing and trusting errant cladograms can only lead to trouble. Too often borrowed cladograms include outgroup taxa and exclude ingroup taxa.

If you want to know why tyrannosaur forelimbs were so short,
just look at any extant bird walking or running on the ground. What are they doing with their forelimbs? Nothing. Birds tuck their forelimbs away. When did they start doing this? Their non-avian theropod ancestors did this, too. Phylogenetic bracketing and morphologlical studies indicate so did tyrannosaurs (Fig. 1). Any bit of useless forelimb left over is a genetic legacy, inherited from ancestors that had longer, feathered limbs (Fig. 2) that also tucked them away when perching, running and walking. Padian reports, “Many authors have agreed that the forelimbs were too small to have been of any functional use.”

The core of Padian’s hypyothesis appears to be,
“there was danger in having excess body parts too close to a carcass.” He also wrote, “The central hypothesis of this paper is that the forelimbs of large tyrannosaurids were reduced phyletically not for any reason connected functionally to the forelimbs themselves, but because they posed a hazard to the survival of individuals large enough to feed communally on a carcass.” Padian also wrote, “The danger of wounds, amputations, infections, disease and ultimate death, it is argued here, would have been a selective force for reduction, irrespective of
relict functionality of the limbs.”

Only if those specific wounds were inflicted selectively and with prejudice prior to mating and commonplace enough in a population over thousands of generations. Ask Padian if he still supports his own hypothesis given these essential parameters.

Padian discusses similar feeding frenzies
in the Komodo dragon (Varanus komodoensis), but does not note any biting of forelimbs. He writes, “As far as I can determine there has been no systematic analysis of bite wounds on the skeletal elements of V. komodoensis, nor an actualistic behavioral study of wounds observed to be inflicted during the feeding of groups on carcasses.”

Padian also discusses cannibalism
in living crocodilians, which have small forelimbs relatively far from the teeth. Padian notes many instances of crocs biting each other during feeding. Here is one instance in video. That did not occur during a feeding frenzy, but from a sneak attack on a resting croc. Since crocs and Komodo dragons use their forelimbs for locomotion, all analogies to these taxa can be dismissed with regard to bipedal theropods that don’t use their forelimbs for locomotion.

Padian is arguing for a scenario
in which shorter fore-limbed tyrannosaurs are often enough biting off the forelimbs of longer-limbed immature tyrannosaurs, causing their death from infection prior to reproduction. In Padian’s hypothesis only the more aggressive shorter fore-limbed tyrannosaurs successfully mate and produce descendants with progressively shorter forelimbs. Does that sound reasonable? Can we apply that hypothesis to all theropods including flightless birds from ostriches to dodos?

Figure 5 Giant Deinocheirus, a contemporary of Mononykus, might have served as the host and dining room for a series of ever smaller and more specialized parasite eaters.

Padian discusses small alvarezsaurids with reduced forelimbs,
like Mononykus (Fig 5), but noted, “in more basal alvarezsaurids, the forelimbs were already greatly reduced and it is difficult to posit or test any kind of function for them.”

Padian ignores ancestral Haplocheirus (Fig 5), which does not have such reduced forelimbs.

In his conclusion, Padian wrote,
“It is possible that we have been looking through the wrong end of the telescope. Perhaps the question should not be “What function were the reduced arms selected to perform?” but “How was the reduction of the arms selected so as to provide another, over-riding benefit to the organism?”

Well put. But, let’s look at flightless birds (Figs 4, 6) for a good start to that answer.

Padian then wrote,
“It seems that no functional or non-functional argument proposed so far can explain anything about the reduction of the arms in tyrannosauroids, except perhaps simple disuse; but the disuse also has to be explained (for example, why the forelimbs are reduced in abelisaurids but not in allosaurids).”

Because evolution follows few rules. To each his own. Whatever works. And, at the same time, convergence is rampant.

Colleagues, don’t take a rare incident, like a croc video, and ascribe that incident to the almost universal appearance of short limbs in theropods (other than soaring birds).

Figure 6. Swan-sized, Pezophaps, the solitaire, is the closest dodo relative. Both were giant flightless pigeons that did not feed in a group frenzy, biting off forelimbs, as envisioned by Padian 2022.

Since forelimb reduction is so commonplace in theropods,
and maybe for similar reasons, let’s pause to wonder, why did Padian focus on tyrannosaurid forelimbs? Was that an academic headline grab? Substitute the word ‘theropod’ for ‘tyrannosaurid’ in the headline and get a sense for what authors and editors are looking for.

Figure 7. The toothless poposaur, Effigia, also has tiny forelimbs. Can we apply Padian’s ‘selective biting + infection + death prior to mating for reproduction’ hypothesis to this taxon, too?

Padian also ignored or omitted
all the larger flightless birds (e.g. the dodo, Raphus, and the solitaire, Pezophaps, Fig 6). He also omitted Effigia (Fig 7), a poposaur with tiny forelimbs. There is no indication that shorter-limbed specimens of these taxa were biting off the longer forelimbs of their competitors prior to mating opportunities leaving only progressively shorter-limbed survivors to mate and produce descendants. Use that fish-eye lens to look at other small forelimb theropods and you’ll soon realize that wings/forelimbs just tend to get smaller if they are not used.

In flightless pterosaurs this is also true.

Padian’s next paper might wonder
how tyrannosaurs got so large while their forelimbs did not keep up (Fig 2). That’s how you look through the other end of the telescope. Hint: it starts with flightlessness, as in azhdarchid pterosaurs and giant birds.

Don’t judge Dr. Padian too harshly on this faux pas.
His body of work is generally robust with many solid contributions to paleontology.

Taxon exclusion
remains the number one problem in paleontology. As established by many paleo workers, sometimes a hypothesis becomes firmly established before the cherry-picking of data begins. Sometimes human nature (= the quest for headlines) gets the best of what ideally should be emotionless and unbiased scientific method seen through a fish-eye lens.

References
Gans C 1975. Limblessness: Evolution and functional corollaries. American Zoologist 15: 455–467.
Padian K 2022. Why tyrannosaurid forelimbs were so short. Acta Palaeontologica Polonica 67 (1), 2022: 63-76 https://doi.org/10.4202/app.00921.2021

reptileevolution.com/tyrannosaurus_clade.htm

Why T-rex had tiny forelimbs

Publicity
ign.com/articles/t-rex-short-arms-new-study

The olingo, Bassaricyon, enters the LRT amid controversy

Everyone who studies it understands
the olingo, Bassaricyon (Figs 1, 3), shares many traits with the kinkajou, Potos (Figs 2, 4). The large reptile tree (LRT, 2070 taxa) nests these two together based on traits.

Figure 1. The olingo, Bassaricyon, in vivo. This is the kind of mammal that clambered through trees during the Jurassic and Cretaceous. It’s a living fossil.

Helgen et al. 2013 report,
“Species of Bassaricyon are primarily forest-living, arboreal, nocturnal, frugivorous, and solitary,
and have one young at a time.”

Figure 2. The kinkajou, Potos, as a museum mount. Compare to the olingo in figure 1.

Bassaricyon gabbi
(Allen 1876) is the extant olingo, traditionally considered a member of the raccoon clade native to Central American rainforests.

Potos flavus
(Schreber 1774) is the extant kinkajou a tropical American relative of the North American raccoon. This fruit-eater has flat molars and a short, primate like muzzle. The tail is prehensile.

Figure 3. Olingo (Bassaricyon) skull in three views. Compare to figure 4.

Unfortunately,
molecule studies, like Koepfli et al. 2007, separate these two taxa. The Koepfli study also suffered from taxon exclusion. The authors wrote, “Cladistic analyses of morphological characters conducted during the last two decades have resulted in topologies that group ecologically and morphologically similar taxa together. Speciifically, the highly arboreal and frugivorous kinkajou (Potos) and olingos (Bassaricyon) define one clade, whereas the more terrestrial and omnivorous coatis (Nasua), raccoons (Procyon), and ringtails (Bassariscus) defne another clade, with the similar-sized Nasua and Procyon joined as sister taxa in this latter group. These relationships, however, have not been tested with molecular sequence data.”

The Koepfli team listed several genera (Fig 5) traditionally included within the family Procyonidae. Their list excludes several ingroup taxa and includes several outgroup taxa according to the LRT results.

Figure 4. Kinkajou (Potos) skull in four views.

Doubling down, the Koepfli team reported,
“Our fndings suggest that procyonid phylogenetic relationships based on morphological evidence are problematic, and further, that phylogenetic hypotheses relating fossil and living taxa based primarily on dental evidence are also open to question because of extensive homoplasy associated with this type of evidence.”

In other words, these scientists are dismissing traits they can see and measure in favor of genes that be affected by endemic viruses over deep time. They are not doubting their genomic results. The authors cherry-pick ingroup taxa, rather than including a wider gamut of fossil and living taxa and then letting the software tell them the interrelationships recovered.

Figure 5. Cladogram from Koepfli et al. 2007 cherry-picks taxa. In the LRT, the coatimundi, Nasua, is the outgroup, also basal to primates and other placentals. In the LRT Potos nests with Bassaricyon. That’s one more reason why you should avoid deep time molecular studies and use traits from a wide gamut of taxa, like the LRT.

The final phylogenetic test
is an adherence to the process of evolution: a gradual accumulation of derived traits at every node. That can only be achieved by including fossil taxa and a wider gamut of tested taxa. It is indeed unfortunate that genes too often deliver false positives. Genes hold great promise, but fail to deliver, and worse. Genes mismatch taxa and biologists fail to see that, preferring instead to embrace untenable results.

Taxon exclusion remains the number one problem
in paleontology.

Trusting deep time genomic results over trait analyses
remains the number two problem.

Figure 6. Subset of the LRT focusing on basal placentals and the clade Carnivora.

Don’t assume paradigms are true. Don’t trust genes. Don’t parrot textbooks.
Don’t borrow cladograms. Build your own cladogram. Run your own tests using traits that recover a gradual accumulation of derived traits (= maximum parsimony). When you have your own LRT, you’ll have a powerful tool you can use with authority. You will have a good grasp of the big picture and all the little details will naturally fall into place, modeling actual evolutionary events, directions, reversals and convergence.

References
Allen JA 1876. Description of a new generic type (Bassaricyon) of Procyonidae from Costa Rica. Proceedings of the Academy of Natural Sciences of Philadelphia 28: 20-23.
Helgen et al. (7 co-authors) 2013. Taxonomic revision of the olingos (Bassaricyon), with
description of a new species, the Olinguito. ZookKeys 324:1–83.
Koepfli K-P et al. (6 co-authors) 2007. Phylogeny of the Procyonidae (Mammalia: Carnivora): Molecules, morphology and the Great American Interchange. Molecular Phylogenetics and Evolution 43: 1076–1095.
von Schreber JCD 1774. Die Säugethiere vol.1 9 p.pl. 42

wiki/olingo – Bassaricyon
wiki/kinkajou – Potos

Basal placentals to scale, including Protictitherium, a new LRT taxon

Lemur-like Protictitherium
(Figs 1, 2) enters the large reptile tree (LRT, 2070 taxa) at the root of the clade that ultimately produced leptictids (= elephant shrews), Andrewsarchus, tenrecs and toothed whales.

Figure 2. Protictitherium skull in situ and in lateral view.

Protictitherium crassum (Kretzoi 1938; Miocene-Pliocene Vallesian–Turolian) is traditionally considered a hyena-like civet, but civets are not related to hyenas. Here Protictitherium nests with Anagale between Notharctus and Onychodectes (Fig 1) as a late-surviving, very basal (Jurassic to Earliest Cretaceous) placental. In size and shape it lines up well with other basal (Early Jurassic) placentals. Protictitherium was considered scansorial (tree-dwelling) and insectivorous by Koufos and Kondairs 2011.

Figure 2. Basal placentals including Vulpavus, Notharctus and Protictitherium to scale. Note how similar these taxa are to one another. Like Solnhofen birds, each one is basal to another clade of placental taxa.

Protictitherium provides post-cranial data
for the transition from arboreal basal placentals to terrestrial anagalids. The palm civet, Nandinia, and the coatimundi, Nasua (Fig 1), provide extant models for size, shape, niche and lifestyle.

References
Kretzoi M 1938. Die Raubtiere von Gombaszög nebst einer Übersicht der Gesamtfauna. Annales Musei Nationalis Hungarici 31:88–157.
Koufos GD and Konidaris GE 2011. Late Miocene carnivores of the Greco-Iranian Province: Composition, guild structure and palaeoecology. Palaeogeography, Palaeoclimatology, Palaeoecology. 305: 215. doi:10.1016/j.palaeo.2011.03.003

wiki/Nasua
wiki/Oodectes
wiki/Protictitherium
wiki/Anagale

Marsupial ‘dogs’ and ‘cats’ close to Deltatherium

Recent scoring changes
in the LRT settled a nagging issue. Now the large reptile tree (LRT, 2070 taxa) moves a clade of three former ‘placental anagalids’ over to marsupial carnivores close to Arctocyon and Deltatherium (Fig. 1). The three moving taxa include Hyainailourous (= Pterodon), Apterodon and the IVPP V12385 specimen assigned to Hapalodectes (Fig. 1). Phylogenetic issues surrounding all these taxa run deep with prior workers.

Traditionally
Arctocyon (Fig. 1) is considered a member of the placental clade ‘Ungulata” close to Mesonychia by the authors of Wikipedia.

That hypothesis is not supported by the LRT (subset Fig 1).

Traditionally
Deltatherium (Fig 1) is considered a placental (= Eutheria). Recently Shelley et al. 2021 reported, “the phylogenetic relationships of this taxon have remained elusive since its discovery, and it has variably been associated with Arctocyonidae, Pantodonta and Tillodontia.” Shelley et al. wrote extensively about the history of Deltatherium interrelationships ‘considered’ in the pre-cladistic era. The authors reported that Zack (2010) “conducted a comprehensive higher-level phylogenetic analysis of Paleogene eutherians and found Deltatherium to be the sister taxon to a clade including numerous arctocyonids (Chriacus, Thryptacodon, Claeonodon, Mentoclaenodon, and Anacodon) and the extinct pangolin Patriomanis (constrained analysis), and he commented that a close relationship with pantodonts and tillodonts was unlikely.”

Here’s a lesson: If you restrict your search for Deltatherium relatives to ‘Paleogene eutherians’, you’re going to fail if it turns out to nest outside the Eutheria.

Shelley et al. continue their review of Deltatherium interrelationships
by reporting more recent workers “have refrained from inferring the phylogenetic affinities of Deltatherium.” Shelley et al. 2021 likewise refrained from making a specific hypothesis and did not mention the term ‘marsupial’ in their text. However, in their discussion Shelley et al. reported, “A well-developed rostral tympanic process on the posteromedial part of the promontorium is a derived feature for Metatheria.” That’s as close as they got to results recovered by the LRT (subset Fig 1).

If you’re having taxonomic problems like this, venture out a little. Add taxa.

Figure 1. Apterodon, Pterodon, Hapalodectes and kin derived from a sister to Thylacinus.

This clade of carnivorous marsupials
includes some (but certainly not all) of the most cat-like and dog-like morphologies in the Mammalia. Hyaena-mimics, like Hyaenodon, are in the next clade over (Fig 1), also close to Thylacinus. Echoing the Placentalia, in the LRT marsupial cat-like taxa nest close to dog-like taxa.

Sometimes it takes a long list of taxa
to understand interrelationships that converge like this. Prior workers overlooked the possibility of convergence and floundered for a century. They didn’t realize creodonts were marsupials close the the Tasmanian wolf, Thylacinus (Fig 1), often with a convergent carnassial tooth (Fig 1). The creodont page at UCMP reports, “Creodonts are an extinct group of carnivorous mammals that were long thought to be the ancestors of modern Carnivora. This is no longer thought to be the case.” They don’t say what ‘the case’ is nowadays. They don’t mention that creodonts were marsupials. Neither does Wikipedia.

Taxon exclusion
continues to be the number one problem in paleontology. Let’s fix that. It’s easy. Just add a few taxa.

References
Shelley SL, Bertrand OC, Brusatte SL and Williamson TE 2021. Petrosal anatomy of the Paleocene Eutherian mammal Deltatherium fundaminis (Cope 1881). Journal of Mammalian Evolution 28:1161–1180.
wiki/Creodonta
wiki/Oxyaenidae
wiki/Hyaenodonta
wiki/Arctocyonia
ucmp.berkeley.edu/mammal/eutheria/creodonta

Th resurrection of the clade Creodonta was posted December 2018:

Resurrecting extinct taxa: Creodonta, Mesonychidae, Desmostylia and Gephyrostegidae

The importance of our moon and plate tectonics for evolution

Life may be very rare in the universe because
where we do find life (here on Earth, subset Fig 1) we find a planet of just the right size in just the right habitable zone that is attended by a large moon that produces daily tides in the oceans. Those tides keep shorelines and tidal pools changing on a daily basis, along with the light-dark cycle for every rotation of the planet.

The moon also keeps the inner earth molten by producing earth tides.
Over deep time a broiling Earth and its cool floating crust produce continental drift. That produces new environments beyond those that are present between the hot equator and the cold poles. This panoply of new and changing environments together with the islands of isolation they often produce greatly encourages the evolution of life forms that are best suited for the many connected niches.

Ocean and Earth tides were more powerful in the early days
of the Earth-moon system when the two were much closer to one another.

Other planets and moons in the solar system don’t have
the variety of environments found here on Earth, whether on a daily basis, or moving from equator to poles, or from ocean to shoreline to mountain, or from rainy to dry to ice bound, or over deep time. Look around. We’re pretty lucky to be here, wherever we are. Things are different everywhere you look. Other planets don’t have that luxury. Sorry, Mars and Venus.

If life did get a start somewhere out there,
it will not have the opportunity to evolve beyond primordial slime if it starts on an unchanging planet without a big moon. A molten Earth is also responsible for planetary magnetism, which produces Van Allen belts, which protects life forms and keeps the planet from losing its oceans.

Figure 1. North American through time starting with the Late Cretaceous.

Those daily and deep time changes in our planet
made us and every other living thing over deep time. As our planet evolved, so did we. Whatever planetary evolution that continues into our deep time future will continue to evolve new niches and lifeforms that are best suited to fit them.

Here is an article about the moon taking 70 percent of Earth’s crust into orbit
which made plate tectonics possible. It is insightful and well written. And it inspired today’s blogpost: spacedaily.com/news/life-01×1.html

Added April 17, 2022:
Public Lecture Jan 2020: How and why the Earth is different, Nick Rogers

Carnivora: a misunderstood clade

Traditionally members of the Carnivora
“all have blade-like carnassial teeth – their fourth upper premolar and first lower molar – which bite together to shear through food.”

Sounds like someone out there is trying to “Pull a Larry Martin”
by assigning a few traits to define or mark this traditional clade.

UCMP Berkeley correctly notes exceptions, but still manages to “Pull a Larry Martin” when they report, “Carnivores can be told by their enlarged canine teeth, by the presence of three pairs of incisors in each jaw (with rare exceptions), and by the shape of their molar teeth.”

Phylogenetically, not all members have ‘carnasial’ teeth.
Phylogenetically all members of the Carnivora have a last common ancestor in the Middle Jurassic close to extant raccoons (Procyon) and kinkajous (Potos, Fig 1). Thereafter, anything goes. Their ancestors were the ancestors of lions, weasels, wolves, seals, sea lions and several ‘bears’ evolving by convergence in several clades according to results recovered in the large reptile tree (LRT, 2070 taxa, subset Fig 2).

Gene studies have also played havoc
with the clade Carnivora as we learned yesterday. The LRT tests traits.

Figure 1. The cheetah, Acinonyx, enters the LRT today. Note the shorter face, longer vertebral column and longer metatarsals.

Today one and a half new carnivores are added to the LRT.
The speedy cheetah, Acinonyx, enters next to Panthera, the lion. The cheetah is a big cat with a longer, more flexible back (a reversal), longer metatarsals and an even shorter face.

Figure 2. Subset of the LRT focusing on Carnivora.

The half a taxon entering today
is the post-crania of Miacis (Fig. 3), a basal sea lion close to the lineage of cats, dogs in the LRT. Earlier the skull of Macis entered as a taxon alongside short-legged Hyopsodus. These additions, like all additions, shed light where needed. A few scores changed, but the topology remained pretty much the same.

Figure 3. Miacis in situ. This Late Paleocene to Late Eocene taxon is basal to sea lions in the LRT and close to the origin of cats and dogs.

If anyone knows of a recent phenomic study of the Carnivora,
please send a citation along. I would like to compare it to the LRT. At present workers seem to be enthralled with genes (references below) and the results are untenable.

References
Agnarsson I, Kunter M and May-Collado LJ 2010. Dogs, cats, and kin: A molecular species-level phylogeny of Carnivora. Molecular phylogenetics and evolution. 54(3):726-745.
Flynn JJ, Finarelli JA, Zehr S, Hsu J and Nedbal MA 2005. Molecular Phylogeny of the Carnivora (Mammalia): Assessing the Impact of Increased Sampling on Resolving Enigmatic Relationships. Journal of Systematic Biology 54:317-337.
Novacek MJ 1992. Mammalian phylogeny: shaking the tree. Nature 365, 121–125. (doi:10.1038/ 356121a0)
O’Leary MA et al. 2013. The placental mammal ancestor and the post–K–Pg radiation of placentals. Science 339, 662–667. (doi:10.1126/ science.1229237)

Civets and cats: Why do they nest together in Wikipedia, but not in the LRT?

theguardian.com/science/2017/jul/26/cats-vs-dogs

Civets and cats: Why do they nest together in Wikipedia, but not in the LRT?

Answer:
Wikipedia reports the results of gene studies. The LRT recovers the results of trait studies. Trait studies can include fossil taxa. Gene studies typically cannot include fossils.

Gene studies split cat-like taxa from dog-like taxa within the clade Carnivora
(= Feliformes and Caniformes). According to Wikipedia, “Feliformia is a suborder within the order Carnivora consisting of “cat-like” carnivorans, including cats (large and small), hyenas, mongooses, viverrids, and related taxa.” The clade Caniformia comprise all other members of the Carnivora.

Trait studies, like the LRT, lump cats with dogs within the clade Carnivora
(Fig 1). Hyenas, aardwolves and hesperocyonids are transitional taxa between cats and dogs.

Figure 1. Subset of the LRT focusing on the placental clade Carnivora.

And civets?
In the large reptile tree (LRT, 2069 taxa, subset Fig 1) civets (Fig 2) are very primitive, so they nest far from these two taxa, just outside of Carnivora, close to basal-most placentals and outgroup marsupials and related lemurs.

These distinctly different tree topologies
shed light on the dangers of false positives arising from currently favored genomic analyses. Even so and seemingly oblivious to the red flags, both paleoacademics and Wikipedia writers continue to trust the strange, non-gradual results of deep time genomic studies. Genes have become so popular that few workers test extant taxa using trait studies. Apparently, nobody wants to attempt to falsify deeply entrenched deep time genomic studies. Perhaps this is so because genes work so well in closely related taxa not separated by deep time. It is unfortunate that gene studies break down to such an extent that sometimes bats nest with horses.

According to Wikipedia,
“Civets have a broadly cat-like general appearance, though the muzzle is extended and often pointed, rather like that of an otter, mongoose or even possibly a ferret. Civets are unusual among feliforms, and carnivora in general, in that they are omnivores or even herbivores.”

Just like their most recent marsupial ancestors (Fig 1). The civet, Civetticis (Fig 2) is the most recent addition to the LRT. Phylogenetically civets also precede primates. Chronologically civets appeared in the Early Jurassic.

Figure 2. The civet, Civettictis, enters the LRT today.

Civettictis civetta
(Schreber 1776; snout rump length = 80cm) is the extant civet. Here it nests between Nandinia and Genetta, not close to cats like Panthera.

The subject of civets, cats and hyenas came up
while viewing a recently published YouTube video on hyenas that used gene studies to lump civets with cats and hyenas. The trait differences are subtle, but many.

Consider the fact
that all tested civets are extant taxa. Given all those dozens of millions of year since the original civets had their genesis in the Jurassic, perhaps it was only natural that they would converge in several ways with the single tested cat, another extant member of the Carnivora with dozens of millions of year to evolve, the lion, Panthera.

References
Schreber JCD 1776. Die Säugthiere in Abbildungen nach der Natur, mit Beschreibungen 3:16.
wiki/Feliformia
wiki/Caniformia

sciencedirect.com/civet

Nagini, described as a ‘snake-like’ Carboniferous ‘amniote’, is not an amniote

Figure 1. Nagini nodule at full scale alongside a skull diagram from Mann, Pardo and Maddin 2022. Colors added here.

Mann, Pardo and Maddin 2022
introduce us to Nagini mazonense (Fig 1), a tiny microsaur taxon found in a Francis Creek Carboniferous nodule exhibiting “extreme axial elongation and corresponding limb reduction.” This taxon “lacks entirely the forelimb and pectoral girdle, thus representing the earliest occurrence of complete loss of a limb in a taxon recovered phylogenetically within amniotes.”

Nagini does not nest ‘within amniotes’ when more taxa are added (Fig 3).

Figure 2. Cladogram from Mann, Pardo and Maddin 2022 suffering from massive taxon exclusion. Colors added here. Compared to figure 3.

The authors made several phylogenetic mistakes
due to taxon exclusion. Nagini and its sisters (e.g. Brachydectes, Fig 4) are not amniotes in the fully resolved large reptile tree (LRT, 2066 taxa. subset Fig 3). Instead they are highly derived microsaurs closer to similar elongate and limbless caecilians and their nearly limbless kin.

Caecilians in the LRT (Fig 3) are not related to frogs and salamanders as they are in the Mann, Pardo and Maddin cladogram (Fig 2).

The basalmost amniotes in the LRT (Figs 3, 5) are not included in the Mann, Pardo and Maddin cladogram (Fig 2).

The basalmost tetrapods and dozens of other taxa in the LRT (Fig 3) are not included in the Mann, Pardo and Maddin cladogram (Fig 2).

Figure 3. Subset of the LRT focusing on basal tetrapods, microsaurs and basal reptiles. The LRT is completely resolved, includes more pertinent taxa and nests Brachydectes and kin close to similar caecilians within Microsauria. The gray triangle points to Brachydectes, a close relative of Nagini, far from the amniotes (= Reptilia). The basal taxon in Archosauromorpha is Gephyrostegus.

Don’t try to grab headlines by claiming to have a Carboniferous amniote
when you have a microsaur. Don’t cherry-pick taxa and omit basal amniotes in your study of basal amniotes and microsaurs. Taxon exclusion is the number one problem in paleontology.

Figure 4. Brachydectes elongatus (Lysorophus tricarinatus) from Carroll and Gaskill 1978 and Wellstead 1991 with colors and new bone identities added. This taxon is closely related to Nagini (Fig 1).

Finding a fossil is step one.
Identifying a fossil is step two. You can only identify a fossil by comparative morphology and phylogenetic analysis. You can only compare morphologies by including a wide gamut of taxa, some closely related, others not. So don’t borrow and don’t cherry-pick. Do the work. More more pertinent taxa always improves a cladogram. More taxa will improve your understanding of tetrapod and reptile evolution. At present, Mann, Pardo and Maddin 2022 lack demonstrate they lack that understanding due to taxon exclusion.

Figure 5. Eusauropleura to scale with ancestral and descendant taxa including Eucritta, Utegenia, Silvanerpeton and Gephyrostegus, the last common ancestors of all reptiles. Note the long, strong legs. Other than Eucritta, these taxa were omitted from Mann, Pardo and Maddin 2022.

According to the commentary by co-author Mann 2022
“we know comparatively little about whether the earliest amniotes were capable of achieving the same range of diverse body plans and ecologies seen in modern amniotes.”

This is a common tactic among paleo writers, telling the reader how little is known. This sets up their heroic entrance. In this case what Mann reports is incorrect when more taxa are added to analysis, as in the LRT. This is data readily accessed for free online.

“Historically early amniotes were thought to have all been roughly similar in body shape and ecology, with only some variation in feeding and display structures, with amniote morphological diversification really kicking into high gear by the late Permian with the diversification of therapsids and then of diapsid reptiles.”

Early amniotes (Fig 5, ironically missing from the Mann, Pardo and Maddin cladogram, Fig 2) are indeed roughly similar in body shape and ecology.

“One of the important ways in which amniotes can diversify is through modifications in limb morphology including the reduction or even complete loss of limbs.”

When more taxa are added this doesn’t happen in basal amniotes, only in highly derived microsaurs close to caecilians. If a large morphological gap is present in your cladogram, that’s a sign to add taxa. Mann is constructing his own scenario by cherry-picking taxa.

“Recently, a diverse group of early tetrapods known as the Recumbirostra, named after their shared adaptation of recumbent snouts (likely for headfirst burrowing), have risen to prominence in research on the origin of amniotes with several recent studies regarding the group as one of the earliest diversifications of reptiles.”

The LRT does not support this hypothesis of interrelationships. Adding taxa splits Recumbirostra apart from Reptilia. Early Carboniferous reptiles, getting used to their new terrestrial niche, improve and lengthen their limbs (Fig 5), just the opposite of the Mann, Pardo and Maddin hypothesis.

“In general, the presence of diverse limb-reduced and axially-elongated forms, including forms like Nagini with complete forelimb loss, at or near the base of Amniota supports the idea that limb reduction and axial elongation is an adaptive mode ancestral to amniotes.”

Just the opposite (see above paragraph). The legs and toes become stronger in basal amniotes (Fig 5) clambering around their swampy-to-dry environs where their dry terrestrial amniotic eggs are deposited.

A valid phylogenetic context demonstrating a gradual accumulation of derived traits is paramount. Don’t write another paper without one. I hate to see yet another new myth grow when simply adding taxa readily falsifies Mann’s conclusions.

References
Mann A, Pardo JD and Maddin HC 2022. Snake-like limb loss in a Carboniferous amniote. Nature Ecology and Evolution https://doi.org/10.1038/s41559-022-01698-y

Mann 2022 commentary
nature.com/posts/a-farewell-to-arms