Fossiomanus and Jueconodon enter the LRT as pre-mammal diggers

As the headlines reported,
(see below) these two late-surviving pre-mammals lived under the feet of Early Cretaceous dinosaurs and probably only came out after dark.

From the Mao et al. 2021 abstract:
“Mammaliamorpha comprises the last common ancestor of Tritylodontidae and Mammalia plus all its descendants. Tritylodontids are nonmammaliaform herbivorous cynodonts that originated in the Late Triassic epoch, diversified in the Jurassic period and survived into the Early Cretaceous epoch. Eutriconodontans have generally been considered to be an extinct mammalian group, although different views exist.”

“Here we report a newly discovered tritylodontid and eutriconodontan from the Early Cretaceous Jehol Biota of China. Eutriconodontans are common in this biota, but it was not previously known to contain tritylodontids.”

Confirmation on those points!
In the large reptile tree (LRT, 1825+ taxa; subset Fig. 4) Fossiomanus nests with Oligokyphus and the tritylodonts. The other new burrowing pre-mammal, Jueconodon nests with Liaocondon, and other eutriconodonts close to Gobiconodon and Repenomamus.

Figure 1. Fossiomanus in situ in two ventral views, plus manus, pes and pelvis reconstructed. Teeth colored. Taphonomically shifted pectoral girdle repaired on right. The current view of the skull material prevents a reconstruction at this time.

Figure 2. Skull of Jueconodon based on data from Mao et al. 2021.

Mao et al. continue:
“These fossils shed light on the evolutionary development of the axial skeleton in mammaliamorphs, which has been the focus of numerous studies in vertebrate evolution and developmental biology. The phenotypes recorded by these fossils indicate that developmental plasticity in somitogenesis and HOX gene expression in the axial skeleton—similar to that observed in extant mammals—was already in place in stem mammaliamorphs. The interaction of these developmental mechanisms with natural selection may have underpinned the diverse phenotypes of body plan that evolved independently in various clades of mammaliamorph.”

Figure 3. Cladogram from Mao et al. 2021, color overlays added here to show how LRT divides these clades. Compare to figure 4.

Usually, ‘No hypotheses like this can proceed without first establishing a valid phylogeny.’ Parts of Mao et al. match the LRT. Unfortunately, Mao et al. follow invalid academic tradtion as they also include and therefore nest multituberculates with pre-mammals, rather than with rodents and plesiadapiformes in the gnawing clade, Glires. Just add pertinent taxa to resolve this problem. So far PhDs have been reluctant to do this and so the myth continues untested except here.

Mao et al. nest Jueconodon between Liaoconodon and Chaoyangodens (Fig. 3). In the LRT (Fig. 4) Jueconodon also nests with Liaoconodon, but Chaoyangodens nests as a monotreme mammal, basal to the echidna and platypus (Tachyglossus and Ornithorhynchus).

Mao et al. nest Fossiomanus with Kayentatherium, basal to four other tritylodontids including Tritylodon and Oligokyphus among mutually tested taxa. In the LRT (Fig. 4) Fossiomanus nests similarly.

Figure 4. Subset of the LRT focusing on pre-mammals with the addition of Fossiomanus and Jueconodon. Compare to original cladogram in figure 3 and to the LRT for a look at related taxa.

Mao et al. mention Liaoconodon often:

1. “The triangular shape of the skull may have been exaggerated by the crush of
   the specimen, but compared to those that have the similar preservation, such as Jeholodens, Liaoconodon, and Chaoyangodens, the triangular shape of Jueconodon is distinctive.
2. The morphology of the mandible is similar to those of other eutriconodontans, such as Liaoconodon (Meng et al., 2011). Given that Liaoconodon was interpreted as a semiaquatic animal (Chen and Wilson, 2015), the similar mandible in both species indicate that the lower jaw and teeth of Jueconodon were not specialized for digging.
3. The ossified Meckel’s cartilage on each side is preserved but displaced from its anatomical position. This suggests that the transitional mammalian middle ear, as best shown in Liaoconodon (Meng et al., 2011), was present in the fossorial eutriconodontans.“

Figure 5. Skull of Liaoconodon.

Figure 6. Liaoconodon in situ.

Mao et al. report, “the Manda cynodont and mammaliaforms that are considered terrestrial.
Compared to extant mammals, Fossiomanus sinesis is superficially similar in body size and shape to the Cape dune mole-rat Bathyergus suillus, the largest subterranean scratch-digger species of the African mole-rats (Montoya-Sanhueza et al., 2019). However, they differ fundamentally in the axial skeleton in that mole-rat has the rodent body plan with the ancestral PV count of mammals.”

References
Mao F-Y, Zhang C, Liu C-Y and Meng J 2021. Fossoriality and evolutionary development in two Cretaceous mammaliamorphs. Nature (advance online publication)
doi: https://doi.org/10.1038/s41586-021-03433-2
https://www.nature.com/articles/s41586-021-03433-2

wiki/Fossiomanus
wiki/Cape_dune_mole-rat

http://www.sci-news.com/paleontology/fossiomanus-sinensis-jueconodon-cheni-09534.html

https://www.amnh.org/explore/news-blogs/research-posts/burrowing-mammal-ancestors-discovered

Fruitafossor: now a Late Jurassic echidna from Colorado

While reviewing the terrestrial descendants of tree shrews
yesterday, the Late Jurassic Fruitafossor (Figs. 1, 2) stuck out as a chronological misfit as it nested in the otherwise Tertiary edentates (= Xenarthrans).

Here is the problem,
and the solution.

A Jurassic edentate? No.
Fruitafossor windscheffeli (Luo and Wible 2005) used to nest in the LRT with digging edentates, like the armadillo-mimic, Peltephilus (Miocene), and for good reason…

Wikipedia reports,
“The teeth of Fruitafossor bear a striking resemblance to modern armadillos and aardvarks. Its vertebral column is also very similar to armadillos, sloths, and anteaters (order Xenarthra). It had extra points of contact among similar to the xenarthrous process that are only known in these modern forms.”

By contrast, Wikipedia concludes,
“Its shoulder-girdle is similar to a platypus or reptile, but many other features are more similar to most other modern mammals.”

What would Larry Martin say?
Run a complete analysis. Don’t rely on one, two or a dozen traits. And the Late Jurassic is so early in mammal evolution that it becomes important, too. There were fewer mammal clades back then. Edentates had not yet arrived.

Figure 1. Several drawings from Zhou and Wible that one must trust for accuracy. The verification data is too fuzzy to validate.

So is Fruitafossor a Late Jurassic edentate?
Or an edentate-mimic in the Late Jurassic?
With current scoring in the LRT, shifting Fruitafossor from the edentates to the base of the Monotremata adds 23 steps. Shifting to Early Cretaceous Lactodens within the Monotremata adds just 17 steps, the lowest number I could find. Lactodens has typical differentiated teeth and five fingers with small, sharp claws, traits not shared with Fruitafossor + edentates. Lactodens nests with the echidnas, Tachyglossus (extant, Figs. 3–5) and Cifelliodon (Early Cretaceous; Fig. 3). The latter has simple blunt teeth and the former is a known digger.

Figure 2. Fruitafossor in situ from Digimorph.org and used with permission and here colorized to an uncertain extent.

So let’s reexamine scored traits… and solve this conundrum.
Has the LRT met its match? Very few skull traits are known from Fruitafossor. Even so, earlier I overlooked or mis-scored the following that gain importance in hindsight:

Fruitafossor:

1. orbit contacts the maxilla
2. 4 rather than 5 sacrals,
3. coracoid present
4. I could not score hind limb length without a pes and estimates won’t do
5. proximal sesamoid of fibula present
6. fibula diameter greater than half of tibia
7. dorsal osteoderms absent (I misinterpreted scattered elements at Digimorph.org)

Tachyglossus:

1. retroarticular process present as in Fruitafossor
2. metacarpal 1 and 2 are the longest as in Fruitafossor
3. longest manual digit 3 as in Fruitafossor
4. manual digit 4 narrower than 3 as in Fruitafossor

Cifelliodon:

1. three molars, as in Fruitafossor

Figure 3. Early Cretaceous Cifelliodon is ancestral to the living echidna, Tachyglossus according to the LRT. The lack of teeth here led to toothlessness in living echidnas. The skull of Tachyglossus is largely fused together, lacks teeth and retains only a tiny lateral temporal fenestra (because the jaws don’t move much in this anteater. Compared to Cifelliodon the braincase is greatly expanded, the lateral arches are expanded and the two elements fuse, unlike most mammals.

Figure 4. Tachyglossus skeleton, manus and x-rays. Note the perforated pelvis.

Figure 5. The echidna (genus: Tachyglossus) in life. This slow-moving spine-covered anteater has digging claws.

Results (as you might imagine, given these changes):
Fruitafossor is an edentate-mimic nesting basal to Cifellidon and Tachyglossus as a Late Jurassic echidna and monotreme in the LRT. Glad to get rid of that problem!

In their original description of Fruitafossor,
Luo and Wible 2005 nested their discovery between a monotreme clade and a clade with the mammal-mimic, Gobiconodon at its base, then a clade with another egg-laying mammal, Tinodon at its base, then a pangolin ancestor, Zhangheotherium, then a rabbit ancestor Henkelotherium, then two other monotremes, Dryolestes, Amphitherium and the carnivorous marsupial, Vincelestes.  Luo and Wible tested Tachyglossus, but not Cifelliodon, which was published in 2018. Note the simple, blunt teeth in Cifelliodon, nearly matching those in Fruitafossor. Given that the only fossil of Fruitafossor is a bit jumbled, it is possible that it, too, had five fingers in vivo, like other monotremes. With only four fingers (Fig. 1) Fruitafossor had a good excuse for pretending to be an edentate.

So, yes, the LRT was up to the challenge.
But it took insight, lacking until now, to provide the correct matrix scoring. I’m happy to announce that the twenty or so corrections made yesterday were added to the 120,000 or so corrections made over the past ten years. With these corrections the LRT gets better and stronger every week. Minimizing taxon exclusion maximizes the opportunity to correctly nest new and enigma taxa with old and established taxa, even if the new and old specimens are incomplete or scattered about.

The earlier August 2017 blogpost for Fruitafossor
was updated yesterday to erase old errors and enter the corrections.

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References
Huttenlocker AD, Grossnickle DM, Kirkland JI, Schultz JA and Luo Z-X 2018. Late-surviving stem mammal links the lowermost Cretaceous of North America and Gondwana. Nature Letters  Link to Nature
Luo Z-X and Wible JR 2005. A late Jurassic digging mammal and early mammal diversification. Science 308:103–107.
Shaw G 1792. Musei Leveriani explicatio, anglica et latina.

wiki/Fruitafossor
digimorph.org/specimens/Fruitafossor_windscheffeli/

 

New genomic estimate misses monotreme-marsupial split by 43 million years

Summary for those in a hurry:
Fossils provide hard evidence. Deep time gene studies provide estimates and false positives too often to trust them.

Zhou et al. 2021 report:
“Our phylogenomic reconstruction shows that monotremes diverged from therians around 187 million years ago, and the two monotremes diverged around 55 million years ago. This estimate provides a date for the monotreme–therian split that is earlier than previous estimates (about 21 million years ago, but agrees with recent analyses of few genes and fossil evidence.”

Let’s stop putting our faith in estimates derived from genomic deep time studies that have proven themselves to be wrong too many times. Here, the Zhou et al. estimate is at least 43 million years too late (Fig. 2) based on Brasilitherium (Fig. 3) fossils and the tree topology recovered by the LRT (Fig. 1).

Figure 1. Subset of the LRT focusing on Metatheria (marsupials) including Paedotherium and Adalatherium.

By contrast with Zhou et al. 
Morganucodon (Late Triassic, 205mya, Fig. 4) is a basal marsupial in the large reptile tree (LRT, 1790+ taxa; subset Fig. 1) based on phenomic (= trait) analysis that includes fossil taxa. Genomic tests are infamous for false positives when dealing with deep time taxa.

Figure 2. Select basal cynodonts and mammals set chronologically. The divergence times for placentals (Eutheria), marsupials (Metatheria) and monotremes (Mammalia) are estimated here.

Brasilitherium,
(Figs. 3, 4) from the Early Norian, Late Triassic, 225mya, is a derived monotreme in the LRT. That means it lived AFTER the monotreme-therian split which must have occurred at least 230mya.

Figure 3. Brasilodon compared to Kuehneotherium, Akidolestes and Ornithorhynchus, the living platypus.

As everyone knows
the platypus and echidna are highly derived monotremes. Megazostrodon (Fig. 4) is the last common ancestor (LCA) of all monotremes and all mammals. Megazostrodon was a Late Jurassic late survivor of that earlier (Middle Triassic?) radiation.

Figure 4. Basal mammals and their proximal ancestors. Here taxa below Megazostrodon are mammals. Those above are not. Hadrocodium is uniquely reduced, but this occurs within the Mammalia.  The dual jaw joint was tentatively present in Pachygenelus.

According to the LRT,
there was no gradual ascent of monotremes leading to marsupials. Rather the monotreme-marsupial split occurred at the origin of mammals and monotremes. How this affects the genes for lactation discussed in the Zhou et al. paper is beyond the scope of this blogpost.

The purpose here
is to emphasize the importance of a broad, proper and valid phylogenetic context before proceeding to the narrow focus of your interests. 42 co-authors using cutting edge genomic techniques hobbled their otherwise excellent and in-depth report by skipping step number one.

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References
Zhou Z et al. (41 co-authors) 2021. Platypus and echidna genomes reveal mammalian biology and evolution. Nature https://doi.org/10.1038/s41586-020-03039-0

 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

wiki/Crown_group
wiki/Repenomamus
wiki/Priacodon

Triassic and Early Jurassic mammal metabolism

Summary, for those in a hurry:
Newham E et al. 2020 attempt to understand metabolic levels (endothermy) for basal mammals and pre-mammals. Unfortunately, the paper suffers from a traditional invalid cladogram in which the monotreme, Sinodelphys (Fig. 1), is portrayed as a marsupial and the marsupials, Morganucodon and Hadrocodium are portrayed as pre-mammals among other issues based on cherry-picking taxa (= taxon exclusion).

Figure 3. Skull and forelimbs of Sinodelphys in situ. Arrow shows the displacement of the entire hand that otherwise appears to be lost beyond the matrix. How fortuitous!

From the Newham et al. text:
“To estimate mammaliaform lifespans, we used cementochronology. This well-established technique, which counts annual growth increments in tooth-root cementum, has been used to record lifespans in extant mammals with >70 species aged using this technique. Despite this potential, cementochronology has not previously been attempted for fossil mammals older than the Pleistocene (2.6 Ma).”

“Only the short-beaked echidna Tachyglossus aculeatus, a monotreme with long lifespan and low metabolic rate, exceeds the distance above the mammalian mean for Kuehneotherium, but not for Morganucodon.” 

Kuehneotherium is a monotreme in the LRT. Morganucodon is a marsupial in the LRT. The keywords: “Ornithorhynchus” and “platypus” are not found in the text.

Morganucodon
(pre-mammal according to Newham et al., mammal according to LRT) has the following characters, according to Newham et al.:

1. “Single replacement of milk teeth, suggests maternal feeding while toothless via mammary gland
2. Improved olfaction and tactile sensitivity suggestive of nocturnality
3. Mandibular depth suggests determinate growth”

Hadrocodium
(pre-mammal according to Newham et al., mammal according to LRT)

1. “Encephalization quotient equivalent to extant mammals.”

Arboroharamiya
(gliding pre-mammal, Multituberculata,  according to Newham et al., gliding mammal (Glires, Carpolestidae) according to LRT).

Castorocauda
(proximal mammal outgroup found with full fur pelage according to Newham et al., but a sister to the much more basal cynodonts, Probainognathus and Chiniquodon in the LRT).

Sinodelphys
(marsupial according to Newham et al., basal monotreme according to the LRT).

Figure 4. Subset of the LRT cladogram of basal Mammalia. Note the traditional clade Metatheria is a grade with new names proposed here.

More from Newham et al. 2020:
“Despite considerable advances in knowledge of the anatomy, ecology and evolution of early mammals, far less is known about their physiology.”

Just the opposite. Newham et al. know more about their physiology than their evolution and interrelationships in the LRT.

“Evidence is contradictory concerning the timing and fossil groups in which mammalian endothermy arose.”

First fix the phylogeny.

“To determine the state of metabolic evolution in two of the earliest stem-mammals, the Early Jurassic Morganucodon and Kuehneotherium, we use separate proxies for basal and maximum metabolic rate. Here we report, using synchrotron X-ray tomographic imaging of incremental tooth cementum, that they had maximum lifespans considerably longer than comparably sized living mammals, but similar to those of reptiles, and so they likely had reptilian-level basal metabolic rates.”

Understood, but probably not the best way to say this, since mammals are reptiles in the LRT. Birds + dinosaurs and pterosaurs + fenestrasaurs likely also had high metabolic rates.

“Measurements of femoral nutrient foramina show Morganucodon had blood flow rates intermediate between living mammals and reptiles, suggesting maximum metabolic rates increased evolutionarily before basal metabolic rates.”

Morganucodon is a basal marsupial. The platypus also has an active mammalian-style lifestyle, but was not tested. Let’s not cherry-pick taxa.

Ornithorhynchus (platypus) metabolism: “Metabolism was 8% less than that of marsupials in general, and 35% lower than that of eutherian mammals.” (Grant and Dawson 1978, not cited in Newham et al. 2020). Note: that’s a bigger jump just between marsupials and placentals.

Figure 3. Subset of the LRT focusing on basal placentals, including multituberculates.

More from Newham et al. 2020:
“Stem mammals lacked the elevated endothermic metabolism of living mammals, highlighting the mosaic nature of mammalian physiological evolution.”

First fix the phylogeny. Nothing proceeds without a valid cladogram.

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References
Grant TR and Dawson TJ 1978. Temperature Regulation in the Platypus, Ornithorhynchus anatinus: Production and Loss of Metabolic Heat in Air and Water. Physiological Zoology 51(4):1–6. https://www.journals.uchicago.edu/doi/abs/10.1086/physzool.51.4.30160956
Newham E et al. (19 co-authors) 2020. Reptile-like physiology in Early Jurassic stem-mammals. Nature Communications 11, Article number: 5121
https://www.nature.com/articles/s41467-020-18898-4

News
https://www.bristol.ac.uk/news/2020/october/ancient-tiny-teeth.html

https://phys.org/news/2020-10-ancient-tiny-teeth-reveal-mammals.html

https://www.sciencetimes.com/articles/27672/20201012/200-million-year-old-first-mammals-lived-reptiles.htm

Célik and Phillips 2020 reshuffle basal mammal phylogeny by excluding traits (and taxa)

Célik and Phillips 2020 attempted to
understand the phylogenetic order of basal mammals by excluding traits. They wrote, “Excluding these character complexes brought agreement between anatomical regions and improved the confidence in tree topology.”

Those issues aside, taxon exclusion mars this study. 
The Célik and Phillips cladogram shuffled together unrelated taxa compared to the large reptile tree (LRT, 1737+ taxa). They cladogram (Fig. 1) mixed pre-mammals with placentals and marsupials chiefly due to taxon exclusion.

By employing so many taxa,
the LRT minimizes taxon exclusion and resolves such issues as the Multituberculata / Haramiyida problem. These taxa nest within Glires in the Placentalia in the LRT. Glires is not otherwise well represented in the Célik and Phillips cladogram.

Figure 1. Cladogram from Célik and Phillips 2020 with color overlay showing distribution of taxa in the LRT.

From the abstract
“The evolutionary history of Mesozoic mammaliaformes is well studied. Although the backbone of their phylogeny is well resolved, the placement of ecologically specialized groups has remained uncertain. Functional and developmental covariation has long been identified as an important source of phylogenetic error, yet combining incongruent morphological characters altogether is currently a common practice when reconstructing phylogenetic relationships.”

“Ignoring incongruence may inflate the confidence in reconstructing relationships, particularly for the placement of highly derived and ecologically specialized taxa, such as among australosphenidans (particularly, crown monotremes), haramiyidans, and multituberculates. The alternative placement of these highly derived clades can alter the taxonomic constituency and temporal origin of the mammalian crown group.”

“Based on prior hypotheses and correlated homoplasy analyses, we identified cheek teeth and shoulder girdle character complexes as having a high potential to introduce phylogenetic error.“

“We showed that incongruence among mandibulodental, cranial, and postcranial anatomical partitions for the placement of the australosphenidans, haramiyids, and multituberculates could largely be explained by apparently non-phylogenetic covariance from cheek teeth and shoulder girdle characters.”

Figure 3. Subset of the LRT focusing on basal placentals, including multituberculates.

Figure 4. Comparing multituberculate origins: Cziki-Sava et al. vs. LRT.

Based on results recovered in the LRT,
I encourage Célik and Phillips to rerun their analysis with a far larger taxon list. A gradual accumulation of derived traits that mirrors evolutionary events will appear whenever taxon exclusion is minimized.

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References
Célik MA and Phillips MJ 2020. Conflict Resolution for Mesozoic Mammals: Reconciling Phylogenetic Incongruence Among Anatomical Regions. Frontiers in Genetics 11: 0651
doi: 10.3389/fgene.2020.00651
https://www.frontiersin.org/articles/10.3389/fgene.2020.00651/full

From Berkeley: 3 more evograms updated

Yesterday we updated an online evogram
produced by the University of California – Berkeley under the tutelage of Professor Emeritus Kevin Padian. Today a few remaining evograms get similar updates.

Figure 1. Evogram from the Berkeley website focusing on bird origins.

The Berkeley evogram on bird origins
(Fig. 1) closely matches that of the large reptile tree (LRT, 1710+ taxa). Only two corrections include: Eoraptor is a basal phytodinosaur, not a theropod. The caption on tyrannosauroids is, “Reduction of III“, but the illustration does not show a reduction of digit 3.

Figure 2. Evogram from the Berkeley website focusing on mammal origins.

The Berkeley evogram on mammal origins
(Fig. 2) mistakenly puts Yanaconodon close to eutherians. By contrast the LRT nests Yanaconodon in a pre-mammal clade. There is no need to add the highly derived Dimetrodon to a pre-mammal cladogram. It left no descendants. Haptodus is a more primitive, more plesiomorphic choice here. We are its descendants. Likewise, the platypus (Ornithorhynchus) is also highly derived. Better to put a basal prototherian, like Sinodelphys or Megazostrodon, in its place. We are their descendants. Duckbilled platypusses are not plesiomorphic nor ancestral to any other mammal.

Figure 3. Evogram from the Berkeley website focusing on tetrapod origins. This is similar to an evogram found in Padian 2013.

The Berkeley evogram on tetrapod origins
(Fig. 3) includes Eusthenopteron, which left no descendants in the LRT. Flatter Cabonnichthys is a better ancestor. Flattened Tiktaalik and Panderichthys switch places here. The latter has four proto-fingers. Ichthyostega and Acanthostega have supernumerary digits and leave no descendants in the LRT. Here flatter basal tetrapods, like Greererpeton, have a skull, body, limbs and fingers more like those of Panderichthys. Dendrerpeton has a shorter torso and longer limbs. Even more so does Gephyrostegus. The loss of lumbar ribs makes room for more and larger amniotic eggs. Contrary to its original description, Tulerpeton does not have supernumerary digits. Gephyrostegus is a more completely known representative reptilomorph. Rather than make the huge morphological jump to Homo, represented here (Fig. 3) by Darwin himself, another living reptile, Iguana, enters the evogram with fewer changes to distinguish it from Gephyrostegus. Smaller steps mark the gradual progress of evolution. Big jumps, like adding Darwin (even as a joke), throw the whole concept into a tizzy. A similar evogram was published in Padian 2013, a paper ironically entitled, “Correcting some common misrepresentations of evolution in textbooks and the media.”

By minimizing taxon exclusion
the LRT does not make the mistakes shown above (Figs. 1-3) in the Berkeley evograms. Due to its large taxon list, the LRT more clearly documents the gradual accumulation of traits that characterizes every evolving vertebrate, and it does so while testing all competing candidates.

Let Kevin Padian at Berkeley know:
It’s time to update those online evograms!

This just in
An email from Anna Thanukos at the UC Museum of Paleontology, “Hi David,  Thanks for your interest in our site.  I wanted to let you know that the material on the page of interest has recently been reviewed by a curator at the Smithsonian and will be updated in a website revamp we are currently developing. Best regards, Anna Thanukos, UC Museum of Paleontology.”

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References
Padian K 2013.  Correcting some common misrepresentations of evolution in textbooks and the media.  Evolution Education and Outreach 6: 1-13.

https://evolution.berkeley.edu/evolibrary/article/evograms_02

https://evolution.berkeley.edu/evolibrary/article/evograms_03

https://evolution.berkeley.edu/evolibrary/article/evograms_04

https://evolution.berkeley.edu/evolibrary/article/evograms_05

https://evolution.berkeley.edu/evolibrary/article/evograms_06

https://evolution.berkeley.edu/evolibrary/article/evograms_07

 

Adelobasileus restored: NOT ‘the oldest mammal’

When Lucas and Hunt 1990
and Lucas and Luo 1993 described the cranium (all that is known) of Adelobasileus (Fig. 1) they concluded it was, ‘the oldest mammal’. 

Figure 1. Adelobasileus restored like Therioherpeton after first nesting together in the LRT. Line drawing for Adelobasileus from Lucas and Luo 1993.

By contrast
the large reptile tree (LRT, 1707+ taxa, subset Fig. x) nests Adelobasileus with the low and wide mammal-mimic cynodont, Therioherpeton (Fig. 1), despite the very few characters that could be scored here. Both also nest with Sinocodon and Haramiyavia in the LRT. Thus Adelobasileus in not the oldest mammal. It is not even a mammal.

Therioherpeton
Fig. 1) was originally described by Bonaparte and Barberena 1975 as ‘a possible mammal ancestor’.

Later
Oliveira 2006 reevaluated Therioherpeton. “Therioherpetidae are distinguished from all other probainognathians by upper teeth with the imbrication angle increasing in the posterior postcanines. In addition, upper and lower postcanine teeth are labio-lingually narrow.” This author did not include Adelobasileus in his cladogram. Oliveira nested Therioherpeton with Riograndia.

Figure 2. Megazostrodon skull in several views. Drawings from Gow 1986. Colors applied here. This is the last common ancestor of all mammals in the LRT.

The last common ancestor of all mammals
in the LRT (subset Fig. x) continues to be Megazostrodon (Fig. 2), from the early Jurassic. Other, more derived mammals, like Morganucodon, are found in the Late Triassic, indicating an earlier origin and radiation.

Figure x. Subset of the LRT focusing on therapsids leading to mammals. Adelobasileus nests with Therioherpeton in this older cladogram that does not list Adelobasileus.

The most recent paper on basal mammals
and their immediate ancestors, King and Beck 2020, shows just how different cladograms can be when taxa are excluded (Fig. 3, click to enlarge). King and Beck mix non-mammals with prototherians, metatherians and eutherians in a mish-mash as compared to the LRT (Fig. x). At least they nest Adelobasileus outside their Mammalia (which should include only Prototherians, Metatherians and all descendants of their last common ancestor, Megazostrodon, Fig. 2).

Figure 3. Click to enlarge. Stem mammal cladogram from King and Beck 2020 showing how different their topology is to the LRT (color overlays, key at left) which has a wider gamut of included taxa. Arrow points to Adelobasileus near top.

Add taxa 
and multituberculates nest with rodents and other taxa nest appropriately with prototherians, metatherians and eutherians as shown in the LRT (subset Fig. x).

The nesting of Adeolbasileus with Therioherpeton
is not quite an original hypotheses. Google the two keywords, “Adelobasileus, Therioherpeton” and you’ll find someone tweeted these two as possible ancestor-descendant taxa, but unfortunately, still considered Adelobasilesus ‘the oldest mammal.’

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References
Bonaparte JF and Barberena MC 1975. A possible mammalian ancestor from the Middle Triassic of Brazil (Therapsida–Cynodontia). Journal of Paleontology 49:931–936.
King and Beck 2020. Tip dating supports novel resolutions of controversial relationships among early mammals. Proceedings of the Royal Society B 287: 20200943.
http://dx.doi.org/10.1098/rspb.2020.0943
Lucas SG and Hunt 1990. The oldest mammal. New Mexico Journal of Science 30(1):41–49.
Lucas SG and Luo Z 1993. Adelobasileus from the upper Triassic of west Texas: the oldest mammal. Journal of Vertebrate Paleontology 13(3):309–334.
Oliveira EV 2006. Reevaluation of Therioherpeton cargnini Bonaparte & Barberena, 1975 (Probainognathia, Therioherpetidae) from the Upper Triassic of Brazil. Geodiversitas 28 (3): 447-465.

http://reptileevolution.com/sinoconodon.htm
wiki/Adelobasileus
wiki/Therioherpeton

Two papers in one: Haramiyidans and Juramaia

Part 1: King and Beck 2020
bring us their views (again), on ‘early mammal relationships‘. Let’s see how they stack up (again) against the validated (thanks to taxon inclusion) results of the large reptile tree (LRT, 1697+ taxa).

From their abstract:
“Many phylogenetic analyses have placed haramiyidans in a clade with multituberculates within crown Mammalia, thus extending the minimum divergence date for the crown group deep into the Triassic. Here, we apply Bayesian tip-dated phylogenetic methods [definition below] to investigate these issues. Tip dating firmly rejects a monophyletic Allotheria (multituberculates and haramiyidans), which are split into three separate clades, a result not found in any previous analysis. Most notably, the Late Triassic Haramiyavia and Thomasia are separate from the Middle Jurassic euharamiyidans.”

Bayesian tip-dated phylogenetic methods = online definition here.

You heard it here first
Earlier (2016) the LRT rejected a monophyletic Allotheria (separating Haramiavia (Fig. 1) and Thomasia), from Megaconus and all the multituberculates (Fig. 2). Haramiavia and Thomasia nest as pre-mammal synapsids (tritylodontids), not far from Pachygenelus. Several dozen nodes away, Megaconus and the multis nest within the placental clade Glires, at a node more highly derived than tree shrews, rodents and rabbits. So far that hypothesis of relationships has not been tested by other workers, despite several invitations to expand their taxon lists.

Figure 1. Haramiyava dentary showing what a more typical stem mammal dentary and teeth look like. Earlier studies linked this clade to multituberculates, but this dentary was cause to reject that association.

According to King and Beck 2020,
“Our analysis places Haramiyavia and Thomasia in a clade with tritylodontids, a result that may be the result of insufficient sampling of non-mammaliaform cynodont characters and taxa, and which we consider in need of further testing (see detailed discussion in the electronic supplementary material).” This confirms relationships first recovered by the LRT.

Figure 2. LRT taxa in the lineage of multituberculates arising from Carpolestes and Paulchoffatia.

The authors continue,
“Our focal dataset was taken from Huttenlocker et al. 2018, which comprises 538 morphological characters scored for 125 mammaliaforms and non-mammaliaform cynodonts.

Unfortunately,
as I mentioned earlier, King and Beck still need to include extant mammals, like montoremes, marsupials, rodents and Daubentonia, rather than rely on fossil taxa exclusively. (See below).

Figure 3. Subset of the LRT focusing on Glires and subclades within.

Part 2: King and Beck 2020 report:
“A second taxon of interest is the eutherian Juramaia (Fig. 4) from the Middle–Late Jurassic Yanliao Biota, which is morphologically very similar to eutherians from the Early Cretaceous Jehol Biota and implies a very early origin for therian mammals. We also test whether the Middle– Late Jurassic age of Juramaia is ‘expected’ given its known morphology by assigning an age prior without hard bounds. Strikingly, this analysis supports an Early Cretaceous age for Juramaia, but similar analyses on 12 other mammaliaforms from the Yanliao Biota return the correct, Jurassic age.”

Figure 4. Juramaia (Late Jurassic, 160 mya) is more completely known and nests between monotremes and therians (marsupials + placentals).

By contrast In the LRT,
Juramaia is a basal protorothere, nesting between Megazostrodon + Sinodelphys and Chaoyangodens, all basal to the extant platypus and echidna in the LRT. Beck and King omit so many key taxa that they do not recover Prototheria, Metatheria and Eutheria.

The same authors publishing on a similar topic in 2019
were reviewed here. The following is one paragraph from that review: King and Beck 2019 bring us a new phylogenetic analysis restricted to Mesozoic mammals. This represents a massive case of taxon exclusion of basal mammals as demonstrated earlier here, because so many basal mammals are still alive! Think of all the tree shrews, arboreal didelphids, and nearly every little creeping taxon in Glires that nest basal to known Mesozoic mammals. You cannot restrict the taxon list to just those extremely rare Mesozoic mammals.

Colleagues: Please use extant mammals in your analyses!
They are guaranteed complete and articulated with soft tissues and gut contents. Figure out your cladogram with as many of these complete specimens as possible. Then… start adding crushed, incomplete and disarticulated fossil taxa. In other words, give yourself a basic education first. Establish a valid tree topology first. Don’t muddle through your studies with questionable traits based on fractured mandibles missing several teeth. As longtime readers know, a valid phylogenetic context is paramount for all further studies.

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References
Huttenlocker AK, Grossnickle DM, Kirkland JI, Schultz JA and Luo Z-X 2018. Late-surviving stem mammal links the lowermost Cretaceous of North America and Gondwana. Nature 558, 108–112. 8. (doi:10.1038/s41586-018-0126-y);
King B and Beck R 2019. Bayesian Tip-dated Phylogenetics: Topological Effects, Stratigraphic Fit and the Early Evolution of Mammals. PeerJ
doi: http://dx.doi.org/10.1101/533885.
King B and Beck RMD 2020. Tip dating supports novel resolutions of controversial relationships among early mammals. Proceedings of the Royal Society B 287: 20200943. http://dx.doi.org/10.1098/rspb.2020.0943

https://pterosaurheresies.wordpress.com/2019/02/07/taxon-exclusion-mars-mesozoic-mammal-study/

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.

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.

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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

https://www.biorxiv.org/content/10.1101/2019.12.19.882829v1.full.pdf