Taxon exclusion mars 2020 study of evolutionary innovation in reptiles

Simões et al. 2020 present
their vision of phenotypic diversity in reptiles (Fig. 1).

Unfortunately they do so
without knowing the last common ancestor of reptiles (Silvanerpeton) and the basal dichotomy of reptiles, both of which lead to a complete misunderstanding of the main branches in the phylogeny of reptiles. That lack of taxa led to a shuffling of the two major clades in the LRT, the new Archosauromorpha and the new Lepidosauromorpha.

For instance,
Simões et al. have no idea that ‘Diapsida’ is an invalid clade, unless restricted to only Archosauromorpha. Lepidosauriformes are the lepidosaur branch of the former ‘Diapsida’. Their figure 3 cladogram of the Lepidosauria omits Tritosauria and flips the order, nesting Iguania as a derived clade, rather than the basal clade it is in the LRT.

The large reptile tree (LRT) with 1746+ taxa remains the overlooked standard by which all smaller studies can be measured for no other reason that it includes more taxa. In the LRT phylogenetic miniaturization occurred at the genesis of many evolutionary novelties. This factor was overlooked in Simões et al. 2020 due to taxon exclusion.

Figure 1. Cladogram from Simoes et al. 2020 suffering from so much taxon exclusion that Archosauromorpha are shuffled within Lepidosauromorpha.

The Simões et al. plan:
“Here, we explore megaevolutionary dynamics on phenotypic and molecular evolution during two fundamental periods of reptile evolution: (i) the origin and early diversification of the major lineages of diapsid reptiles (lizards, snakes, tuataras, turtles, archosaurs, marine reptiles, among others) during the Permian and Triassic periods, and (ii) the origin and evolution of lepidosaurs (lizards, snakes and tuataras) from the Jurassic to the present.”

Lacking pertinent taxa, Simões et al. mistakenly place turtles in diapsids and do not include pterosaurs, rhynchosaurs and tanystropheids in lepidosaurs.

Simões et al. conclude:
“Collectively, our findings suggest a considerably more complex scenario concerning the evolution of reptiles in deep time than previously thought.”

Without a proper phylogenetic context
anything this study presents is suspect or invalid from the get-go. Bring back your math, your charts, your statistics after you have a wide gamut, comprehensive cladogram with proper outgroup taxa, a working last common ancestor and valid branching thereafter, as in the LRT.

Colleagues:
add more taxa. That will expand, clarify and validate your cladograms.

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References
Simões TR, Vernygora O, Caldwell MW and Pierce SE 2020. Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles. Nature 11:3322  https://doi.org/10.1038/s41467-020-17190-9 http://www.nature.com/naturecommunications

New paper on Eldeceeon, one of our earliest reptile ancestors

Ruta, Clack and Smithson 2020
bring us new two new specimens of the amphibian-like reptile, Eldeceeon (pronounced ‘L-D-C-on’, Smithson 1994; Viséan, 335mya), adding to the two previously described specimens (Fig. 1). These two are the basalmost taxa in the Archosauromorpha in the large reptile tree (LRT, 1725+ taxa, subset Figs. 4, 5). The authors confirm a relationship to Silvanerpeton (Fig. 2), the last common ancestor of all reptiles in the LRT. They share a deep pelvis for large egg laying and a large lumbar region  for egg-carrying in females. This trait is shared with males unless all specimens around this node found so far are all females.

Figure 1. The two earlier specimens attributed to Eldeceeon that nest together at the base of the Archosauromorpha. Note the extended lumbar region and deep pelvis ideal for laying large eggs on both specimens.

Unfortunately, 
the authors consider these taxa “either as the most plesiomorphic stem amniote clade or as a clade immediately crownward of anthracosauroids.” 

They didn’t test enough taxa to nest Elcedeceeon and Silvanerpeton as basal amniotes (= reptiles), nor did they test enough taxa to recover a basal dichotomy in the Viséan at the base of the Reptilia. One branch, the Archosauromorpha, gives rise to synapsids and non-lepidosaur diapsids. At its base, Eldeceeon is an amphibian-like reptile that laid (by phylogenetic bracketing) amniotic eggs.

From the abstract:
“A detailed account of individual skull bones and a revision of key axial and appendicular features are provided, alongside the first complete reconstructions of the skull and lower jaw and a revised reconstruction of the postcranial skeleton.”

Actually those first complete reconstructions were done here in 2014. Worse yet, the authors created by freehand one chimaera reconstruction (their figure 7e), not appreciating the distinctions between the two previously known specimens (Fig. 1).

From the abstract
“The late Viséan anthracosauroid Eldeceeon rolfei from the East Kirkton Limestone of Scotland is re-described. Information from two originally described and two newly identified specimens broadens our knowledge of this tetrapod. 

Figure 2. Four cladograms from Ruta, Clack and Smithson 2020 seeking a nesting place for included taxa. Compare to Figure 4, a subset of the LRT. They need more outgroup taxa to solve their self-confessed phylogenetic problems.

From the Discussion
“The most vexing aspect of the Eldeceeon postcranium is the configuration of its rib cage, with long and curved ribs confined to the anterior half of its trunk. We hypothesise that the space between the most posterior trunk ribs and the pelvis was occupied by an unusually large puboischiofemoralis internus 2 (PIFI2).”

All basal amniotes have this sort of lumbar region. Gravid lizards use this space to carry eggs (Fig. 3). Ruta, Clack and Smithson overlook this possibility because their cladograms (Fig. 2) do not nest Eldeceeon and kin among the reptiles.

Figure 3. Extant lizards, A. gravid, B. in the process of laying eggs, C. with egg clutch.

In the LRT Anthracosaurus
(Fig. 4) nests far from Eldeceeon (Fig. 5), Silvanerpeton, Gephyrostegus and other stem reptiles (= Reptilomorpha). Anthracosaurus nests in the same basal tetrapod clade as Ichthyostega and Proterogyrinus in the LRT. So taxon exclusion has mixed up the order of taxa in the cladogram of Ruta, Clack and Smithson 2020. More taxa solve such phylogenetic problems.

Other taxa are also adversely affected by taxon exclusion.
Ruta, Clack and Smithson report, “Eucritta melanolimnetes Clack, 1998 shares characters with groups as diverse as baphetids, temnospondyls, and anthracosaurs (Clack 2001); perhaps unsurprisingly, this combination of features has resulted in alternative phylogenetic placements for this taxon, either as a derived stem tetrapod or as a basal crown tetrapod shifting between alternate positions on either side of the lissamphibian–amniote dichotomy”. In the LRT (subset Fig. 2) Eucritta is a sister to Tulerpeton, the proximal outgroup clade to the Amniota + Gephyrostegus, which may be an amniote, too. It is the proximal outgroup to the Amniota in the LRT and includes all of the basal amniote traits.

Figure 4. Subset of the LRT focusing on basal tetrapods. Colors indicate number of fingers known. Many taxa do not preserve manual digits. Eldeceeon arises after Silvanerpeton. Compare to cladograms in figure 2.

Eldeceeon rolfei (Smithson 1994) ~27 cm in total length, Early Carboniferous ~335 mya, is from the same formation that yielded Silvanerpeton and Westlothiana in the Viséan. Derived from a sister to Tulerpeton, Eldeceeon was basal to Diplovertebron and Solenodonsaurus in the LRT (Fig. 5). Relative to G. bohemicus, the skull of Eldeceeon was shorter and taller. The dorsal ribs are missing from the posterior half of the torso. This is an adaption to carrying larger eggs in gravid females. The pectoral girdle was more gracile. yet still deep. These two specimens nest together, but are distinct enough to warrant distinct species names.

Figure 5. Subset of the LRTfrom 2019 focusing on basal Archosauromorpha including Vaughnictis and Cabarzia nesting at the base of the Protodiapsid-Synapsid split. Note all the large varanopids nest together here in the Synapsida, separate from small varanopids in the Protodiapsida.

Add taxa
to see the big picture. That always solves problems. Taxon exclusion continues to be the number one problem in paleontology.

Don’t create reconstruction chimaeras.
That never works out well. Too often the chimaera is created freehand.

The LRT is free, online and worldwide,
just so workers can check out the current list of sister taxa pertinent to any taxon under study. Someday it will be used. Not this time, but someday.

More on Anthracosaurus
and the traditional clade ‘Anthracosauria’ follows below the References. This clade turns out to be much smaller than current textbooks and lectures might indicate. Anthracosaurus is a terminal taxon leaving no descendants tested in the LRT.

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References
Ruta M, Clack JA and Smithson TR 2020. A review of the stem amniote Eldeceeon rolfei from the Viséan of East Kirkton, Scotland. Earth and Environmental Science Transactions of The Royal Society of Edinburgh (advance online publication)
DOI: https://doi.org/10.1017/S1755691020000079
Smithson TR 1994. Eldeceeon rolfei, a new reptiliomorph from the Viséan of East Kirkton, West Lothian, Scotland. Transactions of the Royal Society of Edinburgh: Earth Sciences 84 (3-4): 377–382.

wiki/Eldeceeon

Figure 3. The complete skull of Anthracosaurus greatly resembles its relative, Neopteroplax. These are basal flathead taxa with orbits high on the skull, distinct from reptilomorphs with smaller skulls and lateral orbits.

https://en.wikipedia.org/wiki/Anthracosauria
“Anthracosauria” is sometimes used to refer to all tetrapods more closely related to amniotes such as reptiles, mammals, and birds, rather than lissamphibians such as frogs and salamanders. An equivalent term to this definition would be Reptiliomorpha. Anthracosauria has also been used to refer to a smaller group of large, crocodilian-like aquatic tetrapods also known as embolomeres.

Gauthier, Kluge and Rowe (1988) defined Anthracosauria as a clade including “Amniota plus all other tetrapods that are more closely related to amniotes than they are to amphibians” (Amphibia in turn was defined by these authors as a clade including Lissamphibia and those tetrapods that are more closely related to lissamphibians than they are to amniotes).

Similarly, Michel Laurin (1996) uses the term in a cladistic sense to refer to only the most advanced reptile-like amphibians. Thus his definition includes Diadectomorpha, Solenodonsauridae and the amniotes.

Laurin (2001) created a different phylogenetic definition of Anthracosauria, defining it as “the largest clade that includes Anthracosaurus russelli but not Ascaphus true“. [Ascaphus is the extant tailed frog.]

Michael Benton (2000, 2004) makes the anthracosaurs a paraphyletic order within the superorder Reptiliomorpha, along with the orders Seymouriamorpha and Diadectomorpha, thus making the Anthracosaurians the “lower” reptile-like amphibians. In his definition, the group encompass the Embolomeri, Chroniosuchia and possibly the family Gephyrostegidae.

None of these apply to Anthrosaurus in the LRT.

Distinct from prior authors, the LRT recovers Limnoscelis, Diadectes and other diadectomorphs deep with the Lepidosauromorpha branch of the Reptilia. More taxa solved this problem, too.

Several book reviews for ‘The Rise of the Reptiles’ by H-D Sues 2019

A new book on evolution,
‘The Rise of Reptiles’ (left), came out last August 2019. Unfortunately, it took this long to come to my attention.  After a short bio on author, Dr. Hans-Dieter Sues, several reviews follow.

According to Amazon.com, author Hans-Dieter Sues is 
“a senior scientist and curator of fossil vertebrates at the Smithsonian’s National Museum of Natural History. He is a coauthor of Triassic Life on Land: The Great Transition.”

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Amazon.com called ‘The Rise of the Reptiles’,
“The defining masterwork on the evolution of reptiles.”

John Long, Finders University, called it,
“A valuable reference book―entertaining read and beautifully illustrated―about how reptiles first evolved and diversified into many lineages, including the one leading to us mammals. The Rise of Reptiles is essential reading for every evolutionary biologist.”

Michael J. Benton, University of Bristol, reported,
“The writing style is clear and easy, the illustrations are excellent, and the whole design and print quality highly attractive. There is no other book like it, and this will stand as a useful reference for many years.”

Jeremy B. Stout, Quarterly Review of Biology, called it, 
“The most complete and current compendiumon reptilian evolution and diversity to date… Few (if any) are better suited to have written this volume than Sues. His impressive research record over the past 40 years has dealt directly with many of the taxonomic groups in this volume, including (nonreptile) synapsids, parareptiles, sauropterygians, crocodylomorphs, and dinosaurs.”

After scientifically testing the various hypotheses put forth by Sues
in the Large Reptile Tree (LRT, 1680+ taxa) his book was found to promote many of the traditional myths and misconceptions that have befuddled reptile cladograms for the past decade. Virtually all of the problems in ‘The Rise of the Reptiles’ can be attributed to too few taxa in the various cited phylogenetic analyses.

Starting with outgroups, Sues reports,
“The group generally considered most closely related to amniotes is Diadectomorpha.” He cites papers from 1980, 2003 and 2007.

Using the last common ancestor method, the tested out-group to the clade Reptilia in the LRT (2020) is the Reptilomorpha. This clade includes the long-limbed taxon, Gephyrostegus, a late survivor from an earlier, probably Late Devonian, radiation. When more taxa are added diadectomorphs nest well within the Lepidosauromorpha branch of the Reptilia (Fig. 5), contra Sues 2019.

Dr. Sues “Pulls a Larry Martin” when he reports
on a few traits he notes are present in his short list of stem-amniote ‘outgroups’.

Those outgroups (diadectomorphs, which are ingroups in the LRT) were gleaned from old studies. Look what happens when you don’t have the correct outgroups and correct last common ancestors. The traits you observe are going to be wrong because you’re not even looking at the correct node. Never rely on a few traits to define a clade. Always rely on the ‘last common ancestor’ method to determine clade membership. And don’t exclude pertinent taxa!

Figure 2. “Classification” of reptiles according to Sues 2019. Color overlay note differences when more taxa are added, as in the LRT.

Sues reported on ‘the oldest known reptile, Hylonomus‘ 323-315mya,
but that was based on a pre-cladistic 1964 study. Sues then hedged that ‘undisputed’ report with two ‘recent phylogenetic analyses’ (1988 and 2006) that, “instead found these taxa [Hylonomus + Palaeothyris] closely related to diapsid reptiles.”

Using the last common ancestor method, the oldest known reptile in the LRT (2020) is Silvarnerpeton (346-323 mya). No hedging required here. All descendants laid amniotic eggs.

Figure 3. Reptilia vs. Amniota in Sues 2019 compared to the LRT.

Sues cites Tsuji and Müller (2009) who defined ‘Parareptilia’ as
“the most inclusive clade containing Milleretta and Procolophon, but not Captorhinus” and that clade includes such diverse taxa as mesosaurs and pareiasaurs (Fig. 4).

If those two are related, that’s a Red Flag. In the LRT mesosaurs nest with similar pachypleurosaurs and other marine diapsids. Pareiasaurs give rise to turtles. As defined, the clade ‘Parareptilia’ is paraphyletic at worst, and a junior synonym of Reptilia at best in the LRT, which includes a wider gamut of taxa.

Figure 4. Parareptilia according to Sues 2019.

Similar problems
attend the cladogram of ‘Eureptilia’ in Sues 2019 (Fig. 6).

More taxa solve this problem, too.

Figure 5. Simplified cladogram of the Reptilia according to Sues 2019 (below in white) compared to a simplified version of the LRT using the same taxa. More taxa reveal an earlier dichotomy that creates two diapsid-grade skull morphologies. 

Dr. Sues has no idea how reptiles diverged
from their Viséan (or earlier) initial radiation. This could have been repaired if he had simply added taxa to his own analysis, rather than relying on published academic papers published decades ago with the same flaws.

Figure 6. The ‘Eureptilia’ according to Sues 2019. This is a paraphyletic clade when more taxa are included, as in the LRT. Since the invalid clade ‘Sauria’ includes lepidosaurs and archosaurs it is half colored blue.

Other than cladograms, Sues 2019
also presents photos and diagrams (Fig. 7). Unfortunately some diagrams don’t match the fossils, leading to confusion at best.

Figure 7. Figure from Sues 2019 showing Youngina capensis and a diagram of the same, that does not match the fossil. DGS color overlay added for comparison. What is the specimen number for this specimen?

Exposing and overturning old and new reptile mythology
is what PterosaurHeresies.Wordpress.com is all about as it supports the website www.ReptileEvolution.com and its centerpiece, the growing online cladogram at: www.ReptileEvolution.com/reptile-tree.htm. A wide-gamut cladogram is a powerful tool providing evidence against invalid traditional hypotheses that exclude pertinent taxa.

I cannot recommend this book.

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References
Sues HD 2019. The Rise of Reptiles: 320 Million Years of Evolution.
Johns Hopkins University Press, Baltimore. xiii + 385 p.; ill.; index.
ISBN: 9781421428673 (hc); 9781421428680 (eb).

 

In memoriam: Professor Jennifer Clack

If you never met her,
here’s your second chance, via YouTube videos.

This week marks the passing of Professor Jennifer Clack (1947-2020),
a renown specialist in Devonian tetrapods, especially Acanthostega (Fig. 1). In the above 4-minute YouTube video from 2017, Clack introduces her concept that the first tetrapods, like her discovery of Acanthostega, had more than five manual digits. This is confirmed by Middle Devonian tetrapod tracks (Fig. 3) with more than five digits.

Figure 1. Acanthostega does not have much of a neck. Note the narrow torso, taller than wide, distinct from lobefin fish that phylogenetically led to basal tetrapods, like Trypanognathus in figure 4.

But not
according to the large reptile tree (LRT) which recovers Acanthostega as a terminal taxon, not a transitional one, far from the main line of tetrapod origins. Four digits are found in Panderichthys, Greererpeton and many other basal tetrapods, as we learned earlier here, here and here. More than five digits are found in only a few derived taxa, including the stem reptile, Tulerpeton, far from the origin of digits.

A more complete and technical account
of basal tetrapod traits is provided by Clack in this 20-minute YouTube lecture video from 2016 (above).

It may be that Clack only saw evolutionary progress
without considering the possibility of evolutionary reversal, as happens when taxa return to a more aquatic niche from a less aquatic niche, reducing the importance of their digits and limbs. In the above video, Clack does not provide a phylogenetic analysis, like the LRT (subset Fig. 2) that includes more primitive, but late-surviving basal tetrapods, all of which follow the pattern of a wider than deep torso, as in ancestral fish with embedded arm bones in their lobefins. Rather, she concentrates on individual traits, which while valuable, set her up for ‘Pulling a Larry Martin‘, rather than concentrating efforts on determining a phylogeny that minimizes taxon exclusion and lets the software determine (= mirror) evolutionary events, as the LRT does while minimizing taxon inclusion bias.

Figure 2. Subset of the LRT focusing on basal tetrapods. Note the displaced positions of Acanthostega and Ichthyostega.

Only after a phylogeny is documented and validated
can one then discuss the various traits and their uses by the creature that possessed them.

Lest we forget
the first tetrapod tracks (Fig. 1, Niedźwiedzki et al. 2010) predate fossil tetrapods, including Acanthostega, by 20 to 30 million years, as we looked at here. And even they had more than five toes. Thus the phylogenetic origin of tetrapods goes back even further. The early Devonian must have provided quite a few niches for such rapid evolution to take place.

Figure 3. Best Devonian Valentia track with various overlays.

We need to look more closely at
Trypanognathus (Fig. 4; latest Carboniferous), which is the most primitive, but by far not the earliest, taxon in the LRT to document fingers and limbs, rather than lobe fins. Note the anterior eyes, wide flat skull and body, and primitive sprawling limbs. Can someone count the fingers and toes on this specimen? I find no more than four digits. Some may be hiding here.

Figure 4. Trypanognathus in situ, colorized to bring out ribs and limbs is the most primitive, but not the earliest taxon with limbs and toes, not lobe fins.

We’ve seen the chronology of several fossil finds
at odds with their phylogeny in the LRT (e.g. multituberculates, bats, Gregorius). That keeps it interesting, but only a wide gamut phylogenetic analysis based on traits will deliver a valid tree topology. As time goes by and more discoveries are made the competing hypotheses will someday converge.

Figure 5. Silvanerpeton from the Upper Viséan (331 mya) is the outgroup taxon for Gephyrostegus and the Amniota.

And one more thing,
Clack 1994 described Silvanerpeton (Fig. 5, Viséan, 335 mya) first as an anthrcosauroid and later (Ruta and Clack 2006) as a stem tetrapod, all without recovering it as the basalmost reptile, as shown in the LRT. Adding taxa, creating a wider gamut phylogenetic analysis, would have brought even more fame to this well-respected paleontologist.

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References
Clack JA 1994. Silvanerpeton miripedes, a new anthracosauroid from the Visean of East Kirkton, West Lothian, Scotland. Transactions of the Royal Society of Edinburgh: Earth Sciences 84 (for 1993), 369–76.
Niedźwiedzki G, Szrek P, Narkiewicz K, Narkiewicz M and Ahlberg PE 2010. Tetrapod trackways from the early Middle Devonian period of Poland Nature 463, 43-48. doi:10.1038/nature08623
Ruta M and Clack, JA 2006 A review of Silvanerpeton miripedes, a stem amniote from the Lower Carboniferous of East Kirkton, West Lothian, Scotland. Transactions of the Royal Society of Edinburgh: Earth Sciences, 97, 31-63.

https://www.zoo.cam.ac.uk/news/professor-jenny-clack-frs-1947-2020

http://www.theclacks.org.uk/jac/Biography.html

https://www.pbs.org/wgbh/nova/link/clack.html
(make sure to click on the parts 2-4 links therein)

 

The affinities of ‘Parareptilia’ and ‘Varanopidae’: Ford and Benson 2020

Readers will know the knives are out for this one
by Ford and Benson 2020 since the large reptile tree (LRT, 1625+ taxa) finds the Parareptilia is polyphyletic and the Varanopidae (1940) is a junior synonym for Synapsida (1903). And yes, Ford and Benson’s cladogram (Fig. 1) suffers from (altogether now): taxon exclusion. The Ford and Benson paper, like many before it, keeps perpetuating the myth of the Parareptilia and other traditional clades.

Figure 1. Cladogram by Ford and Benson 2020, with orange overlay showing taxa in the Archosauromorpha in the LRT. Massive taxon exclusion is the problem with the Ford and Benson tree.

From the abstract:
“Amniotes include mammals, reptiles and birds, representing 75% of extant vertebrate species on land. They originated around 318 million years ago in the early Late Carboniferous and their early fossil record is central to understanding the expansion of vertebrates in terrestrial ecosystems.

By contrast, in the LRT the last common ancestor of all amniotes (= reptiles) is Silvanerpeton from the Viséan (Early Carbonferous, 335mya, not listed in Fig. 1) with a likely genesis earlier since the Viséan includes several other  amphibian-like reptiles, also not listed. Ford and Benson need to dip much deeper into the basal Tetrapoda to figure out which taxon is the last common ancestor of the Amniota and which taxa precede it. They make the mistake of considering Tseajaia and Limnoscelis pre-amniotes.The LRT nests them both deep within Amniota / Reptilia.

“We present a phylogenetic hypothesis that challenges the widely accepted consensus about early amniote evolution, based on parsimony analysis and Bayesian inference of a new morphological dataset.”

That would be great, so long as they include pertinent taxa, which they do not.

“We find a reduced membership of the mammalian stem lineage, which excludes varanopids.”

That’s odd because when you add pertinent taxa, the LRT finds an increased membership in the diapsid/mammal stem lineage, the new Archosauromorpha.

“This implies that evolutionary turnover of the mammalian stem lineage during the Early–Middle Permian transition (273 million years ago) was more abrupt than has previously been recognized.”

No one can make valid implications from the Ford and Benson cladogram. It is largely incomplete.

“We also find that Parareptilia are nested within Diapsida.”

This is only possible due to massive taxon exclusion. Ford and Benson omit many taxa that would change the topology of their tree. The Parareptilia include a diverse and polyphyletic assembly of taxa according to the LRT. Ford and Benson are not aware that Lepidosauria are no longer members of the archosauromorph Diapsida.

“This suggests that temporal fenestration, a key structural innovation with important functional implications, evolved fewer times than generally thought, but showed highly variable morphology among early reptiles after its initial origin.”

Just the opposite. In the LRT fenestration evolved MORE times than generally thought.

“Our phylogeny also addresses controversies over the affinities of mesosaurids, the earliest known aquatic amniotes, which we recover as early diverging parareptiles.”

That can only happen with massive taxon exclusion. We’ve known for several years that mesosaurs nest as derived pachypleurosaurs close to thalattosaurs and ichthyosaurs in the LRT. Those pertinent taxa are omitted in Ford and Benson’s paper.

From the introduction:
“The current paradigm of early amniote evolution was established in the late twentieth century. It includes a deep crown group dichotomy between Synapsida (total group mammals) and Reptilia (total group reptiles, including birds), followed by an early divergence of Parareptilia from all other reptiles (Eureptilia).”

Add taxa and the first dichotomy separates the new Archosauromorpha from the new Lepidosauromorpha. This has been online since July 2011 and represents the current paradigm. Ford and Benson are digging into old myths and traditions.

“Furthermore, both molecular and morphological studies have recovered turtles, which lack fenestrae, as diapsids.”

Since molecular studies do not replicate trait studies in deep time molecular studies must be wrong (probably due to epigenetics) and do not employ fossil taxa. So forget genomics in paleontology. Genomics delivers false positives.

“Our analysis includes 66 early fossil members of the amniote crown group, and four crownward members of the amniote stem group, giving a total of 70 operational taxonomic units.” 

By contrast the LRT includes 1625+ taxa not biased by prior studies, including dozens of basal vertebrates and basal tetrapods.

“The goal of our study is to examine the deep divergences of the amniote crown group.” 

If so, then Ford and Benson need to add dozens to hundreds of more taxa to their incomplete study. A suggested list is found here.

“We excluded recumbirostrans from our analysis. Recumbirostrans have generally been assigned to non-amniote microsaurs, but were recently recovered as early crown group amniotes.”

By contrast the LRT includes seven taxa listed by Wikipedia/Recumbirostra. We learned earlier that previous workers have deleted taxa that otherwise deliver unwanted results. Not sure what is happening in the Ford and Benson paper after their omission of this clade. Those seven recumbirostran taxa nest outside the Reptilia /Amniota in the LRT.

From the Results:
“All our analyses recover parareptiles and neodiapsids as a monophyletic group within Diapsida.”

These are false positive results due to taxon exclusion as shown here.

From the Discussion:
“The sister relationship between parareptiles and neodiapsids, and their relationship to Varanopidae, implies a single origin of temporal fenestration before the common ancestor of these clades.” 

These are false positive results due to taxon exclusion as shown here. We’ve known the clade Diapsida is polyphyletic since July 2011 with a last common ancestor in Early Carboniferous amphibian-like reptiles.

Happy holidays, dear readers. 

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References
Ford DP and Benson RBJ 2020. The phylogeny of early amniotes and the affinities of Parareptilia and Varanopidae. Nature ecology & evolution 4:57–65. SuppData

Modesto SP 2020. Rooting about reptile relationships. Nature Ecology & Evolution 4:10–11.

 

Revision to the LRT: basal tetrapods

Here’s a revision to the LRT
that is still being revised and studied (Fig. 1) following the addition of several taxa and two new characters.  I hope readers will report untenable relationships. Most of the taxa are still related to their prior sisters, but the order has changed here and there. It’s been interesting and enlightening going through this process.

Figure 1. Subset of the LRT focusing on the basal (anamniote) Tetrapoda. The last week has been spent reexamining data and letting the taxa sort themselves out again. Please report any untenable relationships.

A few novel nestings appear here.
As the days go by I will discuss and illustrate many of the interesting clades and sisters that were recovered here. For instance, earlier I reported Spathicephalus nesting with Tiktaalik.

Something that does not jump out immediately
is the genesis of tetrapods with fingers and toes deep enough into the Devonian to produce the highly derived near reptile with long digits, Tulerpeton, by the end of the Devonian, prior to the first appearance of nearly all tetrapod fossils with fingers and toes no sooner than the Early Carboniferous.

More reptile ancestors
Several more basal tetrapods are now in the direct lineage of the clade Reptilia. These formerly nested slightly elsewhere.

Middle Devonian tetrapod tracks
were reported earlier here. That trackmaker remains elusive. So the evidence for their presence is known, but the bones are not.

At ReptileEvolution.com
the web pages and their order will be updated this week. Currently the order does not reflect the tree topology shown above.

 

Eusauropleura: now identified as a late-surviving basalmost reptile

The newest addition
to the large reptile tree (LRT, 1341 taxa) is Eusauropleura digitata (originally Sauropleura, Cope 1868; Romer 1930; Carroll 1970; Late Carboniferous, 310 mya; AMNH 6865; Figs. 1, 2) nests as a late-surviving basalmost reptile in the LRT.

The genesis for this genus
in the earliest Carboniferous is based on the more derived Silvanerpeton from the Viséan (335 mya). A dense layer of belly scales (not shown en masse), a larger manual digit 5, and a taller ilium, among other traits, distinguish this specimen from Gephyrostegus. A larger manus, ischium and giant caudal transverse processes (ribs) relative to the torso are unique traits among close relatives. Note the lack of ribs in the lumbar area, where large amniote eggs develop before they are laid. The eggs were relatively large based on the greater depth of the ischium.

Figure 1. Eusauropleura in situ and slightly reconstructed. Manus reconstruction with PILs enlarged.

Basal to Eusauropleura
are taxa close to the Reptilomorpha – Lepospondyli split. These include Eucritta and Utegenia (Fig. 2) all derived from the Late Devonian reptilomorph, Tulerpeton. This affirms the primitive state of basalmost reptiles, derived from Devonian tulerpetids. Further affirmation comes from the observation that the central vertebral elements of Eusauropleura “are very thin-walled, forming little more than a husk around the large notochord,” according to Carroll 1970.

Figure 2. Eusauropleura to scale with ancestral and descendant taxa including Eucritta, Utegenia, Silvanerpeton and Gephyrostegus, the last common ancestor of all reptiles. Note, none of these specimens preserves ossified carpals.

First considered a microsaur
(Cope 1868), then a gephyrostegid (Romer 1930, 1950; Carroll 1970), Eusauropleura was identified as more primitive than Gephyrostegus (Carroll 1970), but still terrestrial, not aquatic and close to the ancestry of reptiles, but not itself a reptile.

So what is a reptile?
As determined here in 2011, there is no list of traditional reptile skeletal traits that upholds the reptile status of Gephyrostegus. There is a new list. Irregardless of skeletal traits, only the nesting of Gephyrostegus as the last common ancestor of all reptiles in the LRT tells us it was laying eggs with an amnion, the ONLY trait needed to determine its reptile status. Silvanerpeton, from the earlier Viséan, was likely also a reptile because phylogenetic descendants of late-surviving Gephyrostegus are also found in coeval Viséan strata. Reptiles are that old. Given that the last common ancestor of Silvanerpeton and Gephyrostegus must also be a late-surviving member of that basalmost reptile radiation, whether the amnion was fully developed or not, something we may never know given the fragility of an amniotic membrane over 300 million years in stone. Earlier workers did not enter Eusauropleura, Silvanerpeton and Gephyrostegus into a wide gamut phylogenetic analysis and so did not recover a last common ancestor status for these amphibian-like reptiles.

Another specimen attributed to Eusauropleura
AMNH 6860 (Moodie 1909, Carroll 1970), is a bit more jumbled, more incomplete and more difficult to reconstruct. A complete ilium with an elongate posterior process is easy to see in this specimen. Such a process provides attachment points for more than one sacral rib, a traditional reptile trait, but this is difficult to determine in the scattered remains of the fossil. And is this really Eusauropleura?

Yet another specimen attributed to Eusauropleura
PU 16815 is an isolated pectoral girdle, bones lacking in the other specimens and therefore not readily comparable.

Scales
According to Carroll 1970, “Scales, both dorsal and ventral, are conspicuous in these specimens [Gephyrostegus and Eusauropleura]. The body was protected by heavy, oblong scales, overlapping to form a chevron pattern, between the pelvic and pectoral girdles. Were they not associated with the skeleton, they would be difficult to distinguish from those of [more primtive] embolomeres. Laterally the scales assume a more oval outline, become thinner, smaller and less extensively overlapping. The dorsal scales are small, thin and round. Where worn, all the scales exhibit a pattern of fine ridges, running parallel with the margins. These form a pattern of concentric ridges in the dorsal scales, similar to that of [more primitive] discosauriscids. Except for the heavier ossification of the dorsal scales, those of Eusauropleura are generally similar to those of Gephyrostegus.”

References
Carroll RL 1970. The ancestry of reptiles. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 257 (814):267–308. DOI: 10.1098/rstb.1970.0026
Cope ED 1868. Synopsis of the Extinct Batrachia of North America. Proceedings of the Academy of Natural Sciences of Philadelphia 1868:208-221.
Romer AS 1930. The Pennsylvanian tetrapods of Linton, Ohio. Bulletin of the American Museum of Natural History. 59 (2):144–147.
Romer AS 1950. The nature and relationships of the Paleozoic microsaurs: American Journal of Science 248:628-654.

wiki/Eusauropleura

Tulerpeton restoration

A reconstruction
puts the in situ bones back into their in vivo places.

A restoration
imagines the bones and soft tissues that are missing from the data. Adding scaled elements from a sister taxon is usually the best way to handle a restoration as we await further data from the field.

Figure 1. Tulerpeton restored based on the bauplan of Silvanerpeton and to the same scale.

We looked at
Tulerpeton, the Upper Devonian taxon known chiefly from its limbs, earlier. I reconstructed the limbs several ways, but did not attempt a restoration. Here (Fig. 1) that oversight is remedied based on the bauplan of Viséan sister, Silvanerpeton. 

Among the overlapping elements,
in Tulerpeton the pectoral girdle and forelimbs are larger. An extra digit is present laterally.

References
Clack JA 1994. Silvanerpeton miripedes, a new anthracosauroid from the Visean of East Kirkton, West Lothian, Scotland. Transactions of the Royal Society of Edinburgh: Earth Sciences 84 (for 1993), 369–76.
Coates MI and Ruta M 2001 2002. Fins to limbs: What the fossils say. Evolution & Development 4(5): 390–401.
Lebedev OA 1984. The first find of a Devonian tetrapod in USSR. Doklady Akad. Navk. SSSR. 278: 1407–1413.
Lebedev OA and Clack JA 1993. Upper Devonian tetrapods from Andreyeva, Tula Region, Russia. Paleontology36: 721-734.
Lebedev OA and Coates MI 1995. postcranial skeleton of the Devonian tetrapod Tulerpeton curtum Lebedev. Zoological Journal of the Linnean Society. 114 (3): 307–348.
Mondéjar-Fernandez J, Clément G and Sanchez S 2014. New insights into the scales of the Devonian tetrapods Tulerpeton curtum Lebedeve, 1984. Journal of Vertebrate Paleontology 34:1454-1459.

wiki/Silvanerpeton
wiki/Tulerpeton

Diplovertebron and amphibian finger loss patterns

Updated June 13, 2017 with the fact that Diplovertebron is the same specimen I earlier illustrated as Gephyrostegus watsoni. And the Watson 1926 version of Diplovertebron (Fig. 1) was so inaccurately drawn (by freehand) that the data nested is apart from the DGS tracing. Hence this post had deadly errors now deleted.

Figure 2. The gradual loss of basal tetrapod fingers. Unfortunately fingers are not known for every included taxon. Odd Tulerpeton with 6 fingers may result from taphonomic layering of the other manus peeking out below the top one. See figure 6. Mentally delete Diplovertebron from this chart. 

The presence of five manual digits
in Balanerpeton (Figs. 4, 5) sheds light on their retention in Acheloma + Cacops. There is a direct phylogenetic path between them (Fig. 2). Note that all other related clades lose a finger or more. Basal and stem reptiles also retain five fingers.

Figure 3. Utegenia nests as a sister to Diplovertebron.

Distinct from the wide frontals
in Utegenia and Kotlassia,  Balanerpeton (Fig. 4) had narrower frontals like those of Silvanerpeton, a stem reptile.

Figure 4. The basal amphibian, Balanerpeton apparently has five fingers (see figure 5).

As reported
earlier, finger five was lost in amphibians,while finger one was lost in temonospondyls. Now, based on the longest metacarpal in Caerorhachis and Amphibamus (second from medial), apparently manual digit one was lost in that clade also, distinct from the separate frog and microsaur clades. In summary, loss from five digits down to four was several times convergent in basal tetrapods.

Figure 5. DGS recovers five fingers in Balanerpeton with a Diplovertebron-like phalangeal pattern. Two 5-second frames are shown here.

Finally, we have to talk about
Tulerpeton (Fig. 6). The evidence shows that the sixth manual digit is either a new structure – OR – all post-Devonian taxa lose the sixth digit by convergence, since they all had five fingers. Finger 6 has distinct phalangeal proportions, so it is NOT an exposed finger coincident rom the other otherwise unexposed hand in the fossil matrix.

Figure 6. Tulerpeton manus and pes in situ, reconstructed by Lebdev and Coates 1995 and newly reconstructed here. Digit 6 is either a new structure, or a vestige that disappears in all post-Devonian taxa.

References
Fritsch A 1879. Fauna der Gaskohle und der Kalksteine der Permformation “B¨ ohmens. Band 1, Heft 1. Selbstverlag, Prague: 1–92.
Kuznetzov VV and Ivakhnenko MF 1981. Discosauriscids from the Upper Paleozoic in Southern Kazakhstan. Paleontological Journal 1981:101-108.
Watson DMS 1926. VI. Croonian lecture. The evolution and origin of the Amphibia. Proceedings of the Zoological Society, London 214:189–257.

wiki/Diplovertebron

Tulerpeton nests between Ichthyostega and Eucritta

Updated Dec 13, 2017 re-nesting Tulerpeton between Ichthyostega and Eucritta. 

Yesterday we looked at the nesting of Tulerpeton (Lebedev 1984; Latest Devonian; PIN 2921/7) as a basal tetrapod, which is the traditional nesting.

I thank
Dr. Michael Coates for sending a pdf of his 1995 study of Tulerpeton. From the improved data I was able to make new reconstructions of the manus and pes. The differences shift the nesting of Tulerpeton to the last common ancestor of Eucrtta and Seymouriamorpha.

Figure 1. Tulerpeton parts from Lebedev and Coates 1995 here colorized and newly reconstructed. Manus and pes enlarged in figure 2. Note the in situ placement of the pedal phalanges. The clavicle is shown as originally published and withe the ventral view reduced in width to compare its unchanged length to the original lateral view image.

In the new reconstruction
only the manus retained 6 digits, with the lateral sixth digit a vestige. The pes has a new reconstruction with only 5 digits, very much in the pattern of Gephyrostegus and Eucritta. Both have five phalanges on digit 5. In the new reconstructions all of the PILs (Peters 2000) line up in sets.

Figure 2. Tulerpeton manus and pes in situ, reconstructed by Lebdev and Coates 1995 and newly reconstructed here with PILs added. Note the broken mt5 and the reinterpretation of the squarish elements as phalanges, not distal carpals. The tibiale is rotated 90º to cap the tibia.

Lebedev and Coates report:
“A cladistic analysis indicates that Tulerpeton is a reptilomoprh stem-group amniote and the earliest known crown-group tetrapod. The divergence of reptilomorphs from batrachomorphs (frogs and kin) occurred before the Devonian Carboniferous boundary. Polydactyly persisted after the evolutionary divergence of the principal lineages of living tetrapods. Tulerpeton was primarily air-breathing.”

Autapomorphies
Manual digit 6 is present as a novelty. Perhaps it is a new digit after damage. More primitive taxa do not have this digit. An anocheithrum (small bone atop the cleithrum) is present. Metatarsal 1 in Tulerpeton is the largest in the set. The posterior ilium rises. The femur has a large, sharp, fourth (posterior) trochanter.

Scales
on Tulerpeton are also found similar in size and number are also found in related taxa.

Taxon exclusion
and digital graphic segregation AND reconstruction AND comparative anatomy all contributed to the new data scores. As usual, I have not seen the specimen, but I did add it to a large gamut data matrix, the likes of which are not typically employed.

Figure 1. Tulerpeton restored based on the bauplan of Silvanerpeton and to the same scale.

References
Coates MI and Ruta M 2001 (2002). Fins to limbs: What the fossils say. Evolution & Development 4(5): 390–401.
Lebedev OA 1984. The first find of a Devonian tetrapod in USSR. Doklady Akad. Navk. SSSR. 278: 1407–1413.
Lebedev OA and Clack JA 1993. Upper Devonian tetrapods from Andreyeva, Tula Region, Russia. Paleontology36: 721-734.
Lebedev OA and Coates MI 1995. postcranial skeleton of the Devonian tetrapod Tulerpeton curtum Lebedev. Zoological Journal of the Linnean Society. 114 (3): 307–348.
Peters D 2000. Description and Interpretation of Interphalangeal Lines in Tetrapods. Ichnos, 7: 11-41

wiki/Tulerpeton