The skull of PVL 4597 joins its post-crania in the LRT

The PhD thesis of Agustina Lecuona 2013
on the several specimens attributed to the Middle Triassic Gracilisuchus (Fig. 2) is online (PDF). It includes the previously unpublished skull of PVL 4597 (Figs. 1, 2), which the large reptile tree (LRT, 1592 taxa) nests apart from Gracilisuchus, as the last common ancestor of all archosaurs (crocs + dinos only) with or without its skull. We reviewed Gracilisuchus yesterday, so this addition to the LRT is timely.

Figure 1. The skull of PVL 4597 in several views from the 2013 PhD thesis of A. Leucona. Colors added.

Figure 1. The skull of PVL 4597 in several views from the 2013 PhD thesis of A. Lecuona. Colors added.

The differences between PVL 4597 and Gracilisuchus are few (Fig. 2).
So, it is not a surprise that Lecuona considered them congeneric.

However,
the differences are fewer between PVL 4597 and its ancestor, Turfanosuchus (Fig. 4), and  its descendant, Herrerasaurus, the last common ancestor of dinosaurs traditionally and in the LRT. 19 additional steps are added when PVL 4597 is forced to nest with Gracilisuchus in the LRT.

FIgure 2. Comparing PVL 4597 to Gracilisuchus. Despite their many similarities, these two do not nest together in the LRT.

FIgure 2. Comparing PVL 4597 to Gracilisuchus. Despite their many similarities, these two do not nest together in the LRT. Taxon exclusion is the issue with the PhD dissertation and the use of an invalidated analysis from Nesbitt 2011.

Basal members of large clades
are sisters to basal members of sister clades (Fig. 3). We compare those taxa with one another, ignoring the more derived members.

Figure 3. Subset of the LRT focusing on basal archosaurs and their immediate ancestors.

Figure 3. Subset of the LRT focusing on basal archosaurs and their immediate ancestors.

Here (Fig. 4) are the skulls of
Turfanosuchus and Herrerasaurus, taxa closer to PVL 4597 than PVL 4597 is to Gracilisuchus is in the LRT. The long-awaited skull confirms the nesting of the post-crania.

Figure 2. Skull of Turfanosuchus compared to Herrerasaurus, the basalmost dinosaur.

Figure 4. Skull of Turfanosuchus compared to Herrerasaurus, the basalmost dinosaur.

Without PVL 4597, 
the LRT still nests Turfanosuchus and basal bipedal crocs close to the base of the Dinosauria, contra the results of other studies that generally do not include those taxa.

Unfortunately,
Lecuona’s PhD thesis employed a borrowed and flawed cladogram on which she mistakenly trusted in: Nesbitt 2011. Even though Lecuona’s revised cladogram includes the basal bipedal crocs (which nest at derived nodes in her thesis), earlier we dismantled Nesbitt 2011 in a 7-part series ending here. Rescored Nesbitt 2011 resembles the LRT.


References
Lecuona A 2013. Anatomía y relaciones filogenéticas de Gracilisuchus stipanicorum y sus implicancias en el origen de Crocodylomorpha. PhD thesis. PDF
Nesbitt SJ 2011. The early evolution of archosaurs: relationships and the origin of major clades. Bulletin of the American Museum of Natural History 352: 292 pp.

wiki/Gracilisuchus

Gracilisuchus revisited and tweaked

Revised October 30, 2019 and November 4, 2019
as I revise the holotype specimen by deleting the limbs. The nesting does not change.

The basal bipedal crocodylomorph,
Gracilisuchus (Figs. 1-3), was one of the first taxa in the large reptile tree (LRT, 1592 taxa), back when there were about 260? taxa. At the time I used Romer’s 1972 reconstruction (Fig. 5) to score data points. That turned out to be a freshman mistake. Romer filled in the missing taxa with the so-called Tucuman specimen, PVL4597, but kept the hind limbs and feet from the holotype slab. The hips and tail are not preserved in the holotype specimen PULR8 (Fig. 1).

Figure 1. Gracilisuchus revised with new, slightly longer legs  and more precise feet after tracing the holotype. Romer added a pelvis and tail that are erased here.

Figure 1.  Gracilisuchus revised with the subtraction of limbs and tail.  Romer added limbs and a tail that are erased here.

 

 

A larger cladogram problem.
Lecuona, Desojo and Pol 2017 report, “The phylogenetic relationships of G. stipanicicorum were evaluated based on an extensive phylogenetic analysis of Archosauriformes expanding a previous dataset (Nesbitt, 2011) in terms of both taxon and character sampling.”  As we learned earlier in a 7-part series, the analysis by Nesbitt 2011 and all those that followed are flawed throughout. Those analyses include unrelated taxa and exclude pertinent taxa. When scores are corrected or filled in where appropriate the resulting topology closely matches the LRT.

Here’s a good idea:
Don’t trust ANY previously published cladograms. Build your own.

This revision gave me an opportunity to update the text
on the Gracilisuchus page. That was needed due to the large number of additional taxa added near Gracilisuchus over the last 8-9 years. With the loss of limbs data, the current nestings of Gracilisuchus and a headless taxon wrongly attributed (Lecuona and Desojo 2011) to Gracilisuchus, PVL4597, did not change with these corrections. Just goes to show, it’s the taxon list, not the character list, that is key to understanding hypothetical interrelationships.

Basal Crocodylomorpha

Figure 5. Basal Crocodylomorpha, including Gracilisuchus, Saltopus, Scleromochlus and Terrestrisuchus. That’s the old Gracilisuchus pictured here, with tail and hips.

Thanks to
reader Neil P for bringing Gracilisuchus back to my attention.


References
Butler RJ, Sullivan C, Ezcurra MD, Liu J, Lecuona A and Sookias RB 2014. New clade of enigmatic early archosaurs yields insights into early pseudosuchian phylogeny and
the biogeography of the archosaur radiation. BMC Evolutionary Biology 14:1-16.
Lecuona A and Desojo, JB 2011. Hind limb osteology of Gracilisuchus stipanicicorum (Archosauria: Pseudosuchia). Earth and Environmental Science Transactions of the Royal Society of Edinburgh 102 (2): 105–128.
Lecuona A, Desojo JB and Pol D 2017. New information on the postcranial skeleton of Gracilisuchus stipanicicorum (Archosauria: Suchia) and reappraisal of its phylogenetic position. Zoological Journal of the Linnean Society XX:1–40.
Romer AS 1972. The Chañares (Argentina) Triassic reptile fauna. An early ornithosuchid pseudosuchian, Gracilisuchus stipanicicorum, gen. et sp. nov. Breviora 389:1-24.

wiki/Gracilisuchus

Late Devonian origin of four-fingered hand revisited and tweaked

Earlier we looked at the origin of fingers
in basal tetrapods (Fig. 1). The primitive number then, as now, was 4 fingers, 5 toes.

Figure 1. Graphing the presence of fingers and toes in basal tetrapods, updated today with the addition of 4 digits in Panderichthys.

Figure 1. Graphing the presence of fingers and toes in basal tetrapods, updated today with the addition of 4 digits in Panderichthys. Sharp-eyed readers will note the switching of Panderichthys with the Tiktaalik clade here.

Unfortunately,
I overlooked a paper (Boisvert, et al., 2008) that found four proto-digits in the lobefin of Panderichthys (Fig. 2) and provided good data for the Tiktaalik manus that I did not have. With those corrections, a quick review is in order.

Figure 1. From Boisert et al. 2008, colors added. This is their ordering for the evolution of manual digits. Compare to figure 2.

Figure 2. From Boisert et al. 2008, colors added. This is their ordering for the evolution of manual digits. Compare to figure 3 where Panderichthys and Tiktaalik switch places and several taxa are inserted transitional to Acanthostega.

For some reason, fingers are rarely preserved in basal tetrapods,
but most continue to have four. Proterogyrinus (Fig. 2) is an early exception with five. So is Acanthostega (Fig. 2) with eight. See chart above  (Fig. 1) for all tested taxa in the LRT.

Tradition holds that eight is a primitive number,
later reduced to five or four. The large reptile tree (LRT, 1590 taxa, subset Fig. 1) flips that around. Eight is a derived number on a terminal taxon (Acanthostega) leaving no descendants. The primitive number is four (subset Fig. 1).

Boisvert, Mark-Kurik and Ahlberg 2008 used a CT-scanner
to find four proto-digits on the manus of Panderichthys (Fig. 2) and compared those to the traditional basal tetrapod taxa: Eusthenopteron, Tiktaalik and Acanthostega. Note the big phylogenetic leap they show between Tiktaalik and Acanthostega. And note the apparent reversal in Tiktaalik as the metacarpal seems to revert to a ray. These problems are corrected in figure 3.

Figure 3. Forelimb of several basal tetrapods rearranged to more closely fit the LRT. Four fingers turns out to be the primitive number. Five is a recent mutation. Six was a short-lived experiment in Tulerpeton.

Figure 3. Forelimb of several basal tetrapods rearranged to more closely fit the LRT. Compare to figure 2. As discovered here earlier, four fingers turns out to be the primitive number. Five is a recent mutation. Six was a short-lived experiment in Tulerpeton.

The large reptile tree
(LRT, 1590 taxa) recovers a different topology (subset Fig. 1). In the LRT Acanthostega is not a transitional taxon, but an aberrant one returning to a more aquatic lifestyle and leaving no descendants. On the other hand, the four digits in Panderichthys are retained by a wide variety of basal tetrapods. The number jumps to five with the addition of a lateral digit in only a few taxa (Fig. 1). Importantly, in Utegenia (Fig. 4) we see the most primitive appearance of five digits in our lineage despite its late appearance in the fossil record. More derived, but earlier, Late Devonian Tulerpeton had six fingers representing a failed experiment leaving no descendants in the lineage of reptiles, represented by Silvanerpeton in the Early Carboniferous, also pre-dating Utegenia.

So frogs did not lose a finger.
They retained the four that Panderichthys provided them. Four, not five or eight, is the primitive number of digits for basal tetrapods, as discovered earlier here in the LRT. Let me know if there was an earlier discovery for this hypothesis of interrelationships and I will promote that citation.

Occasionally
a salamander will have six fingers. We’ll look at that strange case soon.

Figure 5. Utegenia diagram showing five fingers on each hand. This is the most primitive taxon in our lineage to have all five.

Figure 4. Utegenia diagram showing five fingers on each hand. This is the most primitive taxon in our lineage to have all five.

In the course of this study
I learned that the Tiktaalik clade and Panderichthys needed to switch places on the LRT. This has been updated in most cases (Fig.1).

Figure 2. Tulerpeton manus and pes in situ, reconstructed by Lebdev and Coates 1995 and newly reconstructed here.

Figure 5. Tulerpeton manus and pes in situ, reconstructed by Lebdev and Coates 1995 and newly reconstructed here.

Evidently Boisvert et al. were using
an outdated tree topology and did not recognize the problem that arose between the digits presented by Tiktaalik and those presented by Panderichthys (Fig. 2). Of course that puts Tiktaalik cousins, Koilops and Spathicephalus in the lobefin grade (Fig. 1), lacking fingers. Both currently lack post-cranial data, but were originally thought to be tetrapods.


References
Boisvert CA, Mark-Kurik E and Ahlberg PE 2008. The pectoral fin of Panderichthys and the origin of digits. Nature 456:636–638.

Earliest Paleocene mammals recovered from concretions

Lyson et al. 2019 bring us a peek
into a selection of mammal skulls (Fig. 1) preserved in concretions buried in the first few hundreds of thousands of years (up to 1million years) of sediment following the K-T extinction event (= KPgE) 66mya.

Figure 1. From Lyson et al. 2019 showing skulls of increasing size following the KPgE.

Figure 1. From Lyson et al. 2019 showing skulls of increasing size following the KPgE. These come from a variety of clades, not a single one. Tiny taxa were omitted from every stratum.

 

The illustration of skull through time from Lyson et al. 2019
from one locality (Fig.1 ) suggests that mammals were small immediately following the KPgE and thereafter increased and diversified over time. No doubt that happened in a general sense. However…

Placed into a phylogenetic context
(using the large reptile tree (LRT, 1590 taxa) indicates the skulls are from a wide variety of mammals, not a single clade. Lyson et al. omitted tiny taxa from every stratum, evidently to make them tell this tale.

  1. Didelphodon is a highly derived creodont marsupial in the LRT (Fig. 2).
  2. Baioconodon is a related marsupial not yet in the LRT
  3. Loxolophus A is a third creodont in the LRT
  4. Loxolophus B is a fourth creodont in the LRT
  5. Ectoconus is a basal terrestrial herbivorous placental (= basal condylarth) in the LRT
  6. Carsioptychus (originally Plagioptychus) nests with Sinonyx in the Anagale / tenrec / odontocete clade in the LRT. It was a mesonychid mimic.
  7. Taeniolabis is a highly derived multituberculate member of Glires
  8. Eoconodon nests with Mesonyx or Sinonyx, a mesonychid mimic (Fig. 3). I need more data than just a mandible.

In other words,
these taxa come from a variety of marsupial and placental clades, all with origins deep in the Mesozoic. The increases in skull size in the graphic (Fig. 1) following the extinction event was done by cherry-picking these skulls and omitting small taxa. We know that tiny rodents, primates and tree shrews were present in the earliest Paleocene because we have them today and we have them in the Jurassic. The authors told the story they wanted to tell and my hat is off to them. The publicity rush (see links below) and PBS NOVA special (see YouTube video below) that attend the publication of their paper attests to the industry they tapped into that exists to promote stories that otherwise would not have risen to this level of interest. After all, other fossils found in concretions don’t get this sort of press. 

Even so,
it’s always good to see paleontology told so well on the screen. And discoveries are always worthwhile. Some of these taxa (see list above) had to be added to the LRT to figure out just what they were in a phylogenetic sense, and that’s always interesting as well. 

Figure 6. Didelphodon from Wilson et al. 2016 had a 12 cm long skull.

Figure 2. Didelphodon from Wilson et al. 2016 had a 9 cm long skull.

Figure 7. Eoconodon was either a mesonychid like Mesonyx, or a pre-tenrec mesonychid-mimic like Sinonyx.

Figure 3. Eoconodon was either a mesonychid like Mesonyx, or a pre-tenrec mesonychid-mimic like Sinonyx. You can see how similar the mandibles are to each other. Even the teeth are similar.

References
Lyson TR et al. (15 co-authors) 2019. Exceptional continental record of biotic recovery after the CretaceousâPaleogene mass extinction. Science: eaay2268 (advance online publication) DOI: 10.1126/science.aay2268
Wilson GP, Eddale EG, Hoganson JW, Calede JJ and Vander Linden A 2016. A large carnivorous mammal from the Late Cretaceous and the North American origin of marsupials. Nature Communications 7:13734  PDF

https://science.sciencemag.org/content/early/2019/10/23/science.aay2268

https://www.sciencemag.org/news/2019/10/how-life-blossomed-after-dinosaurs-died

https://www.pbs.org/wgbh/nova/article/fossils-million-years-after-dinosaurs-died/

https://phys.org/news/2019-10-fossil-trove-life-fast-recovery.html

https://www.nationalgeographic.com/science/2019/10/new-fossils-show-mammals-growth-spurt-after-dinosaurs-died-corral-bluffs/

https://www.sciencealert.com/stunning-fossil-trove-shows-how-mammals-flourished-after-the-dinosaurs-died

Nature mistakenly adds 3 pre-mammals to Mammalia

It’s supposed to be the premiere scientific journal,
but Nature is failing more often lately. This time reporter John Pickrell (Sydney, Australia) is breaking with traditional hypotheses regarding mammal origins (Figs. 1–3) recovered decades before the advent of the large reptile tree (LRT, 1588 taxa). In figure one from the Nature article, the author flips the order of Liaconodon, a pre-mammal, with Morganucodon, a mammal. Pickerell does not understand the key trait: a dentary squamosal joint, marks the genesis of mammals. Liaoconodon does not have it, despite its late (more recent) appearance.

More to the point:
Liaoconodon
and the two other taxa mentioned by Pickerell (see below) nest outside the last common ancestor of Mammalia. 

Figure 1. Liaoconodon is a pre-mammal without a mammalian jaw joint (squamosal-dentary). Original art one frame one. Replacement art on frame two. Arrow points to jaw joint. For some reason teeth were omitted from the modern mammal jaw. Nature editor Hentry Gee and author John Pickrell should have noticed this.

Figure 1. Liaoconodon is a pre-mammal without a mammalian jaw joint (squamosal-dentary). Original art one frame one. Replacement art on frame two. Arrow points to jaw joint. For some reason teeth were omitted from the modern mammal jaw. Nature editor Hentry Gee and author John Pickrell should have noticed this.

Here’s what Nature.com reports and shows (Fig. 1)
“The latest finds are also offering clues to the evolution of key mammal features. For instance, the keen hearing of mammals is partly down to tiny bones in the middle ear — the malleus, incus and ectotympanic. But in the reptilian ancestors of mammals, these bones were part of the jaw, and were used for chewing instead of hearing. Mammal forerunners, such as shrew-like Morganucodon from 205 million years ago, sported a prototype of the mammal arrangement that allowed for both functions.”

Outside of this Nature.com article
Morganucodon has been recognized as a basal mammal since its discovery. Liaconodon (Fig. 1) was originally mistakenly considered a triconodont mammal. The LRT corrected that error here in 2016.

Figure x. From Science News, Microdocodon 'hyoids' were misidentified fingers. See figure x.

Figure 2. From Science News, Microdocodon ‘hyoids’ were misidentified fingers. See figure x.

Pickrell reported,
“In July, Luo published a paper revealing a 165-million-year-old vole-sized docodont — a close relative of true mammals — that had the hyoid bones of its throat preserved14. Microdocodon gracilis is the earliest animal known to have been able to suckle like a modern mammal.”

In counterpoint,
Microdocodon (Fig. 2) nests outside the last common ancestor of all mammals in the LRT (subset Fig. 5). So it is not a mammal and did not suckle like a metatherian or eutherian mammal. Microdocodon nests outside the Prototheria (= Monotremata, the egg-laying mammals), which lap milk, not suckle. Worse yet, we looked at Microdocodon earlier here. Those ‘hyoid bones’ were misidentified finger bones, otherwise not identified on the fossil.

Figure 1. Microdocodon throat region. Are those bones hyoids or fingers? If hyoids, then where are the fingers? Note the displaced radius (olive green)  reaching toward the throat. Only impressions of once present fingers are present on the right limb.

Figure 3. Microdocodon throat region. Are those bones hyoids or fingers? If hyoids, then where are the fingers? Note the displaced radius (olive green)  reaching toward the throat. Only impressions of once present fingers are present on the right limb.

Yet another misplaced pre-mammal,
Repenomamus (Fig. 4) went so far as to mimic the mammal jaw joint that rotated between the dentary and the squamosal. THAT DOESN”T MATTER! What matters is the last common ancestor of all living mammals, Megazostrodon, is a mammal. Repenomamus nests outside that clade, despite the fact that it had a convergent mammalian trait and survived into the Cretaceous. I know this can be confusing. The LRT resolves this issue.

Figure x. Contra the caption, Repenomamus is not an early mammal. It is a pre-mammal.

Figure 4. Contra the caption, Repenomamus is not an early mammal. It is a pre-mammal.

Only a phylogenetic analysis
can determine what a taxon or clade is. Convergent traits do not determine this.

Figure x. Subset of the LRT focusing on therapsids, like Repenomamus, leading to mammals.

Figure 5. Subset of the LRT focusing on therapsids, like Repenomamus, leading to mammals.

If you know anyone over at Nature,
or independent reporter, John Pickrell, please pass this url over to them. They are reporting errors. This blogpost can help repair some of them.


References
Pickerell J 2019. How the earliest mammals thrived alongside dinosaurs. An explosion of fossil finds reveals that ancient mammals evolved a wide variety of adaptations allowing them to exploit the skies, rivers and underground lairs. Nature 574, 468-472. Nature.com News Feature Oct. 23, 2019. https://www.nature.com/articles/d41586-019-03170-7

“As many characters as possible…”

Please see Nick Gardiner’s comment and my reply below, as he attempts to discredit this day’s theme with traditional thinking and I reply with an explanation of my niche in paleontology by following this day’s theme.

Grandcolas et al. 2001 push for the use of
“as many characters as possible should be included in the cladistic analysis.” The risk, as seen by Grandcolas et al. not to do so is to, “bias the analysis.” The risk in my opinion is you’ll never run the analysis if you keep looking for more and more characters. Their number, if not infinite, is certainly some multiple factor of legion. In certain circles we call this sort of encouragement snipe hunting.

The authors’ wish/suggestion/push runs counter to my arguments
for the large reptile tree (LRT), and its overlapping satellites, the large pterosaur tree (LPT) and the therapsid skull tree (TST). I have argued that the minimum number of characters and character states should be employed that will separate each and every taxon and each and every node apart from one another, with high Bootstrap scores. After all, the goal of every analysis is to model and replicate actual evolutionary events to the best of our ability, given our detachment from taxa in deep time and the reduction of data to only skeletons or partial crushed, and broken skeletons in most cases. If most of the characters used are general in nature and are set in place before the addition of any included taxon, then no a priori bias can be said to exist with regard to included characters. Case in point: the LRT has successfully used intended generalized reptile traits to nest birds, mammals and fish with high resolution.

Frankly, the authors’ arguments go over my head throughout
as they argue semantics, possibilities and a priori issues; nothing specific. They point out many theoretical errors reported by prior authors. Thankfully they sum it all up neatly with a statement near the conclusion, “Not to use available and logically suitable characters is like suppressing evidence.” 

On that note, the authors should have remembered
that every judicial case has a court date, a moment in time when evidence is no longer sought and gathered, but used. Theory is one thing. Practice is another. At one point or another, you simply have to run the analysis.

The authors conclude,
“Phylogenetics must propose refutable hypotheses: characters should not be included or excluded from the analysis because of a priori ideas regarding their evolution.” I think we can all agree to that.

However, let’s remember, we all lead busy lives.
Seeking characters ad infinitum sooner or later leads to decreasing value for the incremental and extended effort. Seeking just enough characters to recover a fully resolved tree that documents a gradual accumulation of derived traits at every node will still leave you time to eat, sleep, drive, work and brush your teeth.

Adding taxa
is still the best way to add value to a phylogenetic analysis if the LRT, LPT and TST are any indication. All use a large enough character list with variations within to separate virtually all taxa from one another in a way that appears to echo micro-evolutionary processes in deep time from jawless fish to blog readers.

Thanks to Neil for bringing this paper to my attention.


References
Grandcolas P, Deleporte P, Desutter-Grandcolas L and Daugeron C 2001. Phylogenetics and Ecology: As many characters as possible should be included in the cladistic analysis. Cladistics 17:104–110.

Parmastega: not “a sister group to all other tetrapods”

Beznosov, Clack, Lusevics, Ruta and Ahlberg 2019
describe a new Russian basal ‘tetrapod’ Parmastega (Fig. 1), based on a nearly complete skull and pectoral girdle. Dated at 372 million years ago, or 12 million years before Acanthostega (Fig. 1), Ichthyostega and Tulerpeton, this taxon offers insights into the acquisition of basal tetrapod traits.

Parmastega was described as
“a sister group to all other tetrapods.” Of eight published analyses in this paper, most nest Paramastega close to Ventastega (Fig. 1).

Unfortunately,
the Beznosov et al. taxon list includes only the traditional tetrapods typically tested in studies like this and Eusthenopteron. Their taxon list omits many, if not most of the taxa listed in yesterday’s list of taxa transitional between jawless fish and reptiles.

Figure 1. Parmastega compared to scale with Acanthostega and Ventastega.

Figure 1. Parmastega compared to scale with Acanthostega and Ventastega. Both are similar to Parmastega in most regards. The placement of the naris in Ventastega might not have been ventrally, on the jawline, but higher on the snout as shown here.

By contrast,
the large reptile tree (LRT, 1587 taxa) nests Parmastega so close to Acanthostega. As reported yesterday and earlier, a larger taxon list indicates that Acanthostega is not a taxon transitional between fins and feet, but is a derived tetrapod apparently returning to a more aquatic niche. This runs counter to traditional hypotheses put forth by co-authors Ruta, Clack and Ahlberg, the top experts in this niche of paleontology.

A concave rostrum,
elevated orbits and large size mark it as a derived taxon, despite its antiquity. The intertemporal is fused to the supratemporal.

The post-cranial skeleton of Parmastega
was described as “weakly ossified”. That is in direct contrast to Acanthostega and virtually all other taxa in the LRT.

The chronology offered by Parmastega
supports the hypothesis of a radiation of tetrapods much earlier, with the few fossils found in the Late Devonian representing late-surviving radiations of that radiation.


References
Beznosov PA, Clack JA, Lufsevics E, Ruta M and Ahlberg PE 2019. Morphology of the earliest reconstructable tetrapod Parmastega aelidae. Nature 574:527–531.