You heard it here first: Ichthyostega and Acanthostega were secondarily aquatic

In this YouTube video from 2018
Dr. Donald Henderson starts his online slide video presentation by repeating the traditional fin-to-finger story (Fig. 1).

Unfortunately
that story was already out-of-date in 2018 due to taxon exclusion in comparison to and competition with the phylogenetic analysis found in the large reptile tree (LRT, 1817+ taxa; subset Fig. 5).

Not surprisingly, Dr. Henderson thought it was “very peculiar”
that Middle Devonian tetrapod trackways preceded the Late Devonian fossils of tetrapods by tens of millions of years. The LRT solves this problem. Acanthostega and Ichthyostega are not transitional taxa, but dead end taxa with polydactyly not found in other tetrapod taxa. Their phylogenetic ancestors filled the gap between the Middle and Late Devonian, but those fossils have not been found yet in those strata, only in later strata as late survivors of those earlier radiations.

In the middle of the presentation
Dr. Henderson presented his alternative view: that Ichthyostega and Acanthostega were secondarily aquatic tetrapods. His YouTube video is dated January 11, 2018. Only a short month earlier the LRT recovered Ichthyostega and Acanthostega as secondarily more aquatic tetrapods, time-stamped here.

Evidently that was an idea whose time had come.
Or else Dr. Henderson read that hypothesis here and embraced it. Either way, Dr. Henderson did not employ phylogenetic analysis, but came to his solution as a notion to reconcile the Middle Devonian tracks to the late Devonian fossils.

Otherwise
Dr. Henderson’s presentation was mundane. Henderson’s customary family tree of vertebrates (Fig. 1) indicates he had no idea how clades of fish are related to one another at a species level (Fig. 2). He never tested traditional hypotheses, but accepted them without reservation.

Figure 1. Slide from Henderson’s YouTube video with connections between clades highlighted in frame 2.

The fish phylogeny problem was resolved
here in 2019 and continues to evolve with every added taxon.

Figure 2. Shark skull evolution according to the LRT. Compare to figure 1.

Dr. Henderson also presents a traditional lineup
of tetrapods (Fig. 3) that was improved by the LRT by simply adding overlooked taxa (Fig. 4).

Figure 3. Slide from Henderson YouTube presentation modified in frame 2 to reflect the order of basal tetrapods in the LRT. Missing here is Trypanognathus (Fig. 4) and kin, basal tetrapods in the LRT.

Henderson’s traditional lineup is lacking several taxa,
like Trypanognathus (Fig. 4), that are also long, low and with tiny limbs, like Tiktaalik and Panderichthys, but are traditionally never included in fin-to-finger cladograms, other than here in the LRT.

Figure 4. Dorsal and ventral views of Panderichthys and several basal tetrapods demonstrating the low, flat skulls and bodies with small limbs and relatively straight ribs.

It’s nice to have a notion, like Dr. Henderson had.
After all, that’s where all scientific inquiry has its genesis. But you can’t beat a good old, wide gamut phylogenetic analysis to make your notion into a testable hypothesis that covers all the other competing hypotheses. Let’s hope that someday PhDs will adopt a taxon list comparable to the LRT and then let the taxa and their taxonomy tell the tale.

Figure 5. Subset of the LRT focusing on basal tetrapods. Colors indicate number of fingers known. Many taxa do not preserve manual digits.

Colleagues,
follow up those notions with testable analyses. It’s hard work, but it’s the professional thing to do.

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References
https://pterosaurheresies.wordpress.com/2017/12/15/ichthyostega-and-acanthostega-secondarily-more-aquatic/

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

 

A juvenile Eusthenopteron enters the LRT

Fish expert, John Long 1995 (p. 209) wrote:
“The juvenile skull of a crossopterygian fish, Eusthenopteron (Figs. 1,3) has more features in common with that of an early amphibian Crassigyrinus (Fig. 4), that it’s adult skull would have had.”

Long goes on to explain about paedomorphosis and heterochrony during the transition from fish to tetrapod.

Euthenopteron was a good transitional taxon several years ago. Recently it was replaced in the LRT by a flatter taxon, Cabonnichthys.

Figure 1. Eusthenopteron juvenile in situ from Schultze 1984. Large plate ventral to the mandible overlaps a convex ventral margin. The quadratojugal is not labeled here. Several bones are re-labeled here.

Let’s put Long’s 1995 statement to the test
by adding Eusthenopteron ‘junior’ (Schultze 1984) to the large reptile tree (LRT, 1698+ taxa; subset Fig. 5).

Results: The juvenile nested with the adult Eusthenopteron in the LRT, falsifying Long’s statement.
Note: Several bones are relabeled here vs. Schultze’s original designations.

Worthy of note:
The juvenile Eusthenopteron shares several traits with another, often overlooked, small taxon with similar large eyes, Koilops, which nests at the base of a nearby derived node in the LRT (Fig. 5). Based on phylogenetic bracketing, Koilops is also a juvenile. All sister taxa are larger and without juvenile proportions.

Figure 2. Koilops is a flat-headed smaller sister to Elpistostege, but with larger teeth, larger orbits and a shorter snout. These traits indicate Koilops is a juvenile.

So Long’s point about paedomorphosis and heterochrony
was  not correct in this case. His ‘matching tetrapod’, Crassigyrinus (Fig. 4), nests several nodes apart from pre-tetrapods in the LRT (off the subset chart in Fig. 5).

Koilops post-crania remains unknown,
but it nests at the base of Elpistostege, Tiktaalik and Spathicepahlus on one branch, Panderichthys + Tetrapoda on the other. So Koilops likely had lobe fins and a straight tail. Perhaps Koilops was a juvenile elpistostegid ready to mature into something larger, with smaller eyes, more like Elpistostege.

Figure 3. Juvenile and adult Eusthenopteron compared from Schultze 1984. The cranium of the juvenile appears convex here, but was likely flatter based on figure 1.

From the Schultze 1984 abstract:
“A size series of thirty-five specimens of Eusthenopteron foordi Whiteaves, 1881 , shows isometric and allometric changes. As in Recent fishes, the main difference between small (juvenile) and large (adult) specimens is the relative size of the orbit and of the head. With the exception of the caudal prolongation, all fin positions remain isometric to standard length.”

Figure 4. Crassigyrinus has little to no neck.

Contra Long 1995 and all prior basal tetrapod workers, the LRT indicates the transition from fish to tetrapod occurred among flat-head taxa, like Trypanognathus.  Crassigyrinus Fig. 4) is a distinctly different stegocephalid with a taller skull, more like those of the more famous traditional transitional taxa, Ichthyostega and Acanthostega. The new fish-to-tetrapod transitional taxa were recovered by simply adding taxa overlooked by prior workers. Taxon exclusion continues to be the number one problem with vertebrate paleontology today, according to results recovered by the LRT. This free, online resource minimizes taxon exclusion.

Figure x. Subset of the LRT, focusing on fish for July 2020.

Not sure if fish expert John Long
would make the same statement today. Let’s hope things have changed in the last 25 years of vertebrate paleontology.

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References
Long JA 1995. The Rise of Fishes. The Johns Hopkins University Press, Baltimore and London 223 pp.
Schultze H-P 1984. Juvenile specimens of Eusthenopteron foordi Whiteaves, 1881 (Osteolepiform Rhipidistian, Pisces) from the Late Devonian of Miguasha, Quebec, Canada. Journal of Vertebrate Paleontology 4(1):1–16.

wiki/Eusthenopteron

Perhaps Tulerpeton had only 5 fingers (and five toes)

Let’s get right to it.
Tulerpeton (Fig. 1) was originally described with six fingers. If not six fingers, where did that sixth finger come from?

The other hand.
Specifically, the tip of finger 4 from the left hand (Fig. 1) provides a suitable match.  The left hand is otherwise buried in the matrix beneath the well-exposed right hand.

Figure 1. Tulerpeton manus with digit 6 re-identified as the top of digit 4 from the other hand. The drawing at left is the in situ presentation. The diagram at right is the traditional six-finger interpretation. The manus in the middle represents the new hypothesis of digit identity.

Tulerpeton sisters in the LRT
don’t have a digit 6. So, maybe the original description was a mistake.

Likewise, the pes of Tulerpeton
was also originally described with six digits (Fig. 2). However, a new interpretation first discussed here indicated only five toes were present. That sixth digit was created to fill a perceived space produced by broken and displaced phalanges.

Figure 2. Tulerpeton pes reconstruction options using published images of the in situ fossil.

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.
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/Tulerpeton

 

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)

 

Recalibrating clade origins, part 5

Earlier
we looked at the first part, second part, third part and fourth part of Marjanovic’s 2019 chronological recalibration of vertebrate nodes. Today we conclude.

Batrachia (Caudata + Salientia) = Amphibians (= extant Frogs + Salamanders) Marjanovic discusses Triadobatrachus from the Early Triassic (Olenekian, 249mya) and concludes that 249 mya “is a perfectly adequate hard minimum age for this calibration point.” And “290mya may be a defensible soft maximum value.”

After adding Triadobatrachus (Fig. 1) to the large reptile tree (LRT, 1631+ taxa), Gerobatrachus (Early Permian, 300mya) mentioned once by Marjanovic, nests basal to the few tested extant frogs and salamanders. So, 300mya is pretty close to his estimate of 290mya.

Figure 1. Triadobatrachus skull, as originally colorized and dorsal surface redone with tetrapod colors here with bone fusion identified and the maxilla + premaxilla restored. Compare to Rana in figure 2. Distinct from extant frogs, a squamosal is present here.

Figure 2. Skull of the frog, Rana with colors matching those of Triadobatrachus. Here the squamosal and jugal are missing. The quadratojugal is present.

Chondrichthyes (Holocephalii + Elasmobranchii)
= (ratfish + sharks and skates) Marjanovic reports, “By current understanding (Frey et al., 2019), the oldest known crown-chondrichthyan is the stem elasmobranch Phoebodus fastigatus from the middle Givetian. The Givetian, part of the Middle Devonian, …so I propose 385 Ma as the hard minimum age of the chondrichthyan crown-group.”

By contrast, the LRT recovers the whale shark + manta ancestor, Loganellia (Early Silurian, 440mya; Fig. 3) as the oldest known ancestor of sharks and other fish. Sturgeons are more primitive, and therefore must be older, but Ordovician sturgeon and osteostracan fossils have not been found. Taxon inclusion recovers these novel interrelationships.

Figure 2. Loganellia, a thelodont with a whale shark shape including dorsal fin. Image from OldRedSandstone.com. This appears to be Loganellia, not Thelodus.

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Marjanovic reports, “There is not as much interest in phylogeny among specialists of early elasmobranchs than among specialists of early mammals or early dinosaurs.” The LRT does not have that problem. Enigmas are answered with this powerful tool that works well by avoiding tooth-only taxa.

Marjanovic considers the clade Batoidea (skates + rays) to be monophyletic.

In the LRT, so far, three origins for ray-like basal tetrapods have been recovered based on taxon inclusion.

Marjanovic considers the clade Neopterygii (Holosteomorpha + Teleosteomorpha) = (bowfins and gars + other teleosts or bony fish) to be monophyletic.

In the LRT, this hypothesis of relationships has been invalidated.

Marjanovic reports, “I cite 228 references for calibration purposes.”

In the LRT, I’m not sure how many citations I cite for 1631+ taxa, but once again, adding taxa brings new insights to hypothetical interrelationships. Marjanovic was testing the results of a previous publication, but should have done so with a greater authority, with more taxa and with no reference whatsoever to genomics.

Tomorrow: something new. 

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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

Recalibrating clade origins, part 2

Marjanovic 2019 reports on
the origin of several clades based on fossils and molecules. Yesterday we looked at part 1, which focused on the abstract. Today: the origin of several more listed clades.

Gnathostomata (Chondrichthyes + Osteichichthyes)
Marjanovic cautiously proposes the mid-Florian (Early Ordovician, 475 mya) for the origin using traditional taxa and cladograms.

By contrast, the LRT splits off quasi-jawless sturgeons before the appearance of jawed sharks + other bony fish. It also splits off the jawed Loganellia + Rhincodon + Manta clade before the Polyodon + ratfish + sharks + skates clade and the Pachycormus + Hybodus clade before the dichotomy that resulted in the rest of the bony fish (the now polyphyletic ‘Osteichthyes‘)… so direct comparisons are not apples and apples here. Sturgeons first appear much later in the fossil record. Loganellia appears in the Early Silurian with an earlier genesis. So Marjanovic’s estimate may be a little early.

Osteichthyes (Actnopterygii + Sarcopterygii)
Marjanovic reports, “The oldest known uncontroversial crown-group osteichthyan is the oldest known dipnomorph, Youngolepis.” He suggests, “the minimum age for this calibration is the same as that for the next node,” the Silurian/Devonian boundary, 420 mya.

The LRT includes placoderms within one branch of the bony fish, so Entelognathus along with the stem-lungfish Guiyu, both in the Late Silurian are older than Marjanovic suggests with an earlier genesis. Sturgeons, which traditional workers consider a member of the Osteichyes, phylogenetically preceded Longanellia, which is known from Early Silurian strata. So, again we’re not comparing similar cladograms here. The LRT tests a wider gamut of taxa, which is an advantage in that it opens further possibilities than tradition dictates.

Dipnomorpha + Tetrapodomorpha (lungfish + lobe fin ancestors of tetrapods)
Marjanovic reports, “I suggest a hard minimum age of 420mya.” (See above).

The LRT includes Late Siluirian Guiyu within the stem-lungfish clade. so the split occurred earlier.

Tetrapoda (Amphibia + total group of Amniota)
Marjanovic reports, “the richer and better studied Famennian (end-Devonian) record, which has not so far yielded tetrapods close to the crown-group but has yielded more stemward tetrapods and other tetrapodomorphs (Marjanović and Laurin, 2019), should be used to place a soft maximum age around very roughly 365 Ma.”

Figure 1. Tersomius texensis, an amphibamid lepospondyl close to Dendrerpeton.

In the LRT the last common ancestor of Amphibia + Amniota is Tersomius (Fig. 1), a late survivor in the Early Permian of an earlier genesis and radiation. The oldest taxa from this clade in the LRT are the basal amniotes / amphibian-like reptiles, Silvanerpeton and Eldeceeon from the Viséan (335 mya), with a long list of late surviving taxa between them and Tersomius, some eight nodes beyond the Late Devonian Acanthostega and Ichthyostega (365 mya). So the Tournaisian (355 mya) split suggested by Marjanovic seems about right.

Amniota (Theropsida + Sauropsida)
Marjanovic reports, “I refrain from recommending a maximum age other than that of the preceding Node, even though such an early age would imply very slow rates of morphological evolution in the earliest thero- and sauropsids.”

The LRT recovers a different basal dichotomy (Archosauromorpha + Lepidosauromorpha) and a different last common ancestor for all amniotes (Silvanerpeton) than Marjanovic is working with. Silvanerpeton is Viséan in age (~335 mya). In the LRT ‘Amniota’ is a junior synonym for Reptilia.

Crown group of Diapsida (Lepidosauromorpha + Archosauromorpha)
Marjanovic reports, “I cannot express confidence in a maximum age other than that of  Node 106, which I cannot distinguish from the maximum age of Node 105 as explained above. This leaves Node 107 without independent calibrations in the current taxon sample.”

The LRT finds two origins for reptiles with a diapsid skull architecture. So the tradtional clade ‘Diapsida’ is also a junior synonym for Reptilia and Marjanovic is using an outdated and under represented cladogram. Lepidosauromorph diapsids first appear with Paliguana in the earliest Triassic. Archosauromorph diapsids first appear with Erpetonyx and Petrolacosaurus in the Late Carboniferous with an earlier genesis. These taxa are not mentioned by Marjanovic.

Archosauria (Crocodile total group + Bird total group)
Marjanovic reports, “I accept the Permian-Triassic boundary (251.902 ± 0.024 Ma: ICS; rounded to 252) as the soft maximum age on the grounds that a major radiation of archosauromorphs at the beginning of the Triassic seems likely for ecological reasons.”

The LRT restricts membership within the Archosauria to just Crocodylomorpha + Dinosauria. So the maximum age for this dichotomy is younger and the last common ancestor is the PVL 4597 specimen (late Middle Triassic, 230mya) traditionally assigned to Gracilisuchus, but nesting apart from the holotype.

The LRT finds the Archosauriformes first appeared in the Late Permian (260mya), arising from a sister to Youngoides romeri (FMNH UC1528) thereafter splitting into clades arising from the larger Proterosuchus and the smaller Euparkeria.

Alligatoridae (Alligatorinae + Caimaninae)
Marjanovic reports, “Given this uncertainty, I have used a hard minimum age of 65 Ma for present purposes, but generally recommend against using this cladogenesis as a calibration for time trees.”

The LRT does not include pertinent taxa surrounding this split.

Figure 2. Megapodius is the extant bird nesting at the base of all neognathae (all living birds except ratites). And it looks like a basal bird. It also looks a bit like the Solnhofen bird, Jurapteryx. It is easy to imagine diverse forms arising from this bauplan and the LRT indicates that is exactly what happened.

Crown group of Neognathae (Gallanseres + Neoaves)
Marjanovic further defines this clade as, “The last common ancestor of Anas, Gallus and Meleagris on one side and Taeniopygia.” More commonly Marjanovic nests a duck, a chicken and a turkey on one side and a zebra finch on the other as the basal dichotomy of all living birds, sans ostriches, kiwis and kin. Marjanovic reports, “As the soft maximum age I tentatively suggest 115 Ma, an estimate of the mid-Aptian age of the (likewise terrestrial) Xiagou Fm of northwestern China, which has yielded a diversity of stem-birds but no particularly close relatives of the crown.”

Taxa listed by Marjanovic are all highly derived taxa in the LRT where the scrub fowl, Megapodius (Fig. 2) and the tinamou, Crypturus, are basal neognaths. These would have had their genesis in the Earllest Cretaceous given that Early Cretaceous clades that redevelop or retain teeth are more derived.

More tomorrow…

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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

Tetrapod ancestors updated back to Cambrian finless fish

Pictures tell the story, for the most part today.
The large reptile tree (LRT, 1615+ taxa) presents an occasionally novel and growing list of taxa between Cambrian pre-fish and the first listed tetrapod, Laidleria (Fig. 1 bottom). This list is updated from the previous time this list was first presented without so many basal chordates. Note, it still does not include traditional members, Acanthostega and Ichthyostega. which nest at more derived nodes as they venture back into a more fish-like niche.

Figure 1. These taxa are those closest to main line of tetrapod ancestors. That makes these taxa human ancestors, too.

Qiao et al. 2016 report,
“Our findings consistently corroborate the paraphyly of placoderms, all ‘acanthodians’ as a paraphyletic stem group of chondrichthyans, Entelognathus as a stem gnathostome, and the Guiyu-lineage as stem sarcopterygians.”

Figure 2. Traditional cladogram from Lingham-Soliar 2014. This has been invalidated by the LRT.

Figure 3. Subset of the LRT with the addition of several jawless taxa.

References
Brazeau MD and Friedman M 2015. The origin and early phylogenetic history of jawed vertebrates. Nature. 2015;520(7548):490–7. pmid:25903631.
Davis SP, Finarelli JA and Coates MI 2012. Acanthodes and shark-like conditions in the last common ancestor of modern gnathostomes. Nature. 2012;486(7402):247–250. pmid:22699617
Dupret V, Sanchez S, Goujet D, Tafforeau P and Ahlberg PE 2014. A primitive placoderm sheds light on the origin of the jawed vertebrate face. Nature. 2014;507:500–503. pmid:24522530
Lingham-Soliar T 2014. The vertebrate integument volume 1. origin and evolution. Springer.com  PDF
Qiao T, King B, Long JA, Ahlberg PE and Zhu M 2016. Early gnathostome phylogeny revisited: multiple method consensus. PLoS ONE 11(9): e0163157. https://doi.org/10.1371/journal.pone.0163157
Zhu M, Zhao W-J, Jia L-T, Lu J, Qiao T and Qu Q-M. 2009. The oldest articulated osteichthyan reveals mosaic gnathostome characters. Nature. 2009;458:469–474. pmid:19325627
Zhu M, Yu X-B, Ahlberg PE, Choo B, Lu J, Qiao T, et al. 2013. A Silurian placoderm with osteichthyan-like marginal jaw bones. Nature. 2013;502(7470):188–193. pmid:24067611
Zhu M, Yu X-B and Janvier P 1999. A primitive fossil fish sheds light on the origin of bony fishes. Nature. 1999;397:607–610.

https://pterosaurheresies.wordpress.com/2019/10/24/tetrapod-evolution-without-ichthyostega-and-acanthostega/

The origin of the tetrapod quadratojugal

As we’ve seen
over the past several dozen fish additions to the large reptile tree (LRT, 1583 taxa) facial bones homologous with those of tetrapods often divide and fuse. We’ve already seen multipart jugals, lacrimals, nasals and squamosals in fish. This can be confusing and is probably the reason why fish facial bones are traditionally not labeled with tetrapod nomenclature. Expect homology arguments to last for decades, but here all fish facial bones are colored with tetrapod homologs.

Figure 1. Gogonasus skull demonstrating the genesis of the split between the toothy maxilla and the toothless quadratojugal.

The one bone that first appears by a split
of the maxilla into anterior toothy and posterior toothless portions is the quadratojugal. Phylogenetically the quadratojugal first appears on Gogonasus (Fig. 1). Prior taxa lack it. Later taxa have it. Even so, until the cladogram got figured out, this was puzzling.

Figure 2. Subset of the LRT alongside the definitions published in Laurin, Girondot and de Ricqles 2000. Note the Gogonasus node, where the quadratojugal first appears.

Gogonasus andrewsae (Long 1985, Long et al. 1997; Late Devonian, 380 mya; NMV P221807; 30-40cm in length) is the best preserved specimen of its type. This is the crossopterygian transitional between rhizodontids, coelocanths and higher tetrapodomorphs. The maxilla splits in two creating the tetrapod quadratojugal. The squamosal splits in two creating the tetrapodomorph preopercular. A pineal opening appears, so does the tetrapodomorph choana. The lacrimal contacts the external naris. This is the crossopterygian that gave rise to tetrapodomorphs and tetrapods, rhizodontids and gulper eels.

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References
Long JA 1985. A new osteolepidid fish from the Upper Devonian Gogo Formation of Western Australia, Recs. Western Australia Mueum 12: 361–377.
Long JA et al. 1997. Osteology and functional morphology of the osteolepiform fish Gogonasus Long, 1985, from the Upper Devonian Gogo Formation, Western Australia. Recs. W. A. Mus. Suppl. 57, 1–89.

wiki/Gogonasus

Air-breathing Polypterus: it’s in our direct ancestry

The Nile bichir
(genus: Polypterus; Fig. 1) is a small, long-bodied, extant fish at home in hot, swampy, oxygen-starved waters. It has lungs, but no trachea. It breathes through a spiracle. Juveniles have large, pink external gills for breathing underwater. For decades, the big question has been: “What is it?”

According to Wikipedia,
“Polypterus was discovered, described, and named in 1802 by Étienne Geoffroy Saint-Hilaire. It is a genus of 10 green to yellow-brown species. Naturalists were unsure whether to regard it as a fish or an amphibian. If it were a fish, what type was it: bony, cartilaginous, or lungfish? Some regarded Polypterus as a living fossil, part of the missing link between fishes and amphibians, helping to show how fish fins had evolved to become paired limbs.”

Figure 1. The Nile bichir (Polypterus), skull, skeleton and bones colorized for ease of comparison. Compare to the placoderm, Entelognathus, (Fig. 2) and the stem tetrapod Tinirau (Fig. 3).

Surprisingly,
when added to the large reptile tree (LRT, 1447 taxa) Polypterus did not nest with the distinctly different basal actinopterygian, Cheirolepis (Fig. 4), but between the Silurian placoderm, Entelognathus (Fig. 2) and the Middle Devonian stem tetrapod/crossopterygian, Tinirau (Fig. 3). Thus, Polypterus is a very ancient fish, with a genesis predating all tested Devonian crossopterygians and actinopterygians.

Figure 2. The placoderm, Entelognathus, is widely considered the outgroup to the crossopterygians, the stem tetrapods. Compare the skull bones to those of extant Polypterus (Fig. 1) and Middle Devonian Tinirau (Fig. 3).

Romer (1946) wrote (quoted from Wikipedia),
“The weight of Huxley’s opinion is a heavy one, and even today many a text continues to cite Polypterus as a crossopterygian and it is so described in many a classroom, although students of fish evolution have realized the falsity of this position for many years…. Polypterus…is not a crossopterygian, but an actinopterygian, and hence can tell us nothing about crossopterygian anatomy and embryology.” If this were true, Polypterus would have nested with the actinopterygian, Cherolepis, in the LRT.

Hall (2001) reported, 
“Phylogenetic analyses using both morphological and molecular data affirm Polypterus as a living stem actinopterygian.” Remember, a ‘stem’ actinopterygian, by definition, is not an actinopterygian. It’s something else preceding that clade. Currently Polypterus cannot have its genes tested against any other placoderms or crossopterygians, but we can include this taxon in phylogenetic analysis.

So often
paleontologists keep looking, too often in frustration, where they think a taxon should nest (e.g pterosaurs as archosaurs, caseids as synapsids, whales as artiodactyls, etc.), instead of just letting the taxon nest itself in a wide gamut analysis, like the LRT. It’s really that easy and you can be confident of the results because all other candidates are tested at the same time.

Figure 3. The stem tetrapod, Tinirau. Compare to Polypterus (Fig. 1) and Entelogenathus (Fig. 2).

So, where does that leave the basal actinopterygian, Cheirolepis?
In the LRT, Cheirolepis nests with the small crossopterygian, Gogonasus (Fig. 4) and these more circular cross-section taxa form a clade outside of the main line of flat stem tetrapods. That also solves several long-standing problems.

Now the late appearance of the basal fish, Cheirolepis
and other actinopterygians makes sense. They are derived from crossopterygians that have losing their lobe fins while retaining their fin rays.

Figure 4. The former most primitive ray-fin fish, Cheirolepis (Middle Devonian) nests with the crossopterygian, Gogonasus, in the LRT, distinct from Polypterus. Note the fleshy pectoral fins, the anterior advancement  and transformation of the pelvic fin and the loss of the anterior dorsal fin in Cheirolepis.

Placoderms had fleshy fins.
The pectoral fins of Cheirolepis remained lobe-like, while the pelvic fins lost their lobes. That’s the progression, not the other way around.

If you see a fish with great distance
between the pectoral and pelvic fins (e.g. Polypterus, sharks, sturgeons, paddlefish, etc.) it is primitive. In Cheirolepis the distance is shortening. In many derived fish, the pelvic girdle is just beneath the gills. Very strange, when you think about it.

Not only can Polypterus breathe air,
it can lift its chest off the substrate with its robust forelimbs (Fig. 5). It can survive on land for several months at a time. Now those Middle Devonian trackmakers no longer seem so outlandish.

The three flathead fish, Entelognathus, Polypterus and Tinirau,
lead directly to Panderichthys, Tiktaalik and other flattened basal tetrapods.

That makes Polypterus,
like Didelphis, Caluromys and Lemur,  a living representative close to the direct lineage of tetrapods, mammals, primates and humans.

If you’re interested in Polypterus
the above YouTube videos will prove enlightening.

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References
Geoffry Saint-Hillaire E 1802. Description d’un nouveau genre de poisson, de l’ordre des abdominaux. Bull. Sci. Soc. Philom., Paris, 3(61):97-98.
Hall BK 2001. John Samuel Budgett (1872-1904): In Pursuit of Polypterus, BioScience 51(5): 399–407.
Romer AS 1946. The early evolution of fishes, Quarterly Review of Biology 21: 33-69.

wiki/Polypterus
wiki/Tinirau
wiki/Cheirolepis
wiki/Entelognathus