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that story was already out-of-date in 2018 due to taxon exclusion in comparison to and competition with the phylogenetic analysis found in the large reptile tree (LRT, 1817+ taxa; subset Fig.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

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 4. Shark skull evolution according to the LRT. Compare to figure 1.

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. 3) and kin, basal tetrapods in the LRT.

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

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

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.


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.

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.

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.

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.”


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.

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 sister to Spathicephalus, but with teeth, larger orbits and a shorter snout

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 2. Juvenile and adult Eusthenopteron compared from Schultze 1984. The cranium of the juvenile appears convex here, but was likely flatter.

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 5. Crassigyrinus has little to no neck.

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.

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.


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

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 4. Acanthostega does not have much of a neck.

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 4a. Subset of the LRT focusing on basal tetrapods. Note the displaced positions of Acanthostega and Ichthyostega.

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.

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 1. Trypanognathus in situ, colorized to bring out ribs and limbs.

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

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.


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 redone with tetrapod colors here.

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.

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 whale shark shape including dorsal fin. Image from OldRedSandstone.com. This appears to be Loganellia, not Thelodus (Fig. 7).

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


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. 


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

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.

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 3. Traditional cladogram from Lingham-Soliar 2014.

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

Figure 4. Subset of the LRT with the addition of several jawless taxa.

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/

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).

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 Polypterus (Fig. 1) and Tinirau (Fig. 3).

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).

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.

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.


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

An overlooked trackmaker for Middle Devonian tetrapod tracks

Updated August 6, 2019 with new taxa creating a phylogenetic update.
Polypterus, Clarias and Amia are air-breathing fish more primitive than any stem tetrapod. Any of these three could have evolved to a para-tetrapod matching these tracks during the Mid-Devonian.

Ahlberg 2018
discusses the quandary of Middle Devonian (397mya) tetrapod tracks (Zalchemie trackway), some with finger and toe impressions, preceding the Late Devonian (360 mya) appearance of body fossils with fingers and toes.

Figure 1. The Early Carboniferous limbed osteolepid, Pholidogaster,  compared to Middle Devonian Zalchemie tracks to scale.

Figure 1. The Early Carboniferous limbed osteolepid, Pholidogaster, compared to Middle Devonian Zalchemie tracks to scale. Would you consider this a tetrapod, a paratetrapod, or just a fish with legs?

Here
the large reptile tree (LRT, 1308 taxa; subset Fig. 2) provides a solution to the problem. Pholidogaster has toes (fingers not preserved, Fig. 1) yet nests basal to Panderichthys, Tiktaalik, Acanthostega and Ichthyostega. Pholidogaster (Fig. 1) is an Early Carboniferous late survivor of a Middle Devonian first attempt at terrestrial locomotion that produced no extant descendants. Essentially Pholidogaster was an osteolepid with fingers and toes that were not homologous with those found in Tulerpeton and all extant tetrapods (including frogs, salamanders, sirens and amniotes). In other words, fingers and toes were re-invented after the Middle Devonian ancestors of Pholidogaster first gave it a try in the first wave of terrestrial locomotion.

Figure 1. Subset of the LRT focusing on basal tetrapods, colorized according to chronology. Note the wide dispersal of Early Carboniferous taxa, suggesting a Late Devonian radiation as yet largely undiscovered.

Figure 1. Subset of the LRT focusing on basal tetrapods, colorized according to chronology. Note the wide dispersal of Early Carboniferous taxa, suggesting a Late Devonian radiation as yet largely undiscovered. Also note the position of Tulerpeton, basal to all extant tetrapods.

The LRT confirms Ahlberg’s proposition, “As I have previously argued, even Acanthostega may, to some degree, have been secondarily aquatic, descended from more terrestrially competent ancestors.”

The problem may be
that no one has allowed the possibility that osteolepids produced more than one lineage of  limbed and toed descendants. Convergence runs rampant elsewhere. The evidence shows convergence also produced at least two sets of tetrapods, the Tetrapoda and the Paratetrapoda. They existed side-by-side after the first appearance of Tetrapoda until the extinction of the Paratetrapoda.

References
Ahlberg PE 2018. Early vertebrate evolution. Follow the footprints and mind the gaps: a new look at the origin of tetrapods. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, 1–23.

 

 

 

Ichthyostega and Acanthostega: secondarily more aquatic

More heresy here
as the large reptile tree (LRT, 1036 taxa) flips the traditional order of fins-to-feet upside down. Traditionally the late Devonian Ichthyostega and Acanthostega, bridge the gap between lobe-fin sarcopterygians, like Osteolepis.

In the LRT
Acanthostega, ‘the fish with limbs’, nests at a more derived node than its precursor, the more fully limbed, Ossinodus (Fig. 1). Evidently neotony, the retention of juvenile traits into adulthood, was the driving force behind the derived appearance of Acanthostega, with its smaller size, stunted limbs, smaller skull, longer more flexible torso and longer fin tail.

Figure 1. Ossinodus is the more primitive taxon in the LRT compared to the smaller Acanthostega, the tadpole of the two.

Figure 1. Ossinodus is the more primitive taxon in the LRT compared to the smaller Acanthostega, essentially the neotenous ‘tadpole’ of the two.

Likewise
Ichthyostega is more derived than both fully-limbed Ossinodus and Pederpes, which had five toes. As in Acanthostega, the return to water added digits to the pes of Ichthyostega. In both taxa the interosseus space between the tibia and fibula filled in to produce a less flexible crus.

Figure 2. Ossinodus, Pederpes were more primitive than the more aquatic Icthyostega.

Figure 2. Long-limbed Ossinodus and Pederpes were more primitive than the more aquatic Icthyostega.

So, Acanthostega and Ichthyostega were not STEM tetrapods.
Instead, they were both firmly nested within the clade Tetrapoda. Ossinodus lies at the base of the Tetrapoda. The proximal outgroups are similarly flattened Panderichthys and Tiktaalik. The extra digits displayed by Acanthostega and Ichthyostega may or may not tell us what happened in the transition from fins to feet. We need to find a derived Tiktaalik with fingers and toes.

Figure 3. Tiktaalik specimens compared to Ossinodus.

Figure 3. Tiktaalik specimens compared to Ossinodus.

In cases like these
it’s good to remember that ontogeny recapitulates phylogeny. Today and generally young amphibians are more fish-like (with gills and fins) than older amphibians.

It’s also good to remember
that the return to the water happened many times in the evolution of tetrapods. There’s nothing that strange about it. Also the first Devonian footprints precede the Late Devonian by tens of millions of years.

Figure 4. From the NY Times, the traditional view of tetrapod origins.  Red comment was added by me.

Figure 4. From the NY Times, the traditional view of tetrapod origins. 

Phylogenetic analysis teaches us things
you can’t see just by looking at the bones of an individual specimen. A cladogram is a powerful tool. The LRT is the basis for many of the heretical claims made here. You don’t have to trust these results. Anyone can duplicate this experiment to find out for themselves. Taxon exclusion is still the number one problem that is largely solved by the LRT.

You might remember
earlier the cylindrical and very fish-like Colosteus and Pholidogaster convergently produced limbs independently of flattened Ossinodus, here the most primitive taxon with limbs that are retained by every living tetrapod. By contrast, the Colosteus/Pholidogaster experiment did not survive into the Permian.

References
Ahlberg PE, Clack JA and Blom H 2005. The axial skeleton of the Devonian trtrapod Ichthyostega. Nature 437(1): 137-140.
Clack JA 2002.
 Gaining Ground: The origin and evolution of tetrapods. Indiana University Press.
Clack JA 2002. An early tetrapod from ‘Romer’s Gap’. Nature. 418 (6893): 72–76. doi:10.1038/nature00824
Clack JA 2006. The emergence of early tetrapods. Palaeogeography Palaeoclimatology Palaeoecology. 232: 167–189.
Jarvik E 1952. On the fish-like tail in the ichtyhyostegid stegocephalians. Meddelelser om Grønland 114: 1–90.
Jarvik E 1996. The Devonian tetrapod Ichthyostega. Fossils and Strata. 40:1-213.
Säve-Söderbergh G 1932. Preliminary notes on Devonian stegocephalians from East Greenland. Meddelelser øm Grönland 94: 1-211.
Warren A and Turner S 2004. The first stem tetrapod from the Lower Carboniferous of Gondwana. Palaeontology 47(1):151-184.
Warren A 2007. New data on Ossinodus pueri, a stem tetrapod from the Early Carboniferous of Australia. Journal of Vertebrate Paleontology 27(4):850-862.

wiki/Ichthyostega
wiki/Acanthostega
wiki/Ossinodus
wiki/Pederpes

Devonian fish heads

New data on February 27, 2017
focuses on Kenichthys (Zhu and Ahlberg 2004), a sarcopterygian fish in which the posterior naris has migrated to the jaw line, on its way to the inside of the mouth (Fig. A).

Figure A. From Zhu and Ahlberg 2004 demonstrating the migration of the posterior naris in Youngolepis to the rim of the jaw in Kenichthys, and to the inside of the mouth in Eusthenopteron.

Figure A. From Zhu and Ahlberg 2004 demonstrating the migration of the posterior naris in Youngolepis to the rim of the jaw in Kenichthys, and to the inside of the mouth in Eusthenopteron.

In a quest for understanding
the origins of everything reptilian, today we’ll take a look at the skulls of three Devonian fish with skull bones homologous with those of reptiles.

FIgure 1. Cheirolepis skull. Most bones have readily identified homologs with tetrapods, but the medal skull bones and the pineal opening do some shifting. Yes, that's the pineal appearing in the inter frontal.

FIgure 1. Cheirolepis skull. Most bones have readily identified homologs with tetrapods, but the medal skull bones and the pineal opening do some shifting. Yes, that’s the pineal appearing in the inter frontal. DIs the supratemporal split to give rise to temporals? And did the parietals split to give rise to post parietals? Or did the tabulars and post parietals  migrate?

Cheirolepis trailli (Agassiz 1835; Middle Devonian, 390 mya; 30-55?cm in length; Fig. 1) is considered one of the earliest actinopterygian (ray-finned) fish with ‘standard’ dermal skull bones. Those bones were homologous with those of coeval and later sarcopterygian fish, like Eusthenopteron (Fig. 2) and Osteolepis (above right, Fig. 3)and tetrapods, like Ichthyostega. That series of small rostral bones will fuse to become the nasal in tetrapods. The maxilla will become much shallower, the rostrum will lengthen.

In Cheirolepis (now the basal taxon in the large reptile tree, LRT, 955 taxa) the orbit is far forward. The jaws opened up to right angles to form a large gape. The pineal opening pierced the inter-frontal (originally the singular frontal). Note the great depth of the maxilla on the cheek. That doesn’t last in tetrapods. Bony gill covers were present. Those disappear, too. The pectoral fins were lobed and muscular, but the hind fins were not. The pelvis and dorsal fins were large and broad-based. The tail was heterocercal, like a shark’s tail. The body was deep and broad anteriorly, narrower posteriorly. The lumbar  region becomes wider and less streamlined in basal tetrapods.

The homologies of the tabular and postparietal
are questionable here, so two solutions are shown (Fig. 1). The one on the left is likely correct based on the random appearance of post parietals in Osteolepis (Fig. 3) from the random splitting of elongate parietals.

The homologies of the frontals and parietals
are reidentified here for Cheirolepis (Fig. 1) and Eusthenopteron (Fig. 2) based on tetrapod skull bones and the pattern in Osteolepis skull roofing bones (Fig. 3). In their original identity, the pineal opening pierced the parietals. Here the pineal opening migrates from the inter frontal to the frontals, heading toward the parietals in basal tetrapods. The pineal basically follows the lateral eyes as they also migrate posteriorly.

Figure 2. Eusthenopteron skull showing some changes from the Cheirolepis skull.

Figure 2. Eusthenopteron skull showing some changes from the Cheirolepis skull. Here the post parietals have not split rom the parietals. Pink bone on verbal column is the future sacral, the posterior most vertebra with tiny transverse processes (ribs).

Eusthneopteron foordi (Whiteaves 1881; Late Devonian, 385 mya; 1.8m in length) was one of the first fish genera known to share a long list of traits with basal tetrapods.

Distinct from Cheirolepis
Eusthenopteron had choanae (palatal openings for the passage of air, internal nares). The posterior maxilla was not so deep. The orbits were smaller and set further posteriorly. The mandible bones were more like those of tetrapods. Limb bones appear within the pectoral and pelvic fins, but no distinct wrist, ankle, metapodial or digit bones are yet present. Fin rays remain. The jaws were rimmed with tiny teeth. The palate had several large fangs. The tail was not so heterocercal, but stretched out more or less in line with the vertebral column.

Not as visible in these figures…
While all fish have anterior and posterior external naris for odor-laden water to enter and exit, in Eusthenopteron and Osteolepis the posterior naris has migrated to the orbit to become the tear duct. Now, that’s a clue that these fish were spending time poking their eyes above the water and perhaps not gulping air like a lungfish, but breathing and smelling through its new choanae (internal nares).

Figure 3. Osteolepis cranial shield bones from Graham-Smith 1978 and reidentified here (in white)

Figure 3. Osteolepis cranial shield bones from Graham-Smith 1978 and reidentified here (in white). These are due to individual variation.

Variation in the skull shield of Osteolepis (Fig. 4)
is shown above (Fig. 3). Bones originally labeled intertemporals are here considered supratemporals. Original supratemporals are here considered tabulars. Note the random splitting of the parietals, originally considered anterior parietals (APa) and parietals (Pa). Here those bones are parietals and post parietals based on tetrapod homologies. In one Osteolepis specimen (Fig. 3 lower right) extra bones (supernumeraries – sa) appear, but do not appear in related taxa.

Figure 2. Ostelepis has a large bone basal to the pelvic fin. IMHO it is too far back to be a possible ischium, contra Panchen.

Figure 4. Ostelepis, more or less actual size. The heterocercal tail is retained here.

References
Agassiz JLR 1835. On the fossil fishes of Scotland. Report of the British Association for the Advancement of Science, British Association for the Advancement of Science, Edinburgh.
Graham-Smith W 1978. On the Lateral Lines and Dermal Bones in the Parietal Region of Some Crossopterygian and Dipnoan Fishes. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 282 (986):41-105.
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: 1-16.
Whiteaves JF 1881. On some remarkable fossil fishes from the Devonian rocks of Scaumenac Bay, in the Province of Quebec. Annals and Magazine of Natural History. 8: 159–162.
Zhu M and Ahlberg P 2004. The origin of the internal nostril of tetrapods. Nature 432:94-97.

Cheirolepis fossil images
wiki/Cheirolepis
wiki/Eusthenopteron