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.

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. So.a = prefrontal.

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.

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. Newly revised fish subset of the LRT

Figure 5. Newly revised fish subset of the LRT

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

Basal tetrapod cladogram: Marjanovic and Laurin 2016, PeerJ

Recently I added
several basal tetrapod taxa to the large reptile tree (LRT, now 950 taxa) in order to better understand the origin of the clade Reptilia (= Amnlota). Along the way, the software recovered some contra-traditional nestings which revived typically cordial correspondences with Drs. David Marjanovic and Jason Pardo, both of whom have studied basal tetrapods extensively. I don’t have all of the latest literature and I appreciate that these researchers open doors I may not have seen.

Less recently
Marjanovic and Laurin (2016) reexamined a earlier report on lissamphibian origins by Ruta and Coates (2007). Marjanovic and Laurin (ML) report “thousands of suboptimal scores due to typographic and similar errors and to questionable coding decisions: logically linked (redundant) characters, others with only one described state, even characters for which most taxa were scored after presumed relatives. Even continuous characters were unordered, the effects of ontogeny were not sufficiently taken into account, and data published after 2001 were mostly excluded.”

Figure 1. Click to enlarge. Wait 10 seconds for animation to begin. Basal tetrapod tree form Marjanovic and Laurin 2016.

Figure 1. Basal tetrapod tree form Marjanovic and Laurin 2016. After 10 seconds those moving lines that appear on the right will make sense when you CLICK TO ENLARGE and see how they connect taxa on competing trees.

ML document and justify all changes
to the earlier matrix, then add 48 taxa to the original 102. They report,  “From the late19th century to now, the modern amphibians have been considered temnospondyls by some (refs omitted), lepospondyls by others and polyphyletic yet others, with Salientia being nested among the temnospondyls, Gymnophionomorpha among the lepospondyls, and Caudata either in the lepospondyls (all early works) or in the temnospondyls (works published in the 21st century).”

“The present work cannot pretend to solve the question of lissamphibian origins or any other of the controversies in the phylogeny of early limbed vertebrates (of which there are many, as we will discuss). It merely tries to test, and explain within the limitations of the dataset, to what degree the trees found by RC07 still follow from their matrix – the largest published one that has been applied to those questions – after a thorough effort to improve the accuracy of the scoring and reduce character redundancy has been carried out to the best of our current knowledge. However, we think this effort forms a necessary step towards solving any of those problems. Further progress may come from larger matrices…”

“Our matrix has only 276 characters, a strong decrease from the 339 of RC07. For the most part, this is due to our mergers of redundant characters and does not entail a loss of information.”

After all that work and all those changes and additions,
ML report their repaired tree “topology is identical to Ruta and Coates 2007.”

Unfortunately that tree is vastly different
from the one recovered in the LRT, which has far fewer taxa, but an equal or greater gamut. Let’s figure out why the topologies differ and are similar. I’ll start slow with the similarities and the metaphorical ‘low-hanging fruit.’ The difficult topics we will handle later. I took the last few weeks (far too little time) to better understand basal tetrapods having zero knowledge of most taxa before starting. I have not been able to cover all the taxa employed by the ML tree.

Similarities:

  1. Both trees include fish and fish-like tetrapods at the base
  2. Both trees include microsaurs, reptiles and extant amphibians as derived taxa
  3. Both trees agree on the inclusion set for microsaurs and holospondyls
Figure 6. Subset of the large reptile tree focusing on basal tetrapods, updated with Gerrothorax.Figure 6. Subset of the large reptile tree focusing on basal tetrapods, updated with Gerrothorax.

Figure 2. Subset of the large reptile tree focusing on basal tetrapods, updated with Gerrothorax.

Differences:

Due to taxon exclusion,
the ML tree nests several reptiles as non-reptiles. These include:

  1. Sivanerpeton – basal reptile/amniote
  2. Gephyrostegus (bohemicus) –  basal reptile/amniote
  3. Bruktererpeton – Lepidosauromorpha
  4. Solenodonsaurus (+ Chroniosaurus, Chroniosuchus) – Archosauromorpha
  5. Tseajaia – Lepidosauromorpha
  6. Limnoscelis – Lepidosauromorpha
  7. Orobates – Lepidosauromorpha
  8. Diadectes – Lepidosauromorpha
  9. Westlothiana – Archosauromorpha

Where each taxon nests in the LRT follows each dash.

Due to taxon exclusion,
the ML tree nests several taxa as ‘Sauropsida’ a clade that no longer has utility based on the new basal reptile dichotomy Archosauromorpha and Lepidosauromorpha. These include:

  1. Captorhinus – Lepidosauromorpha
  2. Paleothyris/Protorothyris – two distinct Archosauromorpha
  3. Petrolacosaurus – Archosauromorpha

Chroniosuchia
ML report, “Chroniosaurus has a fully resolved position one node more crown ward than Gephyrostegidae, Bruktererpeton or Temnospondyli and one node more rootward than Solenodonsaurus.”  This is a similar nesting to the LRT except that all listed taxa other than Temnospondyli nest within the Reptilia. ML are missing several taxa that would have changed their tree topology (see the LRT for that list).

 

Microbrachis
I caught a little heat for not using the latest drawings of Microbrachis earlier. The new tracings (Fig. 3) come from Vallin and Laurin 2004. Note the tracings of the in situ specimen (color) do precisely match the freehand reconstruction they offered. All scoring changes further cemented prior LRT relationships.

Figure 3. Microbrachis images from Vallin and Laurin 2008. Color added here.

Figure 3. Microbrachis images from Vallin and Laurin 2004. Color added here.

More later.

References
Marjanovic D and Laurin M 2016. Reevaluation of the largest published morphological data matrix for phylogenetic analysis of Paleozoic limbed vertebrates. PeerJ. Not peer-reviewed. 356 pp.
Ruta M and Coates MI 2007
. Dates, nodes and character conflict: addressing the lissamphibian origin problem. Journal of Systematic Palaeontology 5-69-122.
Vallin G and Laurin M 2004. Cranial morphology and affinities of Microbrachis, and a reappraisal of the phylogeny and lifestyle of the first amphibians. Journal of Vertebrate Paleontology: Vol. 24 (1): 56-72 online pdf

wiki/Microbrachis

 

Introducing the Paratetrapoda with a new reconstruction of Pholidogaster

With questions arising
about the phylogenetic nesting of the fish-like paratetrapod Colosteus with Osteolepistoday several putative members of the Colosteidae were added to the large reptile tree (LRT, subset Fig. 1). According to Wikipedia, clade members should include Colosteus, Deltaherpeton, Greererpeton and Pholidogaster.

Figure 6. Subset of the large reptile tree focusing on basal tetrapods, updated with Gerrothorax.Figure 6. Subset of the large reptile tree focusing on basal tetrapods, updated with Gerrothorax.

Figure 6. Subset of the large reptile tree focusing on basal tetrapods, updated with Gerrothorax.

As you can see
(Fig. 1) only one putative member of the Colosteida. Pholidogaster nests with Colosteus. Deltaherpeton nests with Eryops the temnospondyl. Greererpeton nests between temnospondyls and the Neotetrapoda with Ichthyostega at its base.

A new clade
The Paratetrapoda is here defined as Colosteus, Osteolepis, their last common ancestor and all of their descendants. Derived taxa developed tetrapod-like limbs by convergence. The Neotetrapoda is here defined as Ichthyostega, Homo, their last common ancestor and all their descendants. This is the clade that leads to all other tetrapods.

Figure 1. Greererpeton reduced to a blueprint of body parts. Here there may be one extra phalanx on pedal digit 5 and one missing on pedal digit 2 compared to sister taxa. So an alternate is shown with that repair. The skulls at left are juveniles.

Figure 2. Greererpeton reduced to a blueprint of body parts. Here there may be one extra phalanx on pedal digit 5 and one missing on pedal digit 2 compared to sister taxa. So an alternate is shown with that repair. The skulls at left are juveniles.

Greererpeton burkemorani 
(Romer 1969, Smithson 1982, Godfrey 1989; Early Carboniferous, 320 mya; 1.5 m in length). Godfrey thought it nested closer to Proterogyrinus than to Ichthyostega. Here Greererpeton nests between temnospondyls, like Sclerocephalus and Ichthyostega. The skull was flattened with orbits on top of the skull. The lacrimal contacted the naris. The torso included some 41 presacral vertebrae. The pectoral girdle was robust. The limbs were small. The powerful tail was the chief organ of locomotion.

Figure 3. Deltaherpeton skull with colors added.

Figure 3. Deltaherpeton skull with colors added.

Deltaherpeton hiemstrae 
(Bolt JR and Lombard RE 2010; Viséan, Early Carboniferous; Fig. 3) nests with Eryops among the temnospondyls and appears to have a fused nasal/frontal.

Figure 2. Colosteus holotype drawing of the fossil in situ from Hook 1983 compared to the closely related Osteolepis.

Figure 4. Colosteus holotype drawing of the fossil in situ from Hook 1983 compared to the closely related Osteolepis.

Colosteus scutellatus 
(Newberry 1856, Hook 1983; Westphalian, Late Carboniferous, 305 mya; 1m in length; AMNH 6916; Fig. 4) was originally considered a fish (Pygopterus) and renamed by Cope 1869. Here Colosteus nests with Osteolepis and Pholidogaster (Figs. 5, 6) as a paratetrapod convergent with traditional tetrapods. The skull was ovate, the vomers and dentaries had fangs, the fins had transformed to tiny four-fingered limbs. The lacrimal did not reach the external naris. The scales remained large and rhomboid-shaped. Pectoral girdle had not yet evolved an external scapula and coracoid.

Figure 1. Pholidogaster skulls compared to Colosteus and Osteolepis. Panchen reconstruction on left includes a premaxilla that is too wide. At right revised width to fit premaxilla tracing, pectoral girdle and in situ lacrimal and cheek bones.

Figure 5. Pholidogaster skulls compared to Colosteus and Osteolepis. Panchen reconstruction on left includes a premaxilla that is too wide. At right revised width to fit premaxilla tracing, pectoral girdle and in situ lacrimal and cheek bones.

Pholidogaster pisciformis
(Huxley 1862, Panchen 1975; Visean, Early Carboniferous, 340 mya; Figs. 5, 6) was originally considered a labyrindont and an anthracosaur, but here nests with Osteolepis and Colosteus (Fig. 5) among the Paratetrapoda, a clade that developed limbs independent of the Tetrapoda.

The new skull reconstruction (Fig. 5) is narrower than in Panchen 1975 to match the premaxilla and pectoral girdle. The premaxilla carried a lateral fang and the dentary had a corresponding slot for it.

Figure 5. Pholidogaster in situ and with post crania reconstructed based on the Osteolepis bauplan.

Figure 5. Pholidogaster in situ and with post crania reconstructed based on the Osteolepis bauplan. The long straight ribs are actually neural spines that are elevated here. Small bones, like those found in Osteolepis and Eusthenopteron are retained at the bases of unpreserved dorsal and anal fins. The interclavile extends below the jaw. It appears unlikely that this taxon had a neck.

The vertebral column included small bones that were basal to both dorsal fins and anal fin. The long straight unpaired bones once thought to be ribs are here identified as tall slender neural spines. The tail was little different from that found in Osteolepis, including the slight upturn, like a shark’s tail.

The interclavicle and clavicles extended beneath the mandibles. No scapula or coracoid was visible. Those were tiny elements medial to the coracoid and cleithrum. The fingers did not ossify. The pelvis is well ossified with an acetabulum dorsal to the pubis. The hind limb includes metatarsals and a few digits.

The ossified scales that covered the body in Osteolepis and Colosteus are not present here.

Pholdogaster has been known for over 150 years
and if it had only been reconstructed with the present precision I think its fish-like affinities would have been discovered earlier. It’s 150-year-old specific name ‘pisciformis’ points obviously to its fish-like affinities, which were recognized then, but have received less attention in recent studies. It appears unlikely that any paratetrapod had a movable neck.

Remember
we have tetrapods crawling on shore and leaving footprints in the Middle Devonian, millions of years before Acanthostega and Ichthyostega in the latest Devonian. These famous taxa now appear to be conservative relicts retaining fish-like traits, rather than liberal land pioneers inventing tetrapod-like traits.

References
Agassiz L 1843. Recherches Sur Les Poissons Fossiles. Tome I (livr. 18). Imprimerie de Petitpierre, Neuchatel xxxii-188.
Bolt JR and Lombard RE 2010.
 Deltaherpeton hiemstrae, a New Colosteid Tetrapod from the Mississippian of Iowa. Journal of Paleontology. 84 (6): 1135–1151.
Godfrey SJ 1989. The postcranial skeletal anatomy of the Carboniferous tetrapod Greererpeton burkemorani Romer, 1969. Philosophical Transactions of The Royal Society B Biological Sciences 323(1213):75-133.
Hook RW 1983. Colosteus scutellatus (Newberry), a primtiive temnospondyl amphibian from the Middle Pennsylvanian of Linton, Ohio. American Museum Novitates 2770; 1-41.
Huxley TH 1862. On new labyrinthodonts from the Edinburgh Coal-field. Quarterly Journal of the Geological Society London18:291-296.
Panchen AL 1975. A New Genus and Species of Anthracosaur Amphibian from the Lower Carboniferous of Scotland and the Status of Pholidogaster pisciformis Huxley. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 269(900):581-637.
Romer AS 1969. A temnospondylus labyrinthodont from the Lower Carboniferousw. Kirtlandia 6:1-20.
Smithson TR 1982. The cranial morphology of Greererpeton burkemorani Romer (Amphibia: Temnospondyli). Zoological Journal of the Linnean Society 76(1):29-90.

wiki/Greererpeton
wiki/Osteolepis
wiki/Colosteus
wiki/Pholidogaster