Xiphactinus has living relatives in the Amazon

Short one today
because all the work is not yet done with regard to ray fin fish phylogeny. This is just an update.

Previously I overlooked this novel hypothesis of interrelationships.
Now it seems obvious (Fig. 1). But first I had to better understand the crushed skulls of Xiphactinus (Figs. 1, 3) and Portheus (a traditionally junior synonym for Xipactinus, here resurrected due to several differences in the skull and post-crania, Figs. 2,4). Lots of little nips and tucks here.

Figure 1. Revised skull of Xiphactinus.

Figure 1. Revised skull of Xiphactinus.

Figure 2. Revised skull of Portheus.

Figure 2. Revised skull of Portheus.

Figure 2. Xiphactinus fossil. The famous fish-within-a-fish. Note the posterior pelvic fins.

Figure 3. Xiphactinus fossil. The famous fish-within-a-fish. Note the posterior pelvic fins.

Figure 4. Skeleton of Portheus.

Figure 4. Skeleton of Portheus, close to but distinct from Xiphactinus. 

Figure 1. The araimaia, Hopolerythrinus, enters the LRT with the piranha, Serrasalmus.

Figure 5. The araimaia, Hopolerythrinus, nests with the Cretaceous giants, Xiphactinus and Portheus (Figs. 1–4).

Figure 3. Araimaia (Hoplerythrinus) skull.

Figure 6. Araimaia (Hoplerythrinus) skull.

At present these three taxa
share a last common ancestor with an ancestor to Serrasalmus, the piranha.

Figure 8. Subset of the LRT focusing on ray fin fish. Eel-like taxa are highlighted.

Figure 7. Subset of the LRT focusing on ray fin fish. Eel-like taxa are highlighted.

Correction: European eels are neotonous swordfish

Before you say, “That’s crazy!” did you ever notice
that swordfish lack ribs and pelvic fins (Fig. 4)? So do European eels.

More importantly, did you ever notice
that baby swordfish look like eels (Fig. 4)? Okay. With that in mind, let’s start with a little backstory and cover all the bases.

Traditionally swordfish have been allied with 
barracuda, marlin and several extinct billfish, including Blochideae (i.e. Blochius, Fig. 4), based on overall appearance, open sea niche and apex predator status. According to Wikipedia, “They [swordfish] are the sole member of their family, Xiphiidae.” Gregory and Conrad  1937 compared the morphologies of the sailfish and swordfish. Earlier I followed the lead of these experts in nesting the sailfish, Istiophorus (Figs. 5, 7), and the swordfish, Xiphiias, with the barracuda, Sphyraena. That was a mistake.

Today we’ll compare
swordfish and sailfish morphology to two other more closely related taxa: the anchovy, Elops (Fig. 6) and the European eel, Anguilla, which turns out to be more closely related to swordfish despite their outward differences as adults. Turns out that swordfish go through a metamorphosis as they develop from eel-like hatchlings with teeth (Fig. 4).

The LRT scores skeletal traits 
rather than superficial morphologies, which are always prone to reversal and convergence. The large reptile tree (1793+ taxa) is designed to test taxa together that have not been tested together before. Some surprises were recovered earlier using this method here, here and here.

In their description of Bavarichthys
(Fig. 1) Arratia and Tischlinger 2010 did not mention or test the eel, Anguilla, or the swordfish, Xiphias. Turns out, they should have done so.

Recent revisions
of several fish taxa (now that I have 250 fish taxa and the experience that brings to bear) reveal a hitherto overlooked hypothesis of interrelationships between eels and swordfish. Sound crazy? Keep reading. This is one of those ‘moment of discovery’ moments I want to share with you.

Figure 1. Bavarichthys is a big head/ short body anchovy from the Late Jurassic. Now it is ancestral to European eels.

Figure 1. Bavarichthys is a big head/ short body anchovy from the Late Jurassic. Now it is ancestral to European eels.

Let the cheek plates evolve away in Bavarichthys
(Fig. 1) and you’l have the basic skull of both swordfish (Fig. 2) and European eels (Fig. 3). Note the triangular profile, the slender insertion of the nasal between the anterior frontals, the extreme brevity of the post-orbital portion of the skull, including a vertical quadrate. No other tested fish taxa have these traits.

Figure 2. Diagram of the swordfish (Xiphias) skull. Compare to figures 1 and 3.

Figure 2. Diagram of the swordfish (Xiphias) skull. Compare to figures 1 and 3.

Billfish came first. 
The European eel, Anguilla, is derived from swordfish, sailfish and Late Jurassic Bavarichthys. Hatchlings of swordfish are eel-like (Fig. 4) and Bavarichthys-like (Fig. 1). That means European eels are neotonous swordfish. They achieve adulthood while still in the hatchling swordfish stage. European eels also develop traits not found in swordfish, like additional vertebrae and a long, low operculum. European eels don’t develop pelvic fins of dorsal ribs. Neither do swordfish.

Figure 5. Skull of Anguilla, the European eel, compares well with that of Bavarichthys. Note the loss and reduction of preorbital bones.

Figure 3. Skull of Anguilla, the European eel, compares well with that of Bavarichthys. Note the loss and reduction of preorbital bones.

Earlier the LRT nested
Late Jurassic Bavarichthys with closely related anchovies (genus: Elops), then with more closely related European eels (genus: Anguilla). Now it nests basal to both swordfish and European eels.

Other eels,
like the moray eel (Gymnothorax) and electric eel (Electrophorus) nest elsewhere, both near the base of the bony fish. So eels were in the gene pool.

Figure 4. Swordfish ontogeny (growth series). Hatchings have teeth, a short bill and an eel-like body still lacing pelvic fins.

Figure 4. Swordfish ontogeny (growth series). Hatchings have teeth, a short bill and an eel-like body still lacing pelvic fins. Hatchlings go through an eel-like phase and a sailfish-like phase.

Xiphias gladius
(Linneaus 1758; Gregory and Conrad 1937; up to 4.5m in length) is the extant swordfish, nesting between Bavarichthys and Anguilla. 1cm long hatchlings more closely resembled little eels, then growing to little sailfish before reducing the long dorsal fin. The sword is not used to spear, but to slice and maim smaller fish traveling in schools. The pelvic fins and ribs are absent, as in eels. Larger females produce more eggs, up to 29 million.

Figure 5. Skull of the sailfish, Istiophorus. Compare to Elops in figure 6.

Figure 5. Skull of the sailfish, Istiophorus. Compare to Elops in figure 6.

Figure 2. Elops is the extant anchovy. Compare to Bavaricthys in figure 1 and Istiophorus in figure 5.

Figure 6. Elops is the extant anchovy. Compare to Bavaricthys in figure 1 and Istiophorus in figure 5.

Figure 1. Istiophorus, the sailfish, nests with the cobria (Fig. 2) in the LRT, not with the swordfish.

Figure 7. Istiophorus, the sailfish, nests with the anchovy, Elops, not with, but close to the sailfish, Xiphias.

Sailfish have long slender pelvic fins,
like those of anchovies, unlike swordfish and eels. Sailfish have a broad postorbital, like anchovies, unlike swordfish. Sailfish have a zig-zag frontal-nasal suture, like anchovies, unlike swordfish. The list of subtle, but scoreable differences continues. More importantly, no other tested taxa share more traits with swordfish and sailfish than eels and anchovies, respectively.

Figure 8. Subset of the LRT focusing on ray fin fish. Eel-like taxa are highlighted.

Figure 8. Subset of the LRT focusing on ray fin fish. Eel-like taxa are highlighted.

With the sailfish and swordfish gone, where does that leave the lonely barracuda?
In the LRT the barracuda nests with the similar long-bodied remora (Remora) and cobia (Rachycentron), derived from the mahi-mahi (Coryphaena) all with mandibular prognathism. This is non-tradional. Other workers prefer to nest billfish with barracuda.


References
Arratia G and Tischlinger H 2010. The first record of Late Jurassic crossognathiform fishes from Europe and their phylogenetic importance for teleostean phylogeny. Mitteilungen aus dem Museum für Naturkunde in Berlin. Fossil Record; Berlin 13(2): 317–341.
Gregory WK and Conrad GM 1937. The comparative anatomy of the swordfish (Xiphias) and the sailfish (Istiophorus). The American Museum Novitates, 952:1-25.
Linnaeus C von 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.

https://pterosaurheresies.wordpress.com/2020/07/04/bavarichthys-a-late-jurassic-solnhofen-anchovy/

wiki/Istiophoriformes

wiki/Swordfish

 

Pol et al. 2021: Anachronistic look at the origin of the Sauropodomorpha

From the Pol et al. 2021 abstract
“Sauropodomorpha is the first major dinosaurian group that radiated during the Triassic.”

No. That’s not how it works in phylogenetic analysis. Clades don’t radiate alone without a second clade also radiating.

Here’s how it works: From a basal clade, llike Dinosauria (represented by Herrerasaurus), there is always a dichotomy where one branch, like Theropoda (represented by Tawa), splits from the another branch, like Phytodinosauria (represented by Buriolestes). This happens in all phylogenetic analyses as it does in the large reptile tree (LRT 1793+ taxa). Rarely three branches arise to produce an unresolved node. That usually means a mistake in scoring. Such a node is not present in this subset  of the LRT focusing on Sauropodomorpha (Fig. 1).

Figure 2. Subset of the LRT focusing on basal phytodinosauria. Aardonyx nests with Saturnalia here.

Figure 1. Subset of the LRT focusing on basal phytodinosauria. Aardonyx nests with Saturnalia here. The Sauropodomorpha is the sister clade to Ornithischia (cropped off the bottom of the graphic).

From the abstract:
“Sauropodomorpha is one of the three major groups of Dinosauria, along with Theropoda and Ornithischia (Benton, 1983; Novas, 1996), and became the most conspicuous herbivores of terrestrial ecosystems of the Mesozoic.”

Again, this is anachronistic paleontology. There are never three major groups of any vertebrate. There should always be dichotomies. Pol et al. need to add taxa to understand the first dichotomy in the Dinosauria splits the Theropoda from the Phytodinosauria. Several nodes later a dichotomy splits Sauropodomorpha from Ornithischia. Both are plant eaters.

Figure 2. Plateosaurus skeleton digitized.

Figure 2. Plateosaurus skeleton digitized.

From the abstract
“These early lineages are currently referred as basal or early sauropodomorphs (Bronzati, 2017) or more traditionally grouped in Prosauropoda (Sereno, 1999; Galton and Upchurch, 2004), a term now in disuse as most phylogenetic studies in the last decade agree in the paraphyly of this group.”

The first dichotomy in Sauropodomorpha in the LRT splits taxa leading to Plateosaurus (Plateosauridae Marsh 1895 = Prosauropoda Huene 1920, Sereno 1998, Fig. 2) from taxa leading to Brachiosaurus.

Recently Baron, Norman and Barrett 2017 were unable to recover basal Phytodinosauria due to taxon exclusion. They also mixed up basal sauropods with basal plateosaurs.

Figure 1. Tiny forelimbs with three sharp-clawed fingers indicate that Guaibasaurus is a theropod, not a sauropodomorph. Shown to scale with related theropods Marasuchus and Procompsognathus.

Figure 3. Tiny forelimbs with three sharp-clawed fingers indicate that Guaibasaurus is a theropod, not a sauropodomorph. Shown to scale with related theropods Marasuchus and Procompsognathus.

Pol et al. report, 
“Guaibasaurus is included in the table although many studies depicted this taxon as an early theropod or saurischian (see text).”

In the LRT Guaibasaurus (Fig. 3) is indeed a basal theropod, so should not have been included in a study focused on phytodinosaurs or sauropodomorphs. That would be like adding pterosaurs to a study focused on archosaurs. Hah! Who would do THAT? (Everyone else, sadly, each time by excluding pertinent taxa).


References
Baron MG, Norman DB and Barrett PM 2017. A new hypothesis of dinosaur relationships and early dinosaur evolution. Nature, 543: 501–506.
Pol D, Otero A, Apaldetti CA and Martinez RJ 2021.
Triassic sauropodomorph dinosaurs from South America: the origin and diversification of dinosaur dominated herbivorous faunas. Journal of South American Earth Sciences. https://doi.org/10.1016/j.jsames.2020.103145

wiki/Plateosauria
https://pterosaurheresies.wordpress.com/2020/11/24/plateosaurus-enters-the-lrt/

Orodus: another overlooked taxon at the shark-bony fish transition

Another overlooked human ancestor
enters the large reptile tree (LRT, 1793+ taxa) and with it, new light is shed on the history of how we came to be.

Figure 1. Orodus greggi in situ, FMNH specimen. See figure 2 for reconstruction.

Figure 1. Orodus greggi in situ, FMNH specimen. See figure 2 for reconstruction. This black triangle results after Photoshop removal of the original distortion due to perspective visible in the original photo.

Orodus greggi 
(Agassiz 1838, Late Pennsylvanian to Early Permian 300mya, 2m long) is a later surviving descendant at the shark-bony fish split, descending from Hybodus and basal to tiny Prohalecites.

Note: these are both late survivors of a Middle Silurian radiation based on phylogenetic and chronological bracketing. That gives both taxa plenty of time to evolve individual traits that appear, but do not remove both taxa from their phylogenetic order in the LRT.

The mandible of Orodus is massive
(probably a newly evolved trait). The cranium is narrow. The fins are larger than those illustrated by Zangrel 1981. The FMNH specimen preserves skin and gill slits.

Note: the distance between the pectoral fins and skull shrinks in Prohalecites, one way to make five gill opercula shrink to just one.

The FMNH (Field Museum) specimen of Orodus
would make a wonderful project for a PhD candidate. Not much has been written about it. It might be a good idea to run it through an x-ray machine to see the now covered coronoid process.

Figure 2. Orodus reconstructed using DGS from figure 1 alongside Prohalecites x10 and to scale.

Figure 2. Orodus reconstructed using DGS from figure 1 alongside Prohalecites x10 and to scale.

Earlier we looked at
Prohalecites (Fig. 2) a tiny descendent of Orodus also nesting in the LRT between sharks and bony fish and discussed the increasingly common instances of phylogenetic miniaturization at the genesis of major clades.


References
Agassiz L 1838.
 Recherches Sur Les Poissons Fossiles. Tome III (livr. 11). Imprimérie de Petitpierre, Neuchatel 73-140.

wiki/Prohalecites
wiki/Orodus

New genomic estimate misses monotreme-marsupial split by 43 million years

Summary for those in a hurry:
Fossils provide hard evidence. Deep time gene studies provide estimates and false positives too often to trust them.

Zhou et al. 2021 report:
“Our phylogenomic reconstruction shows that monotremes diverged from therians around 187 million years ago, and the two monotremes diverged around 55 million years ago. This estimate provides a date for the monotreme–therian split that is earlier than previous estimates (about 21 million years ago, but agrees with recent analyses of few genes and fossil evidence.”

Let’s stop putting our faith in estimates derived from genomic deep time studies that have proven themselves to be wrong too many times. Here, the Zhou et al. estimate is at least 43 million years too late (Fig. 2) based on Brasilitherium (Fig. 3) fossils and the tree topology recovered by the LRT (Fig. 1).

Figure 7. Subset of the LRT focusing on Metatheria (marsupials) including Paedotherium and Adalatherium.

Figure 1. Subset of the LRT focusing on Metatheria (marsupials) including Paedotherium and Adalatherium.

By contrast with Zhou et al. 
Morganucodon (Late Triassic, 205mya, Fig. 4) is a basal marsupial in the large reptile tree (LRT, 1790+ taxa; subset Fig. 1) based on phenomic (= trait) analysis that includes fossil taxa. Genomic tests are infamous for false positives when dealing with deep time taxa.

Figure 1. Select basal cynodonts and mammals set chronologically. The divergence times for placentals (Eutheria), marsupials (Metatheria) and monotremes (Mammalia) are estimated here.

Figure 2. Select basal cynodonts and mammals set chronologically. The divergence times for placentals (Eutheria), marsupials (Metatheria) and monotremes (Mammalia) are estimated here.

Brasilitherium,
(Figs. 3, 4) from the Early Norian, Late Triassic, 225mya, is a derived monotreme in the LRT. That means it lived AFTER the monotreme-therian split which must have occurred at least 230mya.

Figure 1. Brasilodon compared to Kuehneotherium, Akidolestes and Ornithorhynchus, the living platypus.

Figure 3. Brasilodon compared to Kuehneotherium, Akidolestes and Ornithorhynchus, the living platypus.

As everyone knows
the platypus and echidna are highly derived monotremes. Megazostrodon (Fig. 4) is the last common ancestor (LCA) of all monotremes and all mammals. Megazostrodon was a Late Jurassic late survivor of that earlier (Middle Triassic?) radiation.

Figure 5. Basal mammals and their proximal ancestors. Here taxa below Megazostrodon are mammals. Those above are not. Hadrocodium is uniquely reduced, but this occurs within the Mammalia.  The dual jaw joint was tentatively present in Pachygenelus.

Figure 4. Basal mammals and their proximal ancestors. Here taxa below Megazostrodon are mammals. Those above are not. Hadrocodium is uniquely reduced, but this occurs within the Mammalia.  The dual jaw joint was tentatively present in Pachygenelus.

According to the LRT,
there was no gradual ascent of monotremes leading to marsupials. Rather the monotreme-marsupial split occurred at the origin of mammals and monotremes. How this affects the genes for lactation discussed in the Zhou et al. paper is beyond the scope of this blogpost.

The purpose here
is to emphasize the importance of a broad, proper and valid phylogenetic context before proceeding to the narrow focus of your interests. 42 co-authors using cutting edge genomic techniques hobbled their otherwise excellent and in-depth report by skipping step number one.


References
Zhou Z et al. (41 co-authors) 2021. Platypus and echidna genomes reveal mammalian biology and evolution. Nature https://doi.org/10.1038/s41586-020-03039-0

 

Shocking news! The torpedo is a hammerhead!

This one came as a surprise
as I scored Tetronarce (= the New Zealand torpedo, an electric ray, Fig. 1), I thought:

  1. this taxon is breaking some rules, and
  2. I’ve seen that bizarre nasal before… but where?
Figure 1. Tetronarce fairchildi (originally Torpedo fairchildi Hutton 1872, 1m)

Figure 1. Tetronarce fairchildi (originally Torpedo fairchildi Hutton 1872, 1m). The long red elements are tabular homologs, separated from the rest of the skull.

Tetronarce fairchildi 
(originally Torpedo fairchildi Hutton 1872, 1m) is the extant New Zealand torpedo, an electric ‘ray’ on the outside. Here it nests with Sphyrna, the hammerhead shark, based on its skeleton. So this ‘ray’ is convergent with other rays. Note the broad nasals with open medial architecture, underslung jaws with tiny, single-cusp teeth and shark-like tail. Here the eyeball stalks are preserved, distinct from most other tetrapods tested in the LRT, probably due to careful dissection to get at its cartilaginous skeleton. Two dorsal fins are preserved.

Figure 1. The small hammerhead shark, Sphyrna tutus, is best appreciated in dorsal or ventral view.

Figure 1. The small hammerhead shark, Sphyrna tutus, is best appreciated in dorsal or ventral view.

Skates,
like the guitarfish, Rhinobatos, and the sawfish, Pristis, have an elongate narrow rostrum and nasal. Angel sharks and eagle rays have other distinguishing traits that nest them with each other and not with the aforementioned. So do manta rays. When more rays and skates are added to the LRT that may change. Or not.

Every possibility must always be left open,
as Torpedo gently, but firmly reminds us. Do not be tempted into “Pulling a Larry Martin” here. A short list of traits don’t make a taxon. Only a nesting in a wide gamut phylogenetic analysis can do that.

Yes, outward appearances are very different.
But when you look at the skeletons and test them in phylogenetic analysis no other taxon shares as many traits with hammerheads as torpedoes. Evolutiion leaves clues. It’s up to us to find them. You won’t find a similar laterally extended nasal with a perforated medial architecture in any other tested sharks or rays. Though many skeletal traits are indeed different, taken as a suite of characters no other tested taxon comes closer.

Figure 2. Skull of Sphyrna tutus in three views from Digimorph. org and used with permission. Colors added.

Figure 2. Skull of Sphyrna tutus in three views from Digimorph. org and used with permission. Colors added.

Sphyrna tudes 
(orignally Zygaena tudes Valenciennes 1822; 1.3m in length) is the extant smalleye hammerhead shark. It prefers muddy habitats with poor visibility. Sphyrna has a tendency to inhabit coastal waters along the intertidal zone rather than the open ocean, as their prey item, invertebrates, fish, rays, small crustaceans and other benthic organisms hide in the sands and sediment along these zones. Gestation is 10 months. Females produce 19 pups each year. The eyes and nares are further separated by the lateral expansion of nasals, prefrontals and postfrontals creating the cephalofoil. Compare to Torpedo (above).

The largely overlooked value of the LRT 
comes from testing together taxa that have never been tested together before with a generic character list not designed specifically for sharks and rays, other fish, birds and mammals. Convergence runs rampant in the Vertebrata. Scientists need a wide gamut cladogram that minimizes taxon exclusion and character selection bias.

By the present evidence
the former clade Batoidea has now been divided into quarters. This appears to be a novel hypothesis of interrelationships. If there is a prior publication, let me know so I can promote it.


References
Hutton FW 1872. Catalogue with diagnoses of the species. Ed. Hutton, FW and Hector J (eds), Fishes of New Zealand, pp. 1-88 pls 1-12, Colonial Museum and Geological Survey Department, Wellington.

wiki/Electric_ray
wiki/Sphyrna
wiki/Torpedo_fairchildi

A mystery fish, Stylephorus, enters the LRT as an oarfish-mimic lizardfish

Stylephorus chordatus
(originally Stylophorus chordatus (Shaw 1791, Regan 1924) is an elongate, oceanic fish rarely encountered either in the sea or in the library.

Figure 1. Stylephorus ontogeny and feeding

Figure 1. Stylephorus ontogeny and feeding

According to Wikipedia
“The tube-eye or thread-tail, Stylephorus chordatus, is a deep-sea fish, the only fish in the genus Stylephorus and family Stylephoridae.”

“It is found in deep subtropical and tropical waters around the world, living at depths during the day and making nightly vertical migrations to feed on plankton. It is an extremely elongated fish; although its body grows only to 28 cm (11 in) long, its pair of tail fin rays triple its length to about 90 cm (35 in). Its eyes are tubular in shape, resembling a pair of binoculars”

“It has a tubular mouth through which it sucks seawater by enlarging its oral cavity to about 40 times its original size. It then expels the water through the gills, leaving behind the copepods on which it feeds.”

Traditionally and due to taxon exclusion,
Stylephorus has been nested within the traditional clade Lampriformes (Fig. 2). In the large reptile tree (LRT, 1789+ taxa) members nest in at least three clades.

Figure 3. Traditional Lampriformes now distributed elsewhere in the LRT.

Figure 2. Traditional Lampriformes now distributed elsewhere in the LRT. White taxa have not yet been tested.

As in the telescope fish,
Gigantura (Figs. 2, 4), the eyes of Stylephorus are also elongate. The length of Stylephorus sans tail measures 10 to 11 inches. The tail extends this another 22 to 35 inches. Regan 1924 described Stylephorus from a one and only juvenile specimen (Fig. 1).

Figure 1. Gigantura indica overall. Note the pectoral fins above the gill openings and lack of pectoral fins.

Figure 3. Gigantura indica overall. Note the pectoral fins above the gill openings and lack of pectoral fins.

From the Regan 1924 abstract
“The fish known as Stylophorus chordatus was first described in 1791 by Shaw from a specimen taken swimming at the surface between the islands of Cuba and Martinique.  For more than a hundred years this was the only example known. It was preserved in the Museum of the Royal College of Surgeons, where it was examined by several ichthyologists, including Günther, who placed Stylophorus in the Trachypteridae (see below). In 1887 the specimen was transferred to the Natural History Museum; at some time or other it had been hacked about by an enthusiastic anatomist, so that in 1907, in a memoir on the anatomy and classification of the Allotriognathi, I wrote, “The remarkable Stylophorus has usually been placed with or near the Trachypteridae. The single known specimen is not in good enough condition for me to offer any suggestion as to its relationships.”

Trachypteridae are ribbon fish, characterized by “a long, compressed, tape-like body, short head, narrow mouth and feeble teeth”. Other traditional clade members include Zu cristatus, Trachipterus, and Desmodema (but see figure 2).

Figure 3. Stylophorus skull showing the extruding jaws, completely different from those of Gigantura, figure 4.

Figure 4. Stylophorus skull showing the extruding jaws, completely different from those of Gigantura, figure 4.

Miya et al. 2007 tested the DNA of the tube-eye. They wrote:
“The rare, monotypic deep-sea fish family Stylephoridae has long been considered a member of the order Lampridiformes (opahs, velifers, ribbonfishes), and no systematic ichthyologist has questioned its placement within the order for over 80 years… The resulting trees derived from partitioned Bayesian analyses strongly indicated that S. chordatus is not a lampridiform but is closely related to the order Gadiformes (cod and their relatives). Considering its unique morphologies with no indication of affinities within Gadiformes (or any other presently recognized order), the present results warrant a recognition of the new order for S. chordatus in fish systematics.”

In the LRT Stylephorus was tested against Gadus the Atlantic codfish (newly added, soon to be posted) and all other fish, including oarfish. Stylephorus nested with Gigantura.

Figure 2. Gigantura skull tracings from Konstantinidis and Johnson 2016. Colors added.

Figure 5. Gigantura skull tracings from Konstantinidis and Johnson 2016. Colors added.

Mooi and Gill 2010 wrote
“We contend that the move away from providing character evidence with phylogenies has diminished fish systematics and systematics in general, and amounts to a crisis.”

“The role of morphological characters has largely been reduced to their optimization and reinterpretation on the revealed “truth” of molecule-based topologies. All of this has resulted in a schism between molecular and morphological phylogeneticists.”

“We feel that phylogenetics can only move forward by recognizing that molecules are small-scale morphology; molecular data are not substantively different from larger-scale morphological data and should be treated in much the same manner. “

“Careful investigation of homology and transparent presentation of evidence will keep our work and our science relevant. “

Apparently no one has tested Gigantura 
( Figs. 3, 5, but see below). A wide gamut phylogenetic analysis always resolves and recovers relationships and weeds out convergence. On the other hand, taxon exclusion always leads to confusion.

Deleting Gigantura in the LRT
nests Stylelphorus between sticklebacks and sea horses (likely due to similar mouth parts), not far from oarfish (Regalecus). That’s why Stylephorus has been considered close to oarfish. In the LRT it is an oarfish mimic.

This is NOT a novel hypothesis of interrelationships. 
Long before the pre-cladistic era, Brauer (1901) compared Gigantura with Stylephorus because of their superficial resemblance (e.g. both species have anteriorly directed tubular eyes, silvery coloration, and elongated caudal fin rays). Let’s see if other workers add Gigantura to future Stylephorus analyses.


References
Brauer A 1901. Über einige von der Valdivia-Expedition gesammelte Tiefseefische und ihre Augen. Sitzungsberichte der Gesellschaft zur Beförderung der Gesamten Naturwissenschaften zu Marburg 8: 115–130.
Miya, M. et al. (11 co-authors) 2007. Mitochondrial genome and a nuclear gene indicate a novel phylogenetic position of deep-sea tube-eye fish (Stylephoridae). Ichthyological Research. 54 (4): 323–332.
Mooi RD and Gill AC 2010. Phylogenies without Synapomorphies—A Crisis in Fish Systematics: Time to Show Some Character. Zootaxa 2450:26–40.
Regan CT 1924. The morphology of the rare oceanic fish, Stylophorus chordatus, Shaw; based on specimens collected in the Atlantic by the “Dana” expeditions, 1920–1922. Proceedings of the Royal Society B 96(674): PDF
Shaw G 1791. Description of the Stylephorus chordatus, a new fish. Transactions of the Linnean Society of London, 2d Ser: Zoology 1:90–92.

wiki/Tube-eye

Stockdale and Benton 2021 explain why to avoid super trees and super matrices

…then Nature publishes their supertree/supermatrix
analysis of crocodilians and their ancestors using 175 source trees published since 2010.

Unfortunately
Stockdale and Benton presented their charts and graphs without a valid phylogenetic context due to massive outgroup taxon exclusion. Their in-group appears to be okay.

Stockdale and Benton report, 
“There is no published phylogenetic hypothesis that encompasses all Pseudosuchia, as well as molecular data from living taxa. Therefore, we estimated a new phylogenetic hypothesis for this study.”

Molecular studies rarely, if ever, replicate trait-based studies. It’s no exaggeration to report that everyone know this. So, why even waste time with molecular studies when dealing with deep time taxa?

“A matrix based approach was also ruled out, because collecting character data for such a large matrix from the literature and vetting characters for redundancy would have been impractical.”

Here’s a suggestion: Add all the taxa from the various source cladograms to one study and use only the characters from that one study until resolution starts to falter.

Or start with fewer taxa and fewer characters (about 200 each) to establish the tree topology. Then add more taxa. I can tell you from experience, this works.

“In addition, such a large matrix would have introduced a significant fraction of missing data, which could undermine the quality of a finished tree.”

Here’s a suggestion: employ relatively complete taxa to figure out the tree topology. Then add less complete taxa until resolution starts to falter.

“The phylogenetic hypothesis used in this study is based on a formal supertree analysis. Formal supertrees use a systematic approach to assimilating multiple smaller topologies into a single tree. Liberal formal supertree methods enable a well-resolved consensus topology to be estimated from source trees that are incongruent.”

Both supertree methods enable workers to trust prior studies, rather than examining specimens, photos and engravings. That’s antithetical to standards established by paleontologists for the rest of us.

“The supertree was estimated from a sample of 175 source trees published since 2010, each re-analysed from their original source matrices using Bayesian inference and the MK model. The supertree was dated using the equal method; the dated supertree contained a total of 579 archosauromorph taxa, including 24 extant species.”

And yet, despite their large taxon list, Stockdale and Benton managed to exclude a long list of outgroup taxa found to be pertinent by the LRT (subset Fig. 1), Missing taxa include many basal crocodylomorphs and outgroup poposaurs. Stockdale and Benton also omitted members of the only other clade in the Archosauria (by definition, as recovered in the LRT): Dinosauria. In other words, Herrerasaurus and Junggarsuchus should have been included. And where was Benton’s Scleromochlus?

“This tree was then trimmed to match the 280 pseudosuchian taxa included in the body size data. This phylogenetic approach was implemented to eliminate as many sources of error as possible.”

Trimmed? Sounds subjective. Don’t gloss over this point.

Source errors? The whole idea of using a super tree analysis is to avoid looking at taxa, photos of taxa or the literature. Why not at least peek at the taxa to double-check for possible source errors?

Figure x. Subset of the LRT focusing on Euarchosauriformes and Crocodylomorpha.

Figure 1. Subset of the LRT focusing on Euarchosauriformes and Crocodylomorpha. Fewer derived crocs here, but a wider gamut of outgroup taxa validate the LRT.

Stockdale and Benton (SuppData) report on
the “limitations of informal super trees”

“All supertrees, informal or otherwise, share a common drawback that they are dependent on the accuracy of the source trees from which they are estimated. This is especially true of informal trees where topology is copied from older publications, where the data or methodology may be outdated. Informal supertrees are also entirely subjective, and by definition bias analyses in favour of the author’s own views.”

True. So why didn’t Stockdale and Benton listen to themselves? Why did referees and editors permit this to be published?

Add taxa and the traditional clade ‘Pseudosuchia’ becomes invalid, polyphyletic.

“If there is controversy about the evolutionary relationships within a clade, the number of possible informal supertree topologies may become excessive.”

No. This is professional baloney. There is only one tree and it models actual evolutionary events. It’s our job to recover that one tree (subset Fig. 1).

“For example, the positions of several member clades within the Pseudosuchia differ between analyses. The Thalattosuchia have been resolved as a derived clade within the Neosuchia, a basal sister clade to the Crocodyliformes, or an intermediate clade within the Mesoeucrocodylia but outside the Neosuchia.” 

That means someone or several someones made a mistake. Fix the mistakes. See the Stockdale and Benton 2016 text for other examples they cite.

“It would be difficult to draw meaningful conclusions from so many trees if they are considered equally likely; it is therefore necessary to develop a consensus of these different viewpoints based on the strongest evidence.”

More subjective professional baloney. Consensus of viewpoints? How about just taking a quick peek at some specimens, photos of specimens or even drawings of specimens.

“Supermatrix approaches avoid many of the subjectivity issues associated with informal supertrees. Supermatrices lack a specific technical definition, however the term is broadly used to describe phylogenetic analysis of a single, comprehensive matrix. A supermatrix of the Pseudosuchia would require in excess of 500 taxa. Estimating such a large phylogenetic tree from a single matrix represents a formidable challenge, either in the sheer number of fossils to be examined and their characters scored, or by the integration of existing matrices.”

Quit whining! Do the work. The LRT passed 500 total taxa eight years ago and now includes 3-4x that number (including pterosaurs and therapsid skulls).

Here’s a suggestion: Start with 150 to 200 taxa. That will get you will started with a rough estimate of the final tree topology. Later adding taxa one or two at a time will slowly fill in the gaps and solidify the tree topology.

If two taxa are nearly identical in every detail, they are probably related. Drop one. Pick it up later if you really need to.

First attend to the basic problems. The Stockdale and Benton study has basic issues based on taxon exclusion among outgroup taxa. The ingroup taxon list appears to be just fine.

“Very large morphological character matrices present a significant problem in the accumulation of inapplicable characters.For example, a matrix of crocodile-line archosaurs would likely contain characters relating to the morphology of osteoderms, despite osteoderms being absent in some members.”

That’s no problem for the LRT. For example, the score ‘absent’ is available where appropriate. Consider this paper an example and cautionary tale showing how to get published while whining about what not to do.

“Therefore, it is not reasonable to assume that the time invested in building a very large supermatrix will be rewarded with a high quality phylogenetic analysis.”

This statement was falsified by the LRT with over 2000 taxa. Just do the work. Show your work. Repair bad scores. Report results. If you don’t get one tree go back in there and figure out what went wrong. If a skull-only taxon nests with a skull-less taxon, eliminate one of them.

“Conservative approaches handle incongruences between source trees by presenting them as unresolved nodes in the final topology.”

If something is wrong, fix it. Do the work. Don’t let bad data infiltrate your matrix.

“The MRP method is an example of a liberal supertree approach, where incongruences between source trees are resolved democratically, with the better-supported topology being retained in the final supertree. The MRP method is a pragmatic choice, since it can be implemented using readily available software without consuming excessive computer processing power.”

If something is wrong, fix it. Do the work. Don’t let bad data infiltrate your matrix.

“Studies sceptical of supertrees, such as Gatesy et al., have concluded that these issues are insurmountable and that supertree methods should be avoided altogether.”

Just do the work. Don’t rely on, or trust the work of others.

“A rebuttal by Bininda-Emonds et al. concluded that these problems could be mitigated through careful source tree selection protocols and stated that supertrees are a necessity due to the inherent impracticality of super matrices.”

Stockdale and Benton don’t want to do the necessary work.

From the Stockdale and Benton Discussion Section:
“The supertree identifies the Phytosauria as a monophyletic group within Pseudosuchia, closer to extant crocodilians than to Avemetatarsalia.”

Adding missing taxa (as in the LRT) separates Phytosauria from all other included taxa. “Pseudosuchia” becomes an invalid polyphyletic clade when missing taxa are included. “Avemetatarsalia” is a junior synonym for the older clade Reptilia when missing taxa are included. Professor Benton is infamous for cherry-picking taxa. Better to let a wide gamut analysis tell you which taxa to include and exclude.

As described early in 2012,
adding pertinent taxa separate Pararchosauriformes (Proterosuchus is the last common ancestor) from the Euarchosauriformes (Euparkeria is the last common ancestor). Neither of these taxa are in the Stockdale and Benton taxon list. Their last common ancestor is Younginoides. The clade Archosauriformes begins there. The rest follow (Fig. 1).

Stockdale and Benton attempted to describe
environmental drivers of body size in crocs. Unfortunately, without a valid phylogenetic context, and omitting so many pertinent taxa, the rest of the information they so carefully prepared is hobbled by their own self-confessed lack of effort.

Don’t whine about doing the necessary work.
Get the broad basics right. The you’ll have that powerful cladogram for the rest of your career. Only then do the more focused work.


References
Bininda-Edmons ORP et al. (7 co-authors) 2003. Supertrees are a necessary not-so- evil: a comment on Gatesy et al. Syt. Bio. 52, 724-729. [not sure how this 2003 comment precedes the Gatesy et al. 2004 paper].
Gatesy J, Baker RH and Hayashi C 2004. Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia. Syt. Bio. 53:342-355.
Stockdale MT and Benton MJ 2021. Environmental drivers of body size evolution in crocodile-line archosaurs. Nature Communications Biolody 4:38 https://doi.org/10.1038/s42003-020-01561-5 

https://pterosaurheresies.wordpress.com/2012/01/13/introducing-the-pararchosauriformes/

Some news sources took the bait.
Since Scleromochlus and other basal bipedal crocs were not included, the headline in The Conversation is bogus. Here’s what The Conversation reported.

 

 

 

 

 

Firsthand observation of Gigantura vs. phylogenetic bracketing in the LRT

Konstantinidis and Johnson 2016 report:
“The goal of this paper is to provide a detailed description of the osteology of adult giganturids to resolve the identification and homology of skeletal elements, particularly those of the upper jaw. Based on topological evidence, we conclude that the premaxilla is absent and that the major tooth-bearing bone in the ‘upper jaw’ is the palatine.”

Figure 1. Gigantura indica overall. Note the pectoral fins above the gill openings and lack of pectoral fins.

Figure 1. Gigantura indica overall. Note the pectoral fins above the gill openings and lack of pectoral fins.

By contrast,
phylogenetic bracketing in the large reptile tree (LRT, 1788+ taxa) indicates the traditional interpretation of a large, toothy premaxilla in Giganturus (Figs. 1,2; Brauer 1901Konstantinidis and Johnson 2016; 20 cm long) is correct. Related taxa in the LRT, like Chiasmodon (Fig. 4) and Calamopleurus (Fig. 5) have a similar large, toothy premaxilla and no trace of a large toothy palatine.

This argument
has been going on for several decades in the fish community and will likely not be settled here. Konstantinidis and Johnson 2016 go into great detail regarding the pros and cons of previous and (then) current arguments. For instance they report, “The second problem is more complex and relates to the fact that unbeknownst to Rosen, his ‘juvenile’ Trachinocephalus was in fact still in the larval stage. The placement and arrangement of the infraorbitals undergo major changes ontogentically in synodontids, and those of Rosen’s specimen had not yet transformed.” 

This might require phylogenetic analysis of larval, juvenile and adult specimens.

Or not. Some bones and larvae may have been misidentified.

Figure 2. Gigantura skull tracings from Konstantinidis and Johnson 2016. Colors added.

Figure 2. Gigantura skull tracings from Konstantinidis and Johnson 2016. Colors added.

Konstantinidis and Johnson 2016 report,
“The systematic position of Gigantura has been problematic, in large part because of its bizarre morphological specializations and extreme reduction of many skeletal elements, especially in the skull region.”

There is no extreme reduction, especially in the skull region,demonstrated in the LRT. Sister taxa and related taxa have similar skulls. A valid phylogenetic context is essential before making pronouncements and creating hypotheses. I suspect this issue may be at the base of their arguments.

Figure 3. Konstantinids and Johnson 2016 considered this specimen to be a Gigantura larva. This is a dubious observation.

Figure 3. Konstantinids and Johnson 2016 considered this specimen to be a Gigantura larva. This is a dubious observation. No Gigantura relatives have such tiny eyes set so far back on the skull, among many other traits.

Konstantinidis and Johnson 2016
made comparisons to Bathysaurus (Fig. 6, the deep-sea lizard fish, not related to lizard fish like Trachinocephalus). Bathysaurus has not been tested in the LRT yet, but it does not appear to be related to the clade that includes Gigantura and other fish with large orbits longer than the rostrum length. Rather, Bathysaurus appears to be related to the tripod fish, Bathypterois, which nests with anglers and other taxa unrelated to Gigantura in the LRT.

Note the similarity of the purported Gigantura larva (Fig. 3) to anglers. Maybe this is part of the problem. No cladogram was presented by Konstantinidis and Johnson 2016.

Figure 2. Chiasmodon from Gregory 1938, here colorized. Compared to the lizardfish, Trachinocephalus, in figure 3.

Figure 4. Chiasmodon from Gregory 1938, here colorized. Compared to the lizardfish, Trachinocephalus, in figure 3.

Figure 5. Calamopleurus (Cretaceous) an outgroup taxon to Chiasmodon + Gigantura.

Figure 5. Calamopleurus (Cretaceous) an outgroup taxon to Chiasmodon + Gigantura.

Figure 6. Bathysaurus ferox has not been tested in the LRT, but does not appear to be similar to members of the clade that include Gigantura.

Figure 6. Bathysaurus ferox has not been tested in the LRT, but does not appear to be similar to members of the clade that includes Gigantura.

Figure 1. Bathypterois, the deep sea tripod fish, shown with diagram of jaws and palate from Sulak 2006, then colored and matched to the in vivo specimen.

Figure 7. Bathypterois, the deep sea tripod fish, shown with diagram of jaws and palate from Sulak 2006, then colored and matched to the in vivo specimen.

The clade that includes Gigantura
is among the oldest and most primitive of all bony fish, not far from hybodontid sharks. Related clades include spiny sharks (Acanthodii). The Gigantura clade precedes the major split between the Amia clade of ray fin fish and the other unnamed clade that produced lobefins and placoderms along with several other ray fin fish.


References
Brauer A 1901. Über einige von der Valdivia-Expedition gesammelte Tiefseefische und ihre Augen. Sitzungsberichte der Gesellschaft zur Beförderung der Gesamten Naturwissenschaften zu Marburg 8: 115–130.
Konstantinidis P and Johnson GD 2016. Osteology of the telescope fishes of the genus Gigantura (Brauer, 1901), Teleostei: Aulopiformes. Zoological Journal of the Linnean Society 179(2):338–353.

wiki/Telescopefish = Gigantura

Where do Porolepiformes fit into the LRT?

Traditioinally there are four types of lobefin fish:

  1. Actinista = coelocanths (e.g. Latimeria, Fig. 1)
  2. Dipnoi = lungfish (e.g. Polypterus, Fig. 1)
  3. Osteolepiformes = stem tetrapods (e.g. Osteolepis, Fig. 1)
  4. Porolepiformes = all extinct (e.g. Porolepis, Fig. 1)
Figure 1. Lobefin fish clades in this subset of the LRT.

Figure 1. Lobefin fish clades in this subset of the LRT.

A fifth clade of lobefin fish
was recovered by the large reptile tree (LRT, 1787+ taxa, subset Fig. 1). The Stensioella + Guiyu clade does not nest with placoderms, as other workers posit. Those workers consider Stensioella ‘enigmatic’ and ‘with arcane affinity’. In the LRT Stensioella does not nest with coelochanthiformes either, but with Youngolepis, Guiyu and other flattened big-flipper fish, most of which do not preserve post-crania.

Getting back to Porolepiformes…
This clade starts with a Carboniferous late survivor of a Silurian radiation, Allenypterus (Fig. 2). This odd sort of ‘traditional coelocanth’ had a straight, eel-like tail, a tall, narrow torso and lobe pectoral fins only.

Figure 2. Allenypterus nests with the coelacanth lobefins in the LRT and elsewhere.

Figure 2. Allenypterus nests with the coelacanth lobefins in the LRT and elsewhere.

Quebecius
(Fig. 3) had lobe-fin pectoral fins, but all other fins were ray fins. The body was rounder in cross-section and the eyes were relatively smaller. Marginal teeth were tiny on longer jaws.

Figure 2. Quebecius is similar in most respects to Diplacanthus. The pectoral fin still has a pointed appearance, but the other fins have more typical rays.

Figure 3. Quebecius is similar in most respects to Diplacanthus. The pectoral fin still has a pointed appearance, but the other fins have more typical rays.

Holoptychius serrulatus
(Agassiz 1839, Cope 1897; Middle Devonian to Carboniferous, 50cm to 2.5m long, Fig. 4) had lobe-fins only. The anterior skull + body was rounder in cross-section and the eyes were relatively smaller. This genus is found in marine sandstone. Tiny teeth lined the jaws, but are rarely illustrated due to their minuscule size. Large fangs descend from the palate and rise from the coronoids.

Figure 2. Holoptychius is a basal lobefin in the coelacanth clade.

Figure 4. Holoptychius is a basal lobefin in the coelacanth clade.

Porolepis posnaniensis
(Kade 1858, named by Woodward 1891; Early Devonian, Fig. 5) apparently had a post-crania similar to Holoptychius. They eyes continued their decline in size. Colors are tetrapod homologs often different than labels. The upper squamosal is here the postorbital.

Figure 2. Holoptychius and Porolepis skulls compared.

Figure 5. Holoptychius and Porolepis skulls compared.

Laccognathus panderi 
(Gross 1941,Vorobyeva 2006, Down et al. 2011; Middle to Late Devonian, 390-360mya, Figs. 5, 6) was a marine costal or lagoon bottom dweller with an even wider skull, even smaller eyes and large palatal and coronoid fangs. The two external nares are confluent. Post-crania is largely unknown.

Figure 3. Laccognathus diagram from Downs et al. 2011. Colors and tetrapod homolog labels added.

Figure 6. Laccognathus diagram from Downs et al. 2011. Colors and tetrapod homolog labels added.

Figure 5. Laccognathus specimen in situ from Downs et al. 2011. Colors added.

Figure 7. Laccognathus specimen in situ from Downs et al. 2011. Colors added.

According to Wikipedia
“Porolepiformes was established by the Swedish paleontologist Erik Jarvik (1980), and were thought to have given rise to the salamanders and caecilians independently of the other tetrapods. He based this conclusion on the shapes of the snouts of the aforementioned groups. This view is no longer in favour in Paleontology (Schultz and Trueb 1991).”

“Jarvik also claimed the existence of choanae in porolepiformes which linked them to tetrapods, but this has remained controversial. (Clement 2001). Recent phylogenetic reconstruction places porolepiformes close to lungfishes (Janvier 1996).”

In the LRT 
porolepiformes are closer to coelacanths, catfish and placoderms. Lungfish are closer to tetrapods. Choanae are not present in porolepiformes (Clement 2001).


References
Ahlberg PE1991. A re-examination of sarcopterygian interrelationships, with special reference to the Porolepiformes.
–Zoological Journal of the Linnean Society: Vol. 103, #3, pp. 241-287 [doi: 10.1111/j.1096-3642.1991.tb00905.x]
Clement G 2001. Evidence for lack of choanae in the Porolepiformes. Journal of Vertebrate Paleontology, 21: 795–802.
Downs J, Daeschler E, Jenkins F Jr and Shubin N 2011. A New Species of Laccognathus(Sarcopterygii, Porolepiformes) from the Late Devonian of Ellesmere Island, Nunavut, Canada. Journal of Vertebrate Paleontology. 31 (5): 981–996.|
Janvier P 1996. Early vertebrates. Oxford science publications. 1996, Oxford, New York: Clarendon Press; Oxford University Press.|
Jarvik E 1980. Basic structure and evolution of vertebrates. Vol. 1-2. Academic Press (London).
Schultze H-P and Trueb L1991. Origins of the higher groups of tetrapods: controversy and consensus. Cornell University Press. p. 37.
Vorobyeva EI 2006. A new species of Laccognathus (Porolepiform Crossopterygii) from the Devonian of Latvia. Paleontol. J. Physorg.com. 40 (3): 312–322. doi:10.1134/S0031030106030129.
Woodward AS 1891. Catalogue of the Fossil Fishes in the British Museum (Natural History). Part II. Catalogue of the Fossil Fishes in the British Museum (Natural History) 2.

wiki/Porolepiformes
wiki/Porolepis
wiki/Holoptychus
wiki/Allenypterus
wiki/Quebecius
wiki/Actinistia
wiki/Coelocanth