Recalibrating clade origins, part 2

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

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

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

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

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

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

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

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

Figure 3. Tersomius texensis, an amphibamid lepospondyl close to Dendrerpeton.

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

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

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

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

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

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

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

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

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

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

The LRT does not include pertinent taxa surrounding this split.

Figure 1. Megapodius is the extant bird nesting at the base of all neognathae (all living birds except ratites).

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

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

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

More tomorrow…


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

Recalibrating clade origins, part 1

Marjanovic 2019 reports on
the origin of several clades based on the fossil literature and molecules.

From the abstract:
“Molecular divergence dating has the potential to overcome the incompleteness of the fossil record in inferring when cladogenetic events (splits, divergences) happened, but needs to be calibrated by the fossil record.”

Testing has shown molecular testing leads to false positives over deep time. Phylogenetic testing using the large reptile tree (LRT, 1630+ taxa) has also shown the fossil record to be, at this date, more complete than Marjanovic (and, no doubt, others) imagine with no new clades appearing for quite some time and all known clades demonstrating a gradual accumulation of traits in the LRT.

“Ideally but unrealistically, this would require practitioners to be specialists in molecular evolution, in the phylogeny and the fossil record of all sampled taxa, and in the chronostratigraphy of the sites the fossils were found in.”

Ideally, but unrealistically, paleontologists would be better off omitting genomics and focusing on taxon exclusion within phenomics (trait-studies).

“Paleontologists have therefore tried to help by publishing compendia of recommended calibrations, and molecular biologists unfamiliar with the fossil record have made heavy use of such works.”

To their detriment and the deliver of false positives.

“Using a recent example of a large timetree inferred from molecular data, I demonstrate that calibration dates cannot be taken from published compendia without risking strong distortions to the results, because compendia become outdated faster than they are published.”

It is strongly recommended that no one infer anything from molecular data, including Dr. Marjanovic.

“The present work cannot serve as such a compendium either; in the slightly longer term, it can only highlight known and overlooked problems.”

The number one overlooked problem is genomics.

“Future authors will need to solve each of these problems anew through a thorough search of the primary paleobiological and chronostratigraphic literature on each calibration date every time they infer a new timetree; over 40% of the sources I cite were published after mid-2016. Treating all calibrations as soft bounds results in younger nodes than treating all calibrations as hard bounds.”

All calibrations involving genomics are going to have to be validated with last common ancestors recovered from phenomics. So, why not skip a step and just use phenomics?

“The unexpected exception are nodes calibrated with both minimum and maximum ages, further demonstrating the widely underestimated importance of maximum ages in divergence dating.”

Now let’s see what Marjanovic discovered, because his abstract does not give a clue. It’s an introduction, not a boiled-down synthesis. Comparisons with the LRT will be noted. Marjanovic’s cladogram is the first to include as wide a gamut as the LRT while employing only generic taxa. Unfortunately no fossil taxa are included. Only ten mammals and six birds are included.

Distinct from the LRT, the Marjanovic cladogram
nests turtles with archosaurs (creating the invalid clade, Archelosauria).

More tomorrow…


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

Tungsenia, the earliest stem tetrapod?

This appears to be another case of
taxon exclusion.

Lu et al. 2012
considered Tungsenia paradoxa (Early Devonian; Fig. 1) the earliest known stem-tetrapod (= taxa closer to tetrapods than to lungfish; Fig. 2).

By contrast
in the large reptile tree (LRT, 1630+ taxa; not yet updated) Tungsenia nests with similar and coeval stem-lungfish like Youngolepis (1981), Kennicthys (1993) and Guiyu (2009, Fig. 3), which was published three years earlier and found in Late Silurian strata. So Tungsenia is not the oldest member of this clade either.

Lu et al. considered Guiyu
a basal osteichichthyan (not related to stem-lungfish + stem tetrapods) and together with Psarolepis, made these outgroup taxa in their analysis. The stem tetrapods, Cabbonichthys (1997) and Tinirau (2012) are not mentioned in the Lu et al. text, the latter due to a later publication date.

Figure 1. Skull of Tungsenia from Lu et al. 2012. Tetrapod skull colors added and restored based on related taxa. Here the tooth-bearing portion of the premaxilla is missing. So are the vomers, which may have had fangs, like those of Youngolepis (Fig. 4),

Figure 1. Skull of Tungsenia from Lu et al. 2012. Tetrapod skull colors added and restored based on related taxa. Here the tooth-bearing portion of the premaxilla is missing. So are the vomers, which may have had fangs, like those of Youngolepis (Fig. 4),

Lu et al. were working from a traditional paradigm
that nested rhizodontids, like Barameda, with stem tetrapods. The LRT nests rhizodontids at a more basal node than stem lungfish + stem tetrapods due to the addition of several more basal chordate and basal vertebrate taxa that resolve the basal dichotomy between many ray fin fish and the rest of the ray fin fish + lobe fin fish.

Figure 2. Cladogram from Lu et al. 2012. Overlay approximates the new topology based on the LRT.

Figure 2. Cladogram from Lu et al. 2012. Overlay approximates the new topology based on the LRT. Frame changes every 5 seconds.

In the LRT
the cladogram of basal vertebrates (= fish) differs from traditional cladograms due to the addition of taxa not traditionally tested together. That means if workers expand their taxon list to more or less match the LRT they, too, should recover a similar tree topology. If anyone tries this, let me know your progress, issues, etc.

Lu et al. report,
“Tungsenia resembles Kenichthys, and basal dipnomorphs (for example, Youngolepis and Powichthys) in the medioventrally directed snout, the infraorbital sensory canal running along the suture between the premaxillary and neighbouring bones, the broad orbital tectum and the well-developed basipterygoid processes.” 

Adding taxa
brings more taxa, including Tungsenia, into the stem-lungfish clade.

Figure 1. Feeding strategies for basal vertebrates (fish).

Figure 3. Feeding strategies for basal vertebrates (fish). Stem tetrapods are not shown here, but nest at the lower left. Tungsenia is not listed here, but nests with Youngolepis.

Figure 4. Youngolepis skull. Colors added.

Figure 4. Youngolepis skull. Colors added. Distinct from Tungsenia, Youngolepis had a shorter skull and preserved more jaw elements.


References
Lu J, Zhu M, Long JA, Zhao W, Senden TJ, Jia L and Qiao T 2012. The earliest known stem-tetrapod from the Lower Devonian of China. Nature Communications. 3: 1160. doi:10.1038/ncomms2170

wiki/Tungsenia

Hydrolycus armatus: my what big teeth you have!

Figure 1. Hydrolycus, the dogtooth characin of South America.

Figure 1. Hydrolycus, the dogtooth characin of South America.

Figure 2. Hydrolycus face showing the outsized lower fangs.

Figure 2. Hydrolycus face showing the outsized lower fangs.

Hydrolycus armatus (Jardine 1841, typically .9m, up to 1.1m in length) is the extant dogtooth characin or payara of tropical South America. Here it nests with Amia, the bowfin. The skull is taller and narrower. The anterior teeth are longer. The maxilla extends to the quadrate. The jugal is absent. The postorbital is tiny. The intertemporal, supratemporal and tabular are reduced to narrow rods. A parietal crest is present. The lacrimal is crescent-shaped.

Figure 3. Hydrolycus skull with colors added.

Figure 3. Hydrolycus skull with colors added. That short premaxilla marks this taxon as a basal teleost.

The long teeth
are used for spearing piscine prey.


References
Jardine W 1841. Naturalist’s Library: Ichthyology, Edinburgh.

wiki/Hydrolycus_armatus
wiki/Amia

Revisiting the Dendromaia tiny den-mate

Earlier I attempted a tracing of the 2cm skull of the Dendromaia (Maddin et al. 2020; Figs. 1–3) small den-mate using a low resolution image. That didn’t work out well due to using only one plate and misinterpreting the subtle grays in the photo. Even so, oddly enough, the error-filled scoring nested the small skull close to the same taxa that Maddin et al. nested the specimen.

As you might remember,
the much larger den-mate nested in the large reptile tree (LRT, 1628+ taxa) with Acleistorhinus and other skull-only taxa between the more complete Casea, Eocasea and Eunotosaurus taxa. The large den-mate was probably an herbivore based on phylogenetic bracketing. The tiny den-mate was a likely insectivore.

Today
with higher resolution images of the part and counterpart mated together in Photoshop layers (Fig. 1), the skull of the small den-mate is re-traced and reconstructed in much greater detail. (Still far from perfect.) The resulting plate and counter plate preserve the palate and the mandibles respectively in ventral view. Dorsal sutures are unknown.

Figure 1. The small den mate assigned to the genus Dendromaia traced using DGS methods and reconstructed in figure 2.

Figure 1. The small den-mate assigned to the genus Dendromaia traced using DGS methods and reconstructed in figure 2. Details are difficult to interpret. As before, this is a best guess based on current data.

Details are still difficult to interpret.
As before, this is a best guess based on current data. Now the small Late Carboniferous den-mate nests between two other much larger skull taxa both assigned to the genus Varanosaurus, known from Early Permian skeletons. So the small den-mate must be congeneric with Varanosaurus. The small size of the small den-mate is probably due to its young ontogenetic age.

These taxa are basal synapsids (in the lineage of humans), not protodiapsids.

Figure 3. The small den mate nests between these two specimens assigned to Varanosaurus.

Figure 2. The small den-mate nests between these two specimens assigned to Varanosaurus.

Morphologically flat skulls,
like those in Varanosaurus (Fig. 2) and the small den-mate (Fig. 3), tend to fossilize in dorsal or palatal view (Fig. 1). The shape of the mandible informs the reconstructed width of the skull. The dorsal sutures are best guesses based on phylogenetic bracketing.

Figure 3. Reconstruction of the small den mate based on DGS tracings in figure 1.

Figure 3. Reconstruction of the small den-mate based on DGS tracings in figure 1.

The number of mistakes I’ve made
and corrected over the last eight years is now deep into six figures. These corrections are just the latest set to get corrected. Few other workers are attempting to identify bones to this degree on such tiny specimens. There’s no blueprint for this. Everyone who attempts such tracings are on their own. You might try practicing on some roadkill for starters.


References
Maddin HC, Mann A and Hebert B 2020. Varanopid from the Carboniferous of Nova Scotia reveals evidence of parental care in amniotes. Nature ecology & evolution 4:50–56.

wiki/Varanosaurus
wiki/Dendromaia (not yet posted)

The snakehead (genus: Channa) enters the LRT

Nicknames include
“Frankenfish” and “the fish from Hell”, as if ‘snakehead’ wasn’t evil-sounding enough.

Toothy
Channa (Scopoli 1777) enters the large reptile tree (LRT, 1627+ taxa) basal to all other Teleostei other than the bowfin, Amia, and the Cretaceous ‘swordfish’, Polysphyraena.

Figure 1. Skull of the snakehead fish, Channa, with DGS colors applied.

Figure 1. Skull of the snakehead fish, Channa, with DGS colors applied. Powerful jaw muscles and large teeth characterize this skull.

Channa (Figs. 1, 2) is transitional
and proximally basal to the equally toothy wolffish, Anarchias (Fig. 3) and another ocean-going predator, the swift mahi-mahi, Coryphaena.

Figure 2. Channa andrao in vivo.

Figure 2. Channa andrao in vivo.

Channa sp(Scopoli 1777; 25 cm to 1+m) is the extant snakehead, a predatory freshwater fish nesting here between the bowfin (Amia) and the wolffish (Anarchias). This fish can breathe air and travel across land for short distances seeking new ponds, but this is rare as the pectoral fins are weak and poorly angled for this.

Figure 3. The skull of the wolffish, Anarhichas.

Figure 3. The skull of the wolffish, Anarhichas, usually found in oceanic caves. These are some of the largest teeth in Teleostei, a clade known generally for tiny teeth or no teeth at all. 

Like the bowfin and wolffish,
the dorsal and anal fins are long. The pelvic fins are absent only in some species. Teeth are present on the parasphenoid.

Early Eocene fossils are known,
but the genesis of this genus extends back to the Devonianb based on phylogenetic bracketing. Living relatives include the climbing perch, gouramis and Siamese fighting fish. These are considered members of the Percomorpha, but Channa is not related to Perca in the LRT.


References
Scopoli JA 1777. Introdvctio ad historiam natvralem sistens genera lapidvm, plantarvm, et animalivm hactenvs detecta, caracteribvs essentialibvs donata, in tribvs divisa, svbinde ad leges natvrae. – pp. [1-9], 3-506, [1-34]. Pragæ. (Gerle).

wiki/Channa
wiki/Snakehead_(fish)

Dendromaia: Not mother + juvenile… just roommates

Updated December 26
with new tracings of the small den-mate now nesting as a juvenile Varanosaurus in the LRT.

Figure 1. The large and small Dendromaia specimens in part and counterpart, traced using DGS methods.

Figure 1. The large and small Dendromaia specimens in part and counterpart, traced using DGS methods.

Dendromaia unamakiensis made big news
this week by with headlines like:

  1. 305-Million-Year-Old Fossil Shows Parent Caring for Its Offspring
  2. 300m-year-old fossil is early sign of creatures caring for their young
  3. New Fossil Shows Parental Care Is At Least 300 Million Years Old

That’s the paleo PR machine at work.

Figure 2. Partial reconstructions of the two specimens found together in figure 1.

Figure 2. Partial reconstructions of the two specimens found together in figure 1. The LRT separates these taxa phylogenetically, so the large one is not the parent of the small one, contra Maddin et al. 2020.

Unfortunately,
when both the little one and the big one were added to the large reptile tree (LRT, 1625+ taxa), only the little one nested near where Maddin, Mann and Hebert 2020 recovered it. They were using a taxon list that excluded too many taxa in comparison to the LRT.

Figure 3. Skull of the small specimen. In the LRT it nests with Heleosaurus within the Protodiapsida, a clade not recognized by Maddin et al. due to taxon exclusion.

Figure 3. Skull of the small specimen. In the LRT it nests with Heleosaurus within the Protodiapsida, a clade not recognized by Maddin et al. due to taxon exclusion.

From the Maddin et al. abstract:
“Here we report on a fossil synapsid, Dendromaia unamakiensis gen. et sp. nov., from the Carboniferous period of Nova Scotia that displays evidence of parental care—approximately 40 million years earlier than the previous earliest record based on a varanopid from the Guadalupian (middle Permian) period of South Africa. The specimen, consisting of an adult and associated conspecific juvenile, is also identified as a varanopid suggesting parental care is more deeply rooted within this clade and evolved very close to the origin of Synapsida and Amniota in general. This specimen adds to growing evidence that parental care was more widespread among Palaeozoic synapsids than previously thought and further provides data permitting the identification of potential ontogeny-dependent traits within varanopids, the implications of which impact recent competing hypotheses of the phylogenetic affinities of the group.”

The Maddin et al. cladogram
did not test both specimens separately. The Maddin et al. results nested Dendromaia with the poorly preserved Pyozia near the base of their Varanopidae.

The small specimen
The LRT nested the small specimen (Fig. 1) with Heleosaurus, sharing some traits with sister Mesenosaurus. These nest with other protodiapsids apart from Varanops and the Varanopidae in the clade Synapsida. Protodiapsids and synapsids are both derived from a sister to Vaughnictis their last common ancestor in the LRT.

The large specimen
The LRT nested the large skull-less specimen with several skull+pecs and skull-only taxa (Delorhynchus, Microleter and Acleistorhinus) close to the turtle mimics Eunotosaurus and Eorhynchochelys, which preserve post-crania.

So…
these two roommates are not conspecific parent and young, but distinctly different genera sharing a space. The larger one likely dug the tunnel. The smaller one likely found safe harbor under the thigh of the large one, a robust herbivore based on phylogenetic bracketing.

Perhaps
Maddin et al. might have come to the same conclusion if they had tested the two taxa separately… just to be sure their assertion was confirmed phylogenetically… and added enough taxa to recover a correct tree topology. That’s what the LRT is here for.


References
Maddin HC, Mann A and Hebert B 2020. Varanopid from the Carboniferous of Nova Scotia reveals evidence of parental care in amniotes. Nature ecology & evolution 4:50–56.

http://www.sci-news.com
https://www.theguardian.com
https://www.iflscience.com

The affinities of ‘Parareptilia’ and ‘Varanopidae’: Ford and Benson 2020

Readers will know the knives are out for this one
by Ford and Benson 2020 since the large reptile tree (LRT, 1625+ taxa) finds the Parareptilia is polyphyletic and the Varanopidae (1940) is a junior synonym for Synapsida (1903). And yes, Ford and Benson’s cladogram (Fig. 1) suffers from (altogether now): taxon exclusion. The Ford and Benson paper, like many before it, keeps perpetuating the myth of the Parareptilia and other traditional clades.

Figure 1. Cladogram by Ford and Benson 2020, with orange overlay showing taxa in the Archosauromorpha in the LRT. Massive taxon exclusion is the problem with the Ford and Benson tree.

Figure 1. Cladogram by Ford and Benson 2020, with orange overlay showing taxa in the Archosauromorpha in the LRT. Massive taxon exclusion is the problem with the Ford and Benson tree.

From the abstract:
“Amniotes include mammals, reptiles and birds, representing 75% of extant vertebrate species on land. They originated around 318 million years ago in the early Late Carboniferous and their early fossil record is central to understanding the expansion of vertebrates in terrestrial ecosystems.

By contrast, in the LRT the last common ancestor of all amniotes (= reptiles) is Silvanerpeton from the Viséan (Early Carbonferous, 335mya, not listed in Fig. 1) with a likely genesis earlier since the Viséan includes several other  amphibian-like reptiles, also not listed. Ford and Benson need to dip much deeper into the basal Tetrapoda to figure out which taxon is the last common ancestor of the Amniota and which taxa precede it. They make the mistake of considering Tseajaia and Limnoscelis pre-amniotes.The LRT nests them both deep within Amniota / Reptilia.

“We present a phylogenetic hypothesis that challenges the widely accepted consensus about early amniote evolution, based on parsimony analysis and Bayesian inference of a new morphological dataset.”

That would be great, so long as they include pertinent taxa, which they do not.

“We find a reduced membership of the mammalian stem lineage, which excludes varanopids.”

That’s odd because when you add pertinent taxa, the LRT finds an increased membership in the diapsid/mammal stem lineage, the new Archosauromorpha.

“This implies that evolutionary turnover of the mammalian stem lineage during the Early–Middle Permian transition (273 million years ago) was more abrupt than has previously been recognized.”

No one can make valid implications from the Ford and Benson cladogram. It is largely incomplete.

“We also find that Parareptilia are nested within Diapsida.”

This is only possible due to massive taxon exclusion. Ford and Benson omit many taxa that would change the topology of their tree. The Parareptilia include a diverse and polyphyletic assembly of taxa according to the LRT. Ford and Benson are not aware that Lepidosauria are no longer members of the archosauromorph Diapsida.

“This suggests that temporal fenestration, a key structural innovation with important functional implications, evolved fewer times than generally thought, but showed highly variable morphology among early reptiles after its initial origin.”

Just the opposite. In the LRT fenestration evolved MORE times than generally thought.

“Our phylogeny also addresses controversies over the affinities of mesosaurids, the earliest known aquatic amniotes, which we recover as early diverging parareptiles.”

That can only happen with massive taxon exclusion. We’ve known for several years that mesosaurs nest as derived pachypleurosaurs close to thalattosaurs and ichthyosaurs in the LRT. Those pertinent taxa are omitted in Ford and Benson’s paper.

From the introduction:
“The current paradigm of early amniote evolution was established in the late twentieth century. It includes a deep crown group dichotomy between Synapsida (total group mammals) and Reptilia (total group reptiles, including birds), followed by an early divergence of Parareptilia from all other reptiles (Eureptilia).”

Add taxa and the first dichotomy separates the new Archosauromorpha from the new Lepidosauromorpha. This has been online since July 2011 and represents the current paradigm. Ford and Benson are digging into old myths and traditions.

“Furthermore, both molecular and morphological studies have recovered turtles, which lack fenestrae, as diapsids.”

Since molecular studies do not replicate trait studies in deep time molecular studies must be wrong (probably due to epigenetics) and do not employ fossil taxa. So forget genomics in paleontology. Genomics delivers false positives.

“Our analysis includes 66 early fossil members of the amniote crown group, and four crownward members of the amniote stem group, giving a total of 70 operational taxonomic units.” 

By contrast the LRT includes 1625+ taxa not biased by prior studies, including dozens of basal vertebrates and basal tetrapods.

“The goal of our study is to examine the deep divergences of the amniote crown group.” 

If so, then Ford and Benson need to add dozens to hundreds of more taxa to their incomplete study. A suggested list is found here.

“We excluded recumbirostrans from our analysis. Recumbirostrans have generally been assigned to non-amniote microsaurs, but were recently recovered as early crown group amniotes.”

By contrast the LRT includes seven taxa listed by Wikipedia/Recumbirostra. We learned earlier that previous workers have deleted taxa that otherwise deliver unwanted results. Not sure what is happening in the Ford and Benson paper after their omission of this clade. Those seven recumbirostran taxa nest outside the Reptilia /Amniota in the LRT.

From the Results:
“All our analyses recover parareptiles and neodiapsids as a monophyletic group within Diapsida.”

These are false positive results due to taxon exclusion as shown here.

From the Discussion:
“The sister relationship between parareptiles and neodiapsids, and their relationship to Varanopidae, implies a single origin of temporal fenestration before the common ancestor of these clades.” 

These are false positive results due to taxon exclusion as shown here. We’ve known the clade Diapsida is polyphyletic since July 2011 with a last common ancestor in Early Carboniferous amphibian-like reptiles.

Happy holidays, dear readers. 


References
Ford DP and Benson RBJ 2020. The phylogeny of early amniotes and the affinities of Parareptilia and Varanopidae. Nature ecology & evolution 4:57–65. SuppData

Modesto SP 2020. Rooting about reptile relationships. Nature Ecology & Evolution 4:10–11.

 

4x the pectoral fin phylogenetically splits in two

Sometimes the pectoral fin
phylogenetically splits in two, creating a new structure anterior to the main body of the pectoral fin.

Figure 2. Prionotus, the sea robin, has more of a barracuda-like face. Uniquely, medial spines from the pectoral fin evolve to act like fingers for walking on the sea floor.

Figure 2. Prionotus, the sea robin, has more of a barracuda-like face. Uniquely, medial spines from the pectoral fin evolve to act like fingers for walking on the sea floor.

Sea robins
(genus: Prionotus, Fig. 1) have finger-like appendages anterior to the pectoral fins.

Figure 6. Three views of the skeleton of Manta, colors added. Green represents the maxilla. Note the terminal mouth, distinct from other rays, skates and guitarfish. The pectoral fins do not reach the orbit. The cephalic fins are highly modified maxillae, still gathering food. Note the attachment to the quadrate. The premaxilla extends across the mouth.

Figure 6. Three views of the skeleton of Manta, colors added. The cephalic fins are highly modified anterior portions of the pectoral fins.

Manta ray
(genus: Manta, Fig. 2) extend a subset of the pectoral fin forward to create flexible external mouth scoops.

Figure 3. The threadfin, Polydactylus, also splits the pectoral fin to form threadlike feelers.

Figure 3. The threadfin, Polydactylus, also splits the pectoral fin to form threadlike feelers.

Threadfins
like Polydactylus (Fig. 3), also split the pectoral fin to form sea robin like feelers. Once nested with flatfish, the large reptile tree (LRT, 1625 taxa) nested Polydactylus with the sea robin, Prionotus (above).Figure 1. Spotted eagle ray skull shows the anterior portions of the pectoral fins jointed medially to create a digging snout.

Figure 4. Spotted eagle ray (Aetobatus) skull shows the anterior portions of the pectoral fins joined medially to create a digging snout.Eagle rays
like Aetobatus (Fig. 4), splits then merges the anterior portion of the pectoral fins, creating a snout used for digging in soft sand. Outside it looks like a nose. Inside the pectoral fin structure is apparent.

Hexapod tetrapods
This is the closest tetrapods have come to becoming six-legged, not quite like those seen in the sci-fi movie, Avatar (2009, which considered six appendages inappropriate for the tall blue humanoids, a morphology first imagined by Edgar Rice Burroughs for Barsoom (Mars).

Figure x. Subset of the LRT focusing on basal vertebrates (= fish).

Figure x. Subset of the LRT focusing on basal vertebrates (= fish).

A Google search reveals ‘split pectoral fin’ is also a malady
that affects certain Koi goldfish. Details here.


 

 

 

 

 

Desmatochelys enters the LRT after bone reinterpretation

Certain aspects
of certain turtle skulls have been traditionally misinterpreted, as reported earlier.

Figure 1. The skull of the Cretaceous sea turtle, Desmatochelys, is relabeled here with the addition of color.

Figure 1. The skull of the Cretaceous sea turtle, Desmatochelys, is relabeled here with the addition of color.

A not so recent paper on the sea turtle, Desmatochelys
(Fig. 1), by Cadena and Parham 2015 misidentified several skull bones, here corrected.


References
Cadena EA and Parham. JF 2015. Oldest Known Marine Turtle? A New protostegid from the Lower Cretaceous of Colombia. PaleoBios. 32(1).