Dr. Phil Hastings, Scripps professor and curator of the SIO Marine Vertebrate Collection delivers an online lecture and slide show sponsored by the University of California Television (UCTV). It runs for about an hour.
This is a traditional view of fishes lacking any mention of fossil taxa.
Hastings follows molecular data. Hastings mentions that we humans are indeed members of the Osteichthys. Ichthyologist Neil Shubin and artist Ray Troll are also mentioned.
the large reptile tree (LRT, 1836+ taxa) presents a distinctly different view of fish systematics because it includes fossils and minimizes taxon exclusion.
In this YouTube video from 2018 Dr. Donald Henderson starts his online slide video presentation by repeating the traditional fin-to-finger story (Fig. 1).
that story was already out-of-date in 2018 due to taxon exclusion in comparison to and competition with the phylogenetic analysis found in the large reptile tree (LRT, 1817+ taxa; subset Fig. 5).
Not surprisingly, Dr. Henderson thought it was “very peculiar”
that Middle Devonian tetrapod trackways preceded the Late Devonian fossils of tetrapods by tens of millions of years. The LRT solves this problem. Acanthostega and Ichthyostega are not transitional taxa, but dead end taxa with polydactyly not found in other tetrapod taxa. Their phylogenetic ancestors filled the gap between the Middle and Late Devonian, but those fossils have not been found yet in those strata, only in later strata as late survivors of those earlier radiations.
In the middle of the presentation Dr. Henderson presented his alternative view: that Ichthyostega and Acanthostega were secondarily aquatic tetrapods. His YouTube video is dated January 11, 2018. Only a short month earlier the LRT recovered Ichthyostega and Acanthostega as secondarily more aquatic tetrapods, time-stamped here.
Evidently that was an idea whose time had come.
Or else Dr. Henderson read that hypothesis here and embraced it. Either way, Dr. Henderson did not employ phylogenetic analysis, but came to his solution as a notion to reconcile the Middle Devonian tracks to the late Devonian fossils.
Dr. Henderson’s presentation was mundane. Henderson’s customary family tree of vertebrates (Fig. 1) indicates he had no idea how clades of fish are related to one another at a species level (Fig. 2). He never tested traditional hypotheses, but accepted them without reservation.
Figure 1. Slide from Henderson’s YouTube video with connections between clades highlighted in frame 2.
Figure 4. Dorsal and ventral views of Panderichthys and several basal tetrapods demonstrating the low, flat skulls and bodies with small limbs and relatively straight ribs.
It’s nice to have a notion, like Dr. Henderson had. After all, that’s where all scientific inquiry has its genesis. But you can’t beat a good old, wide gamut phylogenetic analysis to make your notion into a testable hypothesis that covers all the other competing hypotheses. Let’s hope that someday PhDs will adopt a taxon list comparable to the LRT and then let the taxa and their taxonomy tell the tale.
Figure 5. Subset of the LRT focusing on basal tetrapods. Colors indicate number of fingers known. Many taxa do not preserve manual digits.
follow up those notions with testable analyses. It’s hard work, but it’s the professional thing to do.
From Paleocast in September 2017. This YouTube video parallels the large reptile tree (LRT, 1816+ taxa) by describing a wide gamut of vertebrate taxa. Dr. Joseph Keating of the University of Manchester School of Earth of Environmental Science is the professor of this 38-minute PowerPoint presentation.
Some critical thoughts: The presentation starts off with the statement: “You are a fish.” That’s exciting and odd, but there is no monophyletic clade called ‘fish’. Keating’s presentation shows a ladyfish (genus Elops), which is not in the lineage of humans. More accurately:
You are a chordate
You are a craniate
You are a vertebrate
You are a gnathostome, etc.
Comparing shark jaw and pharyngeal ‘bones’ to human counterparts
Keating omitted the upper jaw counterpart in the human of the upper gill element in the shark. Missing elements in the human include the lacrimal, maxilla and premaxilla.
Keating continues with the out-dated tradition
that placental mammals diverged from one another 80 to 90 million years ago. This is falsified by the presence of Maiopatagium, Rugosodon and other members of Glires (= rodents, rabbits and kin) in the Early Jurassic, some 200 million years ago.
Figure 1. Keating’s out-dated cladogram of mammals.
Keating has elephants splitting from edentates (Fig. 1), and dolphins splitting from cattle, neither of which is confirmed by the LRT. But that’s what you get with gene studies. Gosh, I’d hate to spend tens of thousands of dollars on tuition and several years at these universities to be forced to regurgitate these myths.
Keating gets the Archosauromorph/Lepidosauromorph split correct
at about 330 million years ago, but incorrectly puts birds in the Lepidosauromoph clade.
Keating incorrectly marks the genesis of tetrapods
at about 360 million years ago. We have tetrapod trackmakers in the Middle Devonian, at 390 million years ago.
Figure 2. Keating’s illustration of vertebrate skulls with tetrapod homologs colored, as is done here.
To his credit,
Keating colors fish bones with tetrapod homologs (Fig. 2). Everyone knows now how easy that makes comparisons.
Keating correctly reports
that we (and bony fishes) share a last common ancestor with sharks about 450 million years ago, deep in the Ordovician. Keating does not indicate which shark was ancestral to bony fish. (It was Hybodus).
Figure 3. Keating’s photo of human teeth. Maybe I’m missing something here, but those don’t look like human molars.
Keating’s image of human teeth
(Fig. 3) look unlike any human teeth I have ever seen.
Keating’s favorite group is the jawless fishes, splitting from sharks at 500 million years. Sturgeons and paddlefish are not mentioned. Neither are Birkenia, thelodonts, osteostracans and heterostracans.
There are lots of pictures of lampreys and hagfish, if that’s your thing, including how they fit into human cuisine.
When lancelets are introduced, the concept of ‘Vertebrates’ is introduced. Keating reports that gills, brain, eyes, liver, heart, gall bladder, not vertebrae, are characters of vertebrates. Perhaps he is mixing up ‘craniates’ with ‘vertebrates. I think hagfish are inappropriate vertebrates, contra tradition. Call me old-fashioned, but vertebrae should be present in vertebrates.
Figure 4. Keating’s illustration of shark and human facial bones. Labels and dark skull image at lower right added here.
According to Keating,
heterostracans document the earliest evidence of mineralized bone, the exoskeleton. Keating studied this material in detail with a µCT scanner. As everyone knows, heterostracans have a robust exoskeleton. Birkenia documents a much more primitive state of bone development.
have paired fins, the first taxa do this, according to Keating. Thelodusis the most primitive fish with paired fins in the LRT. The osteostracan, Hemicyclaspis, evolves later as a derived thelodont.
Placoderms are discussed with an emphasis on Dunkleosteus.
Due to taxon exclusion Keating has no idea how placoderms originated within the bony fish. Keating mistakenly reports placoderms were the first to develop jaws. Actually paddlefish did this, just following sturgeons.
The talk concludes
with Tiktaalik. Having a neck is a key trait according to Keating. Another unrelated fish with a neck capable of bending the skull left and right is the Lepidogalaxias, the salamander fish, nesting at the base of the bony ray-fin fish.
Here’s a bonus video
for those who have followed the ongoing clash between certain PhDs and this blogsite as it represents the website RepitleEvolution.com on a daily basis. The speaker, Julia Galef, describes the various mindsets involved and the psychological reason for their separate points-of-view.
Here’s a YouTube video featuring Dr. Karma Nanglu (Smithsonian National Museum of Natural History) showing and discussing Cambrian taxa from the Burgess Shale ancestral to living hemichordates, pterobranchs (= graptolites and kin) and enteropneusts = acorn worms).
Nanglu reports, “This talk will guide you through a series of recent studies using Burgess Shale fossils that shine a light on hemichordate origins, one of the most mysterious parts of the animal tree of life. These exceptional fossils reveal unanticipated combinations of morphological and ecological characteristics early in the history of this animal group, including surprising combinations of those found in their modern relatives.”
Unfortunately, when it came time to present last common ancestors at an hour into the presentation, Nanglu left much of the work undone. His graphic showed question marks at the ancestral nodes (Fig. 1).
Figure 1. Frame from Nanglu talk on YouTube (see above) showing stars and question marks on his cladogram of chordate/hemichordate origins.
By contrast and thirty years ago Peters 1991 found hemicordates arose from basal chordates (Fig. 3) like the lancelet, Branchiostoma(Fig. 2), itself derived from nearly featureless roundworms (Fig. 3). You might recall that adult lancelets are sessile feeders, anchoring themselves tail first into sandy and muddy substrates, distinct from their free-swimming tiny hatchlings that more greatly resemble tiny fish in their activity. All this occurred during the Cambrian.
Distinct from chordates,
sessile (= essentially immobile) pterobranchs emphasize and enlarge the suspension feeding cirri made sticky with mucous strands (Fig. 3).
Distinct from chordates,
worm-like enteropneusts emphasize the rostrum (= proboscis, Fig. 3).
gave up the chevron-shaped swimming muscles and internal gill basket found in lancelets and fish. However, enteropneust hatchlings present a vestigial post-anal tail that is resorbed or transformed in adults.
Figure 2. Extant lancelet (genus: Amphioxus) in cross section and lateral view. The gill basket nearly fills an atrium, which intakes water + food, sends the food into the intestine and expels the rest of the water.
Nanglu 2021 confirms this 30-year-old hypothesis of interrelationships (Fig. 3) as he nests chordates basal to hemichordates and echinoderms.
Nanglu also presents
a tube-building, vermiform last common ancestor between pterobranchs and enteropneusts, with post-anal attachment and possible tube building. In Peters 1991 pterobranchs are basal to crinoids, blastoids and other echinoderms, taxa that further emphasize and enlarge the gracile cirri that encircles the mouth of lancelets until the cirri comprise the entire anatomy of the starfish. So starfish are walking on their greatly enlarged and elaborate mouth parts, having given up or absorbed the rest of the ancestral lancelet anatomy.
Figure 3. Chordate evolution, changes to Romer 1971 from Peters 1991. Here echinoderms have lost the tail and gills of the free-swimming tunicate larva.
We looked at chordate origins
in more detail earlier here (summarized in Fig. 3).
References Peters D 1991. From the Beginning – The story of human evolution. Wm Morrow. Romer AS 1971. The Vertebrate Body – Shorter Version 4th ed. WB Saunders.
From Martin Brazeau and the Imperial College London, here’s a new YouTube video (53 minutes) on how and maybe why sharks lost their bony exoskeleton.
The phylogenetic context is wrong. Without testing, Brazeau et al. considered placoderms basal to sharks and bony fish.That’s a traditional mistake. In the large reptile tree (LRT, 1795+ taxa) placoderms are bony fish close to catfish. In the LRT sharks evolved from sturgeons (Fig. 2). Bony fish evolved from hybodontid sharks. The Silurian is when all this happened.
We looked at this subject earlier here (Borrell 2014) and here Brazeau et al. 2020.
Unfortunately, as you’ll see Brazeau et al. include only fossil taxa to determine which taxa were present in the Silurian.
The jawless, (by reversal) anapsid-mimic placoderm, Minjinia (Fig. 3) was featured in Brazeau’s paper and video.
Ironically Brazeau illustrates his talk with an image of the exoskeleton and endoskeleton of the sturgeon Acipenser. which entered the LRT here. He reports the endochondral bone was lost in sturgeons. That is a traditional mistake as revealed by the LRT.
Brazeau correctly reports the origin of bone precedes sharks and is lost in sharks. He just did not realize that placoderms are descendants of sharks, not their ancestors.
References Brazeau et al. (7 co-authors) 2020. Endochondral bone in an Early Devonian ‘placoderm’ from Mongolia. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-020-01290-2 Hu Y, Lu J and Young GC 2017. New findings in a 400 million-year-old Devonian placoderm shed light on jaw structure and function in basal gnathostomes. Nature Scientific Reports 7: 7813 DOI:10.1038/s41598-017-07674-y
correction to the subtitles on the video: “Resighted” = “Recited” (spelling error)
lots of earlier mistakes getting caught in the ray fin fish clade which continues to be under scrutiny (e.g. see yesterday’s post on swordfish). Hope to have all wrinkles ironed out soon. Thank you for your patience. The LRT is an ongoing hypothesis of interrelations subject to change with more data and more understanding.
And a Bonus Video from Joe Rogan featuring Avi Loeb
Finally we know more about an extinct placental clade that no one else recognized as an extinct placental clade. Clade members in the LRT included Patriofelis, Sarkastodon and Kerberos(Fig. 1). Now a living member, the honey badger, Mellivora capensis (also Fig. 1), enters the LRT within this clade.
Marsupials or placentals?
The problem is: these three extinct hyper-carnivores have been traditionally considered creodonts and within that clade: hyaenodonts and oxyaenids. In the large reptile tree (LRT, 1730+ taxa) creodonts are marsupials. Distinct from them, but convergent in many ways, Mellivora, Patriofelis, Sarkastodon and Kerberos nest as clade members within the placental clade, Carnivora. This newly recognized honey badger clade nests between hyper-carnirorous wolverines + short face bears and the stylinodontid + earless seal clade.
The placental honey badger clade
dentally converges with the marsupial creodont clade. Don’t put your trust in teeth, as we learned earlier.
honey badgers are members of the weasel clade, Mustelidae, apart from other mustelids. In the LRT, all derived members of Carnivora, including cats, dogs, bears, seals and sea lions are all derived from the mink/weasel (genus Mustela).
Figure 1. The honey badger clade, Kerberos, Patriolfelis and Sarkastodon. The only living representative is Mellivora to scale.
Mellivora capensis(originally Viverra capensis Scherber 1777; Fig. 2) is the extant honey badger or ratel, traditionally considered close to weasels. This carnivore has few natural predators because of its thick skin and ferocious defensive abilities.
Figure 2. The honey badger (Mellivora capensis) skull.
Imagine the unreasonable viciousness of a honey badger
expanded to the size of Sarkastodon (Fig. 1).
Figure 3. The honey badger (Mellivora capensis) skeleton.
This 3:20 minute honey badger video on YouTube
went viral (95.5 million views) awhile back. Quite the character, now finally understood phylogenetically.
The LRT solves problems
others don’t even think about. Adding taxa is the solution to many phylogenetic problems.
References Schreber, JCDv 1777. “Das Stinkbinksen”. Die Säugethiere in Abbildungen nach der Natur mit Beschreibungen. Erlangen: Wolfgang Walther. pp. 450–451.
A little off-topic today Astronomer, lecturer, author, and voice of science, Carl Sagan
introduced many of us oldsters to the tesseract, a four-dimensional analogue of the cube. YouTube provides a video of that segment from ‘Cosmos; A Personal Voyage’, a PBS television series from 1980. Here (see below) Sagan holds the 3D ‘shadow’ of a hypothetical 4D tesseract. Click to play.
Other producers have provided more recent videos explaining their visions of the fourth dimension and the tesseract using digital animation (see below).
These presentations are barking up the wrong tree.
The fourth dimension is much simpler and very real. We live it every day.
As everyone already knows, time is the fourth dimension. Space-time provides both the third dimension and the fourth dimension, otherwise known as ‘reality’.
‘Now’ and ‘then’ is all there is to the fourth dimension. Nothing more.
Any 3D shape in the now moment has already moved at right angles from the then moment ever since the Big Bang — when space-time began. How far apart those moments are… or how far apart those shapes are… or in what direction those shapes have moved… are historical givens. Alternatively these parameters up to you, if you are planning something that changes from moment to moment, as any engineer, animator or puppeteer can tell you.
Shadows on 2D walls and tesseracts
are just fanciful illusions in space-time, over-thinking while overlooking the obvious and very real point. When you see a graph or chart that has an X, Y and Z axis and wonder how the next axis lies at right angles to these three, just flip the page and show a new X, Y and Z axis chart that charts another moment in time. You are not stuck with just one page representing just one moment. Later, you can animate those pages by projecting them at 24 or 30 frames per second, when you have enough ‘moments’ to make your point.
There’s nothing more to the fourth dimension
than ‘now‘ and ‘then‘, except to say, it’s a one way street and there’s no leap-frogging in time or space.
The tesseract turns out to be a model
of all the possible futures of a 3D object in space-time. That 3D object can go in any direction and end up anywhere in space for a second measurement for every new ‘now‘ moment. As it always turns out, all possible futures are reduced to one real ‘now‘ moment, ready for the next ‘now‘ moment to come along while looking back on a long line of ‘then‘ moments.
No need to complicate things
any further. Somehow this easy solution has been traditionally overlooked. This may be a novel hypothesis. If not, please provide the citation so I can promote it as a precedent.
Willy Saíz created a 3D model of an unidentified genus pterosaur embryo
that appeared here on YouTube back in 2017. You can click the image to view the short video which silently rotates the image with lap dissolves adding muscles and skin.
It reminds me most of the IVPP V 3758 specimenof the giant unnamed anurognathid embryo (Fig. 1). The embryo is a giant because it is nearly as large as most adult anurognathids (Fig. 2).
Figure 1. Click to enlarge. A magnitude of more detail was gleaned from this fossil (the IVPP egg/embryo) using the DGS method.
Unlike the Willy Saíz 3D model the IVPP specimen (Figs. 1, 2) is partly disarticulated, including some of the skull bones. Evidently the leathery egg rolled or was dropped after the egg left the mother’s body, prior to burial and fossilization. Thankfully, due to its leathery shell, every bone stayed inside the ‘package’.
Figure 2. Click to enlarge. Anurognathids to scale. The adult of the IVPP embryo is 8x the size of the embryo, as in all other tested adult/embryo pairings.
Allometric traits are expected
only under the mythical and invalid archosaur hypothesis of pterosaur interrelationships unfortunately supported by the vast majority (= all but 1) of pterosaur workers. For example, Dr. Mark Witton, made the same mistake with a Pterodaustro embryo illustration (Fig. 3). Compare the imagined figure 3 to the traced figures 4 and 5.
Figure 3. Pterodaustro embryo as falsely imagined in Witton 2013. The actual embryo had a small cranium, small eyes and a very long rostrum. Compare to figures 4 and 5.
Are the Witton and Saíz illustrations examples of pseudoscience?
They are not based on reality. They cannot be replicated, except by other imaginative artists. In science the intention and effort should always be to trace and replicate real data with precision (Figs. 1, 4) and thereafter create reconstructions from those tracings (Figs. 2, 5) with minimum freehand input. Unfortunately we live in a topsy-turvy world where precise tracings are considered pseudoscience by Dr. Witton (remember, he called me a crank) and other well-intentioned, but sadly mistaken scientists.
Figure 4. Original interpretations (2 frames black/white) vs. new interpretations (color).
Figure 5. Pterodaustro embryo. Note the adult proportions in most regards.
Similar to other traditional myths, Kuhl et al. 2020 repeat a traditional myth that will never be validated.
From the abstract “In this tree, grebes and flamingos are the sister clade of all other Neoaves,”
Kuhl et al. is a genomic study. These two bird types do not resemble each other (Fig. 1) and do not nest together in phenomic studies, like the large reptile tree (LRT, Subset Fig. 2). Prum et al. 2015 recovered the same false positive relationship. If a study cannot be validated by traits, it is invalid and worthless.
The unanswered question here is, “Why do certain genes resemble one another in these two unrelated taxa?” Now there’s another subject for a PhD thesis.
Figure 1. Flamingo and grebe illustration from Nat Geo article on birds.
Earlier we looked at grebes and flamingoes here in 2017. Apparently there has been no enlightenment among paleontologists since then. Where is the critical thinking?
Continuing from the Kuhl et al. abstract: “All non-passerine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes.” [= nightjars, sailors [= barn swallows?], hummingbirds, unrelated taxa in the LRT]
In the LRT the hoatzin nests between sparrows and parrots because they look alike, both overall, and in detail, location and diet. Relatives
If you have not learned this already,
genomic studies over deep time lead one to madness.
From thepress release: “For the first time, they have been able to clarify the relationship of all families of non-passerine birds and almost all families of passerine birds. The new family tree is based on gene sections that do not code for proteins, but contain sequences that are specific to the families and their genera.”
Better to stick with a phenomic study that makes sense, like the LRT. Chickens and ducks are not related in the LRT. That makes sense because they don’t resemble each other. Parrots and hawks are not related in the LRT. That also makes sense, but genomic studies put each of these two pairs of taxa together.
As mentioned above, we looked at Prum et al 2015 earlier in a three-part series ending here demonstrating several times that genomic studies do not replicate phenomic studies in the sort of deep time that brought us birds (Late Jurassic to the Present).
Genomic studies are EXCELLENT
over short phylogenetic time. For this reason genomic studies are used by the judicial system. For this reason paleontologists think genomic studies should supersede phenomic studies. However, tests document the fact that genomic studies produce mismatches (taxa that do not look alike, Fig. 1) over deep time. Paleontologists realize this, but continue to put their faith in genomic studies, hoping that someday the last common ancestor of flamingoes (genus: Phoenicopterus) and grebes (genus: Aechmophorus) will someday be discovered in the fossil record.
The LRT has already recovered that last common ancestor,
a taxon close to the late-surviving, but extant megapodes, Megapodius and Early Cretaceous Juehuaornis. You’ll notice (Fig. 1) that clade includes nearly all crown birds.
Figure 1. Subset of the LRT focusing on birds. Note the separation of the duck clade from the chicken clade.
The hallmarks of the Scientific Method include:
asking a specific question
devising a hypothesis
experimenting to gather data
analyzing the data, and then
evaluating whether the hypothesis is correct based on the experimental data.
When the data support the hypothesis, the findings can be published or shared. What happens if the findings do not confirm the hypothesis? Answers here.
Kuhl et al. 2020 was a complete waste of time for the nine co-authors, the editors, referees and innumerable readers who all believed the flawed premise of this genomic hypothesis of interrelations. Where is the genomic study that replicates phenomic studies like the LRT? When that happens, we’ll have that long sought validation.
Pertinent Carl Sagan – ‘A way of thinking’ YouTube video.