Sea horse evolution back to large Cretaceous predators

Another series of taxa pulled from the LRT
focusing on phylogenetic miniaturization (PM) in the lineage of sea horses (Fig. 1). PM starts with 60cm-long Early Cretaceous Notelops and similar extant Scomberoides, the queenfish (Fig. 1), which is also (quite obviously) basal to mackerel and tuna.

Figure 1. Seahorse evolution back to Notelops (Early Cretaceous).

Figure 1. Seahorse evolution back to Notelops (Early Cretaceous).

Less obviously,
in the large reptile tree (LRT, 1806+ taxa) another descendant of Scomberoides is the 10x smaller zebra fish (Danio, Fig. 1).

Here’s where it gets interesting…
The sagittal crest present in Scomberoides (Fig. 1) is absent in Danio and the parietals return to meet each other medially, as in basal bony fish like Amia and Prohalecites. This phylogenetic reversal makes creating a cladogram more difficult, due to convergence, but all the more challenging. Danio descendants remains tiny and crestless. I have no data if Scomberoides hatchlings have crests or not. If so that would be a case of neotony leading to Danio.

Relative to Notelops
larger eyes are first seen, not in tiny Danio, but in big Scomberoides (Fig. 1), prior to PM. That increase in orbit size comes at the cost of a reduction in cheek plates that never comes back in descendant taxa. In Scomberoides the circumorbital ring actually overlaps the preopercular (light yellow) and hyomandibular (dark green). That’s a rare trait that makes it a bit difficult to score.

The jugal
(cyan color) in Danio (Fig. 1) is still large, though disconnected from the circumorbital ring where Gregory 1933 labels it the symplectic. According to Wikipedia, the symplectic is “an additional bone linking the jaw to the rest of the cranium.”  That also makes that bone difficult to score. Seeing this bone in a variety of taxa led to the conclusion that it was homologous to the jugal. Starks 1901 listed several synonymies used by various authors for bones of the fish skeleton. None synonymized the jugal and symplectic. That may have changed in the 120 years since. Let me know, if so.

Stickleback stickles
readily seen in Gasterosteus, are first seen in Scomberoides (Fig. 1), though lost in Danio.

Jaw joint migration from behind the orbit
to way out in front of the orbit in this series of taxa starts with Scomberoides, documents a mid-point in Danio, and reaches a conclusion in Gasterosteus (Fig.1).

Figure x. Rayfin fish cladogram. This one represents the latest subset of the LRT.

Figure x. Rayfin fish cladogram. This one represents the latest subset of the LRT.

That’s the utility of the LRT
and the ready-at-your-fingertips online data with all bones colorized using DGS.


References
Starks EC 1901. Synonymy of the fish skeleton. Proceedings of the Washington Academy of Sciences 3:507-539. PDF here.

The Atlantic cod, Gadus mohua, enters the LRT

Sometimes more common and more ordinary fish,
like the Atlantic cod, Gadus (Figs. 1, 2), also enter the large reptile tree (1806+ taxa).

Figure 5. Atlantic cod, Gadus morhua, in lateral view.

Figure 1. Atlantic cod, Gadus morhua, in lateral view.

Actually
it’s only ordinary on the outside. The skull is unique, but like al vertebrates shares a long list of traits with related taxa.

Figure 4. Skull of the Atlantic cod, Gadus. Note the posterior process of the hyomandibular (dark green).

Figure 2. Skull of the Atlantic cod, Gadus. Note the posterior process of the hyomandibular (dark green).

Gadus morhua (Linneaus 1758) is the Atlantic cod, nesting between two open ocean predators, Coryphaena and Rachycentron. Instead of one long dorsal fin, it is split in three. The anal fin is split in two. The chin has a barbel. The postparietal forms a long crest that divides the parietal. The naris is a long opening from snout tip nearly to the orbit.  Note the elongate postfrontal (orange) and hyomandibular (dark green) with accessory processes.

Figure x. Rayfin fish cladogram. This one represents the latest subset of the LRT.

Figure x. Rayfin fish cladogram. This one represents the latest subset of the LRT.


References
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.

wiki/Gadus_Atlantic_cod

Cawley et al. 2020 did not realize Mesozoic pycnodonts were derived from extant bonefish

Cawley et al. 2020
brought us an overview of a clade of Mesozoic fish, the Pycnodontiformes (Fig. 1).

From the abstract
“Two other neopterygian clades possessing similar ecological adaptations in both body morphology (†Dapediiformes) and dentition (Ginglymodi) also occurred in Mesozoic seas.”

Short note: Dapediformes includes Dapedium and kin (taxa related to gars, like Lepisosteus in the LRT). Ginglymodi includes Semionotiformes (Semionnotus) and Lepidotidae (Lepidotes and Lepisosteus (= gars)). These taxa nest basal to catfish + placoderms in the LRT. They are Silurian in origin, not related to Pycnodus (Fig. 2) and Albula (Figs. 1, 3) in the LRT.

From the introduction:
“The overarching goal of this study is to evaluate the success but also final demise of pycnodontiform fishes, which represented the major marine actinopterygian elements from the Late Triassic to Palaeogene.”

Figure 1. Color image from Cawley et al. 2020. Albula added. Taxa below the gray line are Semionotiformes unrelated to pycnodontiformes.

Figure 1. Color image from Cawley et al. 2020. Albula added. Taxa below the gray line are Semionotiformes unrelated to pycnodontiformes.

Unfortunately Cawley et al. fails to mention
the extant pycnodontiform, the bonefish, Albula, which nests with the pycnodontiforms, Flagellipinna and Pycnodus (Agassiz 1835), in the large reptile tree (LRT, 1804+ taxa).

Also unfortunately,
Cawley et al. inappropriately includes several members of the Dapediidae and Semionotiformes (Fig. 1). Due to taxon exclusion the authors don’t realize these taxa nest in the other major clade of bony fish, apart from most ray fins, closer to spiny sharks, placoderms and lobefins, far from Pycnodus and Albula.

Cawley et al. reports, 
“Pycnodontiforms represent a well-defined monophyletic group…”

then admits,
“but the intrarelationships of various taxa and groups remain debated.” The LRT tests virtually all other fish clades.

Figure 2. Pycnodus with bones colorized according to tetrapod homologies. Third frame shows maxilla and lacrimal returned to in vivo positions.

Figure 2. Pycnodus with bones colorized according to tetrapod homologies. Third frame shows maxilla and lacrimal returned to in vivo positions.

Wikipedia reports,
Pycnodontiformes is an extinct order of bony fish. The group evolved during the Late Triassic and disappeared during the Eocene. The group has been found in rock formations in Africa, Asia, Europe, North and South America. The pycnodontiforms were small to middle-sized fish, with laterally-compressed body and almost circular outline. Pycnodontiform fishes lived mostly in shallow-water seas. They had special jaws with round and flattened teeth, well adapted to crush food items. One study links the dentine tubules in pycnodont teeth to comparable structures in the dermal denticles of early Paleozoic fish. Some species lived in rivers and possibly fed on molluscs and crustaceans.”

Figure 1. Albula vulpes skull with highly derived facial bones reidentified here. Note the lateral premaxillary processes and 'floating' cheek bones. Green vertebrae are caudals.

Figure 3. Albula vulpes skull with highly derived facial bones reidentified here. Note the lateral premaxillary processes and ‘floating’ cheek bones. Green vertebrae are caudals.

Pycnodus according to Wikipedia
“The known whole fossils of Pycnodus are around 12 centimetres (5 in) long, and have a superficial resemblance to angelfish or butterflyfish. The animals, as typical of all other pycnodontids, had many knob-like teeth, forming pavements in the jaws with which to break and crush hard food substances, probably mollusks and echinoderms. These teeth are the most common form of fossil.”

According to Wikipedia
Bonefishes live in inshore tropical waters and moves onto shallow mudflats or sand flats to feed with the incoming tide. The bonefish feeds on benthic worms, fry, crustaceans, and mollusks. Ledges, drop-offs, and clean, healthy seagrass beds yield abundant small prey such as crabs and shrimp. It may follow stingrays to catch the small animals they root from the substrate.”

Apparently no one has reported
that pycnodontiformes is an extinct clade within the extant clade Albulidae. Likewise no one has reported that Semionotifomes are not related to Pycnodontiformes. If so, please send the citation so I can promote it here.


References
Agassiz JLR 1835.Recherches sur les Poissons fossiles, 5 volumes. Imprimerie de Petitpierre et Prince, Neuchaatel, 1420 pp.
Bleeker P 1859. xx
Cawley JJ et al. (5 co-authors) 2020.
Rise and fall of Pycnodontiformes: Diversity, competition and extinction of a successful fish clade. Ecology and evolution DOI: 10.1002/ece3.7168

wiki/Pycnodontiformes
wiki/Pycnodus
wiki/Bonefish

Pycnodontiformes Berg 1937
Albulidae Bleeer 1859

 

Dunyu [Galeaspida] enters the LRT

According to Wikipedia
“Galeaspida lived in shallow, fresh water and marine environments during the Silurian and Devonian times (430 to 370 million years ago) in what is now Southern China, Tibet and Vietnam. Superficially, their morphology appears more similar to that of Heterostraci than Osteostraci, there being currently no evidence that the galeaspids had paired fins. However, Galeaspida are in fact regarded as being more closely related to Osteostraci, based on the closer similarity of the morphology of the braincase.”

Figure 1. Galeaspids from Halstead 1985.

Figure 1. Galeaspids from Halstead 1985.

“The defining characteristic of all galeaspids was a large opening on the dorsal surface of the head shield, which was connected to the pharynx and gill chamber, and a scalloped pattern of the sensory-lines. The opening appears to have served both the olfaction and the intake of the respiratory water similar to the nasopharyngeal duct of hagfishes.”

Figure 2. Skull of Dunyu with tetrapod homolog colors applied here.

Figure 2. Skull of Dunyu with tetrapod homolog colors applied here. Note the elongated dorsal opening. In other galeaspids the opining is more oval. On a 72 dpi monitor this image is only slightly smaller than life size.

Dunyu longiforus
(Fig. 2) from the Late Silurian was described by Zhu et al. 2012.

Figure 3. Subset of the LRT focusing on basal chordates, including Dunyu.

Figure 3. Subset of the LRT focusing on basal chordates, including Dunyu.

Here
(Fig. 3) in the large reptile tree (LRT, 1803+ taxa) Dunyu nests between the thelodont, Thelodus, and the osteostracan, Hemicyclaspis (Fig. 3). The resemblance between the three is readily observed. Phylogenetic bracketing (Fig. 3) provides galeaspids with pectoral fins. Closest living relatives are hagfish and sturgeons.


References
Halstead LB 1985. The vertebrate invasion of fresh water. Philosophical Transactions of the Royal Society London B 309:243–258.
Janvier P 1984. The relationships of the Osteostraci and Galeaspia. Journal of Vertebrate Paleontology 4(3):344–358.
Liu YH 1965. New Devonian aganathans from Yunnan. Vertebrata PalAsiatica 9(2):125–134.
Zhu M and Gai Z-K 2006. Phylogenetic relationships of Galeaspids (Agnatha). Vertebrate PalAsiatica 44:1–27.
Zhu M, Liu Y-H, Jia L-T and Gai Z-K 2012. A new genus of eugaleaspidiforms (Agnatha: Galeaspida) from the Ludlow, Silurian of Qujing, Yunnan, Southwestern China. Vertebrata PalAsiatica. 50 (1): 1–7.

wiki/Galeaspida
wiki/Dunyu

Xiphactinus and its ancestors in the LRT

Short one today
told in pictures.

Here are the taxa
(Fig. 1) in the large reptile tree (LRT, 1803+ taxa; subset Fig. 2) in the lineage of Xiphactinus (Fig. 1) a large Late Cretaceous predator from the Niobrara formation, starting with Calamopleurus, the Early Cretaceous bowfin with long, wicked teeth. Calamopleurus likely had a Late Silurian ancestry based on an Early Devonian relative, Doliodus.

Figure 1. Taxa in the lineage of Xiphactinus going back to Salmo, the salmon.

Figure 1. Taxa in the lineage of Xiphactinus going back to Salmo, the salmon.

As mentioned earlier,
wrestling with data on these 90 or so ray-fin bony fish over the last 2-3 months has been a full-time task. Many, many corrections were made. The present subset of the LRT still needs some polishing, but it is settling into a logical model for evolutionary processes distinct from traditional cladograms that do not recognize the origin of bony fish from hybodontid sharks and Gregorius.

Figure x. Rayfin fish cladogram. This one represents the latest subset of the LRT.

Figure x. Rayfin fish cladogram. This one represents the latest subset of the LRT.

The white notch 
that includes mormyrids and piranha (Fig. 2) was covered earlier here.


 

The coatimundi (Nasua) enters the LRT basal to almost all placentals

Traditionally
the coatimundi (Nasua nasua (Figs. 1, 3, 4; originally Viverra nasua Linneaus 1766) is considered a close relative of the raccoon (Procyon), a member of the Carnivora. So it has not gotten the spotlight it deserves.

Figure 1. The coatimundi (Nasua) compared to the ring-tailed lemur (Lemur).

Figure 1. The coatimundi (Nasua) compared to the ring-tailed lemur (Lemur).

By contrast, 
here in the large reptile tree (LRT, 1804+ taxa, Fig. x) Nasua nests outside the Carnivora, alongside Protictis, a Middle Paleocene taxon, and former enigma.

This nesting in the LRT
means the resemblance between coatimumndis and primitive carnivores, like Procyon, primitive primates, like Lemur (Fig. 1), and primitive tree shrews like Tupaia and Ptilocercus, is not mere convergence, but homology.

Overlooked until now,
coatimundis are basal to virtually all placental mammals, including primates and humans. That’s why they look like lemurs. That’s why they look like big tree shrews. That’s why they look like the LRT ancestor of bats, Chriacus, already with those large claws and feet able to rotate 180º enabling head-down descent from trees.

And that’s not all.
Coatimundis also dig with those big claws. So it is no coincidence that Talpa, the mole, is only a few nodes deep in the base of the Carnivora.

It is also worthwhile to compare
Nasua to an outgroup taxon, Caluromys (Fig. 4), an arboreal marsupial close to the base of the Placentalia.

Figure x. Subset of the LRT focusing on Carnivora and basal Placentalia after the addition of Nasua.

Figure x. Subset of the LRT focusing on Carnivora and basal Placentalia after the addition of Nasua. This phenomic cladogram is very different from genomic cladograms you may have seen, some that employ tapirs for outgroups.

Distinct from all members of the Carnivora
in the LRT, Nasua retains three large molars and a vestigial fourth along with a long list of other more subtle traits. Members of the Carnivora have only two molars typically with a large carnassial tooth preceding the upper molars.

Figure 2. Skull of Nasua compared to mid-Paleocene Protictis. The two are a close match and nest together in the LRT.

Figure 2. Skull of Nasua compared to mid-Paleocene Protictis. The two are a close match and nest together in the LRT. Shown about three-fifths life size.

According to Wikipedia
“Adult coatis measure 33 to 69 cm (13 to 27 in) from head to the base of the tail, which can be as long as their bodies. Males can become almost twice as large as females and have large, sharp canine teeth.Coatis have non retractable claws for climbing and digging. They prefer to sleep or rest in elevated places and niches, like the rainforest canopy, in crudely built sleeping nests. Coatis are active day and night but are not nocturnal animals. In the wild, coatis live for about seven years, while in captivity they can live for up to 15 or 16 years. Coatis communicate their intentions or moods with chirping, snorting, or grunting sounds. The pregnant females separate from the group, build a nest on a tree or in a rocky niche and, after a gestation period of about 11 weeks, give birth to litters of three to seven kits. About six weeks after birth, the females and their young will rejoin the band. Females become sexually mature at two years of age, while males will acquire sexual maturity at three years of age.”

The tail is not prehensile, but is used for balance.
Coatis able to rotate their ankles beyond 180°; they are therefore able to descend trees head first.

Figure 3. Skeleton of the coatimundi (Nasua) along with images of the hands, feet, antebrachium and humerus.

Figure 3. Skeleton of the coatimundi (Nasua) along with images of the hands, feet, antebrachium and humerus.

Although Middle Paleocene Protictis
(Fig. 2). nests alongside Nasua, they both had their origin deep in the Jurassic based on Jurassic remains of more derived taxa among the multituberculates. So the coatimundi was a friend, a meal, or at least an observer, of dinosaurs. This genus is a previously overlooked living relative of human ancestors, much more than the agricultural pest some people think.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Figure 4. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

This appears to be a novel hypothesis of interrelationships.
If not, please provide a citation and I will promote it here.


References
Linneaus C 1766. Systema naturae : per regna tria natura, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. 1 (12 ed.). Holmiae: L. Salvii.
wiki/Coati
wiki/South_American_coati

 

 

 

Agnolin 2021 on Brontornis affinities (still excluding parrots and stinkbirds)

Yes, it’s massive taxon exclusion time again
as Agnolin 2021 tells us that Brontornis (Fig. 2) is a giant goose.

We’ve known since 2011
that Brontornis is closely related to Gastornis (Figs. 1, 2) the giant flightless parrot.  Derived from hoatzins first, then sparrows, then even more distantly from fowl (= chickens, pheasants, peacocks), these giant flightless, herbivorous birds have all the hallmarks (= characters) of Ara, the parrot (Fig. 1).

Unfortunately,
these taxa were excluded from Agnolin’s 2021 analysis, again.

Figure 1. Gastornis (=Diatryma) to scale with Ara the parrot (lower right).

Figure 1. Gastornis (=Diatryma) to scale with Ara the parrot (lower right).

Figure 3. Skulls of Gastornis, Brontornis and Ara, the scarlet macaw.

Figure 3. Skulls of Gastornis, Brontornis and Ara, the scarlet macaw.

Agnolin 2007
also considered Brontornis a giant goose (Anseriformes).

Agnolin 2021
wrote, “After few changes in the data matrix, Brontornis results as part of a clade composed by the giant anseriforms designated by Worthy et al. 2017 as Gastornithiformes. This result is in agreement with recent proposals that excluded Brontornis from phorusrhacoid cariamiforms (where it was traditionally nested) and included it among Anseriformes.”

“Finally, the nesting of Brontornis among herbivorous giant anseriforms, together with several aspects of its mandibular morphology reinforces previous thoughts that Brontornis was herbivorous in habits.”

Fowl, sparrows, hoatzin (= stinkbirds) and parrots are all also herbivorous.

Unfortunately Agnolin 2007, 2021 supports
the hypothesis that fowl and geese are closely related in a traditional genomic clade, Galloanseriformes (= chicken + geese). The large reptile tree (LRT, 1803+ taxa; subset Fig. x) does not support that relationship. Rather fowl and geese are widely separated in the LRT where fowl are in cyan (= bright light blue, Fig. x) and geese are in pale magenta (= pinkish purple Fig. x).

Figure 4. Subset of the LRT focusing on birds. Chongmingia is highlighted in yellow in the Scansoriopterygidae.

Figure 4. Subset of the LRT focusing on birds. Chongmingia is highlighted in yellow in the Scansoriopterygidae.

Taxon exclusion
will always come back to haunt/bite you (pick your own favorite cliché). Add taxa as a remedy for this malady. It works every time.


References
Agnolin F 2007. Brontornis burmeisteri Moreno & Mercerat, un Anseriformes (Aves) gigante del Mioceno Medio de Patagonia, Argentina. Revista del Museo Argentino de Ciencias Naturales, n.s.9, 15-25.
Agnolin F 2021. Reappraisal on the Phylogenetic Relationships of the Enigmatic Flightless Bird (Brontornis burmeisteri) Moreno and Mercerat, 1891. Diversity 2021, 13, 90. https://doi.org/10.3390/d13020090
Andors AV 1992. Reappraisal of the Eocene ground bird Diatryma (Aves: Anserimorphae). Science Series Natural History Museum of Los Angeles County. 36: 109–125.
Bourdon E and Cracraft J 2011. Gastornis is a terror bird: New insights into the evolution of the cariamae (Aves, Neornithes). Society of Vertebrate Paleontology 71stAnnual Meeting Program and Abstracts, p. 75
Buffetaut E 2014. Tertiary ground birds from Patagonia (Argentina) in the Tournouër collection of the Muséum National d’Histoire Naturelle, Paris. Bulletin de la Société Géologique de France. 185(3):207–214.
Cope ED 1876. On a gigantic bird from the Eocene of New Mexico. Proceedings of the Academy of Natural Sciences of Philadelphia 28 (2): 10–11.
Hackett S et al. 2008. A phylogenetic study of birds reveals their evolutionary history. Science 320:1763–1768.
Hébert E 1855a. Note sur le tibia du Gastornis pariensis [sic] [Note on the tibia of G. parisiensis]. C. R. Hebd. Acad. Sci. Paris (in French) 40: 579–582.
Hébert E 1855b. Note sur le fémur du Gastornis parisiensis [Note on the femur of G. parisiensis]. C. R. Hebd. Acad. Sci. Paris (in French) 40: 1214–1217.
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Matthew WD, Granger W and Stein W 1917. The skeleton of Diatryma, a gigantic bird from the Lower Eocene of Wyoming. Buletin of the American Museum of Natural History, 37(11): 307-354.
Mustoe GE, Tucker DS and Kemplin KL 2012. Giant Eocene bird footprints from northwest Washington, USA. Palaeontology. 55 (6): 1293–1305.
Owen R 1843. On the remains of Dinornis, an extinct gigantic struthious bird. Proceedings of the Zoological Society of London: 8–10, 144–146.
Prévost C 1855. Annonce de la découverte d’un oiseau fossile de taille gigantesque, trouvé à la partie inférieure de l’argile plastique des terrains parisiens [Announcement of the discovery of a fossil bird of gigantic size, found in the lower Argile Plastique formation of the Paris region]. C. R. Hebd. Acad. Sci. Paris (in French) 40: 554–557.
Prum RO et al. (6 co-authors) 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature doi:10.1038/nature15697
Witmer L and Rose K 1991. Biomechanics of the jaw apparatus of the gigantic Eocene bird Diatryma: Implications for diet and mode of life. Paleobiology. 17 (2): 95–120.
Worthy TH, Degrange FJ, Handley WD and Lee MSY 2017. The evolution of giant flightless birds and novel phylogenetic relationships for extinct fowl (Aves, Galloanseres). Royal Society Open Science 4: 170975. http://dx.doi.org/10.1098/rsos.170975
Wright TF, et al. (ten co-authors) 2008. A Multilocus Molecular Phylogeny of the Parrots (Psittaciformes): Support for a Gondwanan Origin during the Cretaceous. Molecular Biology and Evolution, 25 (10), 2141-2156 DOI: 10.1093/molbev/msn160.

https://pterosaurheresies.wordpress.com/2017/11/06/the-origin-of-giant-birds-gastornis-diatryma-the-giant-parrot/

https://pterosaurheresies.wordpress.com/2017/09/15/lrt-sheds-light-on-gastornis-its-a-giant-flightless-parrot/

 

Carnivora genomic testing: Hassanin et al. 2021

From the abstract:
“The order Carnivora, which currently includes 296 species classified into 16 families, is distributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among species of Carnivora.”

Genomic tests too often do not and can not test fossil taxa leading to a problem with taxon exclusion. Moreover, genomic testing in deep time too often delivers false positives relative to phenomic (trait-based) traits that are designed to produce tree topologies in which all sister taxa greatly resemble one another, modeling micro-evolutionary events. Why this is so remains an unsolved problem. A phenomic cladogram (the LRT, subset Fig. x) that includes fossil taxa is found online here: http://reptileevolution.com/reptile-tree.htm

Figure 2. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Figure 1. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Talpa, the mole (Fig. 1), was excluded here, but nests within Carnivora in the phenomic analysis, the large reptile tree (LRT, 1803+ taxa, subset Fig. x).

Figure 1. Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Figure 2 Nandinia, the palm civet, nests as the proximal outgroup taxon to the Carnivora and all other placental mammals.

Nandinia, the palm civet sure looks like it, but is not a basal member of Carnivora in the LRT, but a basal placental outgroup taxon to the clade Carnivora.

Figure 1. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Figure 3. Mammals at the base of the Placentalia include the outgroup taxon: Caluromys, a basal placental: Genetta, a basal Carnivora: Eupleres, a basal Volitantia: Ptilocercus, a basal Primates: Microcebus, and basal Glires: Tupaia.

Carnivora is the first major clade to split off
from basal Placentalia (Fig. x). Therefore, the proximal outgroup taxon, the woolly oppossum, Caluromys (Fig. 3) , should be included as the outgroup next time.

Figure 2. Subset of the LRT focusing on the Carnivora.

Figure x. Subset of the LRT focusing on the Carnivora.

By chilling contrast,
in the Hassanin et al. 2021 genomic analysis, a hoofed placental, the tapir (Tapirus), was used as the outgroup taxon. Given all other placentals for their choice of outgroup for Carnivora, why did they choose a relative of horses and rhinos? We’ve seen this sort of confused mayhem before and recently in genomic studies. Let’s all pray that the ghost of Alfred Sherwood Romer will come visit Hassanin et al. and all others who think this is a good idea.


References
Hassanin A, Veron G, Ropiquet A, Jansen van Vuuren B, Le´cu A, Goodman SM, et al. 2021. Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes. PLoS ONE 16(2): e0240770. https://doi.
org/10.1371/journal.pone.0240770

A tiny goby, Elacatinus, enters the LRT with the mudskipper

Short one today.
Uncontroversial traditional nesting for the neon goby with another, larger goby, the mudskipper.

Figure 1. Elacatinus the neon goby, full scale on a 72 dpi monitor.

Figure 1. Elacatinus the neon goby, full scale on a 72 dpi monitor.

Elacatinus oceanops (Jordan 1904; 5cm; Figs. 1–3) is the extant neon goby from Bahamas coral. It is common in the aquariaum trade. Here in the large reptile tree (LRT, 1802+ taxa, subset Fig. 1) the neon goby nests with the mudskipper, Periophthalmus (Fig. 4). This clade is derived from the frogfish (Antennaris) clade and basal to deep-sea tripod fish (Bathypterois) and anglers (Lophius) in the LRT.

Figure 1. Elactatinus skull from Gregory 1933 ion dorsal and lateral views.

Figure 2. Elacatinus skull from Gregory 1933 ion dorsal and lateral views.

Note the absence of a lacrimal, 
exposing the palatine completely. The postorbital is also missing.

Figure 2. Elacatinus in vivo in dorsal and lateral views.

Figure 3. Elacatinus in vivo in dorsal and lateral views.

Figure 4. The mudskipper, Periophthalmus, nests with the neon goby, Elacatinus, in the LRT.

Figure 4. The mudskipper, Periophthalmus, nests with the neon goby, Elacatinus, in the LRT.

References
Jordan DS 1904. Ichthyology in the ‘Encyclopædia Americana.’ Science. 19: 767.

wiki/Frogfish
wiki/Periophthalmus
wiki/Elacatinus

Archelon enters the LRT with snapping turtles

This post was set in motion by a recent PBS Eons YouTube video
all about the biggest fossil turtle ever described, Archelon (Figs. 1, 2). Click to play.

The narrator reported
that Archelon (Figs. 1, 2) was not related to living sea turtles, not even to Dermochelys, the living leatherback (Fig. 4). Well that mystery sounds like a job for the LRT. Maybe it can do some good. And it’s good to get back to reptiles for an evening. It’s been awhile…

Figure 1. Classic photos of Archelon in ventral and dorsal views.

Figure 1. Classic photos of Archelon in ventral and dorsal views.

After testing
in the large reptile tree (LRT, 1802+ taxa) Archelon (Figs. 1, 2) nests firmly with Macrochelys, the alligator snapping turtle (Fig. 3). That’s why Archelon is not related to living sea turtles and perhaps why it’s terrestrial origin has remained a mystery until now.

Once again, testing taxa together that have never been tested together before sometimes recovers such unexpected, but inevitable results.

When you see the skulls together
(Figs. 2, 3), the relationship seems obvious. Most turtles do not extend their premaxilla like a hawk beak, but Archelon and snapping turtles do. The skull suture patterns are also distinct from other turtles and shared between only these two of all other turtles tested in the LRT.

Figure 2. Skull of Archelon with colors identifying bones. Compare to Macrochelys in figure 3.

Figure 2. Skull of Archelon with colors identifying bones. Compare to Macrochelys in figure 3.

In the ancient and dangerous Niobrara Sea covering much of North America,
it took a giant, mean-old snapping turtle with flippers to survive in a seaway full of other giant monster reptiles.

Figure 3. Macrochelys skull in three views with colors added to bones. Compare to Archelon in figure 2.

Figure 3. Macrochelys skull in three views with colors added to bones. Compare to Archelon in figure 2. Image from Catalogue of shield reptiles in the collection of the British Museum.

Archelon ischyros
 (Wieland 1896; Late Cretaceous; 4.6m or 15 feet in length; Figs 1,2) is the largest turtle ever documented. Along with ProtostegusArchelon is traditionally considered a member of the Protostegidae. In the LRT Archelon nests with Macrochelys, the alligator snapping turtle (Fig. 3). Distinct from Macrochelys, the naris opens dorsally in Archelon.

Figure 4. Macrochelys skeleton documenting the origin of the open ribs with small fenestrations.

Figure 4. Macrochelys skeleton documenting the origin of the open ribs with small fenestrations.

Archelon is distinct from and parrallel to
other sea turtles, all of which have a shorter, transverse premaxilla and different skull bone patterns (e.g. Fig. 4). Previous workers had already removed protostegids from other sea turtles, but then stopped there. The Archelon relationship to snapping turtles was not tested or known until now. If proposed previously, please send a citation so I can promote it here.

A leathery carapace,
like that of Dermochelys, covered the similarly open ribs of Archelon (Fig. 1), but the two tax are not related. Dermochelys is closer to sea turtles with a traditional hard-shelled carapace.

Figure 4. Skulls of Dermochelys, the extant leatherback turtle. The skull pattern here is distinct from patterns in Archelon and other snapping turtles (above).

Figure 4. Skulls of Dermochelys, the extant leatherback turtle. The skull pattern here is distinct from patterns in Archelon and other snapping turtles (above).

Not sure why snapping turtles and Archelon 
were never shown to be related to one another before. It seems obvious in hindsight. This struck me as low-hanging fruit left by PhDs for armchair amateurs to deduce. It just took one evening to nest this enigma. Let me know if there are any more enigmas lurking out there that need a good nesting. This is the fun part.

Postscript Feb. 19, 2021
Readers have reported that I might have colorized osteoderms or scales instead of bone sutures. Jura sent the images on the left, which I desaturated and burned to bring out details. Those seem to show scalation. The colored images appear to show sutures. Right? Or wrong?

Jura replied: top = sutures, bottom = welded osteoderms. Compare the top image with figure 4 from Sheil 2005′

The Shiel 2005 image of Macrochelys (= Macroclemys) is a diagram drawing from Gaffney 1979. The Gaffney 1979 image is a diagram drawing from Gaffney 1975e.

Figure x. Osteoderms on the left don't always align with bones on the right in these images of Macrochelys.

Figure x. Osteoderms on the left don’t always align with bones on the right in these images of Macrochelys.

Figure y. Macrochelys skull with traditional labels (b&w) and LRT labels (color). The LRT prefrontal rims the orbit, as in all other tetrapods.

Figure y. Macrochelys skull with traditional labels (b&w) and LRT labels (color). The LRT prefrontal rims the orbit, as in all other tetrapods.

It seems to me,
and let me know if this is an error, that everybody recognizes the pair of bones over the naris. Traditionally these are labeled prefrontals (Fig. y), even though they don’t touch the orbit. Other bones have different traditional labels, too. My labels come from pareiasaur and Elginia homologs so those labels come from a valid phylogenetic context. Traditional labels are wrong because the pareiasaur ancestry is not yet widely, if at all, recognized. All other turtle ancestor candidates are tested in the LRT.


References
Gaffney ES 1975e. Phylogeny of the chelydrid turtles: a study of shared derived characters in the skull. Fieldiana:Geol., vol. 33, pp. 157-178.
Gaffney ES 1979. Comparative cranial morphology of recent and fossil turtles. Bulletin of the American Museum of Natural History 164(2):65–376.
Sheil CA 2005. Skeletal development of Macrochelys terrminckii (Reptilia: Testudines: Chelydridae) Journal of Morphology 263:71–106.
Wieland GR 1896. Archelon ischyros: a new gigantic cryptodire testudinate from the Fort Pierre Cretaceous of South Dakota. American Journal of Science. 4th series. 2 (12): 399–412.

wiki/Macrochelys
wiki/Archelon