Mammalian nomenclature problems

Several putative stem mammal clades
have not been recovered in the LRT, like the ‘Notoungulata’ and the ‘Allotheria.‘ Similarly several putative reptile clades were also not recovered.

Now
the base and stem of the mammal clade are showing some nomenclature problems relative to traditional results.

First, I added a few mammals
(Mus, Taeiniolabis, Paulchaffatia) just be sure I was comparing listed taxa (see below) with listed taxa. If you know of any pertinent taxa that will change the current tree topology back to traditional topologies, please let me know. So far, I’m coming up short. These are the changes recovered so far:

Carrano et al. (editors) 2006
reports the following pertinent definitions. Comments follow (not in boldface).

Mammalia Linneaus 1758
The least inclusive clade containing Ornithorhynchus and Mus. In the LRT, Sinoconodon is the last common ancestor and Pachygenelus nests at the base of the outgroup clade, the Trithelodontidae (including the Tritylodontidae). So, no problems with this definition.

Trithelodontidae Broom 1912
The most inclusive clade containing Pachygenelus, but not Tritylodon and Mus. In the LRT Pachygenelus is basal to both Tritylodon and Mus, so the most inclusive clade containing Pachygenelus includes Mammalia and Tritylodontidae, contra prior studies.

Tritylodontidae Kühne 1956|
The most inclusive clade containing Tritylodon, but not Pachygenelus or Mus. In the LRT, this clade is monophyletic, and now includes Repenomamus.

Mammaliamorpha Rowe 1988
The least inclusive clade containing Tritylodon, Pachygenelus and Mus. In the LRT this clade is a junior synonym of the Trithelodontidae (see above).

Mammaliformes Rowe 1988
The most inclusive clade containing Mus, but not Tritylodon or Pachygenelus. In the LRT, this clade is a junior synonym for the clade Mammalia because Pachygenelus is the proximal outgroup taxon to Mammalia.

Theria  Parker and Howell 1897
The least inclusive clade containing Mus and Didelphis. In the LRT this clade is monophyletic and unchanged.

Theriimorpha Rowe 1988
The most inclusive clade containing Mus but not Ornithorhynchus. In the LRT this clade is a junior synonym for Theria.

Metatheria Huxley 1880
The most inclusive clade containing Didelphis, but not Mus. This definition was meant to include all marsupials, but in the LRT the clade that includes most marsupials does not include Didelphiswhich nests basal to and outside both monophyletic Marsupialia and Placentalia. So, strictly speaking, Metatheria in the LRT currently includes only Didelphis and perhaps its sister, Ukhaatherium.

Allotheria Marsh 1880
The most inclusive clade containing Taeniolabis, but not Mus or Ornithorhynchus. This was meant to indicate that Taeniolabis nested outside the Mammalia, but in the LRT Taeniolabis nests with Plesiadapis and Carpolestes and this clade is a sister to the clade containing Mus and the Multituberculata — within the Glires and Placentalia.

Multituberculata Cope 1884
The least inclusive clade containing Taeniolabis and Paulchofattia. This was meant to  include all the multituberculates and have them nest outside of the Mammalia, but in the LRT Taeniolabis nests with Plesiadapis and Paulchofattia nests with Carpolestes. So that is a clade of four taxa at present and it does not include Ptilodus and other multituberculates, the clade with a large and grooved lower last premolar. These traditional multis now need a new clade name. They are derived from a sister to the rodent clade in the LRT and they leave no descendants. Carpolestes is a sister to the ancestor of rodents and multis and Carpolestes (Fig. 1) has a large and barely-grooved lower last premolar, a precursor to that identifying trait in that second clade of multis.

Figure 1. Carpolestes simpsoni skull shows that large lower precursor premolar.

Figure 1. Carpolestes simpsoni skull shows that large lower premolar with just a few grooves. Here in the LRT Carpolestes nests close to the base of the traditional multituberculates that emphasize this trait. But see text for strict definitions of this clade.

References
Editors: Carrano MT et al. 2006. Amniote Paleobiology: Perspectives on the Evolution of Mammals, Birds and Reptiles. University of Chicago Press.  online here.
Kermack KA, Mussett F, Rigney HW 1973. The lower jaw of Morganucodon. Zoological Journal of the Linnean Society.53 (2): 87–175.
Martin T et al. 2015. A Cretaceous eutriconodont and integument evolution of early mammals. Nature 526:380-384. online.

A Modest Proposal for Abbreviating Phalanges

There are several ways to label individual phalanges.

A:
You can say, “phalanx 3, digit 4 of the manus.” Not sure why, but people seem to put the phalanx first.

B:
You can write in a caption, “ph. 3, dig. 4, man.” I’ve seen this dozens of times.

C:
Or you can do what I’ve been doing lately, “m4.3.” And for the pes, “p4.3.”

If I’m starting a sentence with a phalanx, I’ll write “Manual 4.3…” or “Pedal 4.3…”

The old mc3 and mt3 still work for metacarpals and metatarsals.

Occasionally you’ll find a phalanx that is the product of fusion. Then it’s “m4.2+3.

Of course, if a phalanx is lost, and you don’t want to skip a number on your way to the ungual (like skipping the 13th floor on a building), well, you’re on your own. Do the right thing in terms of context and consistency.

Simplify your captions and not only will you save space in your figures plus wear and tear on your keyboard, you’ll also make things easier to understand for the reader. Isn’t “m4.3”  easier to understand anyway?

A modest proposal.

Nomenclature revisions (part 3)

Today’s blog will tag on the heels of “Nomenclature revisions (part 1 and part 2) to highlight a number of putative clades that are in need of revision, are no longer valid or are redundant in light of the new reptile tree (which is larger than any prior attempt and encompasses all the major clades). Today we’ll restrict our scope to the Archosauriformes.

The Euarchosauriformes

Figure 1. The Euarchosauriformes. Click to see more.

Erythrosuchiformes – new clade
A new definition for a monophyletic clade Erythrosuchiformes is proposed to include Erythrosuchus, Triceratops, their last common ancestor and all of its descendants. Vjushkovia had been traditionally considered an erythrosuchid but here it nests outside the Erythrosuchidae.

The Rauisuchia – retained
Rauisuchia was erected by Bonaparte to represent the clade including Rauisuchidae, Prestosuchidae, Poposauridae and Chatterjeeidae. Because Chatterjeea and Poposaurus now nest as dinosaurs, this definition of the Rauisuchia now includes all dinosaurs. Redefined as a more inclusive monophyletic node-based clade, the new Rauisuchia is proposed to include Vjushkovia, Triceratops, their last common ancestor and all of its descendants. Members also include crown-clade Archosauria and Ticinosuchidae (including Stagonolepidae). The more restricted Rauisuchidae now includes Vjushkovia, Smok, the last common ancestor and all its descendants.

Ticinosuchidae – new clade
Yarasuchus
and Ticinosuchus are basal to a clade that includes Qianosuchus and the Stagonolepidae. Within the new Rauisuchia, a definition for a monophyletic Ticinosuchia is proposed to include Ticinosuchus, Triceratops their last common ancestor and all of its descendants. The more restricted Ticinosuchidae is proposed to include Ticinosuchus, Qianosuchus, their last common ancestor and all its descendants.

Archosauria – retained
Still crocs, birds, their last common ancestor and all its descendants. No change here (except no pterosaurs, of course).

Suchia – paraphyletic
Krebs (1974) defined “Suchia,” as “Crocodylotarsi,” but not Parasuchia. Even so, such a clade remains paraphyletic here. “Suchia” had been described by Benton and Clark (1988) as Crocodylomorpha + “rauisuchians” + Stagonolepididae, but not Gracilisuchus =. Here, that assemblage also constitutes a paraphyletic group.

Pseudosuchia – redundant
In the pre-cladistic era, “Pseudosuchia” generally included Stagonolepidae, the old Rauisuchia, Ornithosuchidae and some basal crocodylomorphs. Here these form a a paraphyletic clade.

Gauthier and Padian (1989) defined “Pseudosuchia” as “crocodiles and all archosaurs closer to crocodiles than to birds. Gauthier 1986 and Senter (2004) created equivalent definitions. Unfortunately, here the “Pseudosuchia,” as defined by these authors, is redundant with the Crocodylomorpha.

Crocodylomorpha – retained, redefined
Parrish (1993) cited six synapomorphies from Walker (1964) when he embedded the old Crocodylomorpha within Rauisuchia.

Benton (1990) defined Crocodylomorpha as all archosaurs closer to Eusuchia than to Ornithosuchus or Postosuchus. While it is clear that Benton meant to include a clade similar to the present one, his definition with the present tree topology would include Ticinosuchidae (including Stagonolepidae), which was not his intention.

Sereno (2005) defined Crocodylomorpha as the most inclusive clade containing Crocodylus but not Poposaurus, Gracilisuchus, Prestosuchus and Aetosaurus. The omission of Gracilisuchus excludes a basal taxon in the present Crocodylomorpha.

A new node-based definition for the new Crocodylomorpha is proposed to include Crocodylus, Pseudhesperosuchus, their last common ancestor and all of its descendants. Ticinosuchidae is the outgroup. Scleromochlus, a taxon often nested with dinosaurs and pterosaurs [17–20,23] nests here (Figures 2) within the crocodylomorpha close to Gracilisuchus.

Crocodylotarsi – redundant
Benton and Clark (1988) defined “Crocodylotarsi” as the last common ancestor of crocodiles and Parasuchia. This represented the “crocodilian line” (Parasuchia, Rauisuchidae, Stagonolopedidae, Poposauridae and Crocodylomorpha) as opposed to the “bird line” (Ornithosuchia) as defined by Parrish (1993). In the present study that definition of Crocodylotarsi is redundant with Archosauriformes and furthermore the taxon list is paraphyletic.

Crurotarsi  – redundant
Sereno (1991) defined “Crurotarsi,” as all forms closer to Crocodylus than to Passer [146]. It was meant to include rauisuchians, phytosaurs (parasuchians), stagonolepids, poposaurs, sphenosuchians, and a few other groups including Ornithosuchidae. Here the definition is redundant with Crocodylomorpha. The taxon membership list is paraphyletic and redundant with Archosauriformes.

More coming in part 4. 

As always, I encourage readers to see specimens, make observations and come to your own conclusions. Test. Test. And test again.

Evidence and support in the form of nexus, pdf and jpeg files will be sent to all who request additional data.

References
Benton MJ 1990. Origin and Interrelationships of dinosaurs, In Weishampel DB, Dodson P, and Osmólska H editors. The Dinosauria. 11–30. Berkeley: U Calif Press.
Benton MJ, Clark JC 1988. Archosaur phylogeny and the relationships of the Crocodylia. In Benton MJ editor. The phylogeny and classification of the tetrapods, 295–338. Syst Assoc, Sp Vol 35A, Clarendon:Oxford.
Bonaparte JF 1982. Classification of the Thecodontia. Geóbios, Mém Sp 6: 99–112.
Clark JM and Hernandez RR 1994. A new burrowing diapsid from the Jurassic La Boca formation of Tamaulipas, Mexico, J Vert Paleo 14: 180–195.
Dilkes D 1998. The Early Triassic rhynchosaur Mesosuchus browni and the interrelationships of basal archosauromorph reptiles. Phil Trans R Soc B 353: 501–541.
Gauthier JA 1986.
Saurischian monophyly and the origin of birds, In Padian K editor. The Origin of Birds and the Evolution of Flight, 1–55. Memoirs Calif Acad Sc 8.
Gauthier J, Kluge AG and Rowe T 1988.
Amniote phylogeny and the importance of fossils. Cladistics 4: 105–209.
Gauthier J, Estes R and de Queiroz K 1988. A phylogenetic analysis of Lepidosauromorpha, In Estes R, Pregill G, editors. Phylogenetic relationships of the lizard families, 15–98. Stanford: Stanford U Press.
Gauthier JA 1994. The diversification of the amniotes. In: Prothero DR, Schoch RM editors. Major Features of Vertebrate Evolution: 129-159. Knoxville: Paleo Society.
Gauthier JA, Padian K 1989. The origin of birds and the evolution of flight, In Padian K, Chure DJ editors. The Age of Dinosaurs: Short Courses in Paleontology, No. 2. 121–133. Paleo Soc Depart Geo Sci, Knoxville: U Tenn.
Krebs B 1974. Die Archosaurier. Naturwissenschaften 61: 17–24.
Laurin M 1991.The osteology of a Lower Permian eosuchian from Texas and a review of diapsid phylogeny. Zoological Journal of the Linnean Society 101: 59–95.
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Parrish JM 1993. Phylogeny of the Crocodylotarsi, with reference to archosaurian and crurotarsan monophyly. J Vert Paleo 13:287–308.
Senter P 2004.Phylogeny of Drepanosauridae (Reptilia: Diapsida). J Syst Palaeo 2: 257–268.
Sereno PC 1991. Basal archosaurs: phylogenetic relationships and functional implications. J Vert Paleo 11 (Supp) Mem 2: 1–53.
Sereno PC 2005.
The logical basis of phylogenetic taxonomy. Syst Biol 54: 595-619.
Walker AD 1964. Triassic reptiles from the Elgin area: Ornithosuchus and the origin of carnosaurs. Phil Trans R Soc London. Ser B Bio Sci 248 (744): 53–134.

Nomenclature revisions (part 2)

Today’s blog will tag on the heels of “Nomenclature revisions (part 1) to highlight a number of putative clades that are in need of revision, are no longer valid or are redundant in light of the new reptile tree (which is larger than any prior attempt and encompasses all the major clades).

Diapsida
Laurin (1991) defined the Diapsida as the most recent common ancestor of araeoscelidians, lepidosaurs and archosaurs and all its descendants. Here that definition is redundant with Reptilia because lizards are not related to archosaurs except through Cephalerpeton, the basalmost reptile.

Benton (1990) referred the term Diapsida to the clade stemming from the first amniote with a supratemporal fenestra homologous with that of Aves. That definition may be retained despite the revelation that the diapsid opening of Sphenodon was not homologous with that of Aves because lepidosauriformes were not related to the basal diapsid, Petrolacosaurus. A node-based redefinition of the new Diapsida is proposed to include Petrolacosaurus, Triceratops, their last common ancestor and all of its descendants. It is equivalent to the definition of Benton (1990).

Younginiformes
Taxa traditionally considered “younginiformes,” such as Youngina, Acerosodontosaurus \ and Thadeosaurus do not form a monophyletic group. Here they form a basal assemblage of a larger clade. The Younginimorpha is proposed to include Thadeosaurus, Triceratops, their last common ancestor and all of its descendants.

Prolacertiformes / Protorosauria
Protorosauria no longer include tanystropheids, pterosaurs and kin. Those have all been shifted to the Squamata. The clade Protorosauria has been reduced to only Prolacerta, Protorosaurus, PamelariaBoreopricea and kin, all basal taxa to the Archosaurifomes. Redefined, the new Protorosauria is proposed to include Prolacerta, Protorosaurus, their last common ancestor and all of its descendants. A more inclusive clade, the new Prolacertiformes, is proposed to include both Protorosauria + Archosauriformes. Redefined as a node-based taxon, the new Prolacertiformes is proposed to include Prolacerta, Triceratops, their last common ancestor and all of its descendants. Orovenator is the outgroup taxon.

Archosauriformes
Gauthier (1986) proposed the term “Archosauriformes” to replace the traditional Archosauria (Proterosuchus through Dinosauria). Gauthier’s Archosauriformes retained the Proterosuchidae, Parasuchidae, Proterochampsidae, Euparkeria, Erythrosuchidae, and the Pterosauria, all taxa conventionally thought to lead to and include the Dinosauria. This needs to be revised. Here pterosaurs now nest with lizards, but the other listed clades are retained. Other former outgroups are now added. These include the Choristodera and Youngina. Not all taxa had an antorbital fenestra (see below). Redefined here, the new Archosauriformes is proposed to include Champsosaurus, Triceratops, their last common ancestor and all of its descendants. A specimen of Youngina (UC 1528) nests at the base.

The Basal Division Within the Archosauriformes
The new Archosauriformes divides at its base into two major clades, the Pararchosauriformes and Euarchosauriformes. This division was previously unnoticed  in prior studies due to exclusion of several basal taxa including several specimens of Youngina.

Pararchosauriformes
The Pararchosauriformes includes Chañaresuchus, Champsosaurus, their last common ancestor and all of its descendants. This now extinct clade also includes choristoderes, parasuchians, DoswelliaCerritosaurus and Lagerpeton, among others.

Euarchosauriformes
The Euarchosauriformes includes Proterosuchus, Triceratops, their last common ancestor and all of its descendants. This clade also includes crocodilians and birds among others. It does not include proterochampsids, parasuchians, choristoderes and kin.

More to come in part 3.

As always, I encourage readers to see specimens, make observations and come to your own conclusions. Test. Test. And test again.

Evidence and support in the form of nexus, pdf and jpeg files will be sent to all who request additional data.

References
Benton MJ 1990. Origin and Interrelationships of dinosaurs, In Weishampel DB, Dodson P, and Osmólska H editors. The Dinosauria. 11–30. Berkeley: U Calif Press.
Clark JM and Hernandez RR 1994. A new burrowing diapsid from the Jurassic La Boca formation of Tamaulipas, Mexico, J Vert Paleo 14: 180–195.
Dilkes D 1998. The Early Triassic rhynchosaur Mesosuchus browni and the interrelationships of basal archosauromorph reptiles. Phil Trans R Soc B 353: 501–541.
Gauthier JA 1986.
Saurischian monophyly and the origin of birds, In Padian K editor. The Origin of Birds and the Evolution of Flight, 1–55. Memoirs Calif Acad Sc 8.
Gauthier J, Kluge AG and Rowe T 1988.
Amniote phylogeny and the importance of fossils. Cladistics 4: 105–209.
Gauthier J, Estes R and de Queiroz K 1988. A phylogenetic analysis of Lepidosauromorpha, In Estes R, Pregill G, editors. Phylogenetic relationships of the lizard families, 15–98. Stanford: Stanford U Press.
Gauthier JA 1994. The diversification of the amniotes. In: Prothero DR, Schoch RM editors. Major Features of Vertebrate Evolution: 129-159. Knoxville: Paleo Society.
Laurin M 1991.The osteology of a Lower Permian eosuchian from Texas and a review of diapsid phylogeny. Zoological Journal of the Linnean Society 101: 59–95.
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.