The assembly of the avian body plan (Cau 2018) pt. 1 of 3

Dr. Andrea Cau 2018 summarizes traditional knowledge
on the origin of birds breaking the process into three stages:

1. Huxleyian stage: Early Triassic to Middle Jurassic the earliest ancestors of birds acquired postcranial pneumatisation, an obligate bipedal and digitigrade posture, the tridactyl hand and feather-like integument
2. Ostromian stage: Middle to Late Jurassic is characterised by a higher evolutionary rate, the loss of hypercarnivory, the enlargement of the braincase, the dramatic reduction of the caudofemoral module, and the development of true pennaceous feathers.
3. Marshian stage: Cretaceous. The transition to powered fl ight with the re-organisation of both forelimb and tail as fl ight-adapted organs and the full
   acquisition of the modern bauplan

This is a pretty good plan overall.
Unfortunately Dr. Cau uses an antiquated cladogram (Fig. 1) riddled with taxon exclusion (especially among the outgroups), so the details tend to get a little messed up. Let’s review the pluses and minuses.

The Cau cladogram and LRT
both feature many of the same basal theropods at the beginning, birds at derived nodes and a variety of carnivores in between, with dromaeosaurs then troodontids leading to birds.

Dr. Cau opens his paper
with several paragraphs devoted to nomenclature. He finds the term ‘non-avian’ particularly irksome. Cau employed 132 taxa and 1781 (1431 informative) characters. He reports that he decided not to include pterosaurs as outgroup taxa. That shows wisdom.

Unfortunately
Cau was not wise to largely ignore basal bipedal crocodylomorphs, including such favorites as Scleromochlus and Gracilisuchus. Thankfully Lewisuchus made his list.

So Cau starts off with four very distant outgroup taxa (Euparkeria, Teleocrator, Dormomeron and Lagerpeton), and that is never good (relevant taxon exclusion, again). It also shows a lack of understanding that could have been had with a quick glance at the large reptile tree (LRT, 1213 taxa). That’s what it’s there for.

Cau 2018 Results
3072 shortest trees (vs. LRT has one, fully resolved tree, last time I tested the whole tree).

Here are Cau’s nodes:

1. Teleocrater + Dinosauromorpha: Unfortunately this clade does not include the Crocodylomorpha, so it is invalid. ‘Dinosauromorpha’, at best, is a junior synonym of Archosauria in the LRT.
2. Dinosaurormorpha: (Lagerpetids + Dinosauriformes). Unfortunately this clade does not include the Crocodylomorpha, so it is invalid. When more taxa are added, lagerpetids nest with Tropidosuchus among the chanaresuchidae. Thus,  ‘Dinosauriformes’, at best, is a junior synonym of Archosauria in the LRT.
3. Dinosauriformes: (Marasuchus + Dracohors). More taxa move Lewisuchus into the Crocodylomorpha, Silesaurus into the Poposauria and Pisanosaurus deep into the Phytodinosauria.
4. Dracohors: (includes Megalosaurus, but not Marasuchus). More taxa (e.g. Segisaurus, Procompsognathus) move Marasuchus into the Theropoda and other taxa as listed above in the LRT.
5. Dinosauria: (Eodromaeus, Herrerasauridae, Sauropodomorpha and Ornithoscelida). This is too many taxa and shows a lack of understanding. No basal dichotomy can be made. The LRT defines Dinosauria as Theropoda + Phytodinosauria, their last common ancestor (Herrerasaurus) and all descendants.
6. Ornithoscelida: (Ornithischia + Theropoda) Adding more taxa will split up and invalidate this clade, based on LRT results.
7. Theropoda: (Coelophysoidea + Averostra) In the LRT several theropods are listed as outgroups in the Cau analysis and it includes the phytodinosaur, Chilesaurus. (Daemonosaurus is curiously absent from this paper). Almost toothless Limusaurus should nest with oviraptorids. Elaphrosaurus has not been tested in the LRT. The basalmost coelophysoid (with feathers!), Sinocalliopteryx, nests as a derived compsognathid in the Cau taxon list.
8. Averostra: (Ceratosauria + Tetaneurae) The LRT recovers a clade of large carnivores between Sinocalliopteryx and Compsognathus. This clade includes Proceratosaurus, Deinocheirus, Xiongguanlong, Suchomimus and Spinosaurus, taxa not employed by Cau. These taxa attract Guanlong and Dilong to this basal feathered clade, away from tyrannosaurs. Otherwise, the LRT and Cau both place the same long list of medium to large basal theropods in clades at the base of this clade/grade.

More tomorrow.

References
Cau A 2018. The assembly of the avian body plan: a 160-million-year long process. Invited Paper, Bollettino della Societa Paleontologica Italiana 57(1):1–25.