One final note on the Eodicynodon / Galeops sisterhood issue.
As reported earlier here and here, everyone else nested the dromasaur Galeops (Fig. 1) as the outgroup to the Dicynodontia with Eodicynodon (Barry 1974) at its base. However, by adding taxa, the large reptile tree nested Microurania at the base of the Dicynodontia + Venjukovioidea. Elsewhere Galeops nested as a derived dromasaur, having arisen from their common ancestor a sister to Stenocybus..
It would be great
to see Eodicynodon and Galeops to scale side-by-side for ready comparison, since they nest together in all traditional trees. Like Clark Kent and Superman, they have never been pictured together. So here they are (Fig. 1) for the first time.
Figure 1. Click to enlarge. Eodicynodon the basal dicynodont and Galeops the derived dromasaur. One was terrestrial and one was arboreal. Did dicynodonts arise from dromasaurs? Not likely according to the large reptile tree which nests Stenocybus as their last common ancestor. Eodicynodon was small for a dicynodont. Later forms grew to great size while retaining this basic morphology.
Similar, yes,
but those details were by convergence and common ancestry with Stenocybus. And this origin appears to be distinct from all other therapsids (see below). Overall, a suite of traits nests Eodicynodon and Galeops apart. Likely they did not share the same niche. The large reptile tree found them to be “strange bedfellows” nesting together by default because better nesting partners were not included in analyses.
Tree topology changes
Synapsida, according to Wiki, includes Casesauria, which the large reptile tree nests with Millerettids. So that’s an ongoing problem.
Therapsida, according to Wiki, includes Tetraceratops, which the large reptile tree nests with diadectomorphs and limnoscelids. That’s another ongoing problem.
Anomodontia (dromasaurs + dicynodonts), according to Wiki, are derived from Dinocephalia. which also (according to Wiki) give rise to Theriodonts, which leads to mammals. That puts two plant-eating clades in the middle of a string of carnivores. Not good. Red flag.
On the other hand,
the large reptile tree nested anomodonts with Stenocybus, arising from Ophiacodon/Haptodus. The large reptile tree nested the rest of the therapsids with Nikkasaurus and Biarmosuchus arising out of Archaeothyris/Ophiacodon. Then both Dinocephalians and Theriodonts arise from Phthinosuchus and Eotitanosuchus, which really makes more sense, keeping the carnivorous line carnivorous and the herbivore line distinct.
The trouble is
Stenocybus, Microurania and Nikkasaurus are only known from skulls and, to my knowledge, have not been added to therapsid family trees. They need to be.
References
Barry TH 1974. A new dicynodont ancestor from the Upper Ecca. Annals of the South African Museum 64: 117-136.
Rubidge BS, King GM and Hancox PJ 1994. The postcranial skeleton of the earliest dicynodont synapsid, Eodicynodon from the Upper Permian of South Africa. Palaeontology 37(2):397-408.
The Pterosaur Heresies 
Two points.
1) Can I ask what species/specimen of Venjukovia you put into your tree?
I ask because you criticise phylogenies for missing it out. However the second species of “Venjukovia” (V. invisa) has been renamd Ulemica. To judge from the picture you provide of Venjukovia in previous posts, I suspect it is Ulemica you are using (the type, and now only, species of Venjukovia, is a shoddy jaw with no skull). And Ulemica has been used in many an analysis.
2) on the point “Anomodontia (dromasaurs + dicynodonts), according to Wiki, are derived from Dinocephalia. which also (according to Wiki) give rise to Theriodonts, which leads to mammals. That puts two plant-eating clades in the middle of a string of carnivores. Not good. Red flag.”
Not sure where you get that from wiki, I couldn’t see that. If they do, they are proposing an idea that has been out of date since the 90s. I’m fairly sure they also don’t say theriodonts come from Dinocephalians, which has never, to my knowledge, been suggested by any scientist in history.
Even if these had been suggested, not sure why two herbivorous clades coming from carnivores is a red flag. Given that the primitive condition for tetrapods is carnivory, I’m not sure how you can suggest otherwise for any clade. The vast majority of herbivorous clades come from carnivores. I’m finding it difficult to think of any which didn’t. . Your own tree argues many times for multiple evolution of herbivores from carnivores…
Never heard of Ulemica. I’ll look into it. Re: Theriodonta: Look here: http://en.wikipedia.org/wiki/Therapsida. I’m arguing – against – carnivory arising from herbivory in this case, just the opposite of what you suggest I do. In other words, I agree with you.
On the other hand, snakes and their ancestors, to pull one example, strangely enough, arise from the herbivorous clade, the new Lepidosauromorpha, beginning, as it were with diadectids and captorhinomorphs, among others hundreds of millions of years earlier.
Re: wiki, I think that’s just a way of drawing the phylogeny rather than suggesting an ancestor relationship; the dinocephalian label does appear after the split.
As for the carn/herb transition, sorry for misinterpreting you (although note that dinocephalians and theriodonts are primitively carnivores, so even if the wiki page is suggesting an ancestor relationship, that’s still herbs from carns)
Finally, even if your new lepidosauromorpha is an accurate clade, I don’t think it suggests a herbivorous origin; both diadectomorphs and captorhinids contain carnivorous, insectivorous and herbivorous forms, and the herbivores are the dervived members of the clades in both yours and my trees. Multiple origin of herbivory is the most parsimonious solution in your tree.