The large reptile tree is anchored on about 450 extinct taxa. However, more than a few (39) extant taxa are now included. Today we’ll simply delete all the extinct taxa and see what sort of tree we recover. This will demonstrate what changes to the tree topology occur without extinct taxa, and note how parts of it kind of resemble the latest DNA studies.
Rana the frog nests at the base, perhaps because it is now listed first among the taxa. Or perhaps because it is indeed primitive. Not sure, but if there are no objections?
There is loss of resolution
at the base of the Amniota, where three clades branch off: 1) mammals, 2) turtles and archosaurs and 3) lepidosaurs. This largely matches certain DNA studies, by the way, that nest turtles with archosaurs. Interesting solution to that old problem…
Within the Lepidosauromorpha (sans the turtles)
the clades largely match the large reptile tree. Sphenodontians split from Squamates and Iguania branches off from Scerloglossa thereafter.
Here (Fig. 1) the geckos are separated from the snakes. Instead, amphisbaenids nest with snakes. These ‘odd bedfellows’ appear due to taxon exclusion and loss of limbs.
Here 510 total taxa are reduced to 39, an exclusion of 92 percent. Like other smaller, more focused studies, this one demonstrates the problems they have and, by inference, the value of adding prehistoric taxa. That’s where the transitions are to be found.
The original tree topology is not quite retained.
Turtles transfer from lepidosauromorphs to archosauromorphs. The legless taxa nest together. This tree also nearly echoes DNA studies that have mammals branching off first in the absence of about a dozen taxa that precede synapsids in the large reptile tree.
Word of Warning
No one in their right mind would ever consider turtles the sister taxon to birds and crocs… Yet here they are. Sisterhood varies based on taxon inclusion. This situation is analogous to those that nest pterosaurs with archosaurs and archosauriformes and other such odd nestings.
By the way
I made comments to the recent Reeder et al. morphology + molecules study of squamates here. In short they did not include enough extinct taxa and did not recognize the large number of lepidosaurs that nest between Sphenodontia and Squamata, some of which nest as proximal basal taxa to the Squamata. Without them, the base of their tree did not have the correct roots and so the initial branching also suffered.