provides a teaser abstract that sets up the situation, but provides no solution.
From the abstract
“Since the earliest Triassic, saurian reptiles have been critical components of terrestrial ecosystems. However, molecular and fossil evidence indicates that the divergence between the two constituent lineages (Lepidosauria, Archelosauria [turtles + archosaurs]) took place deep in the Permian Period. A large number of early-diverging stem-archosaur and stemlepidosaur clades have been described from the Permian and Triassic, exhibiting an extraordinary range of bauplans. However, the interrelationships of these stem taxa are poorly resolved, owing to fragmentary records and poor preservation in many groups. As such, the timing of both the initial taxonomic and morphological diversifications of Sauria remain poorly understood. To resolve this phylogenetic uncertainty and the first radiation of crown reptiles, a new phylogenetic data matrix was constructed from a broad sample of Permo-Triassic diapsids. New, three-dimensionally preserved fossils from a number of poorly understood stem groups (e.g., long-necked Tanystropheidae, chameleon-like Drepanosauromorpha) allowed coding of many previously unknown morphologies. Iterations of this data matrix were subjected to both standard parsimony analysis and Bayesian tip-dating methodologies. The results of this analysis suggest that at least ten distinct lineages of Permo-Triassic diapsids survived the PTE, substantially more than went extinct at that time. They do not form a monophyletic Protorosauria clade, a group traditionally considered to include most long-necked, small-headed early archosauromorphs. Instead, these taxa include no fewer than six separate Permo-Triassic diapsid lineages. Indeed, character optimizations strongly suggest that a long-necked, lizard-like bauplan was ancestral for Archosauromorpha. The inclusion of fragmentary fossil material from Early Triassic archosauromorphs indicates that a great deal of morphological diversity existed in saurian groups within the first five million years of the Triassic.**”
*Archelosauria is not recovered in the large reptile tree. Not sure why the molecules do what they do, nesting turtles with archosaurs (hence the clade name).
** This is a teaser abstract. No conclusions are presented. I cannot compare the data here to the cladogram recovered in the large reptile tree.
Pritchard A 2015. Resolving the first radiation of crown reptiles. Journal of Vertebrate Paleontology abstracts