Yes, indeed the basal amniotes are extinct, but if Gauthier is incorrect, i.e. if turtles are descended from an amniote that is more basal to the ancestors of the mammals, then some member of this group of extinct basal amniotes has left descendants but this group nevertheless remains nameless. Gauthier's "Reptilia" would also be polyphyletic or at best paraphyletic if this is the case. I think there is recognition of this fact as some have proposed classifying turtles in their own taxon. That is indeed quite a mess. Gauthier's Reptilia is also heterogeneous, as it includes reptiles which lack endothermic homeothermy and descendants of reptiles that do have a different sort of physiology than most reptiles.

Since you are a paleontologist, you do need to communicate with other paleontologists regarding fossil taxa. Currently, there is no generally agreed informal term for the paraphyletic basal amniotes among cladists so that everyone knows what everyone else is talking about. Under the rigid rules of cladism such a group cannot even have a formal name. They can be called non-mammalian, non-reptilian amniotes, but this is awkward and it is inaccurate since these early amniotes are, as far as one can tell, very much reptilian in their morphology and physiology. Under the system Romer and Simpson used, and the same system that is being used by most biologists, all amniotes can be classified formally in their own Linnaean taxon. The cladists therefore cannot eliminate paraphyletic groups. They simply put these taxa into drawers without any labels. The new system that the cladists are proposing is therefore not progress, but a step away from utility.

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