>>You think amniotes become more homogenous if birds and mammals are removed? >>



Of course I think so. And I am not alone. Other than some dogmatic cladists, a vast majority of biologists consider Reptilia (excluding birds) a natural group and a valid taxon.



>>By what criteria do you judge snakes and crocodiles to be more similar to each other than crocodiles are to birds? Nucleotide sequence? Morphometrics? Embryology? Behavior?>>



Morphologically crocs and snakes are more similar because their scales are more similar to each other. Biochemically snake scales and crocodilian scales are made of the same kind of protein. Feathers, however, are made of a unique protein not found in reptiles.



Physiologically, snakes and crocodilians have more in common with each other and with other reptiles than any reptiles do with birds. All reptiles are ectotherms. They rely on external heat sources and they do not generate a lot of metabolic heat internally. Birds are different. Birds are endotherms and they rely on metabolic heat to maintain a more or less constant body temperature.



If a classification is to be natural, then it must take evolution into account. Since birds have evolved into a different sort of animal than their reptilian ancestor, removing them from their ancestral group Reptila is perfectly consistent with evolutionary theory.



But of course similarity has never been the sole criterion for a natural classification. Snakes and crocodilians do form a monophyletic (paraphyletic if you insist) group with other reptiles. Hence reptiles form a natural group. Their similarities with one another also make such a group far more homogeneous and useful than a "Reptilia" that includes the birds.

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