The traditional system recognizes Reptiles, Birds, and Mammals as three separate classes, recognizable as scaly, feathery, and furry, respectively. The phylogenetic system recognizes all of these as descended from scaly tetrapods, with birds closely related to crocodilians, and turtles as no more closely related to other "reptiles" than are mammals.

The relationship of Aves to Archosaurs such as crocodilians and "dinosaurs" has long been recognized, but not emphasized in taxonomic schemes. This leads to persistent misunderstanding of their evolution: for example, crocodilians are notable among "reptiles" for having vocalizations and a four-chambered heart: special explanations are offered. The phylogenetic perspective makes it clear than vocalization and heart structure are present in the common ancestor of crocs and birds, and therefore in dinosaurs as well. Special explanations are not required, and research focuses on the evolution of common structure and behavior.