Concepts of Phenetic & Patristic distance, and Cladistic relationship

    The above diagram shows the evolutionary and morphological relationships among four taxa A, B, C, & D:
        A & B are most similar phenetically: the morphological difference measured between them on the horizontal axis is smallest.
        B & C are most similar patristically: the amount of change that separate them as measured along the branches of the tree is smallest.
        C & D are most closely related cladistically: of the three branch points in the tree, they have a more recent common ancestor (MRCA) than any other pair in the tree.

    By analogy with an actual tree, A & B are twig tips that are closest together on the outside of a tree ("as the crow flies"), despite being on different branches. B & C are closest together "as the ant runs". C & D are on the same stem "as the branches grow," despite the tips being very far apart.

    Substituting real biological examples for the hypothetical taxa: lizards and crocodiles have a superficial phenetic similarity due to their elongate, scaly bodies and four-footed stance. However, it has long been recognized that crocodiles are more closely related to dinosaurs and birds as Archosauria, which accounts for a number of shared characteristics,e.g., crocs, birds, and (presumably) dinosaurs have four-chambered hearts and make vocal sounds. Within this group, crocodiles and dinosaurs have undergone relatively little morphological change since the Mesozoic, which results in their patristic similarity (e.g., crocodilians and dinosaurs are scaly, terrestrial, diapsid tetrapods). Among Archosauria, one of the two orders of Dinosauria and the many orders of Aves (modern birds) have the closest cladistic relationship (with an MRCA sometime in the Cretaceous period), but because of adaptations associated with the evolution of flight, birds are morphologically distinctive.

    Concepts of morphological similarity and degree of change are rather subjective. Morphological similarity depends on features chosen: crocodile and lizards limbs are quite different, more so that the differences between the latter and the remnants of snake limbs. Limb structures are also quite different between the two orders of dinosaurs, the four-legged Saurischia ("lizard-hipped") and two-legged Ornithischia ("bird-hipped") (the hip joint of the latter is only superficially similar to that of modern birds (Aves), which evolved from the Saurischia). The subjectivity of perceptions of similarity is well-illustrated by films in the "Jurassic Park" franchise. Dinosaurs are depicted so as to resemble living birds, rather than as distinctive terrestrial megafauna in their own right. The recent discovery that many dinosaur species had feathers reinforces the impression that they are bird-like, rather than that birds are dinosaur-like, because of our long association of feathers exclusively with birds.