Phylogenetics and modern definition

By the 21st century, vertebrate paleontologists were beginning to adopt phylogenetic taxonomy, in which all groups are defined in such a way as to be monophyletic; that is, groups include all descendants of a particular ancestor. The reptiles as historically defined would be paraphyletic, since they exclude both birds and mammals, although these also evolved from animals like dinosaurs and early therapsids that were traditionally called reptiles.^[11] Colin Tudge wrote:

Mammals are a clade, and therefore the cladists are happy to acknowledge the traditional taxon Mammalia; and birds, too, are a clade, universally ascribed to the formal taxon Aves. Mammalia and Aves are, in fact, subclades within the grand clade of the

Amniota. But the traditional class Reptilia is not a clade. It is just a section of the clade Amniota: the section that is left after the Mammalia and Aves have been hived off. It cannot be defined by synapomorphies, as is the proper way. It is instead defined by a combination of the features it has and the features it lacks: reptiles are the amniotes that lack fur or feathers. At best, the cladists suggest, we could say that the traditional Reptilia are 'non-avian, non-mammalian amniotes'.^[12]

Despite the early proposals for replacing the paraphyletic Reptilia for a monophyletic Sauropsida, that term was never adopted widely or, when it was, applied consistently.^[13] When Sauropsida was used, it often had the same content or even the same definition as Reptilia. In 1988 Jacques Gauthier proposed a cladistic definition of Reptilia as a monophyletic node-based crown group containing turtles, lizards and snakes, crocodilians, and birds, their common ancestor and all its descendants. Because the actual relationship of turtles to other reptiles was not yet well understood at this time, Gauthier's definition came to be considered inadequate.^[13] A variety of other definitions

were proposed by other scientists in the years following Gauthier's paper. The first such new definition, which attempted to adhere to the standards of the PhyloCode, was published by Modesto and Anderson in 2004. Modesto and Anderson reviewed the many previous definitions, and proposed a modified definition which they intended to retain most traditional content of the group while keeping it stable and monophyletic. They defined Reptilia as all amniotes closer to Lacerta agilis and Crocodylus niloticus than to Homo sapiens. This stem-based definition is equivalent to the more common definition of Sauropsida, which Modesto and Anderson synonymized with Reptilia, since the latter is more well known and more frequently used. Unlike most previous definitions of Reptilia, however, Modesto and Anderson's definition includes birds.^[13]

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