Stem group

A crown group is the smallest monophyletic group, or "clade", to contain the last common ancestor of all extant members, and all of that ancestor's descendants. Extinct organisms can still be part of a crown group: for instance, the extinct dodo is still descended from the last common ancestor of all living birds, so falls within the bird crown group.

Some organisms fall close to but outside a particular crown group. A good example is Archaeopteryx which, although clearly bird-like, is not descended from the last common ancestor of all living birds. Such organisms can be classified within the stem group of a clade. In this example Archaeopteryx is a stem-group bird, but it falls within the vertebrate crown-group. All organisms more closely related to crown-group birds than to any other living group are referable to the bird stem group. As living birds are by definition in the crown group, it follows that all members of the stem-group of a clade are extinct; and thus, stem groups only have fossil members. A crown group and its stem group considered together are known as the total group. Although the stem group is paraphyletic, it can be objectively defined by subtracting the crown group from the total group.

The crown-and-stem group concept, first mooted in 1979, was not commonly used until its reintroduction in the 2000s.

Fossil classification
Stem groups offer a route to classify fossils that otherwise do not obey systematics based on living organisms. Stem group organisms always lack one or more features that are present at the base of the crown group to which they are attached. Thus, Archaeopteryx still retains teeth, unlike crown-group birds. As a group evolves away from the last common ancestor of it and its nearest living relative, it accumulates the distinctive features of its crown group. Hence, the last common ancestor of birds and crocodiles – the first crown group archosaur - was neither bird nor crocodile, and possessed none of the features unique to either. Evolution up the bird stem group allowed the accumulation of distinctive bird features such as the beak and hollow bones, until all were finally present at the base of the crown group.

Paleontological significance
Placing fossils in their right order in a stem group allows the order of these acquisitions to be established, and thus the ecological and functional setting of the evolution of the major features of the group in question. Stem groups thus offer a route to integrate unique palaeontological data into questions of the evolution of living organisms. Furthermore, they show that fossils that were considered to lie in their own separate group because they did not show all the diagnostic features of a living clade, can nevertheless be related to it by lying in its stem group. Such fossils have been of particular importance in considering the origins of the tetrapods, mammals, and animals.

The application of the stem group concept also radically reformed the interpretation of the organisms of the Burgess shale. Their classification in stem groups to extant phyla, rather than in phyla of their own, made the Cambrian explosion much easier to understand without invoking unusual evolutionary mechanisms.