Because homologies result from shared ancestry, only homologies, and not analogies, are useful in constructing phylogenetic trees. However, it turns out that only some homologies are useful. For example, character states that are unique to a given species or other monophyletic group can’t tell us anything about its sister group. They evolved after the divergence of the group from its sister group and so can be used to characterize a group but not to relate it to other groups. Similarly, homologies formed in the common ancestor of the entire group and therefore present in all its descendants do not help to identify sister-group relationships among the descendants of that common ancestor.

What we need to build phylogenetic trees are homologies that are shared by some, but not all, of the members of the group under consideration. These shared derived characters are called synapomorphies. A derived character state is an evolutionary innovation (for example, the change from five toes to a single toe—the hoof—in the ancestor of horses and donkeys). When such a novelty arises in the common ancestor of two taxa, it is shared by both (thus, the hoof is a synapomorphy defining horses and donkeys as sister groups).

In Fig. 23.7, we indicate the major synapomorphies that have helped us construct the phylogeny of vertebrates. For example, the lung is a character present in lungfish and tetrapods, but absent in other vertebrates. Thus, the presence of lungs provides one piece of evidence that lungfish are the sister group of tetrapods. Phylogenetic reconstruction on the basis of synapomorphies is called cladistics.