Clypeasteroid echinoids are a familiar and easily defined clade with a cryptic origin. They first appear in the late Paleocene and are believed to have arisen from cassiduloid ancestry, but identifying sister-group relationships more precisely has proved difficult. Two factors are responsible for this problem, the extreme morphological conservatism of cassiduloids, which has given rise to high levels of character exhaustion, and the origin of crown-group clypeasteroids through paedomorphosis. Previous analyses, based on extant representatives alone or including all Mesozoic to Recent genera, have proved unsatisfactory.

Here a parsimony analysis is undertaken using a restricted set of all stem-group clypeasteroids and cassiduloid taxa that existed immediately prior to the appearance of crown-group clypeasteroids. Inclusion of Togocyamus, the fossil taxon lying closest to the origin of crown-group clypeasteroids, is phylogenetically uninformative because that taxon is highly paedomorphic and has only generalized juvenile characteristics. However, earlier stem-group plesions provide critical data that identify Apatopygidae as extant sister group to the Clypeasteroida. Stratigraphically restricted analyses cannot eradicate the problems that arise from character exhaustion, but can minimize these with respect to specific phylogenetic questions.