Abstract Intraspecific phenotypic variation provides the basic substrate upon which the evolutionary processes that give rise to morphological innovation, such as adaptation, operate. Work in living clades has shown standing population-level variation fuels ecological speciation and gives rise to adaptive radiations. Despite its importance in evolutionary biology, the role of intraspecific variation in shaping phylogenetic and macroevolutionary patterns and processes has remained underexplored. I introduce a model of morphological evolution that accommodates polymorphism. The model describes the stochastic gain and loss of phenotypic character states within taxa, i.e., anagenesis, and the sorting of ancestral polymorphic variation during speciation, i.e., cladogenesis. I explore the behaviour of the model using simulations, then deploy it to reconstruct evolutionary relationships between the highly variable species belonging to the Cretaceous echinoid genus Micraster. The analysis revealed strong statistical support for several contentious relationships. The clade depicts a pattern where morphological variation accumulates within a small number of ancestral lineages and then is sorted into descendants without being fully replenished by anagenetic gains. This disproportionate maintenance of variation within early taxa and loss among later taxa could provide a link between the population processes that maintain intraspecific variation and the radiation and decline of clades.
C. Tomomi Parins-Fukuchi (2025) studied this question.