To a given gene tree topology $G$ and species tree topology $S$ with leaves labeled bijectively from a fixed set $X$, one can associate a set of ancestral configurations, each of which encodes a set of gene lineages that can be found at a given node of the species tree. We introduce a lattice structure on ancestral configurations, studying the directed graphs that provide graphical representations of lattices of ancestral configurations. For a matching gene tree topology and species tree topology $G=S$, we present a method for defining the digraph of ancestral configurations from the tree topology by using iterated cartesian products of graphs. We show that a specific set of paths on the digraph of ancestral configurations is in bijection with the set of labeled histories -- a well-known phylogenetic object that enumerates possible temporal orderings of the coalescences of a tree. For each of a series of tree families, we obtain closed-form expressions for the number of labeled histories by using this bijection to count paths on associated digraphs. Finally, we prove that our lattice construction extends to nonmatching tree pairs, and we use it to characterize pairs $(G,S)$ having the maximal number of ancestral configurations for a fixed $G$. We discuss how the construction provides new methods for performing enumerations of combinatorial aspects of gene and species trees.