Roadblocked monotonic paths and the enumeration of coalescent histories for non-matching caterpillar gene trees and species trees.

Given a gene tree topology and a species tree topology, a coalescent history represents a possible mapping of the list of gene tree coalescences to associated branches of a species tree on which those coalescences take place. Enumerative properties of coalescent histories have been of interest in the analysis of relationships between gene trees and species trees. The simplest enumerative result identifies a bijection between coalescent histories for a matching caterpillar gene tree and species tree with monotonic paths that do not cross the diagonal of a square lattice, establishing that the associated number of coalescent histories for -taxon matching caterpillar trees ( ⩾ 2) is the Catalan number . Here, we show that a similar bijection applies for caterpillars, connecting coalescent histories for a non-matching caterpillar gene tree and species tree to a class of monotonic paths. The result provides a simplified algorithm for enumerating coalescent histories in the non-matching caterpillar case. It enables a rapid proof of a known result that given a caterpillar species tree, no non-matching caterpillar gene tree has a number of coalescent histories exceeding that of the matching gene tree. Additional results on coalescent histories can be obtained by a bijection between permissible roadblocked monotonic paths and Dyck paths. We study the number of coalescent histories for non-matching caterpillar gene trees that differ from the species tree by nearest-neighbor-interchange and subtree-prune-and-regraft moves, characterizing the non-matching caterpillar with the largest number of coalescent histories. We discuss the implications of the results for the study of the combinatorics of gene trees and species trees.