A strengthened bound on the number of states required to characterize maximum parsimony distance

Abstract

In this article we prove that the distance $d_{\mathrm{MP}}(T_1,T_2) = k$ between two unrooted binary phylogenetic trees $T_1, T_2$ on the same set of taxa can be defined by a character that is convex on one of $T_1, T_2$ and which has at most $2k$ states. This significantly improves upon the previous bound of $7k-5$ states. We also show that for every $k \geq 1$ there exist two trees $T_1, T_2$ with $d_{\mathrm{MP}}(T_1,T_2) = k$ such that at least $k+1$ states are necessary in any character that achieves this distance and which is convex on one of $T_1, T_2$. We augment these lower and upper bounds with an empirical analysis which shows that in practice significantly fewer than $k+1$ states are usually required.