Geometric comparison of phylogenetic trees with different leaf sets

Abstract: The metric space of phylogenetic trees defined by Billera, Holmes, and Vogtmann, which we refer to as BHV space, provides a natural geometric setting for describing collections of trees on the same set of taxa. However, it is sometimes necessary to analyze collections of trees on non-identical taxa sets (i.e., with different numbers of leaves), and in this context it is not evident how to apply BHV space. Davidson et al. recently approached this problem by describing a combinatorial algorithm extending tree topologies to regions in higher dimensional tree spaces, so that one can quickly compute which topologies contain a given tree as partial data. In this paper, we refine and adapt their algorithm to work for metric trees to give a full characterization of the subspace of extensions of a subtree. We describe how to apply our algorithm to define and search a space of possible supertrees and, for a collection of tree fragments with different leaf sets, to measure their compatibility.