The isometry group of phylogenetic tree space is $S_n$

Abstract

A phylogenetic tree is an acyclic graph with distinctly labeled leaves, whose internal edges have a positive weight. Given a set of n leaves, the collection of all phylogenetic trees with this leaf set can be assembled into a metric cube complex known as phylogenetic tree space, or Billera-Holmes-Vogtmann tree space. In this largely combinatorial paper, we show that the isometry group of this space is the symmetric group on n elements. This fact is relevant to distance-based analyses of phylogenetic tree sets.