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Classifying tree topology changes along tropical line segments

Shelby Cox

Vol. 14 (2023), No. 1, 71–90
Abstract

The space of phylogenetic trees arises naturally in tropical geometry as the tropical Grassmannian. Tropical geometry therefore suggests a natural notion of tropical path between two trees, given by a tropical line segment in the tropical Grassmannian. It was previously conjectured that tree topologies along such a segment change by a combinatorial operation known as nearest neighbor interchange (NNI). We provide counterexamples to this conjecture, but prove that changes in tree topologies along the tropical line segment are either NNI moves or “four clade rearrangement” moves for generic trees. In addition, we show that the number of NNI moves occurring along the tropical line segment can be as large as n2, but the average number of moves when the two endpoint trees are chosen at random is O(n(log n)4). This is in contrast with O(nlog n), the average number of NNI moves needed to transform one tree into another.

Keywords
phylogenetics, tropical, Grassmannian, ultrametric, trees
Mathematical Subject Classification
Primary: 14T15
Secondary: 05C05, 14T20
Milestones
Received: 30 September 2022
Revised: 21 February 2023
Accepted: 27 March 2023
Published: 28 November 2023
Authors
Shelby Cox
University of Michigan
Ann Arbor, MI
United States