Tropical geometric variation of tree shapes
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Published version
Author(s)
Lin, Bo
Monod, Anthea
Yoshida, Ruriko
Type
Journal Article
Abstract
We study the behavior of phylogenetic tree shapes in the tropical geometric interpretation of tree space. Tree shapes are formally referred to as tree topologies; a tree topology can also be thought of as a tree combinatorial type, which is given by the tree’s branching configuration and leaf labeling. We use the tropical line segment as a framework to define notions of variance as well as invariance of tree topologies: we provide a combinatorial search theorem that describes all tree topologies occurring along a tropical line segment, as well as a setting under which tree topologies do not change along a tropical line segment. Our study is motivated by comparison to the moduli space endowed with a geodesic metric proposed by Billera, Holmes, and Vogtmann (referred to as BHV space); we consider the tropical geometric setting as an alternative framework to BHV space for sets of phylogenetic trees. We give an algorithm to compute tropical line segments which is lower in computational complexity than the fastest method currently available for BHV geodesics and show that its trajectory behaves more subtly: while the BHV geodesic traverses the origin for vastly different tree topologies, the tropical line segment bypasses it.
Date Issued
2022-10-01
Date Acceptance
2022-03-03
Citation
Discrete and Computational Geometry: an international journal of mathematics and computer science, 2022, 68 (3), pp.817-849
ISSN
0179-5376
Publisher
Springer
Start Page
817
End Page
849
Journal / Book Title
Discrete and Computational Geometry: an international journal of mathematics and computer science
Volume
68
Issue
3
Copyright Statement
Copyright © 2022 The Author(s). Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
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Subjects
COALESCENT
Computer Science
Computer Science, Theory & Methods
DISTRIBUTIONS
IDENTIFIABILITY
L-INFINITY OPTIMIZATION
Mathematics
METRICS
Phylogenetic trees
Physical Sciences
Science & Technology
SPACES
Technology
Tree topologies
Tropical geometry
Tropical line segment
Ultrametrics
Publication Status
Published
Date Publish Online
2022-07-12