Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2010.06158

Tropical Geometric Variation of Phylogenetic Tree Shapes

Bo Lin·Anthea Monod·Ruriko Yoshida
View original source ↗Read source document ↗Export metadata ↓

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.

Explore related subjects

math.COmath.AG

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Bo Lin, Anthea Monod, Ruriko Yoshida. 2022-02-19. Tropical Geometric Variation of Phylogenetic Tree Shapes. https://doi.org/10.1007/s00454-022-00410-y

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Adjunctions, Box Products, and Forcing Families

Sidorenko's conjecture states that the number of copies of any given bipartite graph in another graph of given density is asymptotically minimized by a random graph. For bipartite graphs containing a cycle, the forcing conjecture further asserts that asymptotic equality characterizes quasi-random graphs. We establish an adjoint identity for a general class of graph-substitution operators and use it to obtain Sidorenko and forcing results for balanced blow-ups, subdivisions, Cartesian products, and strong products.

math.CO↗
arXiv2026

On the Cost Number of Graphs with Determining Number Two

A distinguishing vertex coloring of a graph $G$ is a vertex coloring such that only the identity automorphism of $G$ preserves the coloring. A graph is $2$-distinguishable if it admits a distinguishing vertex coloring with two colors, and its cost $ρ(G)$ is the minimum size of a color class in such a coloring. The determining number of a graph $G$, denoted by $Det(G)$, is the minimum size of a subset $S\subseteq V(G)$ such that only the trivial automorphism fixes every element of $S$ pointwise. Boutin (J. Combin. Math. Combin. Comput. 85: 161-171, 2013) asked if $ρ(G)$ and $Det(G)$ can be arbitrarily far apart. While the case for $Det(G) = 1$ is trivial, the answer remained unknown for $Det(G) \ge 2$. In this manuscript, we show that if $Det(G)=2$ then not only is $ρ(G)$ bounded, but in fact $ρ(G) \leq 4$. This is the first resolution of Boutin's question for any nontrivial fixed determining number. Moreover, for every fixed $Det(G)= n$, we construct examples giving a lower bound on any possible upper bound for $ρ(G)$ in terms of $n$.

math.CO↗