Phylogenetic invariants for Z₃ scheme-theoretically
In phylogenetics, possible histories of evolution are represented by trees, and to each tree can be associated a certain algebraic variety. Phylogenetic invariants are homogeneous polynomials that vanish on this algebraic variety and are used to distinguish between phylogenetic trees. These invariants form an ideal and a fundamental question is to determine an upper bound for the degree in which this ideal is generated. This question is often addressed for \textit{group-based models}, which are a family of models for which the associated algebraic varieties are known to be toric [\textit{S. N. Evans} and \textit{T. P. Speed}, Ann. Stat. 21, No. 1, 355--377 (1993; Zbl 0772.92012)]; [\textit{L. A. Székely} et al., Adv. Appl. Math. 14, No. 2, 200--216 (1993; Zbl 0794.05014)] and [\textit{M. Michałek}, J. Algebra 339, No. 1, 339--356 (2011; Zbl 1251.14040)]. A conjecture of \textit{B. Sturmfels} and \textit{S. Sullivant} [J. Comp. Biol. 12, 204--228 (2005; Zbl 1391.13058)] reads that the ideal of phylogenetic invariants for a group-based model with (finite) group of symmetries \(G\) is generated in degree at most \(|G|\). This conjecture is verified in the same paper for \(G\cong \mathbb{Z}_2\) and scheme-theoretically for \(G\cong\mathbb{Z}_2\times\mathbb{Z}_2\) in [\textit{M. Michałek}, J. Comb. Theory, Ser. A 120, No. 7, 1672--1694 (2013; Zbl 1316.14098)]. The purpose of the paper under review is to prove this conjecture scheme-theoretically for \(G\cong \mathbb{Z}_3\) (Theorem~1.1). In other words, it is shown that the ideal generated by phylogenetic invariants of degree at most three has the same saturation as the ideal generated by all phylogenetic invariants. The ideal of phylogenetic invariants may be described in terms of \textit{group-based flows}; the main result is proved via a detailed analysis of the combinatorics of these flows.
- Finite phylogenetic complexity of \(\mathbb{Z}_p\) and invariants for \(\mathbb{Z}_3\)
- Phylogenetic invariants for group-based models
- Finite phylogenetic complexity and combinatorics of tables
- Low degree equations for phylogenetic group-based models
- Relevant phylogenetic invariants of evolutionary models
- Constructive degree bounds for group-based models
- Finiteness results for abelian tree models
- Fourier calculus on evolutionary trees
- Geometry of phylogenetic group-based models
- scientific article; zbMATH DE number 1865935 (Why is no real title available?)
- scientific article; zbMATH DE number 835749 (Why is no real title available?)
- Invariants of some probability models used in phylogenetic inference
- Low degree equations for phylogenetic group-based models
- On geometry of binary symmetric models of phylogenetic trees
- On the ideals of equivariant tree models
- On the toric ideal of a matroid
- Phylogenetic invariants for group-based models
- The algebra of \(\mathrm{SL}_3(\mathbb{C})\) conformal blocks
- Toric fiber products
- Toric Ideals of Phylogenetic Invariants
- Toric varieties
- Phylogenetic complexity of the Kimura 3-parameter model
- Low degree equations for phylogenetic group-based models
- Constructive degree bounds for group-based models
- Gorenstein property for phylogenetic trivalent trees
- Phylogenetic invariants for group-based models
- Finite phylogenetic complexity of \(\mathbb{Z}_p\) and invariants for \(\mathbb{Z}_3\)
- Normality of the Kimura 3-Parameter Model
- Finite phylogenetic complexity and combinatorics of tables
- Geometry of phylogenetic group-based models
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