Low degree equations for phylogenetic group-based models

DOI10.1007/S13348-014-0120-0zbMATH Open1332.92040arXiv1402.6945OpenAlexW2031916210WikidataQ61068396 ScholiaQ61068396MaRDI QIDQ2345583FDOQ2345583

Authors: Jesús Fernández-Sánchez, Mateusz Michalek, Marta Casanellas 

Publication date: 22 May 2015

Published in: Collectanea Mathematica (Search for Journal in Brave)

Abstract: Motivated by phylogenetics, our aim is to obtain a system of equations that define a phylogenetic variety on an open set containing the biologically meaningful points. In this paper we consider phylogenetic varieties defined via group-based models. For any finite abelian group $G$, we provide an explicit construction of $codimX$ phylogenetic invariants (polynomial equations) of degree at most $|G|$ that define the variety $X$ on a Zariski open set $U$. The set $U$ contains all biologically meaningful points when $G$ is the group of the Kimura 3-parameter model. In particular, our main result confirms a conjecture by the third author and, on the set $U$, a couple of conjectures by Bernd Sturmfels and Seth Sullivant.

Full work available at URL: https://arxiv.org/abs/1402.6945

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zbMATH Keywords

phylogeneticsabelian groupgroup-based modelsZariski open setphylogenetic variety

Mathematics Subject Classification ID

Applications of graph theory (05C90) Problems related to evolution (92D15) Abelian groups (20K99) Curves in algebraic geometry (14H99)

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Cited In (16)

• Distance to the stochastic part of phylogenetic varieties
• Hilbert polynomial of the Kimura 3-parameter model
• Local equations for equivariant evolutionary models
• Computing algebraic degrees of phylogenetic varieties
• Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry
• Low degree minimal generators of phylogenetic semigroups
• Tying up loose strands: defining equations of the strand symmetric model
• Phylogenetic degrees for claw trees
• Finite phylogenetic complexity of \(\mathbb{Z}_p\) and invariants for \(\mathbb{Z}_3\)
• Phylogenetic invariants for \(\mathbb{Z}_3\) scheme-theoretically
• Normality of the Kimura 3-Parameter Model
• H-representation of the Kimura-3 polytope for the \(m\)-claw tree
• Phylogenetic complexity of the Kimura 3-parameter model
• Phylogenetic invariants for group-based models
• Finiteness results for abelian tree models
• Constructive degree bounds for group-based models

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