Phylogenetic invariants for group-based models

DOI10.18409/JAS.V3I1.15zbMATH Open1353.52008arXiv1011.3236OpenAlexW2964266730MaRDI QIDQ2819992FDOQ2819992

Authors: Maria Donten-Bury, Mateusz Michalek 

Publication date: 13 September 2016

Published in: Journal of Algebraic Statistics (Search for Journal in Brave)

Abstract: In this paper we investigate properties of algebraic varieties representing group-based phylogenetic models. We propose a method of generating many phylogenetic invariants. We prove that we obtain all invariants for any tree for the binary Jukes-Cantor model. We conjecture that our method can give all phylogenetic invariants for any tree. We show that for 3-Kimura our conjecture is equivalent to the conjecture of Sturmfels and Sullivant. This, combined with the results of Sturmfels and Sullivant, would make it possible to determine all phylogenetic invariants for any tree for 3-Kimura model, and also other phylogenetic models. Next we give the (first) example of a non-normal general group-based model for an abelian group. Following Kubjas we also determine some invariants of group-based models showing that the associated varieties do not have to be deformation equivalent.

Full work available at URL: https://arxiv.org/abs/1011.3236

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zbMATH Keywords

phylogenetic treegroup-based modelphylogenetic invariant

Mathematics Subject Classification ID

Lattice polytopes in convex geometry (including relations with commutative algebra and algebraic geometry) (52B20) Applications of commutative algebra (e.g., to statistics, control theory, optimization, etc.) (13P25)

Cited In (23)

• Gorenstein property for phylogenetic trivalent trees
• Local equations for equivariant evolutionary models
• Dimensions of group-based phylogenetic mixtures
• Toric varieties in phylogenetics
• Phylogenetic trees
• Low degree minimal generators of phylogenetic semigroups
• Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model
• Relevant phylogenetic invariants of evolutionary models
• 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
• On the graph labellings arising from phylogenetics
• Toric Ideals of Phylogenetic Invariants for the General Group-Based Model on Claw Trees K 1,n
• Invariants of phylogenies in a simple case with discrete states
• Conformal blocks, Berenstein-Zelevinsky triangles, and group-based models
• Normality of the Kimura 3-Parameter Model
• Geometry of phylogenetic group-based models
• Lie Markov models with purine/pyrimidine symmetry
• H-representation of the Kimura-3 polytope for the \(m\)-claw tree
• Finite phylogenetic complexity and combinatorics of tables
• Phylogenetic complexity of the Kimura 3-parameter model
• Low degree equations for phylogenetic group-based models
• Constructive degree bounds for group-based models

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