Phylogenetic invariants for group-based models

DOI10.18409/JAS.V3I1.15MaRDI QIDQ2819992zbMATH OpenOpenAlexFDO

Authors Maria Donten-Bury, Mateusz Michalek

Publication date 13 September 2016

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

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

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)

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.

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Cited in

(23)

• Gorenstein property for phylogenetic trivalent trees
• Dimensions of group-based phylogenetic mixtures
• Local equations for equivariant evolutionary models
• 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
• 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
• Phylogenetic degrees for claw trees
• Conformal blocks, Berenstein-Zelevinsky triangles, and group-based models
• Invariants of phylogenies in a simple case with discrete states
• Toric Ideals of Phylogenetic Invariants for the General Group-Based Model on Claw Trees K 1,n
• Geometry of phylogenetic group-based models
• Normality of the Kimura 3-Parameter Model
• Lie Markov models with purine/pyrimidine symmetry
• Finite phylogenetic complexity and combinatorics of tables
• H-representation of the Kimura-3 polytope for the \(m\)-claw tree
• 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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