Toric ideals of homogeneous phylogenetic models

We consider the phylogenetic tree model in which every node of the tree is observed and binary and the transitions are given by the same matrix on each edge of the tree. We are able to compute the Grobner basis and Markov basis of the toric ideal of invariants for trees with up to 11 nodes. These are perhaps the first non-trivial Grobner bases calculations in 2^11 indeterminates. We conjecture that there is a quadratic Grobner basis for binary trees. Finally, we give a explicit description of the polytope associated to this toric ideal for an infinite family of binary trees and conjecture that there is a universal bound on the number of vertices of this polytope for binary trees.Comment: 6 pages, 17 figure

Toric fiber products

We introduce and study the toric fiber product of two ideals in polynomial rings that are homogeneous with respect to the same multigrading. Under the assumption that the set of degrees of the variables form a linearly independent set, we can explicitly describe generating sets and Groebner bases for these ideals. This allows us to unify and generalize some results in algebraic statistics.Comment: 19 page

Phylogenetic Algebraic Geometry

Phylogenetic algebraic geometry is concerned with certain complex projective algebraic varieties derived from finite trees. Real positive points on these varieties represent probabilistic models of evolution. For small trees, we recover classical geometric objects, such as toric and determinantal varieties and their secant varieties, but larger trees lead to new and largely unexplored territory. This paper gives a self-contained introduction to this subject and offers numerous open problems for algebraic geometers.Comment: 15 pages, 7 figure

Constructive degree bounds for group-based models

Group-based models arise in algebraic statistics while studying evolution processes. They are represented by embedded toric algebraic varieties. Both from the theoretical and applied point of view one is interested in determining the ideals defining the varieties. Conjectural bounds on the degree in which these ideals are generated were given by Sturmfels and Sullivant. We prove that for the 3-Kimura model, corresponding to the group G=Z2xZ2, the projective scheme can be defined by an ideal generated in degree 4. In particular, it is enough to consider degree 4 phylogenetic invariants to test if a given point belongs to the variety. We also investigate G-models, a generalization of abelian group-based models. For any G-model, we prove that there exists a constant $d$, such that for any tree, the associated projective scheme can be defined by an ideal generated in degree at most d.Comment: Boundedness results for equations defining the projective scheme were extended to G-models (including 2-Kimura and all JC