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.
Recently there have been several attempts to provide a whole set of generators of the ideal of the algebraic variety associated to a phylogenetic tree evolving under an algebraic model. These algebraic varieties have been proven to be useful in phylogenetics. In this paper we prove that, for phylogenetic reconstruction purposes, it is enough to consider generators coming from the edges of the tree, the so-called edge invariants. This is the algebraic analogous to Buneman's Splits Equivalence Theorem. The interest of this result relies on its potential applications in phylogenetics for the wide…
Identifiability is a crucial property for a statistical model since distributions in the model uniquely determine the parameters that produce them. In phylogenetics, the identifiability of the tree parameter is of particular interest since it means that phylogenetic models can be used to infer evolutionary histories from data. In this paper we introduce a new computational strategy for proving the identifiability of discrete parameters in algebraic statistical models that uses algebraic matroids naturally associated to the models. We then use this algorithm to prove that the tree parameters ar…
The general Markov model of the evolution of biological sequences along a tree leads to a parameterization of an algebraic variety. Understanding this variety and the polynomials, called phylogenetic invariants, which vanish on it, is a problem within the broader area of Algebraic Statistics. For an arbitrary trivalent tree, we determine the full ideal of invariants for the 2-state model, establishing a conjecture of Pachter-Sturmfels. For the $κ$-state model, we reduce the problem of determining a defining set of polynomials to that of determining a defining set for a 3-leaved tree. Along the…
Many of the stochastic models used in inference of phylogenetic trees from biological sequence data have polynomial parameterization maps. The image of such a map --- the collection of joint distributions for a model --- forms the model space. Since the parameterization is polynomial, the Zariski closure of the model space is an algebraic variety which is typically much larger than the model space, but has been usefully studied with algebraic methods. Of ultimate interest, however, is not the full variety, but only the model space. Here we develop complete semialgebraic descriptions of the mod…
Group-based models appear in algebraic statistics as mathematical models coming from evolutionary biology, respectively the study of mutations of organisms. Both theoretically and in terms of applications, we are interested in determining the algebraic degrees of the phylogenetic varieties coming from these models. These algebraic degrees are called phylogenetic degrees. In this paper, we compute the phylogenetic degree of the variety $X_{G, n}$ with $G\in\{\mathbb{Z}_2,\mathbb{Z}_2\times\mathbb{Z}_2, \mathbb{Z}_3\}$ and any $n$-claw tree. As these varieties are toric, computing their phylogen…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter. We establish tree identifiability for a number of phylogenetic models, including a covarion model and a variety of mixture models with a limited number of classes. The proof is based on the introduction of a more general model, allowing more states at internal nodes of the tree than at leaves, and the study of the algebraic variety formed by the joint distrib…
Phylogenetic networks are becoming increasingly popular in phylogenetics since they have the ability to describe a wider range of evolutionary events than their tree counterparts. In this paper, we study Markov models on phylogenetic networks and their associated geometry. We restrict our attention to large-cycle networks, networks with a single undirected cycle of length at least four. Using tools from computational algebraic geometry, we show that the semi-directed network topology is generically identifiable for Jukes-Cantor large-cycle network models.
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The fundamental question of whether parameters of such a model are identifiable is difficult to address, due to the complexity of the parameterization. We analyze mixture models on large trees, with many mixture components, showing that both numerical and tree parameters are indeed identifiable in these models when all trees are the same. We also explore the extent …
We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.
In algebraic statistics, the Kimura 3-parameter model is one of the most interesting and classical phylogenetic models. We prove that the ideals associated to this model are generated in degree four, confirming a conjecture by Sturmfels and Sullivant.
We prove identifiability of the tree parameters of the 3-class Jukes-Cantor mixture model. The proof uses ideas from algebraic statistics, in particular: finding phylogenetic invariants that separate the varieties associated to different triples of trees; computing dimensions of the resulting phylogenetic varieties; and using the disentangling number to reduce to trees with a small number of leaves. Symbolic computation also plays a key role in handling the many different cases and finding relevant phylogenetic invariants.
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, a…
The Kimura 3-parameter model on a tree of n leaves is one of the most used in phylogenetics. The affine algebraic variety W associated to it is a toric variety. We study its geometry and we prove that it is isomorphic to a geometric quotient of the affine space by a finite group acting on it. As a consequence, we are able to study the singularities of W and prove that the biologically meaningful points are smooth points. Then we give an algorithm for constructing a set of minimal generators of the localized ideal at these points, for an arbitrary number of leaves n. This leads to a major impro…
The Kimura 3-parameter model is one of the most fundamental phylogenetic models in algebraic statistics. We prove that all algebraic varieties associated to this model are projectively normal, confirming a conjecture of Michalek.
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have arisen on one but not the other. We call these two trees or networks distinguishable from each other. We show that for the binary symmetric model there are no two-taxon trees and networks that are distinguishable from each other, however there are three-taxon trees and networks that are distinguishable from each other. We compare the time parameters for the phy…
Felsenstein's classical model for Gaussian distributions on a phylogenetic tree is shown to be a toric variety in the space of concentration matrices. We present an exact semialgebraic characterization of this model, and we demonstrate how the toric structure leads to exact methods for maximum likelihood estimation. Our results also give new insights into the geometry of ultrametric matrices.
We survey results in algebraic complexity theory, focusing on matrix multiplication. Our goals are (i.) to show how open questions in algebraic complexity theory are naturally posed as questions in geometry and representation theory, (ii.) to motivate researchers to work on these questions, and (iii.) to point out relations with more general problems in geometry. The key geometric objects for our study are the secant varieties of Segre varieties. We explain how these varieties are also useful for algebraic statistics, the study of phylogenetic invariants, and quantum computing.
Phylogenetic models have polynomial parametrization maps. For symmetric group-based models, Matsen studied the polynomial inequalities that characterize the joint probabilities in the image of these parametrizations. We employ this description for maximum likelihood estimation via numerical algebraic geometry. In particular, we explore an example where the maximum likelihood estimate does not exist, which would be difficult to discover without using algebraic methods. We also study the embedding problem for symmetric group-based models, i.e. we identify which mutation matrices are matrix expon…
Methods of phylogenetic inference use more and more complex models to generate trees from data. However, even simple models and their implications are not fully understood. Here, we investigate the two-state Markov model on a tripod tree, inferring conditions under which a given set of observations gives rise to such a model. This type of investigation has been undertaken before by several scientists from different fields of research. In contrast to other work we fully analyse the model, presenting conditions under which one can infer a model from the observation or at least get support for th…
This file, provided as bibliographical information, contains the table of contents and editors' foreword from the proceedings of the July 1996 Warwick EuroConference on Algebraic Geometry.
In this paper we introduce elements of algebraic geometry over an arbitrary algebraic structure. We prove Unification Theorems which gather the description of coordinate algebras by several ways.
Real algebraic geometry adapts the methods and ideas from (complex) algebraic geometry to study the real solutions to systems of polynomial equations and polynomial inequalities. As it is the real solutions to such systems modeling geometric constraints that are physically meaningful, real algebraic geometry is a core mathematical input for geometric constraint systems.
Reflexive functors of modules naturally appear in Algebraic Geometry. In this paper we define a wide and elementary family of reflexive functors of modules, closed by tensor products and homomorphisms, in which Algebraic Geometry can be developed.
In this paper, for a given finitely generated algebra (an algebraic structure with arbitrary operations and no predicates) A we study finitely generated limit algebras of A, approaching them via model theory and algebraic geometry. Along the way we lay down foundations of algebraic geometry over arbitrary algebraic structures.
Some notions of algebraic geometry can be defined for arbitrary varieties of algebras. This leads to universal algebraic geometry. The main idea of the presented theory is to consider interactions between algebra, logic and geometry in algebras from a given variety of algebras.
This paper is a survey of computational issues in algebraic geometry, with particular attention to the theory of Grobner bases and the regularity of an algebraic variety. 1. A geometric introduction to Grobner bases. 2. An algebraic introduction to Grobner bases. 3. Bounds in algebraic geometry, and regularity and complexity questions. 4. Applications.
This paper is a survey on arc spaces, a recent topic in algebraic geometry and singularity theory. The geometry of the arc space of an algebraic variety yields several new geometric invariants and brings new light to some classical invariants.
We study the algebraic and geometric properties of the integral closure of different rings of functions on a real algebraic variety : the regular functions and the continuous rational functions.
These are notes for the Bootcamp volume for the 2015 AMS Summer Institute in Algebraic Geometry. They are based on earlier notes for the "Positive Characteristic Algebraic Geometry Workshop" held at University of Illinois at Chicago in March 2014.
This note is supposed to answer some questions on deformation theory in derived algebraic geometry. We show that derived algebraic geometry allows for a geometrical interpretation of the full cotangent complex and gives a natural setting for deformation and obstruction theories.
Let X be an affine real algebraic set . We investigate on the theory of algebraically constructible functions on X and the description of the semi-algebraic subsets of X when we replace the polynomial functions on X by some rational continuous functions on X.
We develop the idea of using an algebraic-geometry approach to classical differential geometry problems. Consider an orthogonal net constructed according to algebraic-geometric data we obtain a set of smooth orthogonal nets that are Ribaucour transformations of the initial orthogonal net.
This is an expository introduction to tropical algebraic geometry based on my lectures at the Workshop on Tropical Geometry and Integrable Systems in Glasgow, July 4-8, 2011, and at the ELGA 2011 school on Algebraic Geometry and Applications in Buenos Aires, August 1-5, 2011.
This text is a survey of derived algebraic geometry. It covers a variety of general notions and results from the subject with a view on the recent developments at the interface with deformation quantization.
Parametric Cartan theory of exterior differential systems, and explicit cohomology of projective manifolds reveal united rationality features of differential algebraic geometry.
Lecture notes of an algebraic geometry graduate course. The topics covered are as follows. Cohomology: ext sheaves and groups, cohomology with support, local cohomology, local duality. Duality: relative duality, Cohen-Macaulay schemes. Morphisms of schemes: flatness and base change and related topics. Hilbert and Quotient schemes.
An informal discussion of how the construction problem in algebraic geometry motivates the search for formal proof methods. Also includes a brief discussion of my own progress up to now, which concerns the formalization of category theory within a ZFC-like environment.
Tropical algebraic geometry is an active new field of mathematics that establishes and studies some very general principles to translate algebro-geometric problems into purely combinatorial ones. This expository paper gives an introduction to these new techniques with a special emphasis on the recent applications to problems in enumerative geometry.
In this paper, we study group equations with occurrences of automorphisms. We describe equational domains in this class of equations. Moreover, we solve a number of open problem posed in universal algebraic geometry.
