Related papers: Phylogenetic ideals and varieties for the general …
The measure-valued Fleming-Viot process is a diffusion which models the evolution of allele frequencies in a multi-type population. In the neutral setting the Kingman coalescent is known to generate the genealogies of the "individuals" in…
We provide a complete classification of normal phylogenetic varieties coming from tripods, and more generally, from trivalent trees. Let $G$ be an abelian group. We prove that the group-based phylogenetic variety $X_{G,\mathcal{T}}$, for…
In this paper we complete the results of Sullivant and Sturmfels proving that many of the algebraic group-based models for Markov processes on trees are pseudo-toric. We also show in which cases these varieties are normal. This is done by…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
The theory of {\Gamma}-species is developed to allow species-theoretic study of quotient structures in a categorically rigorous fashion. This new approach is then applied to two graph-enumeration problems which were previously unsolved in…
We find generators for the ideals of secant varieties of Segre varieties in several the cases including the Garcia-Stillmann-Ssturmfels conjecture for four factors and prove results about their singularities.
We give an exact solution to the Kolmogorov equation describing genetic drift for an arbitrary number of alleles at a given locus. This is achieved by finding a change of variable which makes the equation separable, and therefore reduces…
We introduce two models for multi-type random trees motivated by studies of trait dependence in the evolution of species. Our discrete time model, the multi-type ERM tree, is a generalization of Markov propagation models on a random tree…
We study a class of Markov chains that model the evolution of a quantum system subject to repeated measurements. Each Markov chain in this class is defined by a measure on the space of matrices. It is then given by a random product of…
Probability modelling for DNA sequence evolution is well established and provides a rich framework for understanding genetic variation between samples of individuals from one or more populations. We show that both classical and more recent…
This paper deals with properties of the algebraic variety defined as the set of zeros of a "deficient" sequence of multivariate polynomials. We consider two types of varieties: ideal-theoretic complete intersections and absolutely…
We introduce a statistical mechanics formalism for the study of constrained graph evolution as a Markovian stochastic process, in analogy with that available for spin systems, deriving its basic properties and highlighting the role of the…
We consider the problem of inferring an ancestral state from observations at the leaves of a tree, assuming the state evolves along the tree according to a two-state symmetric Markov process. We establish a general branching rate condition…
For the multivariate trigonometric polynomials we study convolution with the corresponding the de la Vallee Poussin kernel from the point of view of discretization. In other words, we replace the normalized Lebesgue measure by a discrete…
By exploiting an analogy between population genetics and statistical mechanics, we study the evolution of a polygenic trait under stabilizing selection, mutation, and genetic drift. This requires us to track only four macroscopic variables,…
We consider an algebra of (classical or virtual) tangles over an ordered circuit operad and introduce Conway-type invariants of tangles which respect this algebraic structure. The resulting invariants contain both the coefficients of the…
We propose a Markov chain approach for the evolution of a genealogical line of genomes. Our idealized genome has $N$ sites and each site can be in state $0$ or $1$. At each time step we pick a site at random. If the site is in state $0$ we…
We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated…
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…
The stochastic growth-fragmentation model describes the temporal evolution of a structured cell population through a discrete-time and continuous-state Markov chain. The simulations of this stochastic process and its invariant measure are…