Related papers: Computing algebraic degrees of phylogenetic variet…
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…
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…
As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic methods are efficient,…
Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
We develop the necessary theory in computational algebraic geometry to place Bayesian networks into the realm of algebraic statistics. We present an algebra{statistics dictionary focused on statistical modeling. In particular, we link the…
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…
This paper announces results on the behavior of some important algebraic and topological invariants --- Euler characteristic, arithmetic genus, and their intersection homology analogues; the signature, etc. --- and their associated…
We define phylogenetic projective toric model of a trivalent graph as a generalization of a binary symmetric model of a trivalent phylogenetic tree. Generators of the pro- jective coordinate ring of the models of graphs with one cycle are…
Reconstructing evolutionary trees from molecular sequence data is a fundamental problem in computational biology. Stochastic models of sequence evolution are closely related to spin systems that have been extensively studied in statistical…
The variety of bicommutative algebras is the class of all nonassociative algebras satisfying the polynomial identities $(x_1x_2)x_3=(x_1x_3)x_2$ and $x_1(x_2x_3)=x_2(x_1x_3)$. In this paper we provide a complete description of varieties of…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that…
A bottleneck of a smooth algebraic variety $X \subset \mathbb{C}^n$ is a pair of distinct points $(x,y) \in X$ such that the Euclidean normal spaces at $x$ and $y$ contain the line spanned by $x$ and $y$. The narrowness of bottlenecks is a…
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…
We relate the geometry of the resonance varieties associated to a commutative differential graded algebra model of a space to the finiteness properties of the completions of its Alexander-type invariants. We also describe in simple…