Related papers: Phylogenetic degrees for Jukes-Cantor model
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the…
Hypertoric varieties are quaternionic analogues of toric varieties, important for their interaction with the combinatorics of matroids as well as for their prominent place in the rapidly expanding field of algebraic symplectic and…
Recently Guillemin gave an explicit combinatorial way of constructing "toric" Kahler metrics on (symplectic) toric varieties, using only data on the moment polytope. In this paper, differential geometric properties of these metrics are…
This article studies a large, general class of orthogonal polytopes which we may call "generic orthotopes". These objects emerged from a desire to represent a Coxeter complex by an orthogonal polytope that is particularly nice with respect…
This paper focuses on determining the volumes of permutation polytopes associated to cyclic groups, dihedral groups, groups of automorphisms of tree graphs, and Frobenius groups. We do this through the use of triangulations and the…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
We compute the degree of Stiefel manifolds, that is, the variety of orthonormal frames in a finite dimensional vector space. Our approach employs techniques from classical algebraic geometry, algebraic combinatorics, and classical invariant…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
We present families of combinatorial classes described as trees with nodes that can carry one of two types of "flowers": integer partitions or integer compositions. Two parameters on the flowers of trees will be considered: the number of…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
We introduce a novel intrinsic volume concept in tropical geometry. This is achieved by developing the foundations of a tropical analog of lattice point counting in polytopes. We exhibit the basic properties and compare it to existing…
Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees. These relative labelings are naturally formalized as tanglegrams, which have previously been an object of…
Hypertoric varieties are hyperk\"ahler analogues of toric varieties, and are constructed as abelian hyperk\"ahler quotients of a quaternionic affine space. Just as symplectic toric orbifolds are determined by labelled polytopes, orbifold…
We seek to determine a real algebraic variety from a fixed finite subset of points. Existing methods are studied and new methods are developed. Our focus lies on aspects of topology and algebraic geometry, such as dimension and defining…
In this paper we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
A phylogenetic tree is a tree with a fixed set of leaves that has no vertices of degree two. In this paper, we axiomatically define four other discrete structures on the set of leaves. We prove that each of these structures is an equivalent…
We consider the problem of classifying the dynamics of complex polynomials $f: \mathbb{C} \to \mathbb{C}$ restricted to their basins of infinity. We synthesize existing combinatorial tools --- tableaux, trees, and laminations --- into a new…
It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on…