Related papers: Nested tree space: a geometric framework for co-ph…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
We generalize the notion of tight geodesics in the curve complex to tight trees. We then use tight trees to construct model geometries for certain surface bundles over graphs. This extends some aspects of the combinatorial model for doubly…
Singular theories, characterised by the presence of degeneracies in their Lagrangian or Hamiltonian descriptions, require the systematic implementation of constraints in order to obtain well-defined dynamics. While the symplectic framework…
Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…
This is an expository paper. The geometry of phylogenetic trees is used to present in an accessible and pleasant fashion the results of Deligne, Mumford, and Knudsen about the moduli space of n distinct points on the projective line and its…
We consider a class of infinite weighted metric trees obtained as perturbations of self-similar regular trees. Possible definitions of the boundary traces of functions in the Sobolev space on such a structure are discussed by using…
We present a construction, called the limit of a tree system of spaces (or, less formally, a tree of spaces). The construction is designed to produce compact metric spaces that resemble fractals, out of more regular spaces, such as closed…
The reconstruction of transmission trees for epidemics from genetic data has been the subject of some recent interest. It has been demonstrated that the transmission tree structure can be investigated by augmenting internal nodes of a…
In the present paper we investigate geometric characteristics of compact metric spaces, which can be described in terms of Gromov-Hausdorff distances to simplexes, i.e., to finite metric spaces such that all their nonzero distances are…
Tree-graded spaces are a generalization of $\mathbb{R}$-trees and play an important role in describing the large-scale geometry of relatively hyperbolic groups. We consider a subclass of tree-graded spaces that we call "disjointly…
The inference of evolutionary histories is a central problem in evolutionary biology. The analysis of a sample of phylogenetic trees can be conducted in Billera-Holmes-Vogtmann tree space, which is a CAT(0) metric space of phylogenetic…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
Networks having the geometry and the connectivity of trees are considered as the spatial support of spatiotemporal dynamical processes. A tree is characterized by two parameters: its ramification and its depth. The local dynamics at the…
We consider the existence of the topological entropy of shift spaces on a finitely generated semigroup whose Cayley graph is a tree. The considered semigroups include free groups. On the other hand, the notion of stem entropy is introduced.…
In this paper, we present a flexible and probabilistic framework for tracking topological features in time-varying scalar fields using merge trees and partial optimal transport. Merge trees are topological descriptors that record the…
Nested structure, which is non-random, controls cooperation dynamics and biodiversity in plant-animal mutualistic networks. This structural pattern has been explained in a static (non-growth) network models. However, evolutionary processes…
We already saw in [A1] that the space of dynamically marked rational maps can be identified to a subspace of the space of covers between trees of spheres on which there is a notion of convergence that makes it sequentially compact. In the…
Phylogenetic trees in genetics and biology in general are all binary. We make an attempt to answer one fundamental question: Is such binary branching from the coarsest to the finest scales sustained by data? We convert this question into an…
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…
Many biological systems and artificial structures are ramified, and present a high geometric complexity. In this work, we propose a space-averaged model of branched systems for conservation laws. From a one-dimensional description of the…