Related papers: Phylogenetic flexibility via Hall-type inequalitie…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
In this paper we study tropicalization of Grassmannian and linear varieties. In particular, we study the tropical linear spaces cor- responding to the phylogenetic trees. We prove that corresponding to each subtree of the phylogenetic tree…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
Motivated by geometric origami and the straight skeleton construction, we outline a map between spaces of phylogenetic trees and spaces of planar polygons. The limitations of this map is studied through explicit examples, culminating in…
The metric space of phylogenetic trees defined by Billera, Holmes, and Vogtmann, which we refer to as BHV space, provides a natural geometric setting for describing collections of trees on the same set of taxa. However, it is sometimes…
Recently, there has been a growing interest in the relationships between unrooted and rooted phylogenetic networks. In this context, a natural question to ask is if an unrooted phylogenetic network U can be oriented as a rooted phylogenetic…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
A graph is a $k$-leaf power of a tree $T$ if its vertices are leaves of $T$ and two vertices are adjacent in $T$ if and only if their distance in $T$ is at most $k$. Then $T$ is a $k$-leaf root of $G$. This notion was introduced by…
Given a collection $\C$ of subsets of a finite set $X$, let $\bigcup \C = \cup_{S \in \C}S$. Philip Hall's celebrated theorem \cite{hall} concerning `systems of distinct representatives' tells us that for any collection $\C$ of subsets of…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
In $\tau$-tilting theory, it is often difficult to determine when a set of bricks forms a 2-simple minded collection. The aim of this paper is to determine when a set of bricks is contained in a 2-simple minded collection for a…
The Shub-Smale Tau Conjecture is a hypothesis relating the number of integral roots of a polynomial f in one variable and the Straight-Line Program (SLP) complexity of f. A consequence of the truth of this conjecture is that, for the…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…
Several indices that measure the degree of balance of a rooted phylogenetic tree have been proposed so far in the literature. In this work we define and study a new index of this kind, which we call the total cophenetic index: the sum, over…
Phyllotaxis describes the arrangement of florets, scales or leaves in composite flowers or plants (daisy, aster, sunflower, pinecone, pineapple). As a structure, it is a geometrical foam, the most homogeneous and densest covering of a large…
Trinomial varieties are affine varieties given by a system of equations consisting of polynomials with three terms. Such varieties are total coordinate spaces of normal varieties with torus action of complexity one. For an affine variety…
The Sackin and Colless indices are two widely-used metrics for measuring the balance of trees and for testing evolutionary models in phylogenetics. This short paper contributes two results about the Sackin and Colless indices of trees. One…
In modular invariant models of flavor, observables must be modular invariant. The observables discussed so far in the literature are functions of the modulus $\tau$ and its conjugate, $\bar\tau$. We point out that certain combinations of…