Related papers: On symmetries in phylogenetic trees

Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…

Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…

In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…

In the critical beta-splitting model of a random $n$-leaf rooted tree, clades are recursively split into sub-clades, and a clade of $m$ leaves is split into sub-clades containing $i$ and $m-i$ leaves with probabilities $\propto 1/(i(m-i))$.…

We construct a new bijection between the set of $n\times k$ $0$-$1$ matrices with no three $1$'s forming a $\Gamma$ configuration and the set of $(n,k)$-Callan sequences, a simple structure counted by poly-Bernoulli numbers. We give two…

In analogy to other concepts of a similar nature, we define the inducibility of a rooted binary tree. Given a fixed rooted binary tree $B$ with $k$ leaves, we let $\gamma(B,T)$ be the proportion of all subsets of $k$ leaves in $T$ that…

Tanglegrams are special graphs that consist of a pair of rooted binary trees with the same number of leaves, and a perfect matching between the two leaf-sets. These objects are of use in phylogenetics and are represented with straightline…

Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…

Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…

The alpha model, a parametrized family of probabilities on cladograms (rooted binary leaf labeled trees), is introduced. This model is Markovian self-similar, deletion-stable (sampling consistent), and passes through the Yule, Uniform and…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

Random binary search trees are obtained by recursively inserting the elements $\sigma(1),\sigma(2),\ldots,\sigma(n)$ of a uniformly random permutation $\sigma$ of $[n]=\{1,\dots,n\}$ into a binary search tree data structure. Devroye (1986)…

The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…

We consider the counting problem of the number of \textit{leaf-labeled increasing trees}, where internal nodes may have an arbitrary number of descendants. The set of all such trees is a discrete representation of the genealogies obtained…

We give a short proof of Cayley's tree formula for counting the number of different labeled trees on $n$ vertices. The following nonlinear recursive relation for the number of labeled trees on $n$ vertices is deduced from a combinatorial…

In this paper we investigate an extremal problem on binary phylogenetic trees. Given two such trees $T_1$ and $T_2$, both with leaf-set ${1,2,...,n}$, we are interested in the size of the largest subset $S \subseteq {1,2,...,n}$ of leaves…

P.L. Erdos and L.A. Szekely [Adv. Appl. Math. 10(1989), 488-496] gave a bijection between rooted semilabeled trees and set partitions. L.H. Harper's results [Ann. Math. Stat. 38(1967), 410-414] on the asymptotic normality of the Stirling…

In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general…

A tanglegram consists of two rooted binary trees with the same number of leaves and a perfect matching between the leaves of the trees. Given a size-$n$ tanglegram, i.e., a tanglegram for two trees with $n$ leaves, a multiset of induced…

We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…