Related papers: A bijection between phylogenetic trees and plane o…
A binary phylogenetic network on a taxon set $X$ is a rooted acyclic digraph in which the degree of each nonleaf node is three and its leaves (i.e.degree-one nodes) are uniquely labeled with the taxa of $X$. It is tree-child if each nonleaf…
For a labeled tree on the vertex set $\set{1,2,\ldots,n}$, the local direction of each edge $(i\,j)$ is from $i$ to $j$ if $i<j$. For a rooted tree, there is also a natural global direction of edges towards the root. The number of edges…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…
Certain families of combinatorial objects admit recursive descriptions in terms of generating trees: each node of the tree corresponds to an object, and the branch leading to the node encodes the choices made in the construction of the…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
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…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
We give a combinatorial proof of a recent result of B\'ona by constructing a bijection from the set of all neighbors of leaves of increasing trees of size $n$ to the set of derangements of length $n$.
A recent paper (Manceau and Lambert, 2016) developed a novel approach for describing two well-defined notions of 'species' based on a phylogenetic tree and a phenotypic partition. In this paper, we explore some further combinatorial…
This paper considers the enumeration of ternary trees (i.e. rooted ordered trees in which each vertex has 0 or 3 children) avoiding a contiguous ternary tree pattern. We begin by finding recurrence relations for several simple tree…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
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 construct a refined bijection $\phi$ between alternating permutations and 0-1-2 increasing trees with degree at most 2. It satisfies that the first element of alternating permutation $\pi$ is equal to the first vertex in $\phi(\pi)$ in…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
We introduce some natural families of distributions on rooted binary ranked plane trees with a view toward unifying ideas from various fields, including macroevolution, epidemiology, computational group theory, search algorithms and other…
We consider bicolored maps, i.e. graphs which are drawn on surfaces, and construct a bijection between (i) oriented maps with arbitary face structure, and (ii) (weighted) non-oriented maps with exactly one face. Above, each non-oriented map…
A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines…
A characterization is provided for each natural number except one (1) by means of an ordered pair of elements. The first element is a natural number called the type of the natural number characterized, and the second is a natural number…
A fringe subtree of a rooted tree is a subtree induced by one of the vertices and all its descendants. We consider the problem of estimating the number of distinct fringe subtrees in two types of random trees: simply generated trees and…
We present a simple bijection between permutation matrices and descending plane partitions without special parts. This bijection is already mentioned in work of P. Lalonde (without giving the details); it involves the inversion words of…