Related papers: Involutions on Tip-Augmented Plane Trees for Leaf …
The study of patterns in permutations associated with forests of binary shrubs was initiated by D. Bevan et al.. In this paper, we study five different types of rise statistics that can be associated with such permutations and find the…
Topologically non trivial effects appearing in the discussion of duality transformations in higher genus manifolds are discussed in a simple example, and their relation with the properties of Topological Field Theories is established.
Growth pattern dynamics lie at the heart of morphogenesis. Here, we investigate the growth of plant leaves. We compute the conformal transformation that maps the contour of a leaf at a given stage onto the contour of the same leaf at a…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
Three standard subtree transfer operations for binary trees, used in particular for phylogenetic trees, are: tree bisection and reconnection ($TBR$), subtree prune and regraft ($SPR$) and rooted subtree prune and regraft ($rSPR$). For a…
Motivated by the definition of Duflo involution for fiat $2$-categories, we define certain analogues of Duflo involution for arbitrary finitary $2$-categories and show that such Duflo involutions exist for two classes of finitary…
Let $L$ be an alternating prime non-split link in $S^3$. We use the category of flypes between reduced alternating diagrams for $L$ to classify involutions on $L$. As consequences, we show that the quotient of an alternating periodic link…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
The innumerable shapes of plant leaves present a challenge to the explanatory power of biophysical theory. A model is needed that can produce these shapes with a small set of parameters. This paper presents a simple model of leaf shape…
We discuss a notion of shuffle for trees which extends the usual notion of a shuffle for two natural numbers. We give several equivalent descriptions, and prove some algebraic and combinatorial properties. In addition, we characterize…
Bicubic maps are in bijection with \beta(0,1)-trees. We introduce two new ways of decomposing \beta(0,1)-trees. Using this we define an endofunction on \beta(0,1)-trees, and thus also on bicubic maps. We show that this endofunction is in…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
Let $X$ be a connected non-compact $2$-dimensional manifold possibly with boundary and $\Delta$ be a foliation on $X$ such that each leaf $\omega\in\Delta$ is homeomorphic to $\mathbb{R}$ and has a trivially foliated neighborhood. Such…
We provide a fundamental result for bucket increasing trees, which gives a complete characterization of all families of bucket increasing trees that can be generated by a tree evolution process. We also provide several equivalent…
We introduce the notion of doubly rooted plane trees and give a decomposition of these trees, called the butterfly decomposition which turns out to have many applications. From the butterfly decomposition we obtain a one-to-one…
We exploit a bijection between plane recursive trees and Stirling permutations; this yields the equivalence of some results previously proven separately by different methods for the two types of objects as well as some new results. We also…
Mutation is an operation on 3-manifolds containing an embedded surface of genus 2. It is defined by cutting along the surface and regluing using the `hyperelliptic' involution, and is known to preserve many 3-manifold invariants. I show…
A major task of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. The evolutionary model is given by a Markov chain on a tree. Given samples from the leaves of the Markov chain, the goal is to reconstruct…
We consider the mutation--selection differential equation with pairwise interaction (or, equivalently, the diploid mutation--selection equation) and establish the corresponding ancestral process, which is a random tree and a variant of the…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…