Related papers: Ancestral diversity in fragmentation trees

We introduce and study a model of plane random trees generalizing the famous Bienaym\'e--Galton--Watson model but where births and deaths are locally correlated. More precisely, given a random variable $(B,H)$ with values in $\{1,2,3,…

We consider a pruning of the inhomogeneous continuum random trees, as well as the cut trees that encode the genealogies of the fragmentations that come with the pruning. We propose a new approach to the reconstruction problem, which has…

For any real-valued $k > 1$, we consider the tree rooted at 0, where each positive integer $n$ has parent $\lfloor\frac{n}{k}\rfloor$. The average number of children per node is $k$, thus this definition gives a natural way to extend…

The occurrence and the distribution of patterns of trees associated to natural numbers are investigated. Bounds from above and below are proven for certain natural quantities.

Ancestral state reconstruction is one of the most important tasks in evolutionary biology. Conditions under which we can reliably reconstruct the ancestral state have been studied for both discrete and continuous traits. However, the…

Take a continuous-time Galton-Watson tree. If the system survives until a large time $T$, then choose $k$ particles uniformly from those alive. What does the ancestral tree drawn out by these $k$ particles look like? Some special cases are…

In this article, we construct a generalization of the Blum-Fran\c{c}ois Beta-splitting model for evolutionary trees, which was itself inspired by Aldous' Beta-splitting model on cladograms. The novelty of our approach allows for asymmetric…

We investigate the statistics of trees grown from some initial tree by attaching links to preexisting vertices, with attachment probabilities depending only on the valence of these vertices. We consider the asymptotic mass distribution that…

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…

Given a rooted tree $T$ with leaves $v_1,v_2,\ldots,v_n$, we define the ancestral matrix $C(T)$ of $T$ to be the $n \times n$ matrix for which the entry in the $i$-th row, $j$-th column is the level (distance from the root) of the first…

Aldous, Evans and Pitman (1998) studied the behavior of the fragmentation process derived from deleting the edges of a uniform random tree on $n$ labelled vertices. In particular, they showed that, after proper rescaling, the above…

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.…

Stochastic modeling of phylogenies raises five questions that have received varying levels of attention from quantitatively inclined biologists. 1) How large do we expect (from the model) the ration of maximum historical diversity to…

The classical matrix-tree theorem relates the determinant of the combinatorial Laplacian on a graph to the number of spanning trees. We generalize this result to Laplacians on one- and two-dimensional vector bundles, giving a combinatorial…

We study a universal object for the genealogy of a sample in populations with mutations: the critical birth-death process with Poissonian mutations, conditioned on its population size at a fixed time horizon. We show how this process arises…

We introduce a random graph model based on k-trees, which can be generated by applying a probabilistic preferential attachment rule, but which also has a simple combinatorial description. We carry out a precise distributional analysis of…

The $k$-cut number of rooted graphs was introduced by Cai et al. as a generalization of the classical cutting model by Meir and Moon. In this paper, we show that all moments of the k-cut number of conditioned Galton-Watson trees converges…

Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…

A simple way to model phenotypic evolution is to assume that after splitting, the trait values of the sister species diverge as independent Brownian motions. Relying only on a prior distribution for the underlying species tree (conditioned…

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…