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The path-difference metric is one of the oldest and most popular distances for the comparison of phylogenetic trees, but its statistical properties are still quite unknown. In this paper we compute the expected value under the Yule model of…
The Yule (pure-birth) model is the simplest null model of speciation; each lineage gives rise to a new lineage independently with the same rate $\lambda$. We investigate the expected length of an edge chosen at random from the resulting…
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…
Diversification is nested, and early models suggested this could lead to a great deal of evolutionary redundancy in the Tree of Life. This result is based on a particular set of branch lengths produced by the common coalescent, where…
The Yule branching process is a classical model for the random generation of gene tree topologies in population genetics. It generates binary ranked trees -- also called "histories" -- with a finite number $n$ of leaves. We study the…
Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule…
Inferring the ancestral state at the root of a phylogenetic tree from states observed at the leaves is a problem arising in evolutionary biology. The simplest technique -- majority rule -- estimates the root state by the most frequently…
Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
The paper written in 1925 by G. Udny Yule that we celebrate in this special issue introduces several novelties and results that we recall in detail. First, we discuss Yule (1925)'s main legacies over the past century, focusing on empirical…
For two decades, the Colless index has been the most frequently used statistic for assessing the balance of phylogenetic trees. In this article, this statistic is studied under the Yule and uniform model of phylogenetic trees. The main tool…
Preferential attachment is a popular generative mechanism to explain the widespread observation of power law distributed networks. We introduce an alternative explanation for the phenomenon by allowing the link growth rates to vary across…
In this work we study the limit distribution of an appropriately normalized cophenetic index of the pure-birth tree conditioned on $n$ contemporary tips. We show that this normalized phylogenetic balance index is a submartingale that…
Neutral macroevolutionary models, such as the Yule model, give rise to a probability distribution on the set of discrete rooted binary trees over a given leaf set. Such models can provide a signal as to the approximate location of the root…
The Yule process generates a class of binary trees which is fundamental to population genetic models and other applications in evolutionary biology. In this paper, we introduce a family of sub-classes of ranked trees, called Omega-trees,…
In a recent paper on 'Estimating Species Trees from Unrooted Gene Trees' Liu and Yu observe that the distance matrix on the underlying taxon set, which is built up from expected internode distances on gene trees under the multispecies…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
In a phylogenetic tree, we often don't have information about the time a speciation event (inner node) occured. Under a neutral model for speciation, I develop fast algorithms for calculating the probability that an inner node i is the k-th…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…