相关论文: On the distribution of interspecies correlation fo…
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…
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…
We introduce two models for multi-type random trees motivated by studies of trait dependence in the evolution of species. Our discrete time model, the multi-type ERM tree, is a generalization of Markov propagation models on a random tree…
The Yule model and the coalescent model are two neutral stochastic models for generating trees in phylogenetics and population genetics, respectively. Although these models are quite different, they lead to identical distributions…
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…
A Yule tree is the result of a branching process with constant birth and death rates. Such a process serves as an instructive null model of many empirical systems, for instance, the evolution of species leading to a phylogenetic tree.…
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…
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…
We present a generalization of the Yule model for macroevolution in which, for the appearance of genera, we consider point processes with the order statistics property, while for the growth of species we use nonlinear time-fractional pure…
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…
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…
Understanding the evolution of binary traits, which affects the birth and survival of species and also the rate of molecular evolution, remains challenging. A typical example is the evolution of mating systems in plant species. In this…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…
The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices…
An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both…
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…
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…
The time process of transport on randomly evolving trees is investigated. By introducing the notions of living and dead nodes a model of random tree evolution is constructed which describes the spreading in time of objects corresponding to…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
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…