Related papers: Clades and clans: a comparison study of two evolut…
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…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
Many processes and models --in biological, physical, social, and other contexts-- produce trees whose depth scales logarithmically with the number of leaves. Phylogenetic trees, describing the evolutionary relationships between biological…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
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…
By introducing the notions of living and dead nodes a new model of random tree evolution with continuous time parameter has been constructed. It is assumed that two random variables, the lifetime and the offspring number of living nodes…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
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.…
Modern population genetics studies typically involve genome-wide genotyping of individuals from a diverse network of ancestries. An important, unsolved problem is how to formulate and estimate probabilistic models of observed genotypes that…
We provide a local probabilistic description of the limiting statistics of large preferential attachment trees in terms of the ordinary degree (number of neighbors) but augmented with information on leafdegree (number of neighbors that are…
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…
It is of fundamental importance to determine if and how hierarchical clustering is involved in large-scale structure formation of the universe. Hierarchical evolution is characterized by rules which specify how dark matter halos are formed…
We prove polynomial upper and lower bounds on the expected size of the maximum agreement subtree of two random binary phylogenetic trees under both the uniform distribution and Yule-Harding distribution. This positively answers a question…
We introduce principal differences analysis (PDA) for analyzing differences between high-dimensional distributions. The method operates by finding the projection that maximizes the Wasserstein divergence between the resulting univariate…
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…
Full binary trees naturally represent commutative non-associative products. There are many important examples of these products: finite-precision floating-point addition and NAND gates, among others. Balance in such a tree is highly…
We study two models of an age-biased graph process: the $\delta$-version of the preferential attachment graph model (PAM) and the uniform attachment graph model (UAM), with $m$ attachments for each of incoming vertices. We show that almost…
Hierarchies are frequently used for the organization of objects. Given a hierarchy of classes, two main approaches are used, to automatically classify new instances: flat classification and cascade classification. Flat classification…
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.…