Related papers: Clades and clans: a comparison study of two evolut…
We consider a one-dimensional dyadic branching Brownian motion on $\mathbb{R}$ with positive drift $\beta \in (0,1)$, branching rate $1/2$, reflected at $0$ and killed at a boundary $L > 0$. The killing boundary $L$ is chosen so that the…
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…
The number of extant individuals within a lineage, as exemplified by counts of species numbers across genera in a higher taxonomic category, is known to be a highly skewed distribution. Because the sublineages (such as genera in a clade)…
Simple stochastic models for phylogenetic trees on species have been well studied. But much paleontology data concerns time series or trees on higher-order taxa, and any broad picture of relationships between extant groups requires use of…
We are interested in the quantitative analysis of the compaction ratio for two classical families of trees: recursive trees and plane binary increasing trees. These families are typical representatives of tree models with a small depth.…
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…
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…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…
We study two fringe subtree counting statistics, the number of cherries and that of pitchforks for Ford's $\alpha$ model, a one-parameter family of random phylogenetic tree models that includes the uniform and the Yule models, two tree…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…
Phylogenetic analysis of DNA or other data commonly gives rise to a collection or sample of inferred evolutionary trees. Principal Components Analysis (PCA) cannot be applied directly to collections of trees since the space of evolutionary…
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that…
An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive…
Given a gene-tree labeled topology $G$ and a species tree $S$, the "ancestral configurations" at an internal node $k$ of $S$ represent the combinatorially different sets of gene lineages that can be present at $k$ when all possible…
Principal components (PCA) and hierarchical clustering are two of the most heavily used techniques for analyzing the differences between nucleic acid sequence samples sampled from a given environment. However, a classical application of…
We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age $\tau$ as $\tau^{-\alpha}$. Depending on the exponent $\alpha$, the scaling of tree depth with tree size $n$ displays a…
We introduce the Pitman Yor Diffusion Tree (PYDT) for hierarchical clustering, a generalization of the Dirichlet Diffusion Tree (Neal, 2001) which removes the restriction to binary branching structure. The generative process is described…
In binary classification, imbalance refers to situations in which one class is heavily under-represented. This issue is due to either a data collection process or because one class is indeed rare in a population. Imbalanced classification…
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…
Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates…