Related papers: Clades and clans: a comparison study of two evolut…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
This paper introduces a new classification scheme - head/tail breaks - in order to find groupings or hierarchy for data with a heavy-tailed distribution. The heavy-tailed distributions are heavily right skewed, with a minority of large…
Phylogenetic data arising on two possibly different tree topologies might be mixed through several biological mechanisms, including incomplete lineage sorting or horizontal gene transfer in the case of different topologies, or simply…
The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…
Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…
Kingman's model describes the evolution of a one-locus haploid population of infinite size and discrete generations under the competition of selection and mutation. A random generalisation has been made in a previous paper which assumes all…
We consider a stochastic model for evolution of group-structured populations in which interactions between group members correspond to the Prisoner's Dilemma or the Hawk-Dove game. Selection operates at two organization levels: individuals…
Class imbalance significantly degrades classification performance, yet its effects are rarely analyzed from a unified theoretical perspective. We propose a principled framework based on three fundamental scales: the imbalance coefficient…
Kingman's House-of-Cards model is a simple and celebrated model to describe the evolution of population under the competition of selection and mutation. Letting mutation probabilities vary on generations makes the model more realistic and…
Consider a population evolving as a critical continuous-time Galton-Watson (GW) tree. Conditional on the population surviving until a large time $T$, sample $k$ individuals uniformly at random (without replacement) from amongst those alive…
Several real-world and abstract structures and systems are characterized by marked hierarchy to the point of being expressed as trees. Because the study of these entities often involves sampling (or discovering) the tree nodes in a specific…
It seems paradoxical to have observed the absence of reduced effective population sizes $N_{\mathrm{e}}$ under marine hatchery practices. This paper studies the Ryman-Laikre, or two-demographic-component, model of the hatchery impact…
The Yang and Prentice (YP) regression models have garnered interest from the scientific community due to their ability to analyze data whose survival curves exhibit intersection. These models include proportional hazards (PH) and…
As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A…
We introduce tree linear cascades, a class of linear structural equation models for which the error variables are uncorrelated but need not be Gaussian nor independent. We show that, in spite of this weak assumption, the tree structure of…
In this paper we introduce a model of spatial network growth in which nodes are placed at randomly selected locations on a unit square in $\mathbb{R}^2$, forming new connections to old nodes subject to the constraint that edges do not…
A discrete time branching process where the offspring distribution is generation-dependent, and the number of reproductive individuals is controlled by a random mechanism is considered. This model is a Markov chain but, in general, the…
Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…
We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new…
For many taxa, the current high rates of extinction are likely to result in a significant loss of biodiversity. The evolutionary heritage of biodiversity is frequently quantified by a measure called phylogenetic diversity (PD). We predict…