Related papers: Markovian simulation for ancestors trees
We study a density-dependent Markov jump process describing a population where each individual is characterized by a type, and reproduces at rates depending both on its type and on the population type distribution. We are interested in the…
In this paper I describe a cellular automaton model of a multi-species ecosystem, suitable for the study of emergent properties of macroevolution. Unlike majority of ecological models, the number of coexisting species is not fixed. Starting…
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…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
We analyse sequential Markov coalescent algorithms for populations with demographic structure: for a bottleneck model, a population-divergence model, and for a two-island model with migration. The sequential Markov coalescent method is an…
The goal of this note is to present a general approach to define the net reproduction function for a large class of nonlinear physiologically structured population models. In particular, we are going to show that this can be achieved in a…
We show that each member of a broad class of Markovian population models induces a unique stochastic process on the space of genealogies. We construct this genealogy process and derive exact expressions for the likelihood of an observed…
In this work, we study a family of non-Markovian trees modeling populations where individuals live and reproduce independently with possibly time-dependent birth-rate and lifetime distribution. To this end, we use the coding process…
The focus of this paper is the analysis of real-time systems with recursion, through the development of good theoretical techniques which are implementable. Time is modeled using clock variables, and recursion using stacks. Our technique…
The recursive and hierarchical structure of full rooted trees is applicable to represent statistical models in various areas, such as data compression, image processing, and machine learning. In most of these cases, the full rooted tree is…
We consider a stochastic individual based model where each predator searches during a random time and then manipulates its prey or rests. The time distributions may be non-exponential. An age structure allows to describe these interactions…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
We introduce a model for simulating mutation of prokaryote DNA sequences. Using that model we can then evaluated traditional techniques like parsimony and maximum likelihood methods for computing phylogenetic relationships. We also use the…
We develop a new Markov chain on graph partitions that makes relatively global moves yet is computationally feasible to be used as the proposal in the Metropolis-Hastings method. Our resulting algorithm can be made reversible and able to…
Multitype branching processes (MTBP) model branching structures, where the nodes of the resulting tree are objects of different types. One field of application of such models in biology is in studies of cell proliferation. A sampling scheme…
Certain families of combinatorial objects admit recursive descriptions in terms of generating trees: each node of the tree corresponds to an object, and the branch leading to the node encodes the choices made in the construction of the…
The goal of these lectures is to review some mathematical aspects of random tree models used in evolutionary biology to model gene trees or species trees. We start with stochastic models of tree shapes (finite trees without edge lengths),…
In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
We consider random recursive trees that are grown via community modulated schemes that involve random attachment or degree based attachment. The aim of this paper is to derive general techniques based on continuous time embedding to study…