Related papers: The Sampled Moran Genealogy Process
Randomness is one of the important key concepts of statistics. In epidemiology or medical science, we investigate our hypotheses and interpret results through this statistical randomness. We hypothesized by imposing some conditions to this…
Consider a finite renewal process in the sense that interrenewal times are positive i.i.d. variables and the total number of renewals is a random variable, independent of interrenewal times. A finite point process can be obtained by…
We introduce and analyze a waiting time model for the accumulation of genetic changes. The continuous time conjunctive Bayesian network is defined by a partially ordered set of mutations and by the rate of fixation of each mutation. The…
We consider the discrete-time migration-recombination equation, a deterministic, nonlinear dynamical system that describes the evolution of the genetic type distribution of a population evolving under migration and recombination in a law of…
We show that genealogical trees arising from a broad class of non-neutral models of population evolution converge to the Kingman coalescent under a suitable rescaling of time. As well as non-neutral biological evolution, our results apply…
The distributed genome hypothesis states that the set of genes in a population of bacteria is distributed over all individuals that belong to the specific taxon. It implies that certain genes can be gained and lost from generation to…
In this article, we focus on Bienaym\'e-Galton-Watson processes with linear-fractional offspring distributions. At a fixed generation, we consider a sample of the individuals alive, drawn in two different ways: either through Bernoulli…
We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies.…
These lecture notes introduce the statistical analysis of continuous-time generative models built from Markov dynamics. We begin with the stochastic-calculus foundations of score-based diffusion models, including time reversal, score…
The development of coalescent theory paved the way to statistical inference from population genetic data. In the genomic era, however, coalescent models are limited due to the complexity of the underlying ancestral recombination graph. The…
Coalescence processes have received a lot of attention in the context of conditional branching processes with fixed population size and non-overlapping generations. Here we focus on similar problems in the context of the standard…
We describe briefly in this note a procedure for consistently estimating the marginal likelihood of a statistical model through a sample from the posterior distribution of the model parameters.
Motivated by applications in systems biology, we seek a probabilistic framework based on Markov processes to represent intracellular processes. We review the formal relationships between different stochastic models referred to in the…
We prove the existence of the total length process for the genealogical tree of a population model with random size given by a quadratic stationary continuous-state branching processes. We also give, for the one-dimensional marginal, its…
We consider the problem of inferring a latent function in a probabilistic model of data. When dependencies of the latent function are specified by a Gaussian process and the data likelihood is complex, efficient computation often involve…
We consider an exactly solvable model of branching random walk with random selection, which describes the evolution of a population with $N$ individuals on the real line. At each time step, every individual reproduces independently, and its…
The extremal process of a branching random walk is the point measure recording the position of particles alive at time $n$, shifted around the expected position of the minimal position. Madaule proved that this point measure converges, as…
Bertoin and Le Gall (2003) introduced a certain probability measure valued Markov process that describes the evolution of a population, such that a sample from this population would exhibit a genealogy given by the so-called…
We suggest a simple deterministic approximation for the growth of the favoured-allele frequency during a selective sweep. Using this approximation we introduce an accurate model for genetic hitch-hiking. Only when Ns < 10 (N is the…
We give a closed form of the discrete-time evolution of a recombination transformation in population genetics. This decomposition allows to define a Markov chain in a natural way. We describe the geometric decay rate to the limit…