Related papers: Estimating effective population size changes from …
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)…
Large-scale statistical analysis of data sets associated with genome sequences plays an important role in modern biology. A key component of such statistical analyses is the computation of $p$-values and confidence bounds for statistics…
Consider the random Dirichlet partition of the interval into $n$ fragments with parameter $\theta >0$. We recall the unordered Ewens sampling formulae from finite Dirichlet partitions. As this is a key variable for estimation purposes,…
We present an algorithm for the stochastic simulation of gene expression and heterogeneous population dynamics. The algorithm combines an exact method to simulate molecular-level fluctuations in single cells and a constant-number Monte…
We consider a class of density-dependent branching processes which generalises exponential, logistic and Gompertz growth. A population begins with a single individual, grows exponentially initially, and then growth may slow down as the…
Recent methods have been developed to map single-cell lineage statistics to population growth. Because population growth selects for exponentially rare phenotypes, these methods inherently depend on sampling large deviations from finite…
In population genetics, extant samples are usually used for inference of past population genetic forces. With the Kingman coalescent and the backward diffusion equation, inference of the marginal likelihood proceeds from an extant sample…
Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to…
Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from…
Capture-recapture methods aim to estimate the size of a closed population on the basis of multiple incomplete enumerations of individuals. In many applications, the individual probability of being recorded is heterogeneous in the…
Consider a structured population consisting of $d$ colonies, with migration rates proportional to a positive parameter $K$. We sample $N_K$ individuals, distributed evenly across the $d$ colonies, and trace their ancestral lineages backward…
We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics…
This paper is concerned with sample size determination methodology for prediction models. We propose combining the individual calculations via a learning-type curve. We suggest two distinct ways of doing so, a deterministic skeleton of a…
Computer simulations of complex population genetic models are an essential tool for making sense of the large-scale datasets of multiple genome sequences from a single species that are becoming increasingly available. A widely used approach…
Effective population size (Ne(t)) is a fundamental parameter in population genetics and phylodynamics that quantifies genetic diversity and reveals demographic history. Coalescent-based methods enable the inference of Ne(t) trajectories…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…
We explore the effect of finite population sampling in design problems with many variables cross-classified in many ways. In particular, we investigate designs where we wish to sample individuals belonging to different groups for which the…
We consider outbreak detection settings of endemic diseases where the population under study consists of various subpopulations available for stratified surveillance. These subpopulations can for example be based on age cohorts, but may…
The population protocol model describes collections of distributed agents that interact in pairs to solve a common task. We consider a dynamic variant of this prominent model, where we assume that an adversary may change the population size…
Weak purifying selection, acting on many linked mutations, may play a major role in shaping patterns of molecular evolution in natural populations. Yet efforts to infer these effects from DNA sequence data are limited by our incomplete…