Related papers: Estimating effective population size changes from …
Using a population dynamics inspired by an ensemble of growing cells, a set of fluctuation theorems linking observables measured at the lineage and population levels are derived. One of these relations implies specific inequalities…
Identifiability of evolutionary tree models has been a recent topic of discussion and some models have been shown to be non-identifiable. A coalescent-based rooted population tree model, originally proposed by Nielsen et al. 1998 [2], has…
We analyse numerically the effects of small population size in the initial transient regime of a simple example population dynamics. These effects play an important role for the numerical determination of large deviation functions of…
Mechanisms leading to speciation are a major focus in evolutionary biology. In this paper, we present and study a stochastic model of population where individuals, with type a or A, are equivalent from ecological, demographical and spatial…
The coalescent is a stochastic process representing ancestral lineages in a population undergoing neutral genetic drift. Originally defined for a well-mixed population, the coalescent has been adapted in various ways to accommodate spatial,…
Spatial models where growth is limited to the edge of the expansions have been instrumental to understand the population dynamics and the clone size distribution in growing cellular populations, such as microbial colonies and avascular…
Probability modelling for DNA sequence evolution is well established and provides a rich framework for understanding genetic variation between samples of individuals from one or more populations. We show that both classical and more recent…
A well-established model for the genealogy of a large population in equilibrium is Kingman's coalescent. For the population together with its genealogy evolving in time, this gives rise to a time-stationary tree-valued process. We study the…
We consider the problem of inference for the states and parameters of a continuous-time multitype branching process from partially observed time series data. Exact inference for this class of models, typically using sequential Monte Carlo,…
In this paper we study the iterated birth process of which we examine the first-passage time distributions and the hitting probabilities. Furthermore, linear birth processes, linear and sublinear death processes at Poisson times are…
Sweepstakes reproduction refers to a highly skewed individual recruitment success without involving natural selection and may apply to individuals in broadcast spawning populations characterised by Type III survivorship. We consider an…
In the case of informative sampling the sampling scheme explicitly or implicitly depends on the response variable. As a result, the sample distribution of response variable can- not be used for making inference about the population. In this…
Data describing human interactions often suffer from incomplete sampling of the underlying population. As a consequence, the study of contagion processes using data-driven models can lead to a severe underestimation of the epidemic risk.…
Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a…
Clinical prediction models are estimated using a sample of limited size from the target population, leading to uncertainty in predictions, even when the model is correctly specified. Generally, not all patient profiles are observed…
In this paper, a first sample-based formulation of the recently considered population observers, or ensemble observers, which estimate the state distribution of dynamic populations from measurements of the output distribution is…
A density-dependent branching process is a particle system in which individuals reproduce independently, but in a way that depends on the current population size. This feature can model a wide range of ecological interactions at the cost of…
Stochastic models of sequential mutation acquisition are widely used to quantify cancer and bacterial evolution. Across manifold scenarios, recurrent research questions are: how many cells are there with $n$ alterations, and how long will…
The coalescent is a foundational model of latent genealogical trees under neutral evolution, but suffers from intractable sampling probabilities. Methods for approximating these sampling probabilities either introduce bias or fail to scale…
Recent improvements in high-throughput genotyping and sequencing technologies have afforded the collection of massive, genome-wide datasets of DNA information from hundreds of thousands of individuals. These datasets, in turn, provide…