Related papers: Demographic inference using genetic data from a si…
The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical…
Reconstruction of population histories is a central problem in population genetics. Existing coalescent-based methods, like the seminal work of Li and Durbin (Nature, 2011), attempt to solve this problem using sequence data but have no…
Samples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. Current methods that take advantage of…
Collecting genomics data across multiple heterogeneous populations (e.g., across different cancer types) has the potential to improve our understanding of disease. Despite sequencing advances, though, resources often remain a constraint…
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 first chapter concerns monotype population models. We first study general birth and death processes and we give non-explosion and extinction criteria, moment computations and a pathwise representation. We then show how different scales…
In this article, discrete and stochastic changes in (effective) population size are incorporated into the spectral representation of a biallelic diffusion process for drift and small mutation rates. A forward algorithm inspired by…
Human populations have experienced dramatic growth since the Neolithic revolution. Recent studies that sequenced a very large number of individuals observed an extreme excess of rare variants, and provided clear evidence of recent rapid…
The multivariate hypergeometric distribution describes sampling without replacement from a discrete population of elements divided into multiple categories. Addressing a gap in the literature, we tackle the challenge of estimating discrete…
We consider population dynamics as implemented by the cloning algorithm for analysis of large deviations of time-averaged quantities. Using the simple symmetric exclusion process as a prototypical example, we investigate the convergence of…
Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point…
Macro-level modeling is still the dominant approach in many demographic applications because of its simplicity. Individual-level models, on the other hand, provide a more comprehensive understanding of observed patterns; however, their…
There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case--control…
We consider the problem of estimating the division rate of a size-structured population in a nonparametric setting. The size of the system evolves according to a transport-fragmentation equation: each individual grows with a given transport…
Background: Many different simulation frameworks, in different topics, need to treat realistic datasets to initialize and calibrate the system. A precise reproduction of initial states is extremely important to obtain reliable forecast from…
Variation in a sample of molecular sequence data informs about the past evolutionary history of the sample's population. Traditionally, Bayesian modeling coupled with the standard coalescent, is used to infer the sample's bifurcating…
We explore the use of Intrinsic Dimension (ID) for gaining insights in how populations evolve in Evolutionary Algorithms. ID measures the minimum number of dimensions needed to accurately describe a dataset and its estimators are being used…
This study elaborates some examples of a simple evolutionary stochastic rate process where the population rate of change depends on the distribution of properties--so different cohorts change at different rates. We investigate the effect on…
We consider an empirical likelihood framework for inference for a statistical model based on an informative sampling design and population-level information. The population-level information is summarized in the form of estimating equations…
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…