Related papers: A conditional coalescent for diploid exchangeable …
We review the problem of confounding in genetic association studies, which arises principally because of population structure and cryptic relatedness. Many treatments of the problem consider only a simple ``island'' model of population…
Heterogeneities in environmental conditions often induce corresponding heterogeneities in the distribution of species. In the extreme case of a localized patch of increased growth rates, reproducing populations can become strongly…
This paper extends earlier work by Cox and Durrett, who studied the coalescence times for two lineages in the stepping stone model on the two-dimensional torus. We show that the genealogy of a sample of size n is given by a time change of…
How does social complexity depend on population size and cultural transmission? Kinship structures in traditional societies provide a fundamental illustration, where cultural rules between clans determine people's marriage possibilities.…
Biological aging is characterized by an age-dependent increase in the probability of death and by a decrease in the reproductive capacity. Individual age-dependent rates of survival and reproduction have a strong impact on population…
We consider a model of a population of fixed size $N$ undergoing selection. Each individual acquires beneficial mutations at rate $\mu_N$, and each beneficial mutation increases the individual's fitness by $s_N$. Each individual dies at…
This paper studies the bounded confidence model on growing fully-mixed populations. In this model, in addition to the usual opinion clusters, significant secondary clusters of smaller size appear systematically, while those secondary…
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common…
Studying how diverse human populations are related is of historical and anthropological interest, in addition to providing a realistic null model for testing for signatures of natural selection or disease associations. Furthermore,…
The aim of this paper is to study the large population limit of a binary branching particle system with Moran type interactions: we introduce a new model where particles evolve, reproduce and die independently and, with a probability that…
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 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…
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…
The evolving Kingman coalescent is the tree-valued process which records the time evolution undergone by the genealogies of Moran populations. We consider the associated process of total external tree length of the evolving Kingman…
Recovery of population size history from molecular sequence data is an important problem in population genetics. Inference commonly relies on a coalescent model linking the population size history to genealogies. The high computational cost…
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…
We present an individual based model of evolutionary ecology. The reproduction rate of individuals characterized by their genome depends on the composition of the population in genotype space. Ecological features such as the taxonomy and…
In this paper we study a class of stochastic individual-based models that describe the evolution of haploid populations where each individual is characterised by a phenotype and a genotype. The phenotype of an individual determines its…
Inference of the marginal likelihood of sample allele configurations using backward algorithms yields identical results with the Kingman coalescent, the Moran model, and the diffusion model (up to a scaling of time). For inference of…
We derive the asymptotic behaviour of the genealogy of a logistic branching process in the setting where the equilibrium population size is large. In three regimes on the tail of the offspring distribution we recover the Kingman,…