Related papers: Linkage disequilibrium under recurrent bottlenecks
We consider resequencing studies of associated loci and the problem of prioritizing sequence variants for functional follow-up. Working within the multivariate linear regression framework helps us to account for correlation across variants,…
Quasispecies theory provides the conceptual and theoretical bases for describing the dynamics of biological information of replicators subject to large mutation rates. This theory, initially conceived within the framework of prebiotic…
We study the continuous-time evolution of the recombination equation of population genetics. This evolution is given by a differential equation that acts on a product probability space, and its solution can be described by a Markov chain on…
Maintenance of sexual reproduction and genetic recombination imposes physiological costs when compared to parthenogenic reproduction, most prominently: for maintaining the corresponding (molecular) machinery, for finding a mating partner,…
Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general…
Quantifying population dynamics is a fundamental challenge in ecology and evolutionary biology, particularly for species that are cryptic, microscopic, or extinct. Traditional approaches rely on continuous representations of population…
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…
To introduce selection into a model of coalescence, I explore the use of modified integer partitions that allow the identification of a preferred lineage. I show that a partition-partition transition matrix, along with Monte Carlo discrete…
We introduce an individual-based model for structured populations undergoing demographic bottlenecks, i.e. drastic reductions in population size that last many generations and can have arbitrary shapes. We first show that the…
We study a nonlinear recombination model from population genetics as a combinatorial version of the Kac-Boltzmann equation from kinetic theory. Following Kac's approach, the nonlinear model is approximated by a mean field linear evolution…
Gene duplications are one of major primary driving forces for evolutionary novelty. We took population genetics models of genes duplicate to study how evolutionary forces acting during the fixation of mutant allele at duplicate loci. We…
A key question in the current diversity crisis is how diversity has been maintained throughout evolution and how to preserve it. Modern coexistence theories suggest that a high invasion rate of rare new types is directly related to…
Selective sweeps are typically associated with a local reduction of genetic diversity around the adaptive site. However, selective sweeps can also quickly carry neutral mutations to observable population frequencies if they arise early in a…
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…
In sexual population, recombination reshuffles genetic variation and produces novel combinations of existing alleles, while selection amplifies the fittest genotypes in the population. If recombination is more rapid than selection,…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
When investigating the spreading of a piece of information or the diffusion of an innovation, we often lack information on the underlying propagation network. Reconstructing the hidden propagation paths based on the observed diffusion…
We consider an infinitely large population under stabilising selection and mutation in which the allelic effects determining a polygenic trait vary between loci. We obtain analytical expressions for the stationary genetic variance as a…
For many traits, including susceptibility to common diseases in humans, causal loci uncovered by genetic mapping studies explain only a minority of the heritable contribution to trait variation. Multiple explanations for this "missing…
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…