Wright-Fisher diffusion bridges

DOI10.1016/J.TPB.2017.09.005MaRDI QIDQ725151zbMATH OpenOpenAlexWikidataFDO

Authors Robert Griffiths, Paul A. Jenkins, Dario Spanò

Publication date 1 August 2018

Published in Theoretical Population Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1703.00208

zbMATH Keywords

coalescent processes in Wright-Fisher diffusion bridgesWright-Fisher diffusion bridges

Mathematics Subject Classification ID

Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Genetics and epigenetics (92D10) Problems related to evolution (92D15) Software, source code, etc. for problems pertaining to biology (92-04)

Abstract: {�f Abstract} The trajectory of the frequency of an allele which begins at $x$ at time $0$ and is known to have frequency $z$ at time $T$ can be modelled by the bridge process of the Wright-Fisher diffusion. Bridges when $x=z=0$ are particularly interesting because they model the trajectory of the frequency of an allele which appears at a time, then is lost by random drift or mutation after a time $T$. The coalescent genealogy back in time of a population in a neutral Wright-Fisher diffusion process is well understood. In this paper we obtain a new interpretation of the coalescent genealogy of the population in a bridge from a time $tin(0,T)$. In a bridge with allele frequencies of 0 at times 0 and $T$ the coalescence structure is that the population coalesces in two directions from $t$ to $0$ and $t$ to $T$ such that there is just one lineage of the allele under consideration at times $0$ and $T$. The genealogy in Wright-Fisher diffusion bridges with selection is more complex than in the neutral model, but still with the property of the population branching and coalescing in two directions from time $tin(0,T)$. The density of the frequency of an allele at time $t$ is expressed in a way that shows coalescence in the two directions. A new algorithm for exact simulation of a neutral Wright-Fisher bridge is derived. This follows from knowing the density of the frequency in a bridge and exact simulation from the Wright-Fisher diffusion. The genealogy of the neutral Wright-Fisher bridge is also modelled by branching P'olya urns, extending a representation in a Wright-Fisher diffusion. This is a new very interesting representation that relates Wright-Fisher bridges to classical urn models in a Bayesian setting.

Recommendations

• Analysis and rejection sampling of Wright-Fisher diffusion bridges
• Exact simulation of the Wright-Fisher diffusion
• Comparison and content of the Wright-Fisher model of random genetic drift, the diffusion approximation, and an intermediate model
• Exact simulation of conditioned Wright-Fisher models
• Exact simulation of coupled Wright–Fisher diffusions

Cites work

• scientific article; zbMATH DE number 3954145 (Why is no real title available?)
• scientific article; zbMATH DE number 503432 (Why is no real title available?)
• scientific article; zbMATH DE number 1478492 (Why is no real title available?)
• scientific article; zbMATH DE number 2228141 (Why is no real title available?)
• A coalescent dual process in a Moran model with genic selection
• A transition function expansion for a diffusion model with selection.
• Analysis and rejection sampling of Wright-Fisher diffusion bridges
• Ancestral processes with selection
• Diffusion models in population genetics
• Diffusion processes and coalescent trees
• Exact simulation of the Wright-Fisher diffusion
• Line-of-descent and genealogical processes, and their applications in population genetics models
• Lines of descent in the diffusion approximation of neutral Wright-Fisher models
• NIST handbook of mathematical functions
• On the convergence of diffusion processes conditioned to remain in a bounded region for large time to limiting positive recurrent diffusion processes
• Orthogonal polynomial kernels and canonical correlations for Dirichlet measures
• Simulating allele frequencies in a population and the genetic differentiation of populations under mutation pressure
• The coalescent
• The transition function of a Fleming-Viot process

Cited in

(9)

• Jacobi Processes with Jumps as Neuronal Models: A First Passage Time Analysis
• Dual process in the two-parameter Poisson-Dirichlet diffusion
• Exact simulation of coupled Wright–Fisher diffusions
• An estimator for the recombination rate from a continuously observed diffusion of haplotype frequencies
• Filtering the Wright-Fisher diffusion
• Editorial: Introduction to the Paul Joyce special issue
• Exact simulation of conditioned Wright-Fisher models
• Analysis and rejection sampling of Wright-Fisher diffusion bridges
• On non-local ergodic Jacobi semigroups: spectral theory, convergence-to-equilibrium and contractivity

Describes a project that uses

Uses Software

• DLMF

This page was built for publication: Wright-Fisher diffusion bridges

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q725151)