Coalescence in a random background.

DOI10.1214/105051604000000099MaRDI QIDQ1879889zbMATH OpenOpenAlexFDO

Authors Alison Etheridge, Anja Sturm, N. H. Barton

Publication date 15 September 2004

Published in The Annals of Applied Probability (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/math/0406174

Coalescent identity by descent random environment recombination selection

Diffusion processes (60J60) Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Branching processes (Galton-Watson, birth-and-death, etc.) (60J80) Applications of branching processes (60J85) Interacting random processes; statistical mechanics type models; percolation theory (60K35) Processes in random environments (60K37)

Abstract: We consider a single genetic locus which carries two alleles, labelled P and Q. This locus experiences selection and mutation. It is linked to a second neutral locus with recombination rate r. If r=0, this reduces to the study of a single selected locus. Assuming a Moran model for the population dynamics, we pass to a diffusion approximation and, assuming that the allele frequencies at the selected locus have reached stationarity, establish the joint generating function for the genealogy of a sample from the population and the frequency of the P allele. In essence this is the joint generating function for a coalescent and the random background in which it evolves. We use this to characterize, for the diffusion approximation, the probability of identity in state at the neutral locus of a sample of two individuals (whose type at the selected locus is known) as solutions to a system of ordinary differential equations. The only subtlety is to find the boundary conditions for this system. Finally, numerical examples are presented that illustrate the accuracy and predictions of the diffusion approximation. In particular, a comparison is made between this approach and one in which the frequencies at the selected locus are estimated by their value in the absence of fluctuations and a classical structured coalescent model is used.

Review text

A single genetic locus which carries two alleles labelled \(P\) and \(Q\) is considered. For the Wright-Fisher model a system of algebraic equations is given for the probabilities of identity in state for a sample of size two from such a population. In order to obtain the diffusion approximation it is convenient to work with the continuous time counterpart of the Wright-Fisher model, the Moran model. For such a model, assuming that the frequencies of the selected alleles, \(P\) and \(Q\), have reached stationarity, it is written the generator of the process that encodes the backward in time evolution of the selected allele frequencies and the numbers of ancestors of the sample of neutral alleles alive at time \(t\) before the present, labeled according to their background (\(P\) or \(Q\)). The parameters of the model are rescaled and the form of the generator of the corresponding diffusion appraximation is established. Also the existence of a stochastic process with this generator and convergence of the rescaled processes to this limit are established. A system of differential equations for the distribution of coalescence times and hence, for the probability of identity in state in a sample of size two, is written. An iterative solution to the system is established. The extension to larger samples and more complex genetic backgrounds is indicated. Also, numerical examples are presented that illustrate the accuracy and predictions of the diffusion approximation.

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