Coalescence in a random background.

DOI10.1214/105051604000000099zbMATH Open1060.60100arXivmath/0406174OpenAlexW1983128758MaRDI QIDQ1879889FDOQ1879889

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)

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.

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

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zbMATH Keywords

selectionrandom environmentrecombinationidentity by descentCoalescent

Mathematics Subject Classification ID

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

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Cited In (27)

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• A semigroup representation and asymptotic behavior of certain statistics of the Fisher-Wright-Moran coalescent
• Editorial: Coalescent theory has many new branches
• Developments in coalescent theory from single loci to chromosomes
• Background selection and population differentiation
• Lines of descent in a Moran model with frequency-dependent selection and mutation
• The conditional ancestral selection graph with strong balancing selection
• Asymptotic behavior of a Moran model with mutations, drift and recombination among multiple loci
• The effect of fluctuating selection on the genealogy at a linked site
• A \(\Lambda\)-Fleming-Viot type model with intrinsically varying population size
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• Sampling HIV intrahost genealogies based on a model of acute stage CTL response
• Multi-site adaptation in the presence of infrequent recombination
• An estimator for the recombination rate from a continuously observed diffusion of haplotype frequencies
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• Genealogical distances under low levels of selection
• An approximate sampling formula under genetic hitchhiking
• A coalescent model for the effect of advantageous mutations on the genealogy of a population
• Genealogies in bistable waves
• Random partitions approximating the coalescence of lineages during a selective sweep
• Selective sweeps for recessive alleles and for other modes of dominance
• The effect of recurrent mutation on the linkage disequilibrium under a selective sweep

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