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

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)

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.

Recommendations

• A coalescent dual process in a Moran model with genic selection
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Cites work

• scientific article; zbMATH DE number 3817476 (Why is no real title available?)
• scientific article; zbMATH DE number 3951715 (Why is no real title available?)
• scientific article; zbMATH DE number 3664138 (Why is no real title available?)
• scientific article; zbMATH DE number 1094275 (Why is no real title available?)
• scientific article; zbMATH DE number 3223982 (Why is no real title available?)
• scientific article; zbMATH DE number 3365602 (Why is no real title available?)
• A numerical method for calculating moments of coalescent times in finite populations with selection
• Ancestral processes with selection
• Coalescence in a random background.
• Genealogical processes for Fleming-Viot models with selection and recombination
• Neutral evolution in spatially continuous populations.
• The coalescent
• The coalescent and genealogical process in geographically structured population

Cited in

(27)

• Time reversal of some stationary jump diffusion processes from population genetics
• The common ancestor process revisited
• The coalescence of intrahost HIV lineages under symmetric CTL attack
• Tree-valued Fleming-Viot dynamics with mutation and selection
• Tractable diffusion and coalescent processes for weakly correlated loci
• Looking down in the ancestral selection graph: a probabilistic approach to the common ancestor type distribution
• 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
• The conditional ancestral selection graph with strong balancing selection
• Asymptotic behavior of a Moran model with mutations, drift and recombination among multiple loci
• Lines of descent in a Moran model with frequency-dependent selection and mutation
• The effect of fluctuating selection on the genealogy at a linked site
• Branching-coalescing particle systems
• Sampling HIV intrahost genealogies based on a model of acute stage CTL response
• A \(\Lambda\)-Fleming-Viot type model with intrinsically varying population size
• Multi-site adaptation in the presence of infrequent recombination
• Coalescence in a random background.
• An estimator for the recombination rate from a continuously observed diffusion of haplotype frequencies
• 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
• Selective sweeps for recessive alleles and for other modes of dominance
• The effect of recurrent mutation on the linkage disequilibrium under a selective sweep
• Genealogies in bistable waves
• Random partitions approximating the coalescence of lineages during a selective sweep

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