On the two-locus sampling distribution

DOI10.1007/BF00168175MaRDI QIDQ807449zbMATH OpenOpenAlexWikidataFDO

Authors Stewart N. Ethier, Robert Griffiths

Publication date 1990

Published in Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/bf00168175

zbMATH Keywords

complete linkagedistribution of gametic typesEwens sampling formulagenealogical processesindependent lociinfinitely many neutral allelesjoint distribution of the sample configurationmeasure-valued diffusionnumber of recombination eventstwo-locus stationary diffusion modeltwo-locus version of an urn model

Mathematics Subject Classification ID

Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Genetics and epigenetics (92D10)

Review text

This paper is concerned with the distribution of gametic types in a random sample of size n of a two-locus stationary diffusion model with infinitely many neutral alleles. Two methods are used to study the Ewens sampling formula [\textit{W. J. Ewens}, Theor. Population Biology 3, 87-112 (1972; Zbl 0245.92009)]. The first is due to \textit{G. B. Golding} [Genetics 108, 257-274 (1984)] and includes additional probabilities in systems of linear equations satisfied by the probabilities required. This method allows some members of the sample to be specified at one locus only; it is used for numerical computations. The second method considers the joint distribution of the sample configuration and the number of recombination events, since the time of the most recent ancestor. This new method due to the authors is used to derive a two-locus version of an urn model of \textit{F. M. Hoppe} [J. Math. Biol. 20, 91-94 (1984; Zbl 0547.92009)]. Simulation of the two-locus sampling distribution is possible, when the recombination parameter is not too large. The authors point out that a number of their results may also be derived using genealogical processes analogous to the coalescent. Detailed proofs are collected in a 10 page appendix.

Recommendations

• The neutral two-locus model as a measure-valued diffusion
• The sampling theory of neutral alleles and an urn model in population genetics
• Tractable diffusion and coalescent processes for weakly correlated loci
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• Importance sampling and the two-locus model with subdivided population structure

Cites work

• scientific article; zbMATH DE number 176645 (Why is no real title available?)
• Neutral two-locus multiple allele models with recombination
• Pólya-like urns and the Ewens' sampling formula
• The infinitely-many-sites model as a measure-valued diffusion
• The neutral two-locus model as a measure-valued diffusion
• The sampling theory of selectively neutral alleles
• The use of sample genealogies for studying a selectively neutral m-loci model with recombination

Cited in

(20)

• The use of sample genealogies for studying a selectively neutral m-loci model with recombination
• The effect on genetic sampling distributions of correlations in reproduction
• Recombination as a point process along sequences
• A coalescent dual process for a Wright-Fisher diffusion with recombination and its application to haplotype partitioning
• The neutral frequency spectrum of linked sites
• Consistency of estimators of the population-scaled recombination rate
• Tractable diffusion and coalescent processes for weakly correlated loci
• Closed-form asymptotic sampling distributions under the coalescent with recombination for an arbitrary number of loci
• Importance sampling and the two-locus model with subdivided population structure
• Padé approximants and exact two-locus sampling distributions
• A generalization of the donnelly-tavare-griffiths formula
• Duality between the two-locus Wright-Fisher diffusion model and the ancestral process with recombination
• Duality, ancestral and diffusion processes in models with selection
• Recoverability of ancestral recombination graph topologies
• Asymptotic sampling distributions made easy: loose linkage in the ancestral recombination graph
• The coalescent in two colonies with symmetric migration
• Joint identity among loci under mutation and regular inbreeding
• Which locus has the oldest allele?
• Analytic computation of the expectation of the linkage disequilibrium coefficient \(r^2\)
• An asymptotic sampling formula for the coalescent with recombination

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