Approximating genealogies for partially linked neutral loci under a selective sweep

DOI10.1007/S00285-007-0085-7MaRDI QIDQ2460425zbMATH OpenOpenAlexWikidataFDO

Authors Peter Pfaffelhuber, A. Studeny

Publication date 12 November 2007

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

Full work available at URL https://arxiv.org/abs/q-bio/0611029

zbMATH Keywords

Ancestral recombination graphDiffusion approximationGenetic hitchhikingRandom backgroundYule process

Mathematics Subject Classification ID

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) Genetics and epigenetics (92D10) Problems related to evolution (92D15)

Abstract: Consider a genetic locus carrying a strongly beneficial allele which has recently fixed in a large population. As strongly beneficial alleles fix quickly, sequence diversity at partially linked neutral loci is reduced. This phenomenon is known as a selective sweep. The fixation of the beneficial allele not only affects sequence diversity at single neutral loci but also the joint allele distribution of several partially linked neutral loci. This distribution can be studied using the ancestral recombination graph for samples of partially linked neutral loci during the selective sweep. To approximate this graph, we extend recent work by Schweinsberg & Durrett 2005 and Etheridge, Pfaffelhuber & Wakolbinger 2006 using a marked Yule tree for the genealogy at a single neutral locus linked to a strongly beneficial one. We focus on joint genealogies at two partially linked neutral loci in the case of large selection coefficients alpha and recombination rates ho = O(alpha/logalpha) between loci. Our approach leads to a full description of the genealogy with accuracy of O((log alpha)^{-2}) in probability. As an application, we derive the expectation of Lewontin's D as a measure for non-random association of alleles.

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Cited in

(9)

• An eco-evolutionary approach of adaptation and recombination in a large population of varying size
• Random partitions approximating the coalescence of lineages during a selective sweep
• Selective sweep and the size of the hitchhiking set
• Genealogies of two linked neutral loci after a selective sweep in a large population of stochastically varying size
• Evolution of the ancestral recombination graph along the genome in case of 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
• Approximating selective sweeps
• An approximate sampling formula under genetic hitchhiking

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