Biology – Quantitative Biology – Populations and Evolution
Scientific paper
2011-12-22
Biology
Quantitative Biology
Populations and Evolution
44 pages. 5 figures
Scientific paper
Two major sources of stochasticity in the dynamics of neutral alleles result from the sampling due to finite population size (genetic drift) and the ran- dom genetic background of selected alleles on which neutral alleles are found (linked selection). There is now good evidence that linked selection plays an important role in shaping polymorphism levels in a number of species. One of the best investigated models of linked selection is the recurrent full sweep model, in which newly arisen selected alleles fix rapidly. However, the bulk of selected alleles that sweep into the population may not be destined for rapid fixation in the species. Here we develop a coalescent model that generalizes the recurrent full sweep model to the case where selected alleles do not sweep to fixation. We show that in a large population, only the initial rapid increase of a selected allele affects the genealogy at partially linked sites, such that the subsequent fate of the selected allele often does not matter. We investi- gate the impact of recurrent partial sweeps on levels of neutral diversity, and show that for a given reduction in diversity, the impact of recurrent partial sweeps on the frequency spectrum at neutral sites is determined primarily by the frequency reached by these partial sweeps. Recurrent sweeps of selected alleles to low frequencies can have a profound effect on levels of diversity but can leave the frequency spectrum relatively unperturbed. Indeed we show that in the limit of a high rate of sweeps to low frequency, the resulting coalescent model is identical to the standard neutral model. This general- ized model goes some way towards providing a more flexible framework to describe genomic patterns of diversity.
Coop Graham
Ralph Peter
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