Coalescence, genetic diversity and adaptation in sexual populations
Richard A. Neher, Taylor A. Kessinger, Boris I. Shraiman
(Submitted on 5 Jun 2013)

In diverse sexual populations, selection operates neither on the whole genome — which is repeatedly taken apart and reassembled by recombination — nor on individual alleles which are tightly linked to the chromosomal neighborhood. Those tightly linked alleles affect each others dynamics which reduces the efficiency of selection and distorts patterns of genetic diversity. Inference of evolutionary history from diversity shaped by linked selection requires an understanding of these patterns. Here, we reexamine this problem in the light of recent progress in coalescent theory of rapidly adapting asexual populations. We present a simple but powerful scaling analysis identifying the unit of selection as the genomic “linkage block” with characteristic length \xi_b, which is determined in a self-consistent manner by the condition that the rate of recombination within the block is comparable to the fitness differences between different alleles of the block. We find that an asexual model with strength of selection tuned to that of the linkage block provides an excellent description of genetic diversity and the site frequency spectra when compared to computer simulations of population dynamics. This correspondence holds for the entire spectrum of strength of selection. When fitness differentials arise from the collective contribution of numerous weakly selected polymorphisms, the rate of adaptation increases as the square root of the recombination rate. Linkage block approximation thus provides a simple but powerful tool for understanding interference and collective behavior of dense weakly selected loci.