The pattern of neutral molecular variation under the background selection model.

Abstract

Stochastic simulations of the infinite sites model were used to study the behavior of genetic diversity at a neutral locus in a genomic region without recombination, but subject to selection against deleterious alleles maintained by recurrent mutation (background selection). In large populations, the effect of background selection on the number of segregating sites approaches the effect on nucleotide site diversity, i.e., the reduction in genetic variability caused by background selection resembles that caused by a simple reduction in effective population size. We examined, by coalescence-based methods, the power of several tests for the departure from neutral expectation of the frequency spectra of alleles in samples from randomly mating populations (Tajima's, Fu and Li's, and Watterson's tests). All of the tests have low power unless the selection against mutant alleles is extremely weak. In Drosophila, significant Tajima's tests are usually not obtained with empirical data sets from loci in genomic regions with restricted recombination frequencies and that exhibit low genetic diversity. This is consistent with the operation of background selection as opposed to selective sweeps. It remains to be decided whether background selection is sufficient to explain the observed extent of reduction in diversity in regions of restricted recombination.

The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects

“…Because several demographic estimation methods are based on fitting a demographic model to the SFS, it is also of interest to determine whether BGS can skew the SFS to different extents under different demographic models. Although it is well known that BGS causes a skew of the SFS towards rare variants under equilibrium models ( Charlesworth et al. 1995 ; Nicolaisen and Desai 2013 ), the effect of BGS on the SFS with population size change has not been much explored (but see Johri et al.…”

Genetic architecture, demographic history, and genomic differentiation of Populus davidiana revealed by whole‐genome resequencing

“…However, regions of low differentiation had long‐term balancing selection characteristics (Charlesworth et al., 1995). For example, the dxy and RND values of the regions that were poorly differentiated between the two populations exhibited less differentiation compared with regions exhibiting high differentiation (Figure 6a,b), the level of polymorphism (π) in both N and S populations being significantly high (Figure 6c,d).…”

Background selection as null hypothesis in population genomics: insights and challenges fromDrosophilastudies

“…Selection can distort estimates of demographic events. BGS, for instance, generates a consistent excess of low-frequency variants at neutral sites resulting in negative Tajima's D [64,[92][93][94][95][96][97][98][99]. The predicted magnitude of the skew in the frequency of variants is particularly evident when incorporating DFEs with weakly selected mutations and when recombination is reduced or absent, but it is also expected for a wide range of recombination rates as long as the number of sites under selection is high.…”