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As I read the maintenance or removal of an allele from a population is dependent upon the alleles in its linkage group; so, when an advantageous mutation occurs in the population, variation in nearby alleles that linked to that mutated allele is reduced to fix (maintain) the mutated allele in the population (hitchhiking effect). This is true for deleterious mutations and background selection. But, I cannot understand how background selection can remove the deleterious mutation from the population? Could you please kindly explain to me about it?

Thanks

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    $\begingroup$ can you clarify your question at all? The focal, deleterious mutation is being removed by plain old natural selection (e.g. it would be removed even if it were on a chromosome by itself, unlinked to anything else). "Background selection" is the term for the loss of diversity/alleles in the linked region around the deleterious allele. $\endgroup$ – Ben Bolker Jun 29 '18 at 12:32
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The phrasing in your question is a little unclear which makes it hard to know exactly what is unclear to you. But I'll give it a try hoping that it helps.

Background selection (BGS) is the process by which deleterious mutations reduce genetic diversity at nearby loci. When you say

I cannot understand how background selection can remove the deleterious mutation from the population

I would like to highlight that BGS does not remove the deleterious mutations per say. BGS is caused by deleterious mutations and has for consequence to reduce genetic diversity whether this diversity represent any variant for fitness.

An easy way to get an intuition of this effect is to think of the effective population size. In a Wright-Fisher population, where all individuals have the same probability to reproduce, the effective population size is equal to the population size. Imagine now that half of the individuals in the population carry a mutation that make them completely sterile. If this is the case, then the effective population size is reduced to half the population size. As the effective population is smaller, so is the genetic diversity. Hence, deleterious mutations (and fitness variance in general) reduce the effective population (in comparison to the actual population size).

Now, a single deleterious mutation that disappears in the next generation will affect the entire genome equally. However, repetitive deleterious mutations at specific loci (conserved regions) that stay around for a few generations will affect the effective population size at this region more than at other regions. Yes, the effective population size, for a population, can vary along the genome.

The strength of BGS to affect various statistics such as expected heterozygosity, $D_{XY}$ or $F_{ST}$ is hard to estimate as both hitchhiking (selective sweeps) and BGS leave very similar genetic signature. See for example Matthey-Doret and Whitlock (2018; bioRxiv) (shameless self-citation).

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