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Our latest biorxiv.org/content/10.1101/20 @jdmatheson calls for significant change to the theory of , a phenomenon by which some genomic segments of some individuals don’t count toward an because they contain too many deleterious mutations. 1/5

bioRxivUnlinked background selection reduces neutral diversity more than linked background selectionBackground selection describes the reduction in neutral diversity caused by selection against deleterious alleles at other loci. It is typically assumed that the purging of deleterious alleles affects linked neutral variants, and indeed simulations typically only treat a genomic window. However, background selection at unlinked loci also depresses neutral diversity. We find that for a realistically high genome-wide deleterious mutation rate, the effects of unlinked background selection exceed those of linked background selection. This can be derived from previous approximate analytical approximations of the effects of both kinds of background selection, and we confirm it with simulations that treat multi-locus complexities in a human-like genome. Background selection reduces neutral genetic diversity by a factor that is independent of census population size. Outside of genic regions, the strength of background selection increases with the mean selection coefficient, contradicting the linked theory but in agreement with the unlinked theory. Neutral diversity within genic regions is fairly independent of the strength of selection. ### Competing Interest Statement The authors have declared no competing interest.

Humans have about 2 new deleterious mutations per birth. We wanted to know what happens when deleterious mutation rates are this high. We found that background selection isn’t very important at low mutation rates, and was far more important than we expected at high mutation rates. 2/5

The usual theory assumes that background selection is only relevant to sites that are closely linked to the deleterious mutations along the chromosome. Our results are better explained by a model in which the sheer volume of deleterious mutation load rules too many individuals out of the “effective” population size, with that load mostly occurring at unlinked sites. 3/5

The linked sites theory predicts weaker background selection with large selection coefficients. We found the opposite, as predicted by the unlinked sites theory. Results do not depend on the census population size. This means there are issues with the common pop gen practice of “scaling” parameters to be more convenient while keeping products like sN constant. 4/5

Background selection is often studied by simulating just the linked section of the genome. Our findings show that this can give the wrong results. Simulating the whole genome is computationally expensive, but possible. 5/5

Joanna Masel

Background selection at unlinked sites might not matter if it can be well captured by a lower describing in a 1-locus idealized model. So we added a figure to demonstrate that this isn't the case. 6/5

@JoannaMasel @GenomeBiolEvol @jdmatheson Good insight in the theory and theoretical work, thanks!