The B-value calculator: expected diversity with background selection

Abstract

Background selection (BGS), the indirect effect of purifying selection at linked and unlinked sites, is a key evolutionary process shaping genomic patterns of variation. Calculating the expected diversity at neutral sites experiencing BGS relative to that under strict neutrality (referred to as B-value or simply B) is important for developing null models when performing population genomic inference, in particular, demographic inference and detection of selective sweeps. We extend and integrate previous theory to estimate B-values analytically, assuming no selective interference, with novel expressions to account for gene conversion between proximal sites. Here, we present the B-value calculator, Bvalcalc, an easy-to-use command-line interface written in Python for efficient analytical calculation of expected genome-wide B at single base-pair resolution. Bvalcalc has several modules for calculating diversity as a function of distance from a single selected element or considering the multiplicative effects of all selected elements across the genome, accounting for recombination maps, gene conversion, self-fertilization, single population size changes, and unlinked effects from other chromosomes. We validated the effectiveness of Bvalcalc with comparisons against simulated results, and generated B-maps for the model species Homo sapiens, Drosophila melanogaster and Arabidopsis thaliana as a proof of concept using public data. Bvalcalc is available with documentation at johrilab.github.io/Bvalcalc/.