Fig. 1.

Inference of demography by MSMC (red lines; ten replicates) and fastsimcoal2 (blue lines; ten replicates) with and without BGS, under demographic equilibrium (left column), 30-fold exponential growth (middle column), and ∼6-fold instantaneous decline (right column). The true demographic models are depicted as black lines, with the x-axis origin representing the present day. (a) All genomic sites are strictly neutral. Exonic sites experience purifying selection specified by (b) DFE1, (c) DFE2, and (d) DFE3 (see table 1). Exons represent 20% of the genome, and exonic sites were masked (i.e., excluded) when performing demographic inference, quantifying the effects of BGS alone. The dashed lines represent indefinite extensions of the ancestral population sizes. Detailed methods including command lines can be found at: https://github.com/paruljohri/demographic_inference_with_selection/blob/main/CommandLines/Figure1.txt.