Regional and LD-based signatures of balancing selection associated with antagonistic variants in three independent populations (DGRP, ZI, and SA).

(A) Mean (±SE) residual Tajima’s D (i.e., the residuals of a regression of Tajima’s D on genome-wide estimates of linked selection) for antagonistic windows (blue; ‘antagonistic status = 1’) and nonantagonistic windows (grey; ‘antagonistic status = 0’). (B) Mean (±SE) residual FST (i.e., the residuals of a regression of FST on genome-wide estimates of linked selection) for antagonistic and nonantagonistic windows. Because these are residuals of a regression, residual FST does not vary between 0 and 1. (C) LD (r2) in the ZI population between pairs of antagonistic SNPs (blue, ‘Antag./antag.’), pairs of nonantagonistic SNPs (grey, ‘Control/control’), and mixed pairs (black, ‘Antag./control’). Points represent mean r2 across 25-bp bins; r2 is modelled as a declining exponential function of distance (fitted lines). Data and code underlying this figure can be found at https://doi.org/10.5281/zenodo.2623225. Antag., antagonistic; DGRP, Drosophila Genetic Reference Panel; LD, linkage disequilibrium; SA, South Africa; SNP, single nucleotide polymorphism; ZI, Zambia.