We observed strong evidence for schizophrenia h2SNP enrichment in SNPs under strong background selection (BGS), which was consistent across all the thresholds we examined (Table 1). We also found a significant depletion of h2SNP in SNPs subject to positive selection as indexed by the CLR statistic. These two results are mutually consistent, as calculation of the CLR statistic explicitly controls for the effect of BGS28. This suggests that SNPs under positive selection, but under weak or no BGS, are depleted for association with schizophrenia. No significant relationship between h2SNP and other positive selection or Neanderthal introgression measures was found after correction for multiple testing (Table 1). An LDSR analysis treating BGS measures as a quantitative trait rather than as a binary one confirmed that the relationship between BGS and schizophrenia association was not due to the imposition of arbitrary thresholds to define strong BGS (P = 7.73 × 10−11). We also note that the τc statistic of the LDSC model was significant for BGS, in both the binary (P = 0.041) and quantitative (P = 0.023) analyses (Supplementary Table 8).
