Fig 5. Analysis of linkage disequilibrium supports a polygenic basis of diapause.

(A): Linkage disequilibrium (LD) decay for SNPs with minor allele frequency > 0.05 in the hybrid swarm (blue = A, purple = B, teal = both) contrasted to the DGRP (orange) and the DGRP down-sampled to 34 lines (yellow). Dashed lines indicate parents of the hybrid swarms, while solid lines indicate the hybrid offspring. 10,000 SNPs were randomly sampled and LD (R²) to nearby SNPs at fixed distances was measured. Lines represent median LD; ribbons represent the 95% confidence intervals. (B-D) Long distance LD between pairs of SNPs randomly sampled from 2L and 2R (B), 3L and 3R (C), or sampled from different chromosomes (D). Dashed box plots indicate parental lines.